@article {pmid40672279,
year = {2025},
author = {Dallon, E and Moran, HM and Chidambaran, SR and Kian, A and Huang, BYH and Fried, SD and DiRuggiero, J},
title = {Investigation of the global translational response to oxidative stress in the model archaeon Haloferax volcanii reveals untranslated small RNAs with ribosome occupancy.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.04.08.647799},
pmid = {40672279},
issn = {2692-8205},
abstract = {UNLABELLED: Oxidative stress induces a wide range of cellular damage, often causing disease and cell death. While many organisms are susceptible to the effects of oxidative stress, haloarchaea have adapted to be highly resistant. Several aspects of the haloarchaeal oxidative stress response have been characterized, however little is known about the impacts of oxidative stress at the translation level. Using the model archaeon Haloferax volcanii , we performed RNA-seq and ribosome profiling (Ribo-seq) to characterize the global translation landscape during oxidative stress. We identified 281 genes with differential translation efficiency (TE). Downregulated genes were enriched in ribosomal and translation proteins, in addition to peroxidases and genes involved in the TCA cycle. We also identified 42 small noncoding RNAs (sRNAs) with ribosome occupancy. Size distributions of ribosome footprints revealed distinct patterns for coding and noncoding genes, with 12 sRNAs matching the pattern of coding genes, and mass spectrometry confirming the presence of seven small proteins encoded in these sRNAs. However, the majority of sRNAs with ribosome occupancy had no evidence of coding potential. Of these ribosome-associated sRNAs, 12 had differential ribosome occupancy or TE during oxidative stress, suggesting that they may play a regulatory role during the oxidative stress response. Our findings on ribosomal regulation during oxidative stress, coupled with potential roles for ribosome-associated noncoding sRNAs and sRNA-derived small proteins in H. volcanii , revealed additional regulatory layers and underscore the multifaceted architecture of stress-responsive regulatory networks.<br><br>IMPORTANCE: Archaea are found in diverse environments, including as members of the human microbiome, and are known to play essential ecological roles in major geochemical cycles. The study of archaeal biology has expanded our understanding of the evolution of eukaryotes, uncovered novel biological systems, and revealed new opportunities for applications in biotechnology and bioremediation. Many archaeal systems, however, remain poorly characterized. Using Haloferax volcanii as a model, we investigated the global translation landscape during oxidative stress. Our findings expand current knowledge of translational regulation in archaea and further illustrate the complexity of stress-responsive gene regulation.},
}
@article {pmid40672236,
year = {2025},
author = {Fricker, AD and Barnes, AL and Henzi, A and Duran, LE and Flores, GE},
title = {Time-resolved growth of diverse human-associated Akkermansia on human milk oligosaccharides.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.07.07.663590},
pmid = {40672236},
issn = {2692-8205},
abstract = {UNLABELLED: The infant gut microbiota is strongly influenced by human milk oligosaccharides (HMOs), a set of glycans that comprise a large constituent of milk and reach the large intestine intact. During growth on HMOs, bacteria produce beneficial metabolites including short chain fatty acids (SCFAs) that are important for host health. Select gut microorganisms have unique sets of enzymes capable of catabolizing distinct HMOs leading to host-specific differences in glycan access, and ultimately differences in SCFA production. Here we cultivated three species of human-associated Akkermansia, an early life commensal that is correlated with a healthy metabolic status in adults, on five individual HMOs in two different media backgrounds. Analysis of growth rates, growth yield, metabolic output, and individual HMO consumption through time revealed differences across species that was influenced by growth media. Most notably, A. biwaensis CSUN-19 has robust growth in both media backgrounds paired with nearly complete degradation of all HMOs. Across all conditions, overall SCFA production was generally commensurate with growth, but most strikingly, A. muciniphila MucT and A. biwaensis CSUN-19 produced succinate only when grown in the presence of N-acetyl glucosamine, but not with mucin. The third organism tested, A. massiliensis CSUN-17 had weaker growth, lower degradation of HMOs, but higher production of propionate in media containing N-acetyl glucosamine. Interactions between Akkermansia and HMOs can influence colonization of other early life commensals, potentially influencing health outcomes throughout life. This study highlights the importance of characterizing growth of individual Akkermansia species on distinct HMO leading to fermentation into organic acids.<br><br>IMPORTANCE: Akkermansia are a widely distributed bacterial genus found in the healthy human gut that are capable of degrading host-produced glycans including human milk oligosaccharides (HMOs). Previous end-point experiments demonstrated varying degradation efficiencies across Akkermansia species with A.biwaensis displaying enhanced growth on multiple HMOs. However, the temporal dynamics and growth preferences when offered substrate choice across the lineage are unknown. Here, we characterized the temporal growth dynamics, HMO catabolism, and metabolic output of three Akkermansia species across five HMOs and two media backgrounds. Specifically, we demonstrate that one species, A. biwaensis CSUN-19, has robust growth independent of media background with nearly complete degradation of all HMOs tested. Overall, the species-, HMO-, and media-specific response of Akkermansia may impact the colonization success of each species, ultimately influencing host-microbe and microbe-microbe interactions in the developing infant gut microbiome.},
}
@article {pmid40672213,
year = {2025},
author = {Schroer, HW and Beghini, F and Garay, JAR and Christakis, NA and Bosch, DE},
title = {Metagenomic polymorphic toxin effector and immunity profiling predicts microbiome development and disease-related dysbiosis.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.07.08.662037},
pmid = {40672213},
issn = {2692-8205},
abstract = {Bacteria use antagonistic interbacterial weapons such as polymorphic toxin secretion systems (TSS) to compete for niches in the human gut microbiome. We developed a bioinformatic marker gene approach (PolyProf) to quantify TSS including ∼200 effector and immunity genes and applied it to ∼15,000 publicly available human metagenomes. PolyProf alpha and beta diversity readily distinguished 12 different human disease states. Decision tree machine learning models integrating bacterial taxonomy with PolyProf had near-perfect accuracy (ROC area 1.00) for all 12 disease states. During microbiome development in the first year of life, PolyProf alpha diversity increases, and beta diversity becomes increasingly like the maternal microbiome, influenced by vertical transfer, delivery mode, and breastfeeding. PolyProf is related to strain sharing among adults through social interactions. In summary, interbacterial antagonism with TSS shapes microbiome development and interpersonal strain sharing. Since PolyProf distinguishes diverse adult disease statuses, these dynamics may contribute to non-genetic inheritance.},
}
@article {pmid40672209,
year = {2025},
author = {Arnoldini, M and Sharma, R and Moresi, C and Chure, G and Chabbey, J and Slack, E and Cremer, J},
title = {Quantifying the varying harvest of fermentation products from the human gut microbiota.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.01.05.573977},
pmid = {40672209},
issn = {2692-8205},
abstract = {Fermentation products released by the gut microbiota provide energy and regulatory functions to the host. Yet, little is known about the magnitude of this metabolic flux and its quantitative dependence on diet and microbiome composition. Here, we establish orthogonal approaches to consistently quantify this flux, integrating data on bacterial metabolism, digestive physiology, and metagenomics. From the nutrients fueling microbiota growth, most carbon ends up in fermentation products and is absorbed by the host. This harvest varies strongly with the amount of complex dietary carbohydrates and is largely independent of bacterial mucin and protein utilization. It covers 2-5% of human energy demand for Western, and up to 10% for non-Western diets. Microbiota composition has little impact on the total harvest but determines the amount of specific fermentation products. This consistent quantification of metabolic fluxes by our analysis framework is crucial to elucidate the gut microbiota's mechanistic functions in health and disease.},
}
@article {pmid40672168,
year = {2025},
author = {Joshi, J and Cumbo, F and Blankenberg, D},
title = {Large-scale classification of metagenomic samples: a comparative analysis of classical machine learning techniques vs a novel brain-inspired hyperdimensional computing approach.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.07.06.663394},
pmid = {40672168},
issn = {2692-8205},
abstract = {UNLABELLED: Classical machine learning techniques have revolutionized bioinformatics, enabling researchers to extract knowledge from complex biological data. However, these techniques often struggle with high-dimensional data, where the increasing number of features leads to decreased performance, also affecting models accuracy. To address this problem, we explore hyperdimensional computing (HDC), an emerging brain-inspired computational paradigm that leverages high-dimensional vectors and simple arithmetic operations to represent and manipulate complex patterns, as an alternative approach in the context of supervised machine learning. In this work, we present a comprehensive comparative analysis of HDC against established machine learning techniques across a range of classification tasks. As a representative use case, we focus on classifying heterogeneous metagenomic samples based on their quantitative microbial profiles, using publicly available microbiome datasets. Our results demonstrate that HDC achieves comparable, and in some cases, superior classification accuracy to classical methods. Furthermore, our findings highlight the potential of HDC for improved computational efficiency, particularly when dealing with large-scale datasets, suggesting the HDC-based classifier as a promising tool for bioinformatics research, particularly in areas characterized by high-dimensional data. We also offer a Galaxy powered toolset to analyze your own datasets and generate reproducible workflows and adopt these methods in your own research with ease. Our investigation into the application of a HDC-based supervised machine learning technique for classifying microbial profiles in metagenomic samples yielded promising results, demonstrating the potential of this novel computational paradigm to complement and, in some cases, surpass the performances of well established machine learning techniques.<br><br>IMPORTANCE: The growing complexity and dimensionality of biological data require more efficient and scalable machine learning approaches. HDC offers a novel alternative to conventional methods, showing resilience to high-dimensionality while maintaining competitive accuracy. This study demonstrates the effectiveness of HDC in classifying metagenomic samples based on their microbial composition. Our results suggest that HDC not only matches, but sometimes exceeds the performance of well-established methods. We make this approach accessible to the broader bioinformatics community with an open-source tool fully integrated into the Galaxy platform, facilitating its adoption and reproducibility, with the aim of integrating HDC into mainstream biological data analysis pipelines, especially for complex, high-dimensional tasks in microbiome research.},
}
@article {pmid40672154,
year = {2025},
author = {Wu, L and Kensiski, A and Gavzy, SJ and Song, Y and Lwin, HW and France, M and Kong, D and Li, L and Lakhan, R and Saxena, V and Piao, W and Shirkey, MW and Mas, VR and Lohmar, B and Shu, Y and Bromberg, JS and Ma, B},
title = {Immunosuppressants Rewire the Gut Microbiome-Alloimmune Axis Through Time-Dependent and Tissue-Specific Mechanisms.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.01.02.631100},
pmid = {40672154},
issn = {2692-8205},
abstract = {BACKGROUND: Lifelong immunosuppressive therapy is required to prevent allograft rejection in organ transplantation. Current immunosuppressants effectively suppress adaptive and innate immune responses, but their broad, antigen-non-specific effects often result in severe off-target complications. It remains a significant unmet medical need in transplant medicine.<br><br>RESULTS: In this study we investigated immunosuppressant effects of four major immunosuppressant classes, including tacrolimus, prednisone, mycophenolate mofetil (MMF), and fingolimod (FTY), on the gut microbiome, metabolic pathways, lymphoid architecture and lymphocyte trafficking after up to 30-day chronic exposure. Despite their distinct mechanisms of action and not designed to target the gut, all immunosuppressive drugs induced profound and time-dependent alterations in both intestine gene expression and gut microbiome composition. Progressive alterations from moderate early, drug-specific changes to a strikingly convergent microbial dysbiosis, marked by significant expansion of pathobionts of Muribaculaceae , occurred across all drug classes. Concurrently, all drugs uniformly induced significant suppression of mucosal immunity including B cell, immunoglobulin, and antigen recognition. Time-dependent changes in lymph node (LN) reorganization and cellular composition were also observed, marked by a progressive shift toward pro-inflammatory phenotypes in gut-draining mesenteric LNs and a gradual loss of tolerogenic architecture in peripheral LNs. Drug-specific metabolic alterations and distinct phases of intestinal transcriptional responses were also characterized. Notably, MMF and FTY demonstrated the most robust immunomodulatory properties, and were able to suppress alloantigen-induced inflammation through mediating regulatory T cell distribution and LN remodeling.<br><br>CONCLUSIONS: Together, these findings highlight the underappreciated complexity and temporal dynamics immunosuppressants effects, particularly their impact on the gut and compartmentalized regulation of alloimmune in lymphoid tissues. Understanding these relationships offers new opportunities for refining immunosuppressive strategies to reduce treatment-related off-target complications and improve long-term organ transplant outcomes.},
}
@article {pmid40672125,
year = {2025},
author = {Rattigan, SM and Mbouombouo, IN and Abdou Tahirou, MA and Mostafa, I and Saqeeb, KN and Garba, S and Guindo, O and Ahmed, T and Barratt, MJ and Gordon, JI and Sudfeld, CR and Grais, RF and Isanaka, S},
title = {Acceptability of a Microbiome-Directed Food for the Management of Children with Uncomplicated Acute Malnutrition in Maradi, Niger: Two Randomized Crossover Trials.},
journal = {Current developments in nutrition},
volume = {9},
number = {7},
pages = {107484},
pmid = {40672125},
issn = {2475-2991},
abstract = {BACKGROUND: A novel ready-to-use microbiome-directed food (MDF) has been developed for the management of acute malnutrition using ingredients that promote repair of the gut microbiota of undernourished children.<br><br>OBJECTIVES: This study aims to assess the acceptability of MDF compared with standard nutritional care among children with acute malnutrition.<br><br>METHODS: Two randomized crossover trials consisting of 2 14-d periods of at-home consumption were conducted. Children aged 6 to <24 mo with severe acute malnutrition (SAM) or moderate acute malnutrition (MAM) were individually randomized in a 1:1 ratio to the sequence of receiving MDF then standard nutritional care, or vice versa. Standard nutritional care consisted of ready-to-use therapeutic food for SAM and ready-to-use supplementary food for MAM. The primary outcome was at-home acceptability, defined as the return of &#x2265;75% of sachets empty after the 14-d at-home consumption period. The primary analysis was a noninferiority analysis, in which MDF was considered noninferior if the lower bound of the 95% confidence interval (CI) of the difference in at-home acceptability comparing MDF with standard nutritional care was within -20 percentage points. Secondary outcomes included caregiver's perception of the child's liking, as well as caregiver willingness to use in the future and preference between the 2 foods.<br><br>RESULTS: In all, 128 children with SAM and 146 children with MAM were randomized. MDF was noninferior to standard nutritional care in terms of at-home acceptability among children with SAM (risk difference: -7.0; 95% CI lower bound: -11.6%) and among children with MAM (risk difference: -2.3%; 95% CI lower bound: -6.1%). There were no differences in caregiver willingness to use either food in future.<br><br>CONCLUSIONS: MDF is acceptable for the management of acute malnutrition in children aged 6 to <24 mo in Niger and should be further tested in other populations with a high prevalence of acute malnutrition. Effectiveness of the novel food will be assessed in forthcoming trials.<br><br>TRIAL REGISTRATION NUMBER: This trial was registered at clinicaltrials.gov as NCT05551819.},
}
@article {pmid40671981,
year = {2025},
author = {Ruiz, NI and Herrera Giron, CG and Arragan Lezama, CA and Frias Redroban, SJ and Ventura Herrera, MO and Sanic Coj, GA},
title = {Timing and Protocols for Microbiome Intervention in Surgical Patients: A Literature Review of Current Evidence.},
journal = {Cureus},
volume = {17},
number = {6},
pages = {e86104},
pmid = {40671981},
issn = {2168-8184},
abstract = {Managing the gut microbiome with a personalized approach can significantly improve surgical outcomes, leading to reduced risk of infections, improved immune function, faster recovery and healing, and decreased risk of postoperative complications. This review explores microbiome-based interventions, such as probiotics, prebiotics, synbiotics, and fecal microbiota transplantation, and their roles in perioperative, preoperative, and postoperative care. Electronic databases, such as PubMed, ScienceDirect, and Google Scholar, were searched using topic-related keywords and MeSH terms. The literature search was limited to English-language peer-reviewed articles within the last 10 years, but the majority of the literature was from the last five years. Microbiome interventions have been associated with reduced postoperative complications and enhanced recovery times. The study found that changing the gut microbiome in specific ways, like using probiotics and synbiotics before and after surgery, can lead to better surgical results. For example, these treatments can lower the risk of infection at the surgery site by 40%-80% compared to standard care, help patients recover their bowel function one to two days faster, and reduce hospital stays by up to 30%. They also decrease levels of important inflammation markers like IL-6 and CRP. Using probiotics and synbiotics before surgery and continuing them for two weeks can lower infection rates and enhance recovery while managing inflammation. The beneficial effects of probiotics, prebiotics, and synbiotics support their use as effective strategies in perioperative care. However, people react differently to probiotics, prebiotics, and synbiotics because of factors like genetics, age, hormonal differences between sexes, and variations in gut microbiota based on race. Future research should focus on developing personalized microbiome-based interventions and establishing standardized protocols tailored to individual patient characteristics to enhance their effectiveness.},
}
@article {pmid40671933,
year = {2025},
author = {Zeballos, RS and da Silva Helbingen, MF and Melo, PMP and Alves, FEC and Salvino, CR and Seródio, EP and de Carvalho, ERM},
title = {Post spike syndrome (PSS): Simple solution leading to resolving results, five cases report.},
journal = {IDCases},
volume = {41},
number = {},
pages = {e02278},
pmid = {40671933},
issn = {2214-2509},
abstract = {UNLABELLED: Post-Spike Syndrome (PSS) is an emerging condition associated with the Spike protein, originating from both SARS-CoV-2 infection and mRNA-based therapies. This case series explores the significant clinical impact of PSS, characterized By gut dysbiosis, systemic inflammation, and immune activation, leading to multisystem manifestations such as fatigue, brain fog, neuropathies, and reactivation of pre-existing diseases. A simple therapeutic approach was applied to five patients, resulting in notable symptom improvement.<br><br>METHODS: This case series includes five patients diagnosed with interstitial granulomatous dermatitis, polymyalgia rheumatica, peripheral polyneuropathy, drug-refractory epilepsy, and trigeminal neuralgia. A common pathophysiological mechanism-vasculitis triggered by both SARS-CoV-2 and mRNA-based therapies-was hypothesised. The patients exhibited a satisfactory response to the proposed therapeutic strategy. This is an observational and descriptive study, with data collected retrospectively from medical records at a private clinic in S&#xe3;o Paulo, Brazil.<br><br>CONCLUSION: It is crucial to raise awareness within the medical community About SPIKEOPATHY, particularly in cases of classic pathologies that do not respond to conventional treatments. We believe PSS is currently underestimated. A broad intervention including a focus on restoring the microbiome, in particular Bifidobacterium associated with ivermectin and nattokinase was used as a therapeutic strategy. In other studies, Bifidobacterium has already been shown to significantly reduce harmful bact&#xe9;ria in post-COVID patients. Further studies are needed to confirm these findings and expand our understanding of PSS management.},
}
@article {pmid40671808,
year = {2025},
author = {Mazzoni, C and Ochana, B and Focht, G and Harpenas, E and Quteineh, A and Meyer, EO and Ya'acov, AB and Shmorak, S and Shemer, R and Shteyer, E and Dor, Y and Yassour, M},
title = {Human DNA levels in feces reflect gut inflammation and associate with presence of gut species in IBD patients across the age spectrum.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-6809327/v1},
pmid = {40671808},
issn = {2693-5015},
abstract = {Background Feces are a complex matrix that holds precious information regarding gut processes. Comprehensive fecal DNA sequencing is largely utilized as a non-invasive way to profile the gut microbiome, but is majorly overlooked in other fields. Clinical practice and research on Inflammatory Bowel Diseases (IBD) would greatly benefit from accurate and non-invasive methods to monitor gut inflammation in IBD patients. In IBD, immune cell storming and epithelial cell shedding in the gut increase the amount of human DNA in feces, making fecal DNA profiling a desirable approach to monitor gut inflammation dynamics. Methods We used a combination of sequencing techniques to comprehensively characterize the fecal DNA diversity in a newly established cohort of IBD patients and Controls (SZ cohort, N=134 children, Israel). We performed methylation-based human cell-specific profiling together with shotgun metagenomics to characterize the human and the microbial DNA content in feces, respectively. Moreover, we included a large external validation cohort (LLDeep+1000IBD cohorts, N=689 adults, the Netherlands) in order to extend our findings from the methylation-based profiling to the more broadly-available quantification of human DNA in metagenomics sequencing. Results We found that neutrophil DNA dominates fecal human DNA content in IBD patients, and our measurements were highly correlated with fecal calprotectin levels. Combining neutrophil and other cell type DNA fractions in one metric was able to distinguish between remissive and active cases of IBD. Human reads percentage by metagenomics was well correlated with disease severity and species richness, which had distinct trends in CD and UC over time. We used a combination of species richness, human DNA percentage and microbiome composition data to predict IBD and distinguish CD from UC in both adult and pediatric IBD patient cohorts. Conclusions The comprehensive characterization of human and microbiome fecal DNA is a useful approach to track immune response level and investigate the interaction that the immune system has with gut microbiome richness and composition over time, enriching opportunities for better disease monitoring and thus better treatment of IBD patients.},
}
@article {pmid40671790,
year = {2025},
author = {Nakanishi, M and Martinez, MJ and Sztachelski, P and Leclerc, M and Rosenberg, DW},
title = {Differential susceptibility to colonic ulceration in mice with genetic deletion of Prostaglandin E synthase.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-6977322/v1},
pmid = {40671790},
issn = {2693-5015},
abstract = {BACKGROUND: Prostaglandin E 2 (PGE 2) exerts pleiotropic and context-dependent effects on inflammation, cancer and maintenance of intestinal mucosal homeostasis. To further define its role in intestinal diseases, we genetically inactivated its rate-limiting synthesis, Ptges , in two mouse lines. An unexpected phenotype consisting of spontaneous mucosal ulceration was found exclusively in the colons of strain A mice. This study aims to characterize the phenotype that may have a clinical relevance to NSAID-induced enteropathies.<br><br>METHODS: Mucosal ulcerations were characterized in Ptges -deficient mice maintained on strain A (A/D:KO) and C57BL/6 (B6D:KO) backgrounds. RNA sequencing of colons identified inflammatory signatures in sensitive A/D:KO mice. Microbial dysbiosis was evaluated in the fecal stream using 16S rRNA sequencing. The potential role of genetic and environmental factors in the etiology of differential susceptibility to colonic ulceration was examined through the co-housing experiment and by generating F1 hybrid of A/D:KO and B6D:KO mice.<br><br>RESULTS: Progressive colonic ulcerations develop spontaneously in A/D:KO mice, a phenotype that is absent in B6D:KO mice. RNAseq analysis revealed robust expression of pro-inflammatory genes in A/D:KO mice prior to the development of tissue damage, suggesting a subtle defect in intrinsic immune regulation. In B6D:KO colons, there was potent enrichment of genes associated with protection against mucosal injury in. While distinct gut microbial community structures were identified, co-housing of these mice did not rescue the inflammatory phenotype in A/D:KO , nor confer sensitivity to the colons of B6D:KO mice. However, F1 hybrids of A/D:KO with B6D:KO mice were mostly free of colonic ulceration.<br><br>CONCLUSIONS: These results suggest that genetic blockage of Ptges causes a dramatic shift in the inflammatory milieu in strain A mice, an effect that may be augmented by a complex interaction between genetic background, microbiome and metabolite imbalance. These mice may provide a genetic model for studying interindividual variability in human sensitivity to NSAID-induced colitis.},
}
@article {pmid40671760,
year = {2025},
author = {Zhang, J and Zhi, Y and Xia, G and Feng, D and Lei, S},
title = {A Prospective Observational Study on the Effects of XingQi HuoXue Decoction on Gut Microbiota and Clinical Outcomes in Sepsis Patients with Acute Gastrointestinal Injury.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {3487-3503},
pmid = {40671760},
issn = {1178-6973},
abstract = {BACKGROUND: Therapeutic options for sepsis-associated acute gastrointestinal injury (AGI) remain limited. In this study, we explored the potential of a decoction called XingQiHuoXue (XQHX), which was formulated by us, in patients with septic AGI.<br><br>MATERIALS AND METHODS: It was a non-randomized observational study. Forty-nine patients diagnosed with septic AGI classified as qi stagnation and blood stasis syndrome (QSBSS), a condition characterized by unsmooth flow of qi and blood, were enrolled. The patients were divided into the treatment group (routine treatment and the XQHX) and the control group (routine treatment). Clinical characteristics encompassed demographics, underlying diseases, disease severity and prognostic outcomes. Gut microbiota data were derived from characterization of pre- and post-treatment fecal specimens collected from 15 patients enrolled. The clinical and gut microbiota characteristics were compared between the two groups.<br><br>RESULTS: Among the 49 patients, 30 showed improvement, including 19 patients from the treatment group and 11 from the control group. The difference in the improvement rate between the groups was significant (P < 0.05). With regard to changes in the microbiome composition, the treatment group showed a significant decrease in the abundance of Bacteroides, and Enterobacteriaceae/g- (q = 0.04 and q = 0.006), accompanied by a significant increase in the abundance of Enterococcus (q = 0.01). These changes were not found in the control group. The abundance of Bacteroides and Enterobacteriaceae/g- was positively correlated with the Acute Physiology and Chronic Health Evaluation II and Sequential Organ Failure Assessment score (R = 0.778 and 0.499), while the abundance of Enterococcus showed a negative correlation with the score (R = -0.811 and -0.656).<br><br>CONCLUSION: Our preliminary findings suggest that XQHX may improve the prognosis of patients with septic AGI and QSBSS. The milder disease presentation and better prognosis could be associated with alterations in the gut microbiota induced by XQHX.},
}
@article {pmid40671685,
year = {2025},
author = {Haykal, D and Flament, F and Shadev, M and Mora, P and Puyat, C and Dréno, B and Zheng, Q and Cartier, H and Gold, M and Cohen, S},
title = {Advances in Longevity: The Intersection of Regenerative Medicine and Cosmetic Dermatology.},
journal = {Journal of cosmetic dermatology},
volume = {24},
number = {7},
pages = {e70356},
pmid = {40671685},
issn = {1473-2165},
mesh = {Humans ; *Regenerative Medicine/trends/methods ; Artificial Intelligence ; *Skin Aging/physiology ; *Dermatology/trends/methods ; *Longevity ; Rejuvenation ; *Cosmetic Techniques/trends ; Microbiota ; Skin ; Precision Medicine/methods/trends ; },
abstract = {BACKGROUND: Aging is increasingly recognized as a modifiable biological process influenced by genetic, environmental, and lifestyle factors. Recent advances in regenerative medicine and artificial intelligence (AI) have reshaped the field of cosmetic dermatology, shifting the focus from temporary aesthetic improvements to long-term interventions aimed at preserving skin vitality and longevity.<br><br>AIM: This narrative review aims to synthesize emerging knowledge from 2010 to 2025 on the integration of regenerative strategies, biological modulators, immunologic regulation, microbiome modulation, and AI-driven personalization in the context of aesthetic longevity. The review also discusses translational potential and ethical considerations surrounding these advancements.<br><br>METHODS: A targeted literature search was conducted using PubMed and Scopus to identify peer-reviewed articles from 2010 to 2025. Search terms included "skin aging," "stem cells," "mitochondrial dysfunction," "epigenetic reprogramming," "artificial intelligence in dermatology," and "skin microbiome." Selected studies focused on regenerative and longevity-based interventions with clinical relevance or future applicability in cosmetic dermatology.<br><br>RESULTS: Key findings were categorized into six interconnected domains: regenerative medicine, mitochondrial function, epigenetic modulation, immunological balance, microbiome resilience, and AI-driven innovation. These pillars demonstrate a paradigm shift toward biologically informed, personalized strategies that aim to restore and sustain skin health at the molecular level.<br><br>CONCLUSION: Cosmetic dermatology is undergoing a transformation toward integrative, proactive care that combines regenerative medicine, AI, and personalized interventions. These approaches offer promising, evidence-based solutions for enhancing both aesthetic outcomes and long-term skin function, while also raising important ethical and regulatory considerations for clinical implementation.},
}
@article {pmid40671662,
year = {2025},
author = {Bullon, P and Giampieri, F and Bullon, B and Battino, M},
title = {The Role of Oxidative Stress in Periodontitis.},
journal = {Journal of periodontal research},
volume = {},
number = {},
pages = {},
doi = {10.1111/jre.70016},
pmid = {40671662},
issn = {1600-0765},
abstract = {Periodontitis and noncommunicable diseases share an overall inflammatory state often sustained by concomitant oxidative stress as one of the main processes involved. A huge amount of literature supports such a main pathogenic process, which is also considered the therapeutic target. The attempt to control inflammation by acting on oxidative stress has given largely unsatisfactory results, either as preventive or as treatment approaches. To propose new ideas that will help in this field, the paper reviewed all physiological processes involved in oxidative stress in periodontitis. The discussion considers all of them, considering whether they come from endogenous sources, that is, all the intracellular physiological devices and/or processes that are involved in oxidative stress, such as mitochondria, rough endoplasmic reticulum, peroxisomes, autophagy, and aging, or from exogenous sources, that is, the external factors that affect oxidative stress, such as nutrition, physical activity, psychological status, environmental conditions, microbiome, and drugs. The most important conclusion is that all of them should be taken into consideration in future research since we need to address oxidative stress as part of a specific biological and metabolic cellular state in a multicellular organism. To understand the cellular physiology that underlies oxidative stress and consider this point in treating each of our periodontal patients according to a specific oxidative state could be called personalized/precise oxidative stress therapy (POST) and should include the following points: (1) environmental conditions, (2) individual characteristics, and (3) oxidative state of different intracellular organelles.},
}
@article {pmid40671646,
year = {2025},
author = {Yang, T and Maki, KA and Marques, FZ and Cai, J and Joe, B and Pepine, CJ and Pluznick, JL and Meyer, KA and Kirabo, A and Bennett, BJ and , },
title = {Hypertension and the Gut Microbiome: A Science Advisory From the American Heart Association.},
journal = {Hypertension (Dallas, Tex. : 1979)},
volume = {},
number = {},
pages = {},
doi = {10.1161/HYP.0000000000000247},
pmid = {40671646},
issn = {1524-4563},
abstract = {Although substantial advancements have been made in hypertension research, translation of this research into new pharmacotherapies remains challenging. The need for new therapies is imperative: 15% to 20% of patients with hypertension have treatment-resistant hypertension, which often persists despite aggressive clinical treatments consisting of ≥3 medication classes, including a diuretic. Numerous preclinical studies have demonstrated that alterations in the gut microbiome affect blood pressure, suggesting an important role for this nonconventional cardiovascular risk factor. This innovative association suggests a novel therapeutic opportunity for hypertension: modifying the gut microbiome to control hypertension. In line with this hypothesis, clinical trials have been launched to examine whether hypertension can be managed by targeting the gut microbiome. This American Heart Association Science Advisory aims to outline clinical evidence, raise awareness among the health care community about the importance of the gut microbiome in patients with hypertension, update existing knowledge, identify research gaps, and ultimately facilitate the rapid translation of findings into clinical trials and practice.},
}
@article {pmid40671632,
year = {2025},
author = {Hunt, RL and Oh, J and Jain, A and Kuo, TH and Berardi, D and Jian, W and Song, D and Wu, Q and Goodman, AL and Palm, NW and Zimmermann, M and Johnson, CH and Crawford, JM},
title = {Discovery of a Widespread Polyamine-Low-Molecular-Weight Thiol Hybrid Pathway in Clostridioides difficile.},
journal = {ACS infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1021/acsinfecdis.5c00286},
pmid = {40671632},
issn = {2373-8227},
abstract = {Clostridioides difficile infection can cause severe inflammation in the gastrointestinal (GI) tract, leading to diarrhea, colitis, and an increased risk of colorectal cancer. Colonization of C. difficile is associated with microbial community-level changes in the expression of polyamine and polyamine precursor biosynthesis genes. Polyamines are abundant cationic metabolites that serve indispensable functions for all kingdoms, particularly in gut homeostasis. Catabolism of the polyamine precursors arginine and ornithine offers C. difficile supplemental nutrition while subverting host immunity, yet existing models of C. difficile metabolism are incomplete regarding polyamines with comparable importance in the gut (e.g., spermidine). In this study, we conducted feeding studies with isotope-labeled polyamines and discovered a network of low-molecular-weight thiol (LMWT) molecules termed clostridithiols (CSHs) constructed from polyamines conjugated with N-acetylcysteine (NAC) moieties. NAC is clinically used as a mucolytic agent and is a well-established redox molecule. Through the analysis of a human microbiota diversity collection, we established that these previously uncharacterized hybrid metabolites are widely detected in Firmicutes and Bacteroidetes. A genetic screen using DNA from an alternative CSH producerBacteroides uniformis enabled the identification and validation of a two-gene operon, including a gene encoding a domain of unknown function, that was conserved in both producing organisms and other members of the microbiome. CSH abundance in GI mucosal biopsies positively correlated with colorectal cancer compared with matched healthy control samples. These studies indicate that human microbial metabolism broadly unites polyamine and LMWT functionalities to generate metabolites that may be associated with disease.},
}
@article {pmid40671239,
year = {2025},
author = {Thatcher, C and Damjanovic, K and Kuek, F and Laffy, PW and Bourne, DG and Høj, L},
title = {Bacterial Dynamics in Newly Settled Acropora kenti: Insights From Inoculations With Individual Probiotic Candidates.},
journal = {Environmental microbiology},
volume = {27},
number = {7},
pages = {e70143},
doi = {10.1111/1462-2920.70143},
pmid = {40671239},
issn = {1462-2920},
support = {RRAP-ECT3//Department of Climate Change, Energy, the Environment and Water/ ; //AIMS@JCU/ ; },
mesh = {*Anthozoa/microbiology/growth &amp; development ; *Probiotics ; Animals ; *Microbiota ; *Bacteria/genetics/classification/isolation &amp; purification ; Pseudoalteromonas ; Halomonas/physiology ; Rhodobacteraceae/physiology ; },
abstract = {Bacterial probiotics hold promise for enhancing coral health and stress resilience; however, their application to coral juveniles, which are critical for restorative aquaculture, remains underexplored. Here, we show that the microbiome of newly settled Acropora kenti is amenable to manipulation, with individual probiotic candidates inducing distinct microbiome responses that differed in their stability after the final inoculation. Three of the eight tested strains, Halomonas smyrnensis, Endozoicomonas acroporae and Roseivivax lentus, remained prevalent in the microbiome at least 5 days post-inoculation. Notably, aggregates of Endozoicomonas cells were observed exclusively in the corresponding treatment, marking the first report of coral-associated microbial aggregates (CAMAs) in early life stage acroporids and the first induced through bacterial manipulation. In the Pseudoalteromonas rubra treatment, the inoculum was detected at low relative abundance but induced a microbiome shift that persisted beyond the final inoculation. While no significant coral health benefits were observed in this short 17-day experiment, the Ruegeria arenilitoris strain unexpectedly induced tissue regression and mortality. The described experimental system offers a systematic approach for tracking bacterial dynamics in newly settled corals, facilitating the identification of potentially beneficial strains and the exclusion of harmful ones to inform the design of probiotic consortia for coral aquaculture.},
}
@article {pmid40671160,
year = {2025},
author = {Wang, S and Kong, F and Zhang, X and Dai, D and Li, C and Cao, Z and Wang, Y and Wang, W and Li, S},
title = {Disruption of hindgut microbiome homeostasis promotes postpartum energy metabolism disorders in dairy ruminants by inhibiting acetate-mediated hepatic AMPK-PPARA axis.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {167},
pmid = {40671160},
issn = {2049-2618},
support = {32130100//National Natural Science Foundation of China/ ; },
mesh = {Animals ; Female ; *Gastrointestinal Microbiome/physiology ; Cattle ; *Energy Metabolism ; *AMP-Activated Protein Kinases/metabolism ; *Liver/metabolism ; Homeostasis ; *Postpartum Period/metabolism ; *PPAR alpha/metabolism/genetics ; *Acetates/metabolism ; 3-Hydroxybutyric Acid/blood ; Ruminants/microbiology ; },
abstract = {BACKGROUND: Postpartum energy metabolism disorders pose a significant challenge to the health and productivity of dairy ruminants, yet their underlying pathogenesis remains poorly understood. The critical role of the gut microbiota in regulating host metabolic processes via the "gut-liver axis" has garnered increasing attention, but its specific mechanisms in dairy ruminant energy metabolism disorders are still unclear. This study uses dairy cows as a model and employs a large-scale case-control analysis to systematically investigate the pathophysiological basis of postpartum energy metabolism disorders through the lens of the "gut-liver axis."<br><br>RESULTS: Postpartum energy metabolism disorders in dairy cows are characterized by elevated blood &#x3b2;-hydroxybutyrate (BHB) and aspartate aminotransferase (AST) levels, and hepatic steatosis. A random forest model based on gut microbiota effectively predicts disease occurrence (AUC&#x2009;=&#x2009;0.74). Multi-omics (metagenomics, metabolomics, and transcriptomics) analysis further identified key microbes, including Faecousia species (sp017465625 and sp017380435), Methanosphaera species (sp016282985), and Bifidobacterium globosum. These microbes regulate acetate concentration in the gut, which is significantly correlated with key genes in the hepatic PPAR and PI3K-AKT pathways, as well as with blood BHB levels. Primary hepatocyte culture experiments further confirmed that sodium acetate effectively inhibits hepatic fat deposition induced by mixed fatty acids through the hepatic AMPK-PPARA axis and reduces the production of BHB in the culture medium.<br><br>CONCLUSION: This study demonstrates that key gut microbes and their metabolic product (acetate) inhibit the occurrence of metabolic disorders through the hepatic AMPK-PPARA axis. These findings provide new insights and potential therapeutic targets for understanding and mitigating postpartum metabolic disorders in dairy&#xa0;ruminants. Video Abstract.},
}
@article {pmid40671070,
year = {2025},
author = {Chen, YT and Sun, YT and Lee, HF and Lin, YC and Chen, MJ},
title = {Probiotic supplementation regulated swine growth performance, fecal odor reduction and carcass characteristics by modulating intestinal microbiome.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {74},
pmid = {40671070},
issn = {2524-4671},
support = {110-2321-B-002-020//National Science and Technology Council, Taiwan/ ; },
abstract = {BACKGROUND: Using probiotics as a substitute for antibiotic growth promoters and reducing odor has received increasing attention in animal science. Despite the extensive investigation into the effects of probiotic administration on swine growth performance and odor reduction by short study durations, the analysis of carcass characteristics and potential mechanistic insights involving gut microbiota and downstream pathways is still few.<br><br>METHODS: A total of 48 crossbred LYD [(Landrace x Yorkshire) x Duroc] piglets (equal numbers of males and females) were randomly assigned to one of four dietary treatments: control (CON), Lactobacillus kefiranofaciens M1 (M1), M1&#x2009;+&#x2009;Bacillus amyloliquefaciens S20 (SA group) and M1&#x2009;+&#x2009;S20&#x2009;+&#x2009;Bacillus subtilis S14 (SAM group). During the nursery phase (4-8 weeks), pigs were pair-housed and monitored for diarrhea. From 8 to 19 weeks of age, pigs were individually housed and fed grower-finisher diets. Growth performance, blood biochemistry, fecal enzyme activity, and odor-related metabolites were assessed at multiple time points. At market weight (~&#x2009;110&#xa0;kg), six pigs per group were slaughtered for carcass and cecal microbiota analysis.<br><br>RESULTS: The results demonstrated that administration of the probiotics led to increased body weight and average daily weight gain, particularly notable during the weaning and finishing periods. Additionally, the SA and SAM groups significantly reduced skatole concentration in feces. Furthermore, probiotic supplementation was associated with increased carcass weight, with the SAM group exhibiting significantly higher tenderloin weight than the CON group. Microbiota analysis revealed taxa exhibiting significant differences in abundance among groups, with corresponding LEfSe findings.<br><br>CONCLUSION: Administering Bacillus subtilis S14 and B. amyloliquefaciens S20 (SA group) impacted growth performance, reduced fecal odor, and enhanced pig carcass quality. The identified probiotic strains hold promise as feed additives, offering a potential solution to challenges encountered by the swine industry.},
}
@article {pmid40671045,
year = {2025},
author = {Khan, I and Panaiotov, S and Attia, KA and Mohammed, AA and Uzair, M and Khan, I and Li, Z and Xie, X},
title = {Integrated analysis of blood microbiome and metabolites reveals key biomarkers and functional pathways in myocardial infarction.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {797},
pmid = {40671045},
issn = {1479-5876},
support = {22JR5RA19//Gansu Provincial Science and Technology Program/ ; 24ZDCA004//Science and Technology Program gansu province/ ; },
mesh = {Humans ; *Biomarkers/blood/metabolism ; *Myocardial Infarction/microbiology/blood/metabolism ; *Microbiota ; Male ; Middle Aged ; *Metabolomics ; Female ; Metabolome ; Signal Transduction ; RNA, Ribosomal, 16S/genetics ; Aged ; Case-Control Studies ; Bacteria ; },
abstract = {BACKGROUND: Myocardial infarction (MI) has been linked to changes in the blood microbiome, yet the interplay between microbiome and metabolome remains poorly understood. This study integrates blood microbiome profiling and metabolomic analysis to uncover biomarkers and pathways associated with MI.<br><br>METHODS: Using 16&#xa0;S rRNA sequencing and LC-MS metabolomics, blood samples from 24 MI patients and 24 healthy controls were analyzed. Microbial diversity, key taxa, metabolites, and their functional implications were evaluated.<br><br>RESULTS: While alpha and beta diversity of the microbiome showed no significant differences, three bacterial taxa (Proteobacteria, Gammaproteobacteria, and Bacilli) and twenty metabolites (e.g., UPD-L-Ara4O, Urotensin-related peptide, and 9-hydroxy octadecanoic acid) were identified as potential biomarkers, achieving an AUC of 0.99-1. Functional pathway analysis revealed upregulation in glycerolipid metabolism and mTOR signaling pathways, which were significantly correlated with clinical markers of MI.<br><br>CONCLUSION: This integrative approach highlights the diagnostic potential of blood microbiome-metabolome dynamics in MI and suggests mechanistic pathways that could guide future interventions.},
}
@article {pmid40670979,
year = {2025},
author = {Petat, H and Hassel, C and Michel, A and Charbonnier, C and Plantier, JC and Marguet, C},
title = {Microbiosthma: a prospective study following respiratory microbiota in young children with severe preschool wheezing to better understand their respiratory future.},
journal = {BMC pulmonary medicine},
volume = {25},
number = {1},
pages = {342},
pmid = {40670979},
issn = {1471-2466},
mesh = {Child, Preschool ; Female ; Humans ; Infant ; Male ; Bronchoalveolar Lavage Fluid/microbiology ; *Dysbiosis/microbiology ; *Microbiota ; Prospective Studies ; *Respiratory Sounds/etiology ; *Respiratory System/microbiology ; Sputum/microbiology ; },
abstract = {Preschool wheeze is a frequent infant disease, which can be severe. A continuous infection/inflammation loop at the heart of the pathophysiology is described, which could lead to a dysbiosis. In this context, the main objective of the "Microbiosthma" project is to assess whether dysbiosis of the upper and lower respiratory microbiomes could constitute a physiopathological biomarker of severe preschool wheeze in young children. This project will be divided into three parts: (i) determine the basal composition of the respiratory microbiomes (ii) monitor these microbiomes longitudinally over the course of the severe preschool wheeze, with a one-year follow-up, and (iii) assess the role of immune cell activation and inflammation in the pathogenesis of severe preschool wheeze. The "Microbiosthma" project is a bicentric, prospective study. Bronchial fibroscopy is performed on children aged < 24 months with severe preschool wheeze. One hundred infant nasopharyngeal, bronchoalveolar lavage and sputum samples will be collected over 2 years, and patients will be followed for 12 months. This collection started in September 2023. Microbiome analyses will use a metatranscriptomic approach and immunological analyses for all samples collected. For immunological analysis, key inflammatory cytokines in bronchoalveolar lavage samples will be measured. Host sequencing data obtained by NGS sequencing will be analysed for transcriptomic signatures of inflammatory profiles. The aim of the "Microbiosthma" project is to understand the respiratory microbiome of the physiopathological process involved in the development of severe preschool wheeze. This original project will therefore identify the nature of potential dysbiosis, the relationship between different respiratory microbiomes and the potential role of the immune system in this pathogenesis. The registration number is NCT06044051 (CCP Nord-Ouest, 07/11/2023).},
}
@article {pmid40670830,
year = {2025},
author = {Mahooti, M and Safaei, F and Firuzpour, F and Abdolalipour, E and Zare, D and Sanami, S and Safavi, M and Mirdamadi, S},
title = {Exploring the role of inflammatory regulatory effects of probiotics as adjuvants in cancer development management with considering possible challenges: a comprehensive review.},
journal = {Inflammopharmacology},
volume = {},
number = {},
pages = {},
pmid = {40670830},
issn = {1568-5608},
abstract = {Probiotics have gained significant interest due to their versatile therapeutic and preventive potential. These beneficial microorganisms have primarily been studied in gastrointestinal disorders and, due to their inflammatory regulatory effects, have then been investigated for their effects on a wide range of conditions, from acute illnesses and chronic diseases to inflammation-related diseases, including cancer. Probiotics can not only restore microbiome balance following different treatments, from antibiotic therapy to some cancer treatments, but also, with their immunomodulatory and inflammatory regulation effects, they can induce potent immune responses in different conditions with minor side effects. Moreover, as they can secrete anti-inflammatory cytokines as well as reduce pro-inflammatory cytokines as well as chemokine, they can be applied to prevent the development of many inflammation disorders. Therefore, studies have been directed to survey probiotic adjuvant effects, especially regarding their potential in the reduction of inflammation to become chronic. Probiotics, as an adjuvant, can increase the antigens displayed to related cells and thus activate different immune response compartments. Moreover, probiotic adjuvant can modulate inflammation in cancer development, making them strong candidates for regulating inflammation. With the increase and improvement in our knowledge about the adjuvant role of probiotics in the inflammatory processes underlying cancer development, it is pivotal to review current studies in this field. Therefore, the current study strives to provide a review of the latest studies regarding the probiotic's adjuvant effect in the field of immunology and oncology research to benefit the scientific community.},
}
@article {pmid40670809,
year = {2025},
author = {Talat, A and Zuberi, A and Khan, AU},
title = {Unravelling the Gut-Microbiome-Brain Axis: Implications for Infant Neurodevelopment and Future Therapeutics.},
journal = {Current microbiology},
volume = {82},
number = {9},
pages = {390},
pmid = {40670809},
issn = {1432-0991},
support = {BT/PR40148/BTIS/137/20/2021//Department of Biotechnology, Ministry of Science and Technology, India/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Brain/growth &amp; development/physiology ; Infant ; *Neurodevelopmental Disorders/therapy/microbiology ; Dysbiosis ; Probiotics ; Infant, Newborn ; Animals ; },
abstract = {The microbiome-gut-brain axis signifies the intricate interplay between gut microbiome and brain, facilitated by bidirectional communication channels. The brain modulates gut function through the hypothalamic-pituitary-adrenal axis and the autonomic nervous system, while the gut influences central nervous system (CNS) function through microbial metabolites, neurotransmitters, and gut hormones. Early brain development in infants is shaped by mother to neonate microbiome transmission, mode of birth, gestational length, breastfeeding, maternal and infant antibiotic exposure, and acquired infections. Dysbiosis in the gut microbiome is associated with various neurodevelopmental disorders in children such as attention-deficit hyperactivity disorder (ADHD) and autism spectrum disorder (ASD). In this review, we elucidate the pivotal role of the microbiome-gut brain axis in a child's neural development, exploring factors modulating this intricate interaction. Furthermore, we discuss the potential future therapeutic avenues that can support optimal neurodevelopment, such as probiotics, prebiotics, synbiotics, postbiotics, CRISPR/Cas9, fecal microbiota transplant, and phage therapy.},
}
@article {pmid40670795,
year = {2025},
author = {Grießhammer, A and de la Cuesta-Zuluaga, J and Müller, P and Gekeler, C and Homolak, J and Chang, H and Schmitt, K and Planker, C and Schmidtchen, V and Gallage, S and Bohn, E and Nguyen, TH and Hetzer, J and Heikenwälder, M and Huang, KC and Zahir, T and Maier, L},
title = {Non-antibiotics disrupt colonization resistance against enteropathogens.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {40670795},
issn = {1476-4687},
abstract = {Non-antibiotic drugs can alter the composition of the gut microbiome[1], but they have largely unknown implications for human health[2]. Here we examined how non-antibiotics affect the ability of gut commensals to resist colonization by enteropathogens[3]. We also developed an in vitro assay to assess enteropathogen growth in drug-perturbed microbial communities. Pathogenic Gammaproteobacteria were more resistant to non-antibiotics than commensals and their post-treatment expansion was potentiated. For 28% of the 53 drugs tested, the growth of Salmonella enterica subsp. enterica serovar Typhimurium. (S. Tm) in synthetic and human stool-derived communities was increased, and similar effects were observed for other enteropathogens. Non-antibiotics promoted pathogen proliferation by inhibiting the growth of commensals, altering microbial interactions and enhancing the ability of S. Tm to exploit metabolic niches. Drugs that promoted pathogen expansion in vitro increased the intestinal S. Tm load in mice. For the antihistamine terfenadine, drug-induced disruption of colonization resistance accelerated disease onset and increased inflammation caused by S. Tm. Our findings identify non-antibiotics as previously overlooked risk factors that may contribute to the development of enteric infections.},
}
@article {pmid40670792,
year = {2025},
author = {Lee, KK and Liu, S and Crocker, K and Wang, J and Huggins, DR and Tikhonov, M and Mani, M and Kuehn, S},
title = {Functional regimes define soil microbiome response to environmental change.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {40670792},
issn = {1476-4687},
abstract = {The metabolic activity of soil microbiomes has a central role in global nutrient cycles[1]. Understanding how soil metabolic activity responds to climate-driven environmental perturbations is a key challenge[2,3]. However, the ecological, spatial and chemical complexity of soils[4-6] impedes understanding how these communities respond to perturbations. Here we address this complexity by combining dynamic measurements of respiratory nitrate metabolism[7] with modelling to reveal functional regimes that define soil responses to environmental change. Measurements across more than 1,500 soil microcosms subjected to pH perturbations[8,9] reveal regimes in which distinct mechanisms govern metabolite dynamics. A minimal model with two parameters, biomass activity and growth-limiting nutrient availability, predicts nitrate utilization dynamics across soils and pH perturbations. Parameter shifts under perturbation reveal three functional regimes, each linked to distinct mechanisms: (1) an acidic regime marked by cell death and suppressed metabolism; (2) a nutrient-limited regime in which dominant taxa exploit matrix-released nutrients; and (3) a resurgent growth regime driven by exponential growth of rare taxa in nutrient-rich conditions. We validated these model-derived mechanisms with nutrient measurements, amendment experiments, sequencing and isolate studies. Additional experiments and meta-analyses suggest that functional regimes are widespread in pH-perturbed soils.},
}
@article {pmid40670788,
year = {2025},
author = {Kumar, A and Sun, R and Habib, B and Deng, T and Bencivenga-Barry, NA and Palm, NW and Ivanov, II and Tamblyn, R and Goodman, AL},
title = {Identification of medication-microbiome interactions that affect gut infection.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {40670788},
issn = {1476-4687},
abstract = {Most people in the USA manage their health by taking at least one prescription drug, and drugs classified as non-antibiotics can adversely affect the gut microbiome and disrupt intestinal homeostasis[1,2]. Here we identify medications that are associated with an increased risk of gastrointestinal infections across a population cohort of more than one million individuals monitored over 15 years. Notably, the cardiac glycoside digoxin and other drugs identified in this epidemiological study are sufficient to alter the composition of the microbiome and the risk of infection with Salmonella enterica subsp. enterica serovar Typhimurium (S. Tm) in mice. The effect of digoxin treatment on S. Tm infection is transmissible through the microbiome, and characterization of this interaction highlights a digoxin-responsive β-defensin that alters the microbiome composition and consequent immune surveillance of the invading pathogen. Combining epidemiological and experimental approaches thus provides an opportunity to uncover drug-host-microbiome-pathogen interactions that increase the risk of infections in humans.},
}
@article {pmid40670741,
year = {2025},
author = {Rey, F and Vemuganti, V},
title = {Gut bacteria make a molecule that promotes plaque build-up in arteries.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {40670741},
issn = {1476-4687},
}
@article {pmid40670700,
year = {2025},
author = {Liu, Y and Zhang, W and Guo, L and Li, H and Zhu, J and Li, X and Zhang, X and Yang, X and Xu, Y and Shen, Q and Yang, T and Wei, Z},
title = {Development of a chemotactic SynCom bioorganic fertilizer for biocontrol of bacterial wilt in tobacco fields.},
journal = {Applied microbiology and biotechnology},
volume = {109},
number = {1},
pages = {168},
pmid = {40670700},
issn = {1432-0614},
support = {2022XM03//the Key Research and Development Project of Guizhou Province of China National Tobacco Corporation/ ; 2022XM03//the Key Research and Development Project of Guizhou Province of China National Tobacco Corporation/ ; 2022XM03//the Key Research and Development Project of Guizhou Province of China National Tobacco Corporation/ ; 2022XM03//the Key Research and Development Project of Guizhou Province of China National Tobacco Corporation/ ; 110202202015//the Key Projects of China National Tobacco Corporation/ ; 110202202015//the Key Projects of China National Tobacco Corporation/ ; 110202202015//the Key Projects of China National Tobacco Corporation/ ; 110202202015//the Key Projects of China National Tobacco Corporation/ ; No. 42477125//the National Natural Science Foundation of China/ ; No. 42477125//the National Natural Science Foundation of China/ ; No. 42477125//the National Natural Science Foundation of China/ ; No. 42477125//the National Natural Science Foundation of China/ ; No. 42477125//the National Natural Science Foundation of China/ ; No. 42477125//the National Natural Science Foundation of China/ ; No. 42477125//the National Natural Science Foundation of China/ ; No. 42477125//the National Natural Science Foundation of China/ ; },
mesh = {*Nicotiana/microbiology/growth &amp; development ; *Fertilizers ; *Plant Diseases/microbiology/prevention &amp; control ; Rhizosphere ; Soil Microbiology ; *Chemotaxis ; *Ralstonia solanacearum/growth &amp; development ; Pseudomonas/genetics/physiology ; Bacillus/genetics/physiology ; Bacteria/genetics/classification/isolation &amp; purification ; },
abstract = {Bacterial wilt caused by Ralstonia solanacearum is one of the most severe plant diseases all over the world. Currently, many scientists are using SynCom (synthetic microbial community) to control this disease. However, designing of highly efficient SynCom remains challenging. In this study, we isolated 372 bacteria with different morphologies from the rhizosphere soil of healthy tobacco plants in a diseased field. Based on the antagonistic activity, compatibility, and presence of cheA gene, a marker gene of chemotaxis, we constructed a chemotactic SynCom comprising two Pseudomonas strains and one Bacillus strain. In vitro experiments revealed that vitamin C, propionic acid, and esculetin significantly promoted the growth and antagonistic ability of chemotactic SynCom strains. Next, we optimized the proportion of organic fertilizer to support the growth of the SynCom strains. The application of the bioorganic fertilizer containing chemotactic SynCom can protect diseased tobacco field from R. solanacearum invasion and enhance yields. Finally, rhizosphere bacterial community analysis showed that phyla Bacillota and Chloroflexiota were significantly enriched. This study highlights the potential of chemotactic SynCom for effective biocontrol, offering a new approach for managing bacterial wilt and enhancing crop yields. KEY POINTS: • The bioorganic fertilizer containing chemotactic SynCom suppresses R. solanacearum and boosts tobacco yields. • Root exudate-selected prebiotics enhance the antagonistic effects of SynCom against pathogens. • SynCom bioorganic fertilizer regulates the rhizosphere microbiome, enriching beneficial bacterial phyla.},
}
@article {pmid40670579,
year = {2025},
author = {Eswaran, S and Gebert, L and Schraven, S and Treichel, N and Ritz, T and Hamm, S and Seeger, A and Kiessling, F and Clavel, T and Dreschers, S and Wagner, N and Schippers, A},
title = {Intercellular adhesion molecule-1 protects against adipose tissue inflammation and insulin resistance but promotes liver disease activity in western-diet fed mice.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {25884},
pmid = {40670579},
issn = {2045-2322},
mesh = {Animals ; *Intercellular Adhesion Molecule-1/genetics/metabolism ; *Insulin Resistance ; Mice ; *Diet, Western/adverse effects ; Male ; *Inflammation/metabolism/pathology ; *Adipose Tissue/metabolism/pathology ; Liver/metabolism/pathology ; Gastrointestinal Microbiome ; *Fatty Liver/metabolism/pathology/etiology ; Mice, Inbred C57BL ; Adipose Tissue, White/metabolism/pathology ; },
abstract = {Metabolic dysfunction associated steatotic liver disease (MASLD) presents a growing global health problem. Disease progression is promoted not only by hepatic leukocyte accumulation but also by inflammatory signals from adipose tissue and an altered gut microbiome. To determine the contribution of intercellular adhesion molecule-1 (ICAM-1) to MASLD pathogenesis, male mice with an ICAM-1 mutation (Icam1[tmBay]) and wild type (WT) mice were compared in 12 and 24-week feeding experiments with a Western-style diet (WD) containing 40 kcal% fat, 20 kcal% fructose, and 2% cholesterol. WD-induced MASLD was accompanied by increased ICAM-1 expression in liver, epididymal white adipose tissue (EWAT), and intestine in WT mice. WD-fed Icam1[tmBay] mice exhibited increased circulating neutrophils, higher frequencies of inflammatory leukocytes in EWAT, and a worsened glucose tolerance when compared to WT mice. In contrast, the mutation resulted in reduced WD-induced liver disease activity and less accumulation of intrahepatic leukocytes. WD-feeding caused substantial changes in fecal microbiota with decreased microbial diversity that differed between the mouse strains. In conclusion, ICAM-1 positively regulates adipose tissue homeostasis and protects from insulin resistance but promotes liver damage in diet-induced obesity. This points to organ-specific roles for ICAM-1 and the potential of liver-specific targeting of ICAM-1 for treatment of MASLD.},
}
@article {pmid40670440,
year = {2025},
author = {Liu, GH and Li, J and Yan, LX and Deng, HP and Quan, MH and Zuo, YW},
title = {Impact of rhizosphere quantitative microbiome and soil properties on alkaloid levels in Lycoris aurea herb.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {25806},
pmid = {40670440},
issn = {2045-2322},
support = {32070367; 31470403//National Natural Science Foundation of China/ ; 32070367; 31470403//National Natural Science Foundation of China/ ; 2024NSCQ-MSX2167//Chongqing Natural Science Foundation/ ; 2024NSCQ-MSX2167//Chongqing Natural Science Foundation/ ; },
mesh = {*Rhizosphere ; *Soil Microbiology ; *Alkaloids/metabolism/analysis ; *Microbiota ; *Lycoris/microbiology/metabolism/chemistry ; *Soil/chemistry ; Bacteria/genetics/classification ; Fungi/genetics/classification ; },
abstract = {Lycoris aurea Herb is a plant renowned for its striking appearance and medicinal properties, particularly the production of alkaloids such as lycorine and galanthamine, which have therapeutic potential in treating diseases. Understanding the interaction between L. aurea and its rhizosphere microbiome is crucial, as the microbiome influences plant health, nutrient availability, and metabolite biosynthesis. This study investigated the interplay between rhizosphere microbiome and alkaloid levels in L. aurea using genetically identical plant samples collected from two ecologically distinct regions. The findings revealed that higher levels of lycorine and galanthamine correlated with specific soil physicochemical properties such as higher acid phosphatase activity and higher sodium and manganese levels. Additionally, quantitative Accu16STM and AccuITSTM sequencing demonstrated distinct bacterial and fungal diversities in the high alkaloids-producing group compared with the low alkaloids-producing group. Our study found that the abundance of four dominant bacterial phyla Acidobacteriota, Proteobacteria, Actinobacteriota, and Planctomycetota was higher in the low-alkaloid content group, whereas the dominant fungal phylum Ascomycota was more abundant in the high-alkaloid content group. Linear discriminant analysis revealed distinct variations in bacterial and fungal taxa, with the high-alkaloid content group containing ten bacterial indicators, such as Kitasatospora and Acidimicrobiaceae, and ten fungal taxa, including Boletales, Vandijckomycella and Sclerodermataceae. Functional annotations of microbial taxa revealed differences in metabolic functions such as chitinolysis and nitrate reduction in the high alkaloid groups, respectively. Moreover, Spearman correlation analysis underscored the relationships between microbial diversity and soil characteristics, particularly emphasizing the role of soil pH in influencing microbial populations. In conclusion, this research provides valuable insights into the environmental and rhizosphere microbial dynamics of L. aurea, offering implications for alkaloid biosynthesis and pharmacology.},
}
@article {pmid40670389,
year = {2025},
author = {Arias, SL and van Wijngaarden, EW and Balint, D and Jones, J and Crawford, CC and Shukla, PJ and Silberstein, M and Brito, IL},
title = {Environmental factors drive bacterial degradation of gastrointestinal mucus.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {133},
pmid = {40670389},
issn = {2055-5008},
mesh = {Humans ; *Mucus/microbiology/metabolism ; *Bacteria/metabolism/genetics ; *Gastrointestinal Microbiome ; Peptide Hydrolases/metabolism ; *Gastrointestinal Tract/microbiology/metabolism ; *Intestinal Mucosa/microbiology/metabolism ; Bacterial Proteins/metabolism ; Oxidative Stress ; Bacteroides fragilis/metabolism ; },
abstract = {The mucus layer lining the gastrointestinal tract is essential for gut health, providing a protective barrier while maintaining host-microbiome symbiosis. Its disruption is a hallmark of diseases like ulcerative colitis, yet how bacterial activity impacts mucus structure remains unclear. We developed a method to collect human-cell-derived mucus that mimics human colonic mucus and used it to investigate mucus degradation by commensal bacteria. Glycan foraging by species such as Bacteroides thetaiotaomicron and Bacteroides fragilis did not alter mucus rheology. Instead, secreted proteases were the primary drivers of degradation. Protease activity by B. fragilis and Bifidobacterium longum subsp. infantis was nutrient-dependent, while Enterococcus faecalis was further influenced by oxygen. Under oxidative stress, E. faecalis upregulated carbohydrate metabolism and virulence genes. These results reveal that bacterial mucus degradation is context-dependent and shaped by environmental factors. Our findings underscore the value of human cell-derived mucus models for understanding bacteria-mucus interactions in health and disease.},
}
@article {pmid40670379,
year = {2025},
author = {Shi, W and Lv, M and Wang, R and Saleem, M and Wang, L and Li, M and Wang, B and Lin, R and Xu, B and Yang, C and Ning, T and Zhou, B and Gao, Z},
title = {Geocaulosphere soil bacterial community drives potato common scab outcomes beyond pathogen abundance.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {134},
pmid = {40670379},
issn = {2055-5008},
support = {2024M751875//China Postdoctoral Science Foundation/ ; 42407427//National Natural Science Foundation of China/ ; 42377309//National Natural Science Foundation of China/ ; 2023YFD20014003//Shandong Provincial "811" Project of First-class Discipline Construction, the National Key R&amp;D Program of China/ ; 2023BCF01015//Key R&amp;D Program of Ningxia Hui Autonomous Region of China/ ; M2023-07//State Key Natural Science Foundations of China Laboratory of Microbial Technology Open Projects Fund/ ; SDAIT-16-01//Potato Innovation Program for the Chief Expert of Shandong Province/ ; 2021CXGC010804//Shandong Province Key R&amp;D Program/ ; },
mesh = {*Solanum tuberosum/microbiology ; *Soil Microbiology ; *Plant Diseases/microbiology ; *Microbiota ; *Bacteria/classification/genetics/isolation &amp; purification ; Metagenomics ; Soil/chemistry ; },
abstract = {The assembly mechanisms of soil microbiome during plant disease progression remain incomplete. This study linked potato common scab (PCS) severity to destabilized soil microbiome dynamics in potato geocausphere soil (GS) through integrated metagenomic analysis and culture-based experiments. Across four Shandong fields, PCS-infected GS exhibited an 11.66% reduction in bacterial α-diversity (Shannon index) and elevated stochastic community assembly. Bacterial community structure explained 39.28% (GS) and 15.96% (bulk soil) of PCS variance, outperforming pathogen abundance contributions (14.39% GS, 7.33% BS). Two microbial interaction patterns emerged in GS: 1) synchronized shifts between pathogens and beneficial taxa as PCS intensified; 2) stochastic assembly governing entire communities but deterministic processes dominating specialized subgroups. These results propose a microbial stability framework connecting soil microbiome structural rules to plant disease progression, emphasizing community-level dynamics over pathogen-centric explanations.},
}
@article {pmid40669940,
year = {2025},
author = {Robillard, K and Varshney, P},
title = {Current Food Allergy Treatment Options.},
journal = {Immunology and allergy clinics of North America},
volume = {45},
number = {3},
pages = {403-418},
doi = {10.1016/j.iac.2025.04.007},
pmid = {40669940},
issn = {1557-8607},
mesh = {Humans ; *Food Hypersensitivity/therapy/immunology/diagnosis/etiology ; Allergens/immunology ; Probiotics/therapeutic use ; *Desensitization, Immunologic/methods ; Medicine, Chinese Traditional ; Anaphylaxis ; Disease Management ; },
abstract = {Food allergy is a significant health issue affecting millions of people worldwide, and the prevalence is increasing. Food allergy impacts physical health, finances, school and work attendance, mental health, and quality of life. Historically, allergen avoidance, anaphylaxis education, and prompt use of intramuscular epinephrine were the only treatment options. Now, there are 2 Food and Drug Administration-approved products (Palforzia and Xolair), which can help reduce the risk of severe food allergy reactions. There is ongoing research regarding the use of immunotherapy (oral, sublingual, and epicutaneous), other monoclonal antibodies (eg, dupilumab), probiotics and microbiome manipulation, and traditional Chinese medicine.},
}
@article {pmid40669623,
year = {2025},
author = {Zhan, Y and Liang, J and Zhou, S and Zhang, C and Chen, X and Gao, L and Zhao, J and He, Y and Zhao, M and Lu, Q},
title = {Structure characterization and repair of UVB-induced skin inflammation of rhamnomannan derived from Roseomonas mucosa DL-1.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {145903},
doi = {10.1016/j.ijbiomac.2025.145903},
pmid = {40669623},
issn = {1879-0003},
abstract = {The skin microbiome plays a crucial role in both (epi-) dermal immune and defense responses, with the skin commensal microbiota being closely associated with various skin diseases. While the therapeutic applications of skin microbiota are expanding, there are still gaps in the understanding of specific mechanisms and applications. In this study, a low-molecular-weight exopolysaccharide (DLEPS) derived from Roseomonas mucosa DL-1 was structurally analyzed using nuclear magnetic resonance and methylation techniques. The analysis revealed that DLEPS is a rhamnomannan, with a primary chain composed of galactose, rhamnose and mannose. The effect of DLEPS on Ultraviolet radiation b (UVB) radiation was investigated both in vitro and in vivo. Pretreatment with DLEPS prior to UVB exposure led to a dose-dependent reduction in apoptosis of HaCaT cells, alongside inhibition of the apoptosis-related YAP-p73 pathway. Additionally, topical application of DLEPS alleviated UVB-induced skin damage in C57BL/6J mice, significantly reducing skin inflammation, lowering serum levels of IL-1β and IL-6, and increasing levels of IL-10. These findings support the therapeutic potential of DLEPS in mitigating UVB-induced skin inflammation.},
}
@article {pmid40669611,
year = {2025},
author = {Song, S and Li, F and Zhao, B and Xu, Y and Liu, Z and Liu, J and Hou, Q and Chen, J and Chen, M and Liu, Z and Zhou, M and Wu, X and Wang, X},
title = {Sparfloxacin ameliorates DSS-induced ulcerative colitis by suppressing cellular senescence, JAK/NF-κB signaling pathway and modulation of the gut microbiota-metabolite axis.},
journal = {Biochemical pharmacology},
volume = {241},
number = {},
pages = {117167},
doi = {10.1016/j.bcp.2025.117167},
pmid = {40669611},
issn = {1873-2968},
abstract = {The progression of ulcerative colitis (UC) involves immune dysregulation, intestinal barrier dysfunction, and microbial dysbiosis while existing targeted therapies present challenges, including adverse effects and economic burdens. UC is characterized by persistent intestinal inflammation, manifesting as abdominal pain, hematochezia, and malnutrition. Prolonged uncontrolled inflammation may lead to colorectal cancer or severe complications, significantly impairing quality of life. Recent studies have revealed a significant correlation between pathological accumulation of senescent cells and UC pathogenesis, suggesting anti-senescence therapeutics as potential interventions. In this study, we identified sparfloxacin (SPA), a fluoroquinolone antibiotic, through high-throughput screening as an effective senolytic agent that markedly alleviates DSS-induced murine colitis. Mechanistically, combining cellular and animal experiments with transcriptomic, untargeted metabolomic, and metagenomic analyses, we demonstrated sparfloxacin's tripartite therapeutic effects: ① Senescence inhibition via downregulation of p16/p21 expression; ② Effective suppression of aberrant JAK/NF-κB signaling activation with a concomitant reduction in pro-inflammatory cytokines (TNF-α, IL-6); ③ Gut microbiota remodeling characterized by increased probiotic abundance and elevated levels of beneficial metabolites. This study for the first time elucidates the molecular mechanism whereby SPA ameliorates UC through coordinated multi-target actions involving senescence inhibition, anti-inflammatory effects, and microbiome restoration. Our findings not only expand the clinical applications of fluoroquinolones but also provide a theoretical foundation for developing integrated UC treatment strategies targeting cellular senescence.},
}
@article {pmid40669221,
year = {2025},
author = {Mishra, S and Yang, X},
title = {How to safeguard soil health against silver nanoparticles through a microbial functional gene-based approach?.},
journal = {Environment international},
volume = {202},
number = {},
pages = {109680},
doi = {10.1016/j.envint.2025.109680},
pmid = {40669221},
issn = {1873-6750},
abstract = {Silver nanoparticles (AgNPs), a major anthropogenic stressor, can threaten soil health by disrupting vital microbial processes critical to maintaining key soil functions such as nutrient cycling, organic matter decomposition, and soil structure formation. Their safe use demands proactive strategies to preserve soils, a globally essential and non-renewable resource that acts as the ultimate sink for nanoparticles released into ecosystems. As functionally critical components of soil ecosystems, microorganisms warrant central consideration in developing nanotoxicity mitigation strategies. This review establishes a framework for soil health protection through systematic examination of (a) AgNPs-mediated ecotoxicological impacts on soil ecosystems, (b) microbial community tolerance thresholds, and (c) ecosystem functions most vulnerable to AgNPs exposure. Through bibliometric analysis of 61 studies, we synthesized comprehensive data on AgNPs-tolerant/sensitive microbial taxa and functional genes, while highlighting critical research gaps and priority research area. Our assessment identifies the following key challenges in predicting AgNPs ecotoxicity in soil systems: (1) a wide toxicity dose-response range, with significant effects observed even at environmentally relevant concentrations (≤1.0 mg/kg), (2) high microbial taxonomic heterogeneity complicating targeted identification, as most taxa remain unculturable, uncharacterized, or classifiable only at higher taxonomic ranks, and (3) limited knowledge of soil-AgNPs-environment interactions hindering identification of critical factors controlling AgNPs toxicity in soils. We then demonstrate how functional gene analysis can improve toxicity prediction accuracy and identify compromised soil processes. This functional genomics approach outperforms taxonomic characterization in predicting AgNPs impacts on soil health by directly quantifying disturbances to critical ecosystem processes. This framework will guide future research in predicting AgNPs' impacts on soil microbial functionality and overall soil health, while offering a broadly applicable approach to assess toxicity for other emerging anthropogenic stressors, including engineered nanomaterials, pesticides, microplastics, and other soil contaminants.},
}
@article {pmid40669177,
year = {2025},
author = {Meng, T and Wang, Z and Li, H and Ouyang, Z and Yang, C and Lian, T and Zhang, Y and Li, H and Bao, P and Liu, D},
title = {The Effects of Azithromycin Modified Triple Antibiotic Paste in Resolving Periapical Inflammation.},
journal = {International dental journal},
volume = {75},
number = {5},
pages = {100895},
doi = {10.1016/j.identj.2025.100895},
pmid = {40669177},
issn = {1875-595X},
abstract = {OBJECTIVE: This study aimed to assess the anti-inflammatory and antibacterial properties of traditional and modified triple antibiotic paste. The 16S rDNA was employed to analyse the root canal microbial community's characteristics pre- and post-treatment.<br><br>METHODS: Rabbits with periapical inflammation (AP) were treated with both pastes. Micro-CT was performed to compare the periapical lesion area, followed by HE staining. Inflammatory factors and microorganism were collected for analysis. T-tests and ANOVA were used to analyse the effects of the 2 pastes on tooth discoloration.<br><br>RESULTS: Compared with the control group, apical lesions and the expression of inflammatory cytokines was decreased, along with a reduction in bone destruction. Antibacterial experiments showed that the 2 antibiotics had similar effects on the common pathogens of AP. Compared with the TAP, mTAP does not cause discoloration of teeth. 16Sr DNA analysis revealed variations in periapical bacteria composition. The contents of common pathogens of AP in TAP and mTAP groups were lower than those in control group.<br><br>CONCLUSIONS: Azithromycin has the potential to serve as an alternative to minocycline. The 16S rDNA data highlights the intricate nature of the root canal microbiome, promising deeper insights into the correlation between microbes and inflammation.},
}
@article {pmid40669008,
year = {2025},
author = {Sulaiman, NNY and Mohamad Nizam, NB and Mohd Noor, NA and Lim, SM and Ramasamy, K and Alabsi, AM and Ismail, MF},
title = {An updated systematic review and appraisal of the pathophysiologic mechanisms of probiotics in alleviating depression.},
journal = {Nutritional neuroscience},
volume = {},
number = {},
pages = {1-21},
doi = {10.1080/1028415X.2025.2531357},
pmid = {40669008},
issn = {1476-8305},
abstract = {Gut-brain axis has emerged as a promising strategy for managing depression. Probiotic supplements, which modulate the gut microbiome, are suggested to enhance gut-brain communication and improve depressive symptoms and cognitive function. However, the acceptance of probiotics in managing depression remains contentious. This study aimed to evaluate the effects of probiotics on depression through meta-analysis and to assess their mechanisms of action, focusing on changes in gut microbial composition and neural mechanisms. A total of 12 randomized controlled trials from PubMed, Web of Science, and Scopus, up to January 1, 2024, were included. Nine studies consistently demonstrated improvements in depressive symptoms, gut microbiota, inflammatory markers, cognitive function, and mood regulation. The meta-analysis indicated a significant reduction in depressive symptoms with probiotics compared to placebo, with a mean difference of - 1.94 (95% CI = -3.56 to - 0.32, p = 0.02, I2 = 69%). The Hamilton Depression Rating Scale (HAM-D), which showed substantial improvement, with a mean difference of - 3.27 (95% CI = -6.42 to - 0.12, p = 0.04, I2 = 82%), is a preferred tool for further studies due to its comprehensive symptom coverage and strong psychometric properties. Probiotic strains such as Lactobacillus plantarum subspecies JYLP-326 and Bifidobacterium breve CCFM1025 were particularly effective, while multi-strain probiotics generally showed more consistent effects than single-strain interventions. Probiotics show promising potential in alleviating depression through their anti-inflammatory effects, gut microbiota modulation, cognitive function enhancement, and possible influence on brain structure and neurotransmitter systems. Despite some variability in trial results, this review provides updated insights for medical practitioners, highlighting probiotics as a viable treatment option for depression.},
}
@article {pmid40668619,
year = {2025},
author = {de Groot, R and Reedijk, D and Faucher, Q and Mihaila, SM and Masereeuw, R},
title = {Strategies for overcoming ABC transporter mediated drug resistance in colorectal cancer.},
journal = {American journal of physiology. Cell physiology},
volume = {},
number = {},
pages = {},
doi = {10.1152/ajpcell.00412.2025},
pmid = {40668619},
issn = {1522-1563},
support = {101107439//EC | HORIZON EUROPE Framework Programme (Horizon Europe)/ ; 24.005.009//NWO (Netherlands Organization for Scientific Research/ ; },
abstract = {Colorectal cancer (CRC) remains a leading cause of cancer-related mortality, with multidrug resistance (MDR) significantly limiting the effectiveness of chemotherapy. A major contributor to MDR is the overexpression of ATP-binding cassette (ABC) transporters, such as P-glycoprotein (ABCB1/P-gp), breast cancer resistance protein (ABCG2/BCRP), and multidrug resistance-associated proteins (ABCC/MRPs). These transporters actively efflux chemotherapeutic agents, reducing their intracellular drug accumulation and efficacy. This review outlines both clinical and emerging strategies that aim to overcome ABC transporter-mediated resistance in CRC. Herein, we detail the functional role of ABC transporters in CRC, followed by clinically tested approaches - such as pharmacological inhibitors, natural compound inhibitors, as well as nanoparticle-based drug delivery systems - that have been explored to circumvent resistance. Additionally, we discuss emerging preclinical approaches, including CRISPR/Cas9 gene-editing, RNA interference, epigenetic modulators, and gut microbiome-targeted interventions, that hold promise for future therapeutic translation. By integrating clinically validated and experimental strategies, this review highlights the importance of a multimodal approach to effectively circumvent MDR in CRC and optimize personalized treatment strategies to improve clinical outcomes.},
}
@article {pmid40668089,
year = {2025},
author = {Chen, Q and Liu, C and Tao, J and Zeng, W and Zhu, Z and Yao, C and Shang, Y and Tang, J and Jin, T},
title = {Insights into microbial dysbiosis and Cutibacterium acnes CAMP factor interactions in acne vulgaris.},
journal = {Microbial genomics},
volume = {11},
number = {7},
pages = {},
pmid = {40668089},
issn = {2057-5858},
mesh = {*Acne Vulgaris/microbiology/pathology ; *Dysbiosis/microbiology ; Humans ; Animals ; Mice ; RNA, Ribosomal, 16S/genetics ; *Virulence Factors/genetics/metabolism ; *Propionibacterium acnes/genetics/pathogenicity ; Skin/microbiology ; Disease Models, Animal ; Keratinocytes/microbiology ; Microbiota ; Female ; },
abstract = {Acne vulgaris is a common skin condition marked by the formation of comedones, papules, pustules and nodules, with its underlying causes still not fully understood. This study explores the impact of microbial dysbiosis and virulence factors on acne development. Through high-throughput 16S rRNA sequencing, we identified significant disruptions in the skin microbiome, particularly in comedones. Key virulence factors of Cutibacterium acnes, known as Christie-Atkins-Munch-Peterson (CAMP) factors, were assessed using both in vitro and in vivo models. Among these, CAMP2 and CAMP5 demonstrated the highest inflammatory and haemolytic activities in keratinocytes. Topical anti-IL-8 treatment in a murine model effectively reduced inflammation and suppressed CAMP expression. Structural analysis of CAMP3 uncovered distinct pathogenic features that, alongside CAMP5, were found to aggravate acne-like inflammation and sebaceous gland atrophy. These findings advance our understanding of the interplay between microbial dysbiosis and CAMP factors in acne pathogenesis, offering potential avenues for therapeutic intervention.},
}
@article {pmid40668000,
year = {2025},
author = {Jiang, D and Hurst, JH and Mohamed, G and Kelly, MS and Roper, J and Surana, NK},
title = {Decreased Microbiota-Driven Tyrosine Metabolism Is Associated With Symptomatic COVID-19 in Children.},
journal = {The Journal of infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/infdis/jiaf325},
pmid = {40668000},
issn = {1537-6613},
abstract = {BACKGROUND: The gut microbiota has been implicated in driving coronavirus disease 2019 (COVID-19) disease severity, but the underlying mechanisms remain unknown. We investigated the relationship between the gut microbiota and development of symptomatic COVID-19 in children.<br><br>METHODS: We prospectively collected stool and plasma samples from 229 children who were exposed to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), including 45 COVID-19 negative, 57 with asymptomatic COVID-19, and 127 with symptomatic COVID-19. We performed shotgun metagenomic sequencing on the stool samples to characterize the microbial taxa and functional profiles. Plasma cytokine levels were measured in SARS-CoV-2-infected individuals.<br><br>RESULTS: Children with symptomatic COVID-19 had reduced microbial biodiversity and decreased functional capacity for several metabolic pathways, including a reduction in the tyrosine biosynthesis pathway, as compared to SARS-CoV-2-uninfected children or those with asymptomatic infection. The abundance of the tyrosine biosynthesis pathway was associated with plasma levels of interferon alpha (IFN-&#x3b1;), which were lower in children with symptomatic COVID-19.<br><br>CONCLUSIONS: Our findings highlight a relationship between the ability of the gut microbiota to metabolize tyrosine and the development of COVID-19 symptoms in children. More generally, our study suggests that the gut microbiota may help protect against more severe forms of COVID-19, potentially by modulating IFN-&#x3b1;.},
}
@article {pmid40667988,
year = {2025},
author = {Gless, BH and Sereika-Bejder, BS and Jensen, I and Bojer, MS and Tsiko, K and Schmied, SH and Vitolo, L and Toledo-Silva, B and De Vliegher, S and Ingmer, H and Olsen, CA},
title = {Mapping of quorum sensing interaction network of commensal and pathogenic staphylococci.},
journal = {mBio},
volume = {},
number = {},
pages = {e0096725},
doi = {10.1128/mbio.00967-25},
pmid = {40667988},
issn = {2150-7511},
abstract = {Staphylococci utilize secreted autoinducing peptides (AIPs) to regulate group behavior through a process called quorum sensing (QS). For pathogenic staphylococci, such as Staphylococcus aureus, QS regulates the expression of major virulence factors, and QS inhibition has been proposed as an alternative to antibiotics for the treatment of infections with methicillin-resistant S. aureus (MRSA). Here, we surveyed the interaction map between QS systems of the pathogens S. aureus, Staphylococcus epidermidis, and Staphylococcus lugdunensis and all the currently known staphylococcal AIPs, covering 21 different species. We identified six of these ribosomally synthesized and post-translationally modified peptides (RiPPs) in this study and compiled the full collection of AIPs by chemical synthesis. The resulting mapping provided 280 QS interactions that were divided into human- and animal-associated staphylococci, showing substantial differences in inhibitory potencies between the groups. AIPs of the bovine-associated species Staphylococcus simulans displayed potential as QS inhibitors toward the investigated strains and were therefore chosen as a starting point for a structure-activity relationship study. This study provides insights into the requirements for QS interference, yielding the most potent inhibitors reported to date for S. epidermidis and S. lugdunensis. Furthermore, we tested an S. simulans AIP as an anti-virulence agent in an assay to assess the risk of acquired suppression of the inhibitory effect, and we established an assay set-up to successfully monitor agr deactivation of virulent MRSA by the QS inhibitor. Finally, a peptide was shown to attenuate skin infection caused by MRSA in a mouse model. Our results reveal a complex network of staphylococcal interactions and provide further impetus for the investigation of QS modulation in the targeting of antibiotic-resistant pathogens.IMPORTANCEBacteria from the Staphylococcus genus produce macrocyclic peptides, called autoinducing peptides (AIPs), used in inter-cell communication with their kin. Differences in AIP sequence and length produced by different staphylococcal species can result in communication interference, altering the physiology of co-inhabiting staphylococci in complex microbiotas. Opportunistic pathogens like Staphylococcus aureus regulate the expression of toxins using this peptide-mediated communication, and its inhibition has, therefore, been proposed as a strategy to target infections caused by methicillin-resistant S. aureus (MRSA). The systematic mapping of AIP activities, structure-activity relationship studies, and evaluation of resistance development provided in this paper, therefore, serve as a resource for the future discovery of inhibitory peptides for the investigation of bacterial communication.},
}
@article {pmid40667611,
year = {2025},
author = {Choi, I and Kim, KA and Kim, SC and Park, D and Nam, KT and Cha, JH and Baek, S and Cha, J and Jo, HY and Jung, M and Zeng, MY and Matei, I and Bullman, S and Ahn, JB and Han, YD and Kim, HS and Lee, I},
title = {Secretory IgA dysfunction underlies poor prognosis in Fusobacterium-infected colorectal cancer.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2528428},
pmid = {40667611},
issn = {1949-0984},
mesh = {*Colorectal Neoplasms/microbiology/immunology/pathology ; Animals ; *Immunoglobulin A, Secretory/immunology/metabolism/genetics ; Humans ; Mice ; *Fusobacterium nucleatum/immunology/physiology ; *Fusobacterium Infections/immunology/microbiology/complications ; Prognosis ; Gastrointestinal Microbiome ; Tumor Microenvironment ; Female ; Male ; Tumor-Associated Macrophages/immunology ; Mice, Inbred C57BL ; Disease Models, Animal ; Plasma Cells/immunology ; },
abstract = {Fusobacterium nucleatum (Fn) is commonly enriched in colorectal cancer (CRC) and associated with poor outcomes, though its mechanisms remain unclear. Our study investigated how Fn affects the tumor microenvironment through single-cell transcriptomic analyses of 42 CRC patient tissues, comparing Fn-positive and Fn-negative tumors. We discovered that Fn impairs IgA plasma cell development and secretory IgA (sIgA) production by disrupting communication with tumor-associated macrophages. Additional experiments in germ-free mice, together with our re-analysis of a publicly available single-cell RNA-seq data set from a CRC mouse model with an intact gut microbiome-both models having been orally gavaged with Fn-jointly validated the causal role of Fn in impairing sIgA induction. We identified a dysregulated IgA maturation (IGAM) module in Fn-positive patients, indicating compromised mucosal immunity and increased bacterial infiltration. This IGAM signature effectively stratified Fn-positive patients, suggesting potential for targeted therapeutic approaches. Our findings reveal that Fn disrupts sIgA production, increasing tumor microbial burden and worsening prognosis through chronic inflammation in Fn-positive CRC.},
}
@article {pmid40667520,
year = {2025},
author = {Miyamae, N and Ogai, K and Kunimitsu, M and Okamoto, S and Fujiwara, M and Nagai, M and Okuwa, M and Oe, M},
title = {Changes in the Skin Microbiome of a Patient with Head and Neck Cancer with Severe Radiodermatitis: A Case Report.},
journal = {Case reports in oncology},
volume = {18},
number = {1},
pages = {958-964},
pmid = {40667520},
issn = {1662-6575},
abstract = {INTRODUCTION: Identifying the skin microbiome associated with severe radiodermatitis could lead to the development of preventive care strategies and early healing interventions, which are currently lacking. In this study, we investigated changes in the skin microbiome of a patient with head and neck cancer who developed severe radiodermatitis from the initiation of radiation therapy to the resolution of dermatitis.<br><br>CASE PRESENTATION: An 82-year-old male underwent chemoradiotherapy with cisplatin (69.96 Gy/33 fractions) for recurrent laryngeal cancer after a total laryngectomy. At baseline, Cutibacterium accounted for 64.3% of the skin microbiome and Staphylococcus for 23.2%. During the occurrence of moist desquamation associated with severe radiodermatitis, Cutibacterium decreased sharply to 0.2%, whereas Staphylococcus increased to 91.0%. Species-level analysis revealed that Staphylococcus aureus was dominant at 50.6%, whereas Staphylococcus hominis and Staphylococcus epidermidis were identified at 0.4% and 1.7%, respectively.<br><br>CONCLUSION: These findings demonstrated that changes in the skin microbiome occur during the progression of severe radiodermatitis. The reduction in Cutibacterium and overgrowth of Staphylococcus, particularly Staphylococcus aureus, suggest their involvement in the development of severe radiodermatitis in patients with head and neck cancer.},
}
@article {pmid40667443,
year = {2025},
author = {Wei, J and Ding, W and Song, K and Zhang, Y and Luo, Q and Qi, C},
title = {Next-generation probiotics and engineered BEVs for precision therapeutics in osteoporosis.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1581971},
pmid = {40667443},
issn = {2296-861X},
abstract = {Osteoporosis, characterized by reduced bone density and increased fracture risk, faces limitations with conventional therapies due to adverse effects and poor gut microbiota modulation. Emerging strategies leveraging probiotics and bacterial extracellular vesicles (BEVs) offer novel therapeutic potential by targeting the gut-bone axis. Engineered probiotics and next-generation formulations enhance osteoprotection via immunomodulation, metabolite production (e.g., SCFAs), and neuroendocrine regulation. BEVs, as biocompatible nanocarriers, enable targeted delivery of osteogenic factors while circumventing colonization challenges. Synthetic biology advances facilitate precision engineering of probiotics and BEVs, improving therapeutic efficacy and scalability. This review highlights pre-clinical and clinical progress, challenges in standardization and safety, and future directions for microbiome-based interventions to revolutionize osteoporosis management. Integrating engineered probiotics with BEV technology promises transformative approaches for bone health restoration.},
}
@article {pmid40667442,
year = {2025},
author = {Zhang, X and Chen, K and Lan, H and Chen, H and Chen, H and Yang, P and He, N and Hung, W and Zeng, Z and Liu, C},
title = {Effect of Bifidobacterium longum subsp. infantis YLGB-1496 on common diseases in pediatrics: a randomized, blinded, placebo-controlled trial.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1585504},
pmid = {40667442},
issn = {2296-861X},
abstract = {INTRODUCTION: Respiratory, gastrointestinal, and allergic diseases can significantly impact both the physical and mental health of children, affecting their overall quality of life. This study aimed to evaluate the preventive effects and safety of Bifidobacterium longum subsp. infantis YLGB-1496 in relation to respiratory, gastrointestinal, and allergic diseases in children.<br><br>METHODS: Eligible healthy children were randomly assigned to either an intervention group (IG, n = 50), which received the probiotic, or a control group (CG, n = 50), which received a placebo, for a duration of 3 months. The primary outcome was the morbidity of upper respiratory tract infections (URTIs). Gut microbiota profiles were assessed via fecal 16S rRNA sequencing. Fecal immune biomarkers, including cytokines, immunoglobulins, and short-chain fatty acids (SCFAs), were measured to evaluate immune and metabolic responses.<br><br>RESULTS: The morbidity of URTIs over the 3-month intervention and follow-up period was significantly lower in the IG than in the CG. The incidence of upper respiratory tract infections (URTIs) over the 3-month intervention and follow-up period was significantly lower in the IG than in the CG, based on intention-to-treat (ITT) analysis [34.0% (17/50) vs. 58.0% (29/50), &#x3c7;[2] = 5.797, p = 0.016]. Per protocol (PP) analyses yielded similar results [36.2% (17/47) vs. 60.4% (29/48), &#x3c7;[2] = 5.59, p = 0.018]. YLGB-1496 supplementation significantly increased the relative abundance of Bifidobacterium bifidum, Bifidobacterium kashiwanohense PV2, and Bifidobacterium longum, while reducing Bacteroides thetaiotaomicron levels in the IG compared to the CG (p < 0.05). Additionally, YLGB-1496 reduced fecal levels of pro-inflammatory factors (IL-1&#x3b2; and IFN&#x3b3;) levels, and increased levels of immunoglobulin (IgA, IgG, and IgM) and SCFAs (including butyric acid and total SCFAs).<br><br>CONCLUSION: Daily administration of YLGB-1496 at a dosage of 1.5 &#xd7; 10[10] CFU for 3 months significantly reduced the episodes of cough, fever, dry stool (defined as Bristol stool scale type 1-3), and eczematous changes of the skin. It also decreased the morbidity of URTIs, bronchopneumonia, and eczema, while beneficially modulating gut microbiome composition and immune function without any adverse effects.<br><br>CLINICAL TRIAL REGISTRATION: https://www.isrctn.com/ISRCTN12824613, identifier: ISRCTN12824613.},
}
@article {pmid40667355,
year = {2025},
author = {Amarnani, A and Rivera, CF and Cornwell, M and Weinstein, T and Gottesman, SRS and Loomis, C and Azad, Z and Lee, A and Prasad, J and Barnes, B and Yi, M and Ullah, N and Gisch, N and Ruggles, K and Ramkhelawon, B and Silverman, GJ},
title = {Pathogenic strains of a gut commensal drive systemic platelet activation and thromboinflammation in lupus nephritis.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.06.20.641288},
pmid = {40667355},
issn = {2692-8205},
abstract = {Imbalances in the gut microbiome have been linked to increased intestinal permeability and disease flares in systemic lupus erythematosus (SLE). Our study revealed that patients with flares of lupus nephritis (LN) and intestinal expansions of the anaerobic commensal, Ruminococcus gnavus (RG), displayed whole blood transcriptome profiles indicative of platelet, neutrophil, and myeloid cell activation, a profile reminiscent of sepsis. Serum analysis confirmed elevated serum levels of Platelet Factor 4 and neutrophil extracellular traps, which significantly correlated with levels of IgG-antibody to a novel lipoglycan (LG) produced by pathogenic RG strains, which was also documented in an independent LN cohort. To test for causality, in vivo mouse models further demonstrated that gut colonization with LG-producing RG strains, as well as a single intraperitoneal challenge with an LG preparation, caused platelet activation and megakaryocytosis in bone marrow and spleen. Mice colonized with RG strains that produce LG developed cellular infiltration of the kidneys by neutrophils and monocytes. Hence, RG expansions during renal flares may identify a specific LN flare endotype driven by thromboinflammatory mechanisms. Antibodies that arise from immune exposure to the RG lipoglycan may serve as a surrogate biomarker, helping to elucidate the impact of the relationship between gut microbiota communities and clinical outcomes in patients afflicted by LN. [208].},
}
@article {pmid40667290,
year = {2025},
author = {Rutkowski, N and Yang, B and Gray-Gaillard, E and Ruta, A and Mejías, JC and Patatanian, M and Cherry, C and Stivers, KB and Ramanujam, S and Price, NL and Housseau, F and Pardoll, DM and Sears, CL and Elisseeff, JH},
title = {Antibiotic-induced microbiota depletion impairs the pro-regenerative response to a biological scaffold in mice.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.06.23.661121},
pmid = {40667290},
issn = {2692-8205},
abstract = {UNLABELLED: Therapeutic biological scaffolds promote tissue repair primarily through the induction of type 2 immunity. However, systemic immunological factors-including aging, sex, and previous infections-can modulate this response. The gut microbiota is a well-established modulator of immune function across organ systems, yet its influence on type 2-mediated repair remains underexplored. Here, we establish a bidirectional relationship between the gut microbiota and biological scaffold-mediated tissue repair. Utilizing a conventionalized germ-free mouse, we demonstrate that scaffold implantation induces compositional and functional changes in the gut microbiome, particularly affecting amino acid biosynthesis. Additionally, in a model of antibiotic-induced microbiota depletion (AIMD), we show that dysbiosis disrupts key immune regulators of type 2 immunity, including reductions in eosinophils, pro-regenerative macrophages, and IL-4-producing CD4 [+] T cells. At 6 weeks post-scaffold implantation, we observed a significant decrease in myocytes with centrally located nuclei alongside an upregulation in pro-fibrotic gene expression with antibiotic treatment. These findings provide insights into the influence of the gut microbiota on type 2-mediated tissue repair.<br><br>SIGNIFICANCE STATEMENT: Antibiotics are routinely administered perioperatively to prevent infection during surgeries and biomaterial implantation. Here, we demonstrate that antibiotic-induced microbiota depletion disrupts the type 2 immune response critical for biomaterial-mediated tissue repair. Our findings highlight the gut microbiota as a determinant of constructive healing and a potential contributor to inter-individual variability in responses to biologic scaffolds.},
}
@article {pmid40667084,
year = {2025},
author = {Mohssen, M and Zayed, AA and Kigerl, KA and Du, J and Smith, GJ and Schwab, JM and Sullivan, MB and Popovich, PG},
title = {Precision Prediction of Microbial Ecosystem Impact on Host Metabolism Using Genome-Resolved Metagenomics.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.06.27.661827},
pmid = {40667084},
issn = {2692-8205},
abstract = {Microbes drive ecosystem function through their physical interactions and metabolic transformations. However, since microbiomes are ecologically and metabolically interconnected, it is challenging to predict emergent ecosystem responses once the microbiome is disturbed. While it is widely acknowledged that mammalian gut dysbiosis influences host metabolism, mechanistic links that predict these effects are understudied. This study employs a genome-resolved eco-systems biology approach, using a high-resolution 'spinal cord-gut axis' model system and dataset, to predict how dysbiotic gut metabolism impacts overall mammalian health. By scaling and combining temporally resolved network analytics and consensus statistical methods, key microbial species were identified that predict overall host physiology and presumably control the gut ecosystem. In silico validation by pathway-centric functional analyses and comparative genomics revealed that key bacteria, sometimes exclusively, encode functions linking microbial and host metabolisms. Notably, spinal-mediated disturbances in the ecosystem shifted gut microbial nitrogen metabolism from urease-to amino acid-dependent pathways, with patterns that varied by host sex and bacterial species. Overall, this research challenges the traditional paradigm that only the host maintains whole-body nitrogen balance and instead invokes the microbiome as an environmentally-sensitive regulatory organ that can dictate health or disease by influencing mammalian whole-body elemental balance.},
}
@article {pmid40666980,
year = {2025},
author = {Markey, L and Qu, EB and Mendall, C and Finzel, A and Materna, A and Lieberman, TD},
title = {Microbiome diversity of low biomass skin sites is captured by metagenomics but not 16S amplicon sequencing.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.06.24.661265},
pmid = {40666980},
issn = {2692-8205},
abstract = {UNLABELLED: Established workflows for microbiome analysis work well for high microbial biomass samples, like stool, but often fail to accurately define microbial communities when applied to low microbial biomass samples. Here, we systemically compare microbiome analysis methods -16S rRNA sequencing, shallow metagenomics, and qPCR PMP™ panels-as well as extraction methods across skin swab samples and mock community dilutions. While extraction method minimally impacted results, with no significant signal for method-specific contamination or bias, we observed critical differences in inferred composition across analysis methods for low biomass samples. Metagenomic sequencing and qPCR revealed concordant, diverse microbial communities on low biomass leg skin samples, whereas 16S amplicon sequencing exhibited extreme bias toward the most abundant taxon. Both qPCR and metagenomics showed that female genital tract bacteria dominated the leg skin microbiome in about half of female subjects. Metagenomics also enabled sub-species analysis, which demonstrated that individuals have consistent within-species diversity across high-biomass forehead and low-biomass leg skin sites. This work illustrates that shallow metagenomics provides the necessary sensitivity and taxonomic resolution to characterize species and strain-level diversity in extremely low biomass samples, opening possibilities for microbiome discovery in previously unexplored niches.<br><br>IMPORTANCE: Despite the importance of the skin microbiome in health and disease, there have been far fewer studies characterizing the microbiome of skin compared to that of the gut. In part, this is because microbiome methods were initially developed for bacteria-rich samples like stool and these methods perform poorly on bacteria-poor samples like skin swabs. The perceived difficulty of getting reliable data from such low biomass sites has limited the scope and types of analyses performed. Here we demonstrate that shotgun, whole-genome, metagenomic sequencing recovers the full input from even very dilute control community samples, and reveals a highly diverse population even on very low biomass skin sites. We describe a streamlined sample processing and analysis pipeline which can be applied broadly to characterize low biomass microbiome samples and reveal new host-microbiome interactions.},
}
@article {pmid40666978,
year = {2025},
author = {Chatman, CC and Majumder, EL},
title = {Acute exposure to groundwater contaminants mixture of nitrate, atrazine and imidacloprid impacts growth kinetics of poultry cecal microbiomes and significantly decreases Caco-2 cell viability.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.06.15.659797},
pmid = {40666978},
issn = {2692-8205},
abstract = {UNLABELLED: Atmospheric deposition, and agricultural runoff or erosion events have substantially contributed to groundwater pollution throughout the USA. This can become troublesome in states like Wisconsin where 68% of the population rely on groundwater for their drinking water source. As such, exposome research must account for the complexity and frequency of environmental exposures. This study aimed to elucidate chemical-biological interactions and adverse outcome pathways associated with an environmentally relevant mixture of agricultural chemicals detected in Wisconsin groundwater via in vitro and in silico methodologies. Using in vitro models, we determined that a ternary mixture of environmentally relevant concentrations of nitrate, atrazine and imidacloprid resulted in an overt decline in growth rate to the poultry cecal microbiome compared to each chemical singularly. Further, there was a decrease in Caco-2 cell viability in various two-chemical combinations. In silico methods analyzed contaminants detected in Wisconsin groundwater wells from across the state and prioritized two groundwater wells as potential for health concerns. Prioritized chemicals in these groundwater wells were linked to nine gene targets and several adverse outcome pathways. In all, the results demonstrated that there is chemical-biological interaction between these model organisms agricultural and chemical mixtures at real world exposure concentrations.<br><br>HIGHLIGHTS: in silico methods were able to predict potential adverse effects for communities utilizing these groundwater wells 8 out of 9 chemicals prioritized with in silico tools were herbicides A ternary mixture of nitrate, imidacloprid and atrazine resulted in a decline in growth rate for poultry cecal microbiomeCaco-2 cells significantly impacted by two-chemical combinations but not ternary mixtures.},
}
@article {pmid40666935,
year = {2025},
author = {Sheikh, A and Scano, C and Xu, J and Ojo, T and Conforti, JM and Haberman, KL and King, B and Martinez, AS and Pujol, M and Watkins, J and Lotter, J and Lin, EL and Zechmann, B and Sevcik, A and Sayes, C and Gallagher, ES and Lang, SP and Mell, J and Ehrlich, GD and Taube, JH and Greathouse, KL},
title = {Outer membrane vesicles from Bacteroides fragilis contain coding and non-coding small RNA species that modulate inflammatory signaling in intestinal epithelial cells.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.06.25.661399},
pmid = {40666935},
issn = {2692-8205},
abstract = {Alterations to the community structure and function of the microbiome are associated with changes to host physiology, including immune responses. However, the contribution of microbe-derived RNAs carried by outer membrane vesicles (OMVs) to host immune responses remain unclear. This study investigated the role of OMVs and OMV-associated small RNA (sRNA) species from pathogenic and commensal Bacteroides fragilis (ETBF and NTBF respectively) in eliciting different immune responses from intestinal epithelial cells. To distinguish the differences in the sRNA profiles of the two strains and their OMVs, RNA-seq, qRT-PCR, and northern blotting were conducted to identify enrichment of discrete sRNA species in OMVs, which were also differentially expressed between the two strains. Specifically, both coding and non-coding RNAs were enriched in OMVs from NTBF and ETBF, with BF9343_RS22680 and BF9343_RS17870 being significantly enriched in ETBF OMVs compared to NTBF. To understand the effects of OMVs on pattern recognition receptors, reporter cells of Toll-like receptor (TLR) activation were treated with OMVs, demonstrating activation of TLRs 2, 3, and 7. Treatment of Caco-2 and HT29-MTX cells with OMVs demonstrated increased expression of IL-8. Surprisingly, we discovered that degradation of RNase-accessible RNAs within ETBF OMVs, but not NTBF OMVs, resulted in vesicles with enhanced capacity to stimulate IL-8 expression, indicating that these extravesicular RNAs exert an immunosuppressive effect. This suggests a dual role for OMV-associated RNAs in modulating host immune responses, with implications for both bacterial pathogenesis and therapeutic applications. Graphical Abstract.},
}
@article {pmid40666868,
year = {2025},
author = {Yang, Y and Wang, T and Huang, D and Wang, XW and Weiss, ST and Korzenik, J and Liu, YY},
title = {Deep Learning Transforms Phage-Host Interaction Discovery from Metagenomic Data.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.05.26.656232},
pmid = {40666868},
issn = {2692-8205},
abstract = {Microbial communities are essential for sustaining ecosystem functions in diverse environments, including the human gut. Phages interact dynamically with their prokaryotic hosts and play a crucial role in shaping the structure and function of microbial communities. Previous approaches for inferring phage-host interactions (PHIs) from metagenomic data are constrained by low sensitivity and the inability to accurately capture ecological relationships. To overcome these limitations, we developed PHILM (P hage- H ost Interaction L earning from M etagenomic profiles), a deep learning framework that predicts PHIs directly from the taxonomic profiles of metagenomic data. We validated PHILM on both synthetic datasets generated by ecological models and real-world data, finding that it consistently outperformed the co-abundance-based approach for inferring PHIs. When applied to a large-scale metagenomic dataset comprising 7,016 stool samples from healthy individuals, PHILM identified 90% more genus-level PHIs than the traditional assembly-based approach. In a longitudinal dataset tracking PHI dynamics, PHILM's latent representations recapitulated microbial succession patterns originally described using taxonomic abundances. Furthermore, we demonstrated that PHILM's latent representations served as more discriminative features than taxonomic abundance-based features for disease classifications. In summary, PHILM represents a novel computational framework for predicting phage-host interactions from metagenomic data, offering valuable insights for both microbiome science and translational medicine.},
}
@article {pmid40666844,
year = {2025},
author = {Alves, G and Ogurtsov, AY and Yu, YK},
title = {Biological Function Assignment Across Taxonomic Levels in Mass-Spectrometry-Based Metaproteomics via a Modified Expectation Maximization Algorithm.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.06.12.659309},
pmid = {40666844},
issn = {2692-8205},
abstract = {A major challenge in mass-spectrometry-based metaproteomics is accurately identifying and quantifying biological functions across the full taxonomic lineage of microorganisms. This issue stems from what we refer to as the "shared confidently identified peptide problem". To address this issue, most metaproteomics tools rely on the lowest common ancestor (LCA) algorithm to assign biological functions, which often leads to incomplete biological function assignments across the full taxonomic lineage of identified microorganisms. To overcome this limitation, we implemented an expectation-maximization (EM) algorithm, along with a biological function database, within MiCId workflow. Using synthetic datasets, our study demonstrates that the enhanced MiCId workflow achieves better control over false discoveries and improved accuracy in microorganism identification and biomass estimation compared to Unipept and MetaGOmics. Additionally, the updated MiCId offers improved accuracy and better control of false discoveries in biological function identification compared to Unipept, along with reliable computation of function abundances across the full taxonomic lineage of identified microorganisms. Reanalyzing human oral and gut microbiome datasets using the enhanced MiCId workflow, we show that the results are consistent with those reported in the original publications, which were analyzed using the Galaxy-P platform with MEGAN5 and the MetaPro-IQ approach with Unipept, respectively.},
}
@article {pmid40666811,
year = {2025},
author = {Li, X and Chen, J and Xu, C and Li, Y and Li, K},
title = {Galla chinensis alleviated liver damage induced by acetaminophen by regulating intestinal microbiota.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1589946},
pmid = {40666811},
issn = {1664-302X},
abstract = {INTRODUCTION: Drug-induced liver injury is a common condition of therapeutics and requires solutions other than drugs. Dietary supplements and herbal products have beneficial potential against liver failure and are often associated with changes in intestinal flora. This study was designed to investigate Galla chinensis (GC) potential in alleviating drug-induced liver injury.<br><br>METHODS: The treatment group and model group were administered 0.5 mL of GC oil daily for 14 days, followed by induction of acute drug-induced liver injury using Acetaminophen (APAP) on the 15th day via intraperitoneal injection. Serum biochemical analysis and intestinal bacteria 16S rRNA sequencing were conducted to explore the anti-drug liver injury activity of GC.<br><br>RESULTS: The results showed that GC treatment alleviated the increased liver organ index caused by APAP. Furthermore, serum biochemical analysis revealed that GC therapy reduced alanine transaminase (ALT) and aspartate transaminase (AST) levels, indicating a protective effect against APAP-induced liver injury. Additionally, GC demonstrated the ability to regulate the diversity and composition of intestinal microbes and help increase the prevalence of beneficial microbes such as Faecalibaculum and Odoribacter while reducing the prevalence of pathogenic bacteria, including Corynebacterium, Rikenella, Bacillus, Phocaeicola, and Alloprevotella.<br><br>DISCUSSION: Our findings indicate that GC plays a significant role in mitigating drug-induced liver injury by improving gut microbiome composition, reducing plasma ALT and AST levels, and inhibiting oxidative stress and inflammatory responses. The study further demands investigations to make pharmaceutical products to be used as nutraceuticals against drug-induced toxicities.},
}
@article {pmid40666810,
year = {2025},
author = {He, B and Zhang, P and Bai, X and Li, W and Zou, S},
title = {Compartment-specific dynamics of soil microbiota along a Pinus armandii plantation chronosequence in karst mountain ecosystems.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1626892},
pmid = {40666810},
issn = {1664-302X},
abstract = {Soil microbiomes play pivotal roles in mediating plant diversity maintenance by regulating multifunctional ecosystem services during plant development. However, how different stand age of plants influence soil microbial communities in various soil compartments remains poorly understood. Through Illumina-based 16S rRNA and ITS amplicon sequencing, we systematically investigated the successional trajectories of soil microbiome in Pinus armandii plantations spanning various developmental phases. Key findings revealed that stand age exerted a stronger influence on microbial restructuring than soil compartment, significantly altering community composition in both soil types. Alpha diversity (Shannon and Chao1 indices) exhibited a U-shaped trajectory with stand age, except for fungal Chao1 in bulk soil. While dominant bacterial and fungal phyla remained relatively stable, community composition displayed significant stage-dependent variations. Co-occurrence network analysis demonstrated lower fungal network complexity compared to bacterial networks, with rhizosphere soils harboring more intricate interactions compared to bulk soils. Community assembly mechanisms diverged: deterministic processes dominated bacterial assembly, whereas stochasticity governed fungal communities. Soil properties exerted significant influences on microbial composition and diversity: bacterial composition correlated strongly with pH and stoichiometric ratios (C/N, C/P, N/P), while fungal composition showed stronger associations with TN, TP, and AN. Our results demonstrate that P. armandii plantations maintain core phylum-level microbial populations while developing stage-specific diversity patterns. Crucially, bacteria and fungi exhibit divergent responses to stand development, highlighting their divergent ecological strategies in adapting to nutrient-limited karst ecosystems.},
}
@article {pmid40666793,
year = {2025},
author = {Riedmüller, J and Monteiro, A and Männer, K and Saliu, EM and Vahjen, W and Zentek, J},
title = {Effects of different doses and preparations of zinc oxide in weanling piglets on performance, intestinal microbiota and microbial metabolites.},
journal = {Translational animal science},
volume = {9},
number = {},
pages = {txaf073},
pmid = {40666793},
issn = {2573-2102},
abstract = {For years, high zinc levels (up to 3000 mg/kg feed) have been used to aid piglets during the weaning phase. However, studies revealed drawbacks like antimicrobial resistance and environmental impact. Since 2022, the EU limits zinc inclusion levels to 150 mg total zinc per kg. Therefore, alternative strategies for replacing high levels of zinc are of great interest. This study compares a potentiated zinc oxide source (HiZox[®]) and feed grade zinc oxide at various levels on piglet performance, fecal consistency and fecal microbiome. The trial involved a total of 1,440 healthy weaned piglets (DanBred × Duroc; 50% barrows, 50% gilts; initial BW 10.1 ± 1.46 kg) over the 28-day duration of the experimental period. Piglets were randomly assigned to 12 treatment groups, each consisting of 12 pens, with 10 piglets per pen. The trial comprised two periods: the starter period (days 1 to 14) focused on comparing the two zinc products, while all animals received a diet supplemented with 150 mg/kg of potentiated ZnO in the grower period (days 15 to 28). Treatment groups receiving feed grade ZnO were denoted as Z150, Z300, Z600, Z900, Z1500, and Z3000, while corresponding groups with the potentiated ZnO product were labeled H150, H300, H600, H900, H1500, and H3000, respectively. Body weight (BW) and feed intake (FI) were measured for every pen at days 1, 14 and 28. Fecal samples were collected on the same days. During the starter phase (days 1 to 14), potentiated ZnO significantly improved average daily gain (ADG) compared to feed-grade ZnO (P ≤ 0.001), with the highest values observed at 3000 mg/kg (H3000: 247 g/d vs. Z3000: 233 g/d). Feed intake (FI) was also higher in potentiated ZnO groups (P ≤ 0.001), and feed conversion ratio (FCR) was more efficient (e.g., H3000: 1.2 vs. Z3000: 1.24; P = 0.001). In the grower phase residual effects from the starter phase persisted: animals previously fed potentiated ZnO had improved FCR (P = 0.003). Fecal microbiota analysis revealed that higher zinc levels reduced Lactobacillus abundance (P ≤ 0.001) and increased the presence of genera typical of adult pigs, such as Clostridium sensu stricto 1 and Terrisporobacter (P < 0.01). In conclusion, based on the observed shift in fecal microbiota composition characterized by a reduction in lactobacilli and an increase in proteobacteria due to heightened dietary zinc levels, it is advised to adjust zinc supplementation to 150 mg/kg after the initial 2 wk post-weaning.},
}
@article {pmid40666732,
year = {2025},
author = {Cantas, L and Goll, R and Fenton, CG and Paulssen, RH and Sørum, H},
title = {Impact of fecal microbiota transplantation in dogs.},
journal = {Frontiers in veterinary science},
volume = {12},
number = {},
pages = {1505226},
pmid = {40666732},
issn = {2297-1769},
abstract = {BACKGROUND: The digestive tract hosts a variety of microorganisms. These microorganisms "micro-organs" play multiple crucial roles in physiological, immunological, and metabolic processes in the body. The manipulation and transplantation of "micro-organs" have lately gained increasing interest in human medicine with promising clinical outcomes, whereas much less is known in veterinary practice.<br><br>OBJECTIVES: The goals of this pilot study were to evaluate the safety and impact of Fecal Microbiota Transplantation (FMT) for dogs suffering from non-infectious digestive disorders.<br><br>ANIMALS: Seven client-owned adult dogs with idiopathic persistent diarrhea (>3&#x202f;weeks) and very poor skin-coat conditions received the intervention (FMT) and were evaluated in a private veterinary clinic.<br><br>METHODS: Transplants have been taken from healthy donors and were administered rectally to recipients. Objective clinical examinations with analyses of blood and feces samples on day 0 (pre-FMT) and days 14-28 (post-FMT) were performed. Besides the conventional blood hematology and biochemistry analyses, 16S rRNA sequencing analysis was used in fecal samples.<br><br>RESULTS: No FMT-related complications occurred. Five of seven (71%) patients demonstrated improved fecal parameters associated with better overall clinical outcome, whereas four of the five (80%) recovered recipients showed molecular correlation with the donor gut microbiota after rectal FMT. There were insignificant changes shown for the conventionally analyzed blood samples. The serum cobalamin levels showed a tendency to increase in recovered recipients.<br><br>CONCLUSION: FMT was easy to apply and displayed certain health benefits in this study. Our findings reveal the important role of a "re-gained" gut microbiome balance in the overall health of dogs. Further research is needed to identify the dynamics and interplay between the different bacterial phyla that may have an impact on the stimuli of host immunologic and metabolic responses.},
}
@article {pmid40666332,
year = {2025},
author = {Golan, Y and Nyquist, SK and Liu, Z and Ennis, D and Zhao, J and Blair, E and Khan, AR and Prahl, M and Gaw, SL and Yassour, M and Engelhardt, BE and Flaherman, VJ and Ahituv, N},
title = {Genomic characterization of normal and aberrant human milk production.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.06.22.25329156},
pmid = {40666332},
abstract = {Breastfeeding is essential for reducing infant morbidity and mortality, yet exclusive breastfeeding rates remain low, often due to insufficient milk supply. The molecular causes of low milk production are not well understood. Fresh milk samples from 30 lactating individuals, classified by milk production levels across postpartum stages, were analyzed using genomic and microbiome techniques. Bulk RNA sequencing of milk fat globules (MFG), milk cells, and breast tissue revealed that MFG-derived RNA closely mirrors luminal milk cells. Transcriptomic and single-cell RNA analyses identified changes in gene expression and cellular composition, highlighting key genes (GLP1R, PLIN4, KLF10) and cell-type differences between low and high producers. Infant microbiome diversity was influenced by feeding type but not maternal milk supply. This study provides a comprehensive human milk transcriptomic catalog and highlights that MFG could serve as a useful biomarker for milk transcriptome analysis, offering insights into the genetic factors influencing milk production.},
}
@article {pmid40666331,
year = {2025},
author = {Quinn-Bohmann, N and Gibbons, SM},
title = {Metabolic modeling reveals determinants of synbiotic efficacy in a human intervention trial.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.06.24.25330246},
pmid = {40666331},
abstract = {Synbiotic interventions show variable effects across individuals, likely driven by ecological interactions with the endogenous microbiota and the host diet. Rationally predicting individual-specific success or failure of probiotic and prebiotic interventions remains an outstanding challenge. In this study, we leverage microbial community-scale metabolic models (MCMMs) to predict probiotic engraftment and shifts in microbiota-mediated short-chain fatty acid (SCFA) production in response to a synbiotic intervention. Using data from a placebo-controlled synbiotic intervention trial, involving a cocktail of five probiotic strains and the prebiotic inulin, we validate model engraftment predictions with quantitative PCR (qPCR), demonstrating that MCMMs accurately predict probiotic engraftment outcomes in the treatment group with over 85% accuracy. Engraftment varied by species, with Akkermansia muciniphila and Bifidobacterium infantis displaying higher engraftment rates than Clostridium beijerinckii, Anaerobutyricum hallii , and Clostridium butyricum . Furthermore, MCMMs predicted significant increases in butyrate and propionate production following synbiotic treatment. MCMM-predicted changes in propionate production in the treatment group were negatively associated with changes in C-reactive protein (CRP), a blood marker of systemic inflammation, from baseline to 12 weeks after the synbiotic intervention. Finally, we explore MCMM-predicted responses to a wider range of synbiotic combinations in a larger observational cohort, suggesting that personalized prebiotic selection can augment probiotic efficacy. These findings highlight the potential of metabolic modeling to inform precision microbiome therapeutics.},
}
@article {pmid40665938,
year = {2025},
author = {Chen, Q and Wang, F and Ma, G and Liu, C and Zhu, T and Wang, K and Wang, H},
title = {Microbial agents suppress jujube black spot disease and enhance jujube quality by regulating soil physicochemical and microbial properties.},
journal = {Pest management science},
volume = {},
number = {},
pages = {},
doi = {10.1002/ps.70062},
pmid = {40665938},
issn = {1526-4998},
support = {//Central Guidance of Local Science and Technology Development Special Foundation of Shandong Province (YDZX2021088)/ ; //Open Project of Research Center of Pesticide Environmental Toxicology, Shandong Agricultural University (HJDL202407)/ ; //Shandong Provincial Key Research and Development Program (2024TSGC0619)/ ; },
abstract = {BACKGROUND: Jujube black spot disease, caused by the soil-borne pathogenic fungus Alternaria alternata, threatens the sustainability of the jujube industry by adversely affecting yield. However, it is unclear whether microbial agents can increase yield by improving soil, inhibiting jujube black spots, and regulating microbial communities.<br><br>RESULTS: Bacillus velezensis strain SDTB038 had significant inhibitory effects on A. alternata, and sound field control effects (the control effects after two applications were 39.71% and 41.97%). SDTB038 had good saline-alkali tolerance and grew well in Potato Dextrose Broth medium containing 1%-7% NaCl or over pH range of 4-10. Upon application of B-1, multiple soil parameters were significantly improved, including levels of soil organic matter, total nitrogen and available potassium, and the activities of soil urease, alkaline phosphatase, catalase and sucrase. In a Tai'an jujube orchard, soil organic matter reached 16.54&#x2009;g/kg, soil organic carbon 28.51&#x2009;g/kg, and total nitrogen content 1.93&#x2009;g/kg, consistent with the data trend in the Kashi area. Furthermore, applying B-1 resulted in a more complex interaction network among soil microorganisms. B-1 promoted the enrichment of beneficial microorganisms such as Bacillus spp. and Sphingomonas spp., while significantly reducing Alternaria spp. and Fusarium spp. levels. This increased jujube yield and overall quality (single fruit weight increased by 1.22-1.72 times).<br><br>CONCLUSION: This study fills a gap in current research on the application of microbial agents to prevent and control of jujube diseases, and has important theoretical and practical significance. &#xa9; 2025 Society of Chemical Industry.},
}
@article {pmid40665935,
year = {2025},
author = {Bak, MTJ and Olivera, PA and Hernandez-Rocha, C and Borowski, K and Turpin, W and Leibovitzh, H and Milgrom, R and Stempak, J and Silverberg, M and Lee, SH},
title = {Isolated Anastomotic Ulcers Are Associated with a Higher Long-Term Risk for Postoperative Recurrence and a Differential Mucosa-Associated Microbiome Composition in Patients with Crohn's Disease Following Ileocolic Resection.},
journal = {Inflammatory bowel diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/ibd/izaf147},
pmid = {40665935},
issn = {1536-4844},
support = {/DK/NIDDK NIH HHS/United States ; 5U01DK062423/NH/NIH HHS/United States ; },
abstract = {BACKGROUND: The clinical relevance and underlying mechanism of isolated anastomotic ulcers (IAUs) following ileocolic resection (ICR) in patients with Crohn's disease (CD) are poorly understood. This study aimed to assess the postoperative recurrence (POR) risk and the mucosa-associated microbiome composition in CD patients with or without IAUs among those with a healthy neo-terminal ileum (TI).<br><br>METHODS: CD patients who underwent ICR and without any ulcerations in the neo-TI (SES-CD &#x2264;2) at first postoperative ileocolonoscopy were identified from an ongoing prospective multicenter study. The primary study outcome was time to POR measured from the first postoperative ileocolonoscopy. Cox proportional hazard models were used to assess the association of IAUs with time to POR. The mucosa-associated microbiome at first ileocolonoscopy was assessed by sequencing the 16S rRNA gene using biopsies taken from both sides of the anastomosis.<br><br>RESULTS: Sixty patients were included, of whom 27 patients had IAUs (45.0%) at first ileocolonoscopy. Median time to first postoperative ileocolonoscopy was 6.5 months (interquartile range [IQR] 5.3-8.1). During a median follow-up duration of 3.0 years (IQR 1.4-5.5) after first postoperative ileocolonoscopy, POR was observed in 53.3%. After adjustment for clinical risk factors, IAUs were independently associated with POR (adjusted hazard ratios 5.4; 95% CI 2.4-12.4; P&#x2005;<&#x2005;.001). At the ileal and colonic side of the anastomosis, a significantly higher abundance of Klebsiella was associated with IAUs (q&#x2005;<&#x2005;0.05).<br><br>CONCLUSIONS: IAUs in CD patients with otherwise healthy neo-TI at first postoperative ileocolonoscopy are associated with long-term POR. In addition, a differential mucosa-associated microbiome composition was observed in patients with IAUs, specifically the proteobacteria Klebsiella, suggesting that putative taxa are related to these lesions. Further validation studies in larger cohorts, along with mechanistic studies, are still required.},
}
@article {pmid40665871,
year = {2025},
author = {Bucking, C and Terblanche, JS and Regan, MD},
title = {The ins and outs of integrative digestive biology.},
journal = {The Journal of experimental biology},
volume = {228},
number = {14},
pages = {},
doi = {10.1242/jeb.250770},
pmid = {40665871},
issn = {1477-9145},
support = {RGPIN-2021-03606//Natural Sciences and Engineering Research Council of Canada/ ; RGPIN-2021-03109//Natural Sciences and Engineering Research Council of Canada/ ; },
mesh = {Animals ; *Digestive System Physiological Phenomena ; *Gastrointestinal Tract/physiology ; },
abstract = {The digestive system facilitates exchanges between animals and their environments. It not only converts resources into energy and growth but also shapes ecosystem processes through waste outputs, all while mediating an animal's relationship with complex microbial communities. The Special Issue: The Integrative Biology of the Gut delves into many aspects of this expansive relationship. Further, this Commentary collects the special issue papers under themes to highlight and explore the physiology of the digestive system and the plasticity that enables its acclimatization to dietary and environmental changes. The themes that have been identified portray the gastrointestinal (GI) tract as an integrative moderator of physiology, and show that when this system is explored using novel techniques or by asking innovative questions, one can reveal phenomena with applications well beyond digestive biology. Further, we discuss how embracing multidisciplinary approaches - including systems biology, evolutionary comparisons and environmental considerations - will allow us to use the unique physiology of the GI tract to form critical insights into evolved organismal biology, microbial symbioses and ecological stewardship. Ultimately, the pivotal role of the GI tract in connecting internal physiology with external ecological dynamics across taxa exemplifies its value as a model system.},
}
@article {pmid40665828,
year = {2025},
author = {Arroyo-Calatayud, M and Haberl, EM and Olivares, L and Collado, MC and Schaubeck, M},
title = {Impact of extensively hydrolyzed infant formula on the probiotic and postbiotic properties of Lactobacillus fermentum in an in vitro co-culture model.},
journal = {Food &amp; function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d4fo06330a},
pmid = {40665828},
issn = {2042-650X},
abstract = {Early gut homeostasis is a balance between dietary antigen exposure, gut barrier function, microbiome establishment and orchestration of innate and adaptive immune responses. Imbalances during this early time of development can lead to increased susceptibility to immune reactions like allergy. Especially for infants with a predisposition to allergies and who cannot be exclusively breastfed, there are different human milk substitutes, including hydrolyzed infant formula, which are supposed to prevent allergy-associated mechanisms. The physiologic mechanism beyond the destruction of cow's milk allergenic structures in those formulas are currently not fully understood. Therefore, our aim was to elucidate the impact of hydrolyzed infant formula on intestinal homeostasis and presumed mechanisms behind the beneficial effects. In this study, we used a triple co-culture in vitro model of gut inflammation and homeostasis, including enterocyte-, goblet- and macrophage-like cells in a transwell setup, to assess the effect of extensively hydrolyzed (eHF) infant formula compared to standard cow's milk-based infant formula with intact protein (iPF). These formulas were combined or not with heat-inactivated Limosilactobacillus fermentum CECT 5716 (Lf) to test the effect of probiotic compounds in combination with different types of infant formula (i.e. eHF and iPF) on the intestinal barrier and cytokine production. Under LPS-inflammatory trigger, eHF and eHF + Lf increased mucus production and MUC2 mRNA expression, restored epithelial barrier integrity and increased secretion of regulatory TGFβ, compared to respective controls. These results suggest a beneficial role for eHF, and especially eHF + Lf, in restoring intestinal homeostasis and attenuating pro-inflammatory responses.},
}
@article {pmid40665733,
year = {2025},
author = {Hao, X and Wu, T and Li, X and He, Q and Qin, Y and Zhang, N and Yu, H and Jiang, Y and Gao, F},
title = {Dietary energy improves Holstein heifer conception through rumen microbiota interactionsfers during initial breeding.},
journal = {Animal bioscience},
volume = {},
number = {},
pages = {},
doi = {10.5713/ab.25.0141},
pmid = {40665733},
issn = {2765-0189},
abstract = {OBJECTIVE: This study aimed to elucidate how graded dietary energy levels regulate the hypothalamic-pituitary-gonadal axis in Holstein heifers during initial breeding, with a focus on rumen microbiota-host interactions.<br><br>METHODS: Forty-four pubertal heifers (398.96 &#xb1; 6.56 kg BW; 12.72 &#xb1; 0.02 months) were stratified by body condition score (BCS) and estrous cyclicity, then randomly allocated to control (CON, 8.64 MJ/kg DM NEL) or high-energy (HE, 9.50 MJ/kg DM NEL) diets (n = 22/group). Although practical constraints limited pen replication, we implemented rigorous matching procedures: Pens were matched for surface area (120 m&#xb2;), feed bunk space (0.8 m/head) and growth performance, serum biochemical/immune/antioxidant markers, reproductive hormones, rumen fermentation parameters, microbiota, and metabolome profiles were analyzed.<br><br>RESULTS: Results The HE group exhibited elevated gonadotropins (FSH, LH) and prolactin (PRL), indicating enhanced hypothalamic-pituitary activity. Serum triglycerides increased, while immune markers showed the altered state of immunoregulation characterized by significant increases in IL-2 and IL-6, reductions in IL-4, and decreases in TNF-&#x3b1; and IFN-&#x3b3;. Antioxidant capacity improved with lower MDA levels. Rumen pH decreased, accompanied by elevated total VFA, bacterial crude protein(BCP), acetic acid, propionic acid, butyric acid, and valeric acid concentrations. Microbial shifts included Treponema and Prevotellaceae_UCG_003 showing positive correlations with PRL and LH, while Ruminococcus was associated with acetyl-CoA precursors through enriched pyruvate metabolism.<br><br>CONCLUSION: High-energy diets (9.50 MJ/kg NEL) enhance hypothalamic-pituitary signaling and rumen fermentation efficiency, advancing first-service conception rates by 15% (55% vs. 70%) in pasture-based systems. This strategy optimizes reproductive management in intensive dairy operations through microbiota-driven metabolic modulation.},
}
@article {pmid40665731,
year = {2025},
author = {Zhou, X and Shen, X},
title = {Evaluation of garlic skin as a forage source for goats: Effects on performance, antioxidant capacity , immune function and.},
journal = {Animal bioscience},
volume = {},
number = {},
pages = {},
doi = {10.5713/ab.25.0169},
pmid = {40665731},
issn = {2765-0189},
abstract = {OBJECTIVE: This study aimed to evaluate the effects of garlic skin as a feed ingredient on growth performance, antioxidant capacity, immune function, and rumen health in goats.<br><br>METHODS: Twelve male black goats with similar body conditions were randomly assigned to two groups. The control group (CON) was fed a basal diet, while the experimental group (GAS) received a diet supplemented with garlic skin for 60 days.<br><br>RESULTS: Results showed that goats' final weight (FW) and average daily gain (ADG) significantly increased in the GAS group compared to the CON group (p < 0.05). The GAS group exhibited enhanced activities of total superoxide dismutase (T-SOD), glutathione peroxidase (GSH-Px), catalase (CAT), and higher total antioxidant capacity (T-AOC) levels, while malondialdehyde (MDA) content significantly decreased (p < 0.05). Immunoglobulin A (IgA) and immunoglobulin G (IgG) levels were significantly elevated, along with increased concentrations of anti-inflammatory cytokines interleukin-4 (IL-4) and interleukin-10 (IL-10), whereas pro-inflammatory cytokines interleukin-1&#x3b2; (IL-1&#x3b2;), interleukin-6 (IL-6), and tumor necrosis factor-&#x3b1; (TNF-&#x3b1;) were significantly reduced (p < 0.05). The rumen fluid of GAS group showed significant increases in ammonia nitrogen, acetate, propionate, and total volatile fatty acids, with a reduction in the acetate-to-propionate ratio (p < 0.05). Significant improvements were also observed in rumen papilla height, width, and density (p < 0.05). 16S rDNA analysis revealed enhanced microbial diversity and enrichment of functional bacterial groups, such as Firmicutes and Christensenellaceae_R-7_group, involved in fiber degradation and volatile fatty acid production. Key metabolites, including 5-methylthioribose and glucose 6-phosphate, were positively correlated with growth and antioxidant capacity, while 21-deoxycortisol negatively affected metabolic balance.<br><br>CONCLUSION: In conclusion, garlic skin supplementation enhanced antioxidant and immune function, optimized rumen fermentation, improved microbial composition, and promoted goat health and productivity.},
}
@article {pmid40665422,
year = {2025},
author = {Gfeller, V and Schneider, M and Bodenhausen, N and Horton, MW and Wille, L and Oldach, KH and Studer, B and Hartmann, M and Messmer, MM and Hohmann, P},
title = {Crop genotype modulates root rot resistance-associated microbial community composition and abundance of key taxa.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {89},
pmid = {40665422},
issn = {2524-6372},
support = {GRS-082/19//Gebert R&#xfc;f Foundation, Schwiez/ ; GRS-082/19//Gebert R&#xfc;f Foundation, Schwiez/ ; GRS-082/19//Gebert R&#xfc;f Foundation, Schwiez/ ; GRS-082/19//Gebert R&#xfc;f Foundation, Schwiez/ ; GRS-082/19//Gebert R&#xfc;f Foundation, Schwiez/ ; GRS-082/19//Gebert R&#xfc;f Foundation, Schwiez/ ; GRS-082/19//Gebert R&#xfc;f Foundation, Schwiez/ ; Root2Res (EU Horizon Europe no. 101060124 and Swiss State Secretariat for Education, Research and Innovation no 23.00050)//European Commission (European Union) and Swiss State Secretariat for Education, Research and Innovation (Switzerland)/ ; Root2Res (EU Horizon Europe no. 101060124 and Swiss State Secretariat for Education, Research and Innovation no 23.00050)//European Commission (European Union) and Swiss State Secretariat for Education, Research and Innovation (Switzerland)/ ; Root2Res (EU Horizon Europe no. 101060124 and Swiss State Secretariat for Education, Research and Innovation no 23.00050)//European Commission (European Union) and Swiss State Secretariat for Education, Research and Innovation (Switzerland)/ ; Root2Res (EU Horizon Europe no. 101060124 and Swiss State Secretariat for Education, Research and Innovation no 23.00050)//European Commission (European Union) and Swiss State Secretariat for Education, Research and Innovation (Switzerland)/ ; LIVESEED (EU Horizon 2020 no. 727230 and Swiss State Secretariat for Education, Research and Innovation no. 17.0009)//European Commission (European Union) and Swiss State Secretariat for Education, Research and Innovation (Switzerland)/ ; RYC2022-037997-I//MICIU/AEI/10.13039/501100011033 and FSE+/ ; },
abstract = {BACKGROUND: Plants are constantly challenged by pathogens, which can cause substantial yield losses. The aggressiveness of and damage by pathogens depends on the host-associated microbiome, which might be shaped by plant genetics to improve resistance. How different crop genotypes modulate their microbiota when challenged by a complex of pathogens is largely unknown. Here, we investigate if and how pea (Pisum sativum L.) genotypes shape their root microbiota upon challenge by soil-borne pathogens and how this relates to a genotype's resistance. Building on the phenotyping efforts of 252 pea genotypes grown in naturally infested soil, we characterized root fungi and bacteria by ITS region and 16 S rRNA gene amplicon sequencing, respectively.<br><br>RESULTS: Pea genotype markedly affected both fungal and bacterial community composition, and these genotype-specific microbiota were associated with root rot resistance. For example, genotype resistance was correlated (R[2]&#x2009;=&#x2009;19%) with root fungal community composition. Further, several key microbes, showing a high relative abundance, heritability, connectedness with other microbes, and correlation with plant resistance, were identified.<br><br>CONCLUSIONS: Our findings highlight the importance of crop genotype-specific root microbiota under root rot stress and the potential of the plant to shape its associated microbiota as a second line of defense.},
}
@article {pmid40665363,
year = {2025},
author = {Liu, Y and Hou, J and Qi, Z and Yang, L and Du, Z and Wu, Y and Song, Q and Li, X and Sun, J and Chen, P and Guan, X and Li, L},
title = {Prenatal psychological stress mediates vertical transmission of gut microbiome to the next generation affecting offspring depressive-like behaviors and neurotransmitter.},
journal = {BMC psychology},
volume = {13},
number = {1},
pages = {791},
pmid = {40665363},
issn = {2050-7283},
support = {S202210471038//College Student Innovation and Entrepreneurship Training Program in Henan/ ; 81973596//National Natural Science Foundation of China/ ; 212102310341//Science and Technology Innovation Talents in Universities of Henan Province/ ; 20B360004//Key Scientific Research Foundation of the Higher Education Institutions of Henan Province/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; Pregnancy ; Female ; *Stress, Psychological/metabolism/microbiology ; *Prenatal Exposure Delayed Effects/metabolism/microbiology/psychology ; Rats ; *Depression/microbiology/metabolism ; *Neurotransmitter Agents/metabolism ; *Dysbiosis/microbiology/metabolism ; Male ; Disease Models, Animal ; Rats, Sprague-Dawley ; Behavior, Animal ; Prefrontal Cortex/metabolism ; Feces/microbiology ; },
abstract = {OBJECTIVE: Prenatal stress has been proven to be associated with dysbiosis of the gut microbiota. Despite the established phenomenon that psychological stress can be transmitted to offspring and the ability of maternal gut microbiota to colonize the offspring's gut through vertical transmission, the intricate relationships linking cross-generational depression with the microbiome remain poorly understood.<br><br>METHODS: We utilized combined fear stress stimuli to establish a pregnancy psychological stress (PPS) rat model, in which offspring exhibited trans-generational depression-like behavior. The relationship between vertical transmission of the gut microbiome, intergenerational effects, and psychological stress in offspring was investigated using microbiology and metabolomics.<br><br>RESULTS: We demonstrated that the vertical transmission of co-altered species from PPS dams to their puberty offspring was strongly associated with dysbiosis of the gut microbiota in the offspring. In terms of microbial function, both PPS dams and their offspring exhibited upregulation of glycine, glutamate, and serine metabolism in fecal samples, as revealed by untargeted metabolomics. Additionally, this microbial trans-generational effect was reflected in the prefrontal cortical tissue of PPS offspring, where serine in the pathway and its interconverted glycine was significantly increased. Furthermore, the co-altered species and metabolites of the pathway formed a highly correlated module with disordered inflammatory factors and neurotransmitters in the prefrontal cortex tissue of PPS offspring. This indicates that the microbiome plays a significant role in prefrontal cortex neuroinflammation as well as neurotransmitter disorders in depression-like offspring.<br><br>CONCLUSIONS: Our findings highlight the gut microbiome as a plausible mediator of prenatal stress effects on offspring neurodevelopment, though further mechanistic validation is required.},
}
@article {pmid40665305,
year = {2025},
author = {Zhang, W and Xiang, Y and Ren, H and Liu, Y and Wang, Q and Ran, M and Zhou, W and Tian, L and Zheng, X and Qiao, C and Liu, Y and Yan, M},
title = {The tumor microbiome in cancer progression: mechanisms and therapeutic potential.},
journal = {Molecular cancer},
volume = {24},
number = {1},
pages = {195},
pmid = {40665305},
issn = {1476-4598},
support = {YJSCX2024-78HYD//Postgraduate Research &amp; Practice Innovation Program of Harbin Medical University/ ; No.82472867//National Natural Science Foundation of China/ ; YQ2024H003//The Outstanding Young Scholar Project of the Natural Science Foundation of Heilongjiang Province/ ; },
mesh = {Humans ; *Neoplasms/microbiology/therapy/pathology/etiology/metabolism ; Tumor Microenvironment/immunology ; *Microbiota ; Disease Progression ; Animals ; Signal Transduction ; },
abstract = {The tumor microbiome (TM) comprises diverse microbial communities, such as bacteria, fungi, and viruses. Recent advancements in microbial sequencing technologies have improved our understanding of the distribution and functional roles of microbes in solid tumors. The TM is formed through several mechanisms, such as direct invasion of mucosal barriers, diffusion from adjacent normal tissues, metastasis of tumor cells, and dissemination via blood and lymphatic circulation. Microbes play a critical role in the tumor microenvironment (TME), and the TM has a heterogeneous composition in different types of cancer. This heterogeneity affects tumor development, progression, and response to treatment. The TM modulates tumor cell physiology and immune responses via several signaling pathways, such as WNT/β-catenin, NF-κB, toll-like receptors (TLRs), ERK, and stimulator of interferon genes (STING). Extensive studies have characterized the role of TM in tumor progression, revealing the importance of genetic abnormalities, epigenetic changes, metabolic regulation, invasion and metastasis, and chronic inflammatory responses. The role of TM in cancer treatment, especially in immunotherapy, has received increasing attention, demonstrating significant regulatory potential. This review provides an in-depth overview of the development of TM detection technologies, explores its potential origins and heterogeneity, and elucidates the mechanisms by which TM contributes to tumorigenesis or tumor suppression. Furthermore, this review explored how TM can be used in cancer treatment, offering a comprehensive perspective on targeted and personalized approaches.},
}
@article {pmid40665254,
year = {2025},
author = {Pinto-Cardoso, S and Chávez-Torres, M and López-Filloy, M and Ávila-Ríos, S and Romero-Mora, K and Peralta-Prado, A},
title = {Patterns of immune recovery in people living with HIV who initiated antiretroviral therapy as late presenters.},
journal = {BMC infectious diseases},
volume = {25},
number = {1},
pages = {917},
pmid = {40665254},
issn = {1471-2334},
abstract = {BACKGROUND: Some people living with HIV-1 (PWH) do not reconstitute their CD4 + T cell counts despite complete inhibition of HIV-1 replication on antiretroviral therapy (AR); these are known as immunological nonresponders (INR). This is a retrospective analysis to estimate the prevalence of INR in a hospital-based cohort of PWH who initiated ART with severe immunodeficiency and/or opportunistic infections. We also explored mechanisms of poor immune recovery, with emphasis on the gut microbiome.<br><br>METHODS: All PWH included in this study achieved virologic suppression (plasma viral load&#x2009;<&#x2009;200 copies of HIV-1/mL) six months after ART initiation and remained virally suppressed thereafter. INR and immunological responders (IR) were defined according to the CD4&#x2009;+&#x2009;T cell counts after 24-months on ART initiation (<&#x2009;350 or &#x2265; 350 cells/&#xb5;L, respectively). Both INR (n&#x2009;=&#x2009;15) and IR (n&#x2009;=&#x2009;15) were matched for nadir CD4 (<&#x2009;200 cells/&#xb5;L). Uninfected individuals at high-risk of HIV infection were also included (n&#x2009;=&#x2009;40). We assessed indirect markers linked to HIV disease progression (markers of innate immune activation and enterocyte damage) and gut dysbiosis using cryopreserved plasma and stool samples using Enzyme-Linked immunosorbent Assay and 16S ribosomal DNA sequencing.<br><br>RESULTS: The estimated prevalence of INR after 24-months on ART was 50%. Microbial translocation, gut epithelial damage and gut dysbiosis persisted in PWH on ART, yet were not different between INR and IR. After adjusting for multiple comparisons, we found that INR had lower alpha diversity (Shannon) and higher levels of sCD163 compared with PWoH (p&#x2009;=&#x2009;0.013 and p&#x2009;=&#x2009;0.017, respectively). No differentially-abundant genera were identified; differences in the gut microbiome were primarily driven by a Prevotella and Bacteroides gradient, which is linked to sexual practices (men who have sex with men, MSM). Indeed, in our cohort, most INR were non-MSM, while PWoH were all MSM.<br><br>CONCLUSIONS: In the Instituto Nacional de Enfermedades Respiratorias, a tertiary reference centre, a disproportionate number of individuals are diagnosed with HIV-1 with severe immunodeficiency and/or opportunistic infections; they represent a high-risk population for the INR phenotype. Our data on possible mechanisms of the INR phenotype linked to the gut microbiome yielded modest results, precluding any decisive conclusions. Interventions to boost the immune function in this at-risk population are warranted and deserving of further studies.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12879-025-11318-2.},
}
@article {pmid40665229,
year = {2025},
author = {Curtis, A and Harrison, F and Kavanagh, K},
title = {Proteomic characterization of Aspergillus fumigatus - host interactions using the ex-vivo pig lung (EVPL) model.},
journal = {Virulence},
volume = {16},
number = {1},
pages = {2530675},
pmid = {40665229},
issn = {2150-5608},
mesh = {Animals ; *Aspergillus fumigatus/pathogenicity/physiology/metabolism/genetics ; Swine ; *Lung/microbiology/immunology ; Proteomics ; *Host-Pathogen Interactions ; Disease Models, Animal ; *Proteome/analysis ; },
abstract = {Aspergillus fumigatus is an opportunistic fungal pathogen of the human airway that can cause a variety of chronic infections, typically in the context of pre-existing lung damage. The interaction of A. fumigatus with ex-vivo pig lung (EVPL) samples was characterized at the proteomic level to provide insights into how the fungus may interact with pulmonary tissue in vivo. This model has many advantages, because pigs share 90% immunological homology with humans and display many anatomical similarities. EVPL also retains resident immune cells, has richer cellular complexity compared to in-vitro models, and has a microbiome. Label-free quantitative proteomic analysis identified the metabolism and development of A. fumigatus on the EVPL alveolar sections; at 48 h, there was an increased abundance of proteins associated with carbon metabolism (e.g. malate dehydrogenase (+8.2 fold increase)), and amino acid metabolism and biosynthesis (e.g. 5-methyltetrahydropteroyltriglutamate - homocysteine S-methyltransferase, (+5.04 fold)) at 72 h. Porcine tissue remained responsive to the pathogen with proteins that increased in abundance associated with innate immune recruitment (e.g. protein S100-A8 (+28.5 fold) and protein S100-A9 (calgranulin-B) (+7.25 fold)) at 24 h, while proteins associated with neutrophil degranulation (e.g. elastase, neutrophil (-2.74 fold)) decreased in abundance. At 96 h, the infected tissue demonstrated enhanced abundance of fibrotic markers (e.g. fibrillin 1, collagen type IV alpha 1 chain, and alpha 2 chain, increased by + 16.44, +15.42 and + 11.95 fold, respectively). These results validate the use of this model for studying pathogen-host interactions and highlight how A. fumigatus interacts with pulmonary tissue during colonization.},
}
@article {pmid40665216,
year = {2025},
author = {Ali, N and Jiang, Q and Akhtar, K and Luo, R and Jiang, M and He, B and Wen, R},
title = {Biochar and manure co-application improves soil health and rice productivity through microbial modulation.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {914},
pmid = {40665216},
issn = {1471-2229},
abstract = {UNLABELLED: Individual applications of biochar (B) or organic manure (M) have been reported to improve soil fertility and plant performance. Their synergistic effects on paddy soil physicochemical properties, microbial communities, and rice productivity remain under explored. This study investigated the effects of B (20 t ha[− 1]), M (15 t ha[− 1]), and their combined application (BM, 10 + 7.5 t ha[− 1]) on soil physicochemical properties, microbial communities, rice plant growth and yield. Our findings revealed that B, M, and BM significantly improved soil physicochemical properties compared to control (CK). BM enhanced total nitrogen and available phosphorus by 34% and 26%, respectively, compared to CK. Soil pH, soil organic carbon, available nitrogen, and available potassium showed higher values in all treatments compared to the CK, with no significant differences among B, M, or their combined applications. Chlorophyll a, b, plant growth, dry matter and yield attributes showed the trend of BM > M > B > CK. These changes were attributed to the enhancement of beneficial soil bacteria, including Proteobacteria, Firmicutes, Actinobacteria and Bacteroidota in the BM treatment. Individual biochar treatment reduced Chloroflexi and Firmicutes but increased Proteobacteria and Actinobacteria. In contrast, individual manure application enhanced Firmicutes and Nitrospirota. Among fungal communities, Chaetomium and Pinnularia showed higher relative abundances in the combined treatment, playing roles in organic matter decomposition and plant growth, respectively. We conclude that the integrated use of biochar and manure enhances rice performance primarily by fostering a soil microbiome conducive to nutrient cycling and plant growth. Combined B + M application is therefore recommended as a sustainable strategy for improving paddy soil quality and crop yield.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12870-025-06834-x.},
}
@article {pmid40665110,
year = {2025},
author = {Ruiz, A and Sanahuja, I and Torrecillas, S and Gisbert, E},
title = {Anatomical site and environmental exposure differentially shape the microbiota across mucosal tissues in rainbow trout (Oncorhynchus mykiss).},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {25653},
pmid = {40665110},
issn = {2045-2322},
support = {PRE2019-091259//Ministerio de Ciencia e Innovaci&#xf3;n/ ; FJC2020-043933-I//Ministerio de Ciencia e Innovaci&#xf3;n/ ; RYC2021-031414-I//Ministerio de Ciencia e Innovaci&#xf3;n/ ; PID2023-147976OR-C21//Ministerio de Ciencia e Innovaci&#xf3;n/ ; },
mesh = {Animals ; *Oncorhynchus mykiss/microbiology ; *Microbiota ; Skin/microbiology ; *Mucous Membrane/microbiology ; Gills/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; *Environmental Exposure ; Gastrointestinal Microbiome ; },
abstract = {This study investigates the diversity, structure, and composition of the fish microbiota across different mucosal organs by comparing the bacterial communities in the oropharyngeal cavity, posterior intestine, gills, and skin of farmed rainbow trout (Oncorhynchus mykiss), along with water and biofilm samples from the surrounding environment. Four distinct skin regions across the dorsal-ventral and anterior-posterior axes were also compared in fish weighing 390.5 ± 36.8 g. Sample analyses showed that lower values of richness (observed) and diversity (Shannon and Faith indices) were observed in the posterior intestine compared to the gills, skin, and environmental (water and biofilm) samples (P < 0.05). Similarly, the oropharynx showed higher Faith diversity values than the intestine (P = 0.01). Furthermore, bacterial community structures differed significantly across organs based on unweighted and weighted UniFrac distances (P = 0.001 for both), with the posterior intestine showing the greatest divergence from other mucosal sites. Indeed, Pseudomonadota was the most abundant phylum across all sample types, except for the posterior intestine, where Firmicutes, particularly the genus Mycoplasma, showed a clear predominance. The posterior intestine showed facultative anaerobic genera, while the other mucosae and environmental samples were mainly composed of strictly aerobic members, like Flavobacterium and Crocinitomix. The microbial communities across the different skin regions were highly heterogeneous: while the dorsal area showed a consistent microbiota, the ventral region exhibited differences between the anterior and posterior sections in bacterial structure and composition at the genus level (P < 0.05). For instance, Candidatus Piscichlamydia was very abundant in the gills and ventral-anterior skin, but was scarcely detected in the rest of skin areas. Overall, these findings suggest a high differentiation of bacterial communities across fish organs, tailored to the specific physiological and environmental characteristics of each mucosal tissue, with a stronger modulation by the surrounding environment in the external mucosae and a higher influence of host innate factors in inner organs, such as the intestine.},
}
@article {pmid40665053,
year = {2025},
author = {Reicher, L and Shilo, S and Godneva, A and Lutsker, G and Zahavi, L and Shoer, S and Krongauz, D and Rein, M and Kohn, S and Segev, T and Schlesinger, Y and Barak, D and Levine, Z and Keshet, A and Shaulitch, R and Lotan-Pompan, M and Elkan, M and Talmor-Barkan, Y and Aviv, Y and Dadiani, M and Tsodyks, Y and Gal-Yam, EN and Leibovitzh, H and Werner, L and Tzadok, R and Maharshak, N and Koga, S and Glick-Gorman, Y and Stossel, C and Raitses-Gurevich, M and Golan, T and Dhir, R and Reisner, Y and Weinberger, A and Rossman, H and Song, L and Xing, EP and Segal, E},
title = {Deep phenotyping of health-disease continuum in the Human Phenotype Project.},
journal = {Nature medicine},
volume = {},
number = {},
pages = {},
pmid = {40665053},
issn = {1546-170X},
abstract = {The Human Phenotype Project (HPP) is a large-scale deep-phenotype prospective cohort. To date, approximately 28,000 participants have enrolled, with more than 13,000 completing their initial visit. The project is aimed at identifying novel molecular signatures with diagnostic, prognostic and therapeutic value, and at developing artificial intelligence (AI)-based predictive models for disease onset and progression. The HPP includes longitudinal profiling encompassing medical history, lifestyle and nutrition, anthropometrics, blood tests, continuous glucose and sleep monitoring, imaging and multi-omics data, including genetics, transcriptomics, microbiome (gut, vaginal and oral), metabolomics and immune profiling. Analysis of these data highlights the variation of phenotypes with age and ethnicity and unravels molecular signatures of disease by comparison with matched healthy controls. Leveraging extensive dietary and lifestyle data, we identify associations between lifestyle factors and health outcomes. Finally, we present a multi-modal foundation AI model, trained using self-supervised learning on diet and continuous-glucose-monitoring data, that outperforms existing methods in predicting disease onset. This framework can be extended to integrate other modalities and act as a personalized digital twin. In summary, we present a deeply phenotyped cohort that serves as a platform for advancing biomarker discovery, enabling the development of multi-modal AI models and personalized medicine approaches.},
}
@article {pmid40664985,
year = {2025},
author = {Boutin, S and Laforest-Lapointe, I},
title = {Reproducing plant microbiome research reveals site and time as key drivers of apple tree phyllosphere bacterial communities.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {25620},
pmid = {40664985},
issn = {2045-2322},
mesh = {*Malus/microbiology ; *Microbiota ; *Bacteria/genetics/classification/isolation &amp; purification ; *Plant Leaves/microbiology ; Flowers/microbiology ; RNA, Ribosomal, 16S/genetics ; Reproducibility of Results ; },
abstract = {Manipulating plant microbiomes is foreseen as a key biocontrol avenue to tackle the accelerating challenges of global change in agriculture. Several recent studies have identified the spatiotemporal dynamics of phyllosphere microbial communities, stressing the need to understand plant microbiome drivers to design efficient biocontrol interventions. Yet, these works are often performed on small sample counts, rarely provide sufficient information on the relative impact of time or local environment, and are seldom repeated to assess reproducibility. To address these limits, we performed a longitudinal sampling across multiple orchards of contrasting agricultural practices to study the ecological drivers of phyllosphere bacterial communities of apple tree (Malus domestica, Borkh.). We sampled up to eight apple cultivars at six orchards (three conventional, three organic) in the Eastern Townships (Canada) in 2022 and 2023. In contrast with common cross-sectional microbiome studies, our work builds on a two-year sampling design, thus allowing for the evaluation of the reproducibility of previous plant microbiome research. Our results support previous findings indicating that site and time are major drivers of apple tree bacterial community structure, yet their relative influence vary across the two sampling years. In addition, our data showed that leaf and flower bacterial alpha diversity is lower at organic sites compared to conventional sites. Overall, this study provides a comprehensive longitudinal multi-site study design highlighting the value of assessing reproducibility in plant microbiome studies and paving the way for future research in this field.},
}
@article {pmid40664880,
year = {2025},
author = {Smolander, N and Fuchs, B and Helander, M and Puigbò, P and Tamminen, M and Saikkonen, K and Mathew, SA},
title = {Glyphosate and phosphate treatments in soil differentially affect crop microbiomes depending on species, tissue and growth stage.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {25502},
pmid = {40664880},
issn = {2045-2322},
support = {355917//Research Council of Finland/ ; 311077//Research Council of Finland/ ; },
mesh = {Glyphosate ; *Glycine/analogs &amp; derivatives/pharmacology ; *Soil Microbiology ; *Microbiota/drug effects ; *Crops, Agricultural/microbiology/growth &amp; development/drug effects ; *Phosphates/pharmacology ; Fertilizers ; *Herbicides/pharmacology ; RNA, Ribosomal, 16S/genetics ; *Soil/chemistry ; Plant Roots/microbiology/drug effects ; Solanum tuberosum/microbiology/growth &amp; development/drug effects ; Bacteria/genetics/drug effects/classification ; Avena/microbiology/growth &amp; development/drug effects ; Plant Leaves/microbiology ; Vicia faba/microbiology/growth &amp; development ; },
abstract = {Glyphosate-based herbicides (GBHs) are widely used for controlling weeds by inhibiting the shikimate pathway. However, the effects of GBH on non-target organisms, such as shikimate pathway-containing microbes, are understudied. Furthermore, the complex interactions between GBH and fertilizers are difficult to predict. Hence, we experimentally investigated the effects of GBH and phosphate fertilizer on the composition of endophytic bacterial communities of potato, faba bean and oat during early and late summer using 16S rRNA gene sequencing, and on plant growth in late summer. GBH treatments significantly affected bacterial communities of early and late summer potato roots and late summer faba bean roots, while phosphate treatments significantly affected bacterial communities of late summer potato leaves, tubers and early summer faba bean leaves. The treatments reduced bacterial diversity in potato and oat and the abundance of putatively beneficial bacteria in potato and faba bean. However, these treatments increased the aboveground biomass of all crops. Thus, agrochemicals had variable effects across crops, tissues and growth stages. While improved crop yield is often prioritized in chemical-intensive farming, the effects of microbiome shifts on crop health need further investigation.},
}
@article {pmid40664808,
year = {2025},
author = {Lombardo-Hernandez, J and Mansilla-Guardiola, J and Aucello, R and Botta, C and García-Esteban, MT and Murciano-Cespedosa, A and Muñoz-Rodríguez, D and Quarta, E and Mateos González, &#xc1; and Juan-Llamas, C and Rantsiou, K and Geuna, S and Cocolin, L and Herrera-Rincon, C},
title = {An in vitro neurobacterial interface reveals direct modulation of neuronal function by gut bacteria.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {25535},
pmid = {40664808},
issn = {2045-2322},
support = {FPU23/02273//Spanish Ministry of Universities FPU Predoctoral Fellowship/ ; PID2023-147361NA-I00//Ministerio de Ciencia e Innovaci&#xf3;n/ ; PR3/23-30827//Universidad Complutense de Madrid/ ; },
mesh = {Animals ; *Neurons/microbiology/metabolism/physiology/cytology ; Rats ; *Gastrointestinal Microbiome ; Gene Expression Profiling ; *Lactobacillus plantarum/physiology ; Transcriptome ; Cells, Cultured ; Calcium Signaling ; Neuronal Plasticity ; },
abstract = {Interactions between bacteria and somatic cells are increasingly important for understanding cellular communication mechanisms. While the gut microbiome's influence on the gut-brain axis is established, direct interactions between bacteria and neurons are poorly explored, especially regarding bidirectional information exchange. We developed an in vitro model using the foodborne bacterium Lactiplantibacillus plantarum and rat cortical neural cultures to study neuronal responses to bacterial presence through morphological, functional, and transcriptomic analyses. We found that L. plantarum adheres to neuronal surfaces without penetrating the soma. Real-time calcium imaging showed enhanced Ca[2][+] signaling dependent on bacterial concentration and active metabolism. Neurons exhibited changes in neuroplasticity-related proteins such as Synapsin I and pCREB, indicating functional modulation. Transcriptomic profiling revealed significant gene expression changes affecting networks linked to neurological conditions and bioelectrical signaling. Together, our results provide proof-of-concept for targeted neuronal responses induced by bacterial contact, offering key resources and transcriptomic data to advance the study of bacteria-driven neural modulation within the gut-brain axis.},
}
@article {pmid40664314,
year = {2025},
author = {Li, Y and Zhang, S and Li, C and Shen, J and Cao, P and Sun, Y and Ma, X and An, B},
title = {Prebiotics chronotherapy alleviates depression-like behaviors in FMT mice through enhancing short-chain fatty acids receptors and intestinal barrier.},
journal = {Journal of affective disorders},
volume = {},
number = {},
pages = {119885},
doi = {10.1016/j.jad.2025.119885},
pmid = {40664314},
issn = {1573-2517},
abstract = {BACKGROUND: Prebiotics interventions to restore microbiome homeostasis may have long-lasting benefits for mental health especially in adolescence. However, the anti-depressants of prebiotics, particularly in prebiotics chronotherapy, orchestrated remain unknown. We aimed to elucidate the underlying mechanisms of prebiotics in light of maximum antidepressant effects by appropriate dosing timing.<br><br>METHODS: Adolescent depression mouse model was made by fecal microbiota transplantation (FMT) from major depressive disorder (MDD) adolescent patients. Sodium Butyrate (SB), one of SCFAs, was intragastrically administrated to mice at Zeitgeber time 4 (ZT4: the highest short-chain fatty acids (SCFAs) receptor-activated timing) or ZT16 (the lowest SCFA receptor-activated timing) for the last 2&#x202f;weeks within 4-week-FMT exposure. The success of modeling and antidepressant effects of SB chronotherapy were determined by changes in depression-like behaviors, inflammation, neurotrophy, neuron functions, circadian rhythm, and barrier systems.<br><br>RESULTS: SB alleviated depressive symptoms at ZT4 with better efficacy over ZT16. SB decreased inflammation, upregulated neurotrophy, restored functions, and re-established circadian rhythm. Notably, SB increased the expressions of SCFAs receptors to repair the intestinal barrier and blood-brain barrier, thereby alleviating depressive symptoms.<br><br>LIMITATION: Only one prebiotic with one disease was involved.<br><br>CONCLUSION: SB supplementation could be a promising therapeutic tactic for restoring the integrity of barrier systems by enhancing the intestinal SCFAs receptors. Alignment SB supplementation with circadian clocks might help to obtain better antidepressant efficacy, which may generate novel insights into diseases related to diseases with barrier system impairment and optimize interventions to improve health and human well-being.},
}
@article {pmid40664260,
year = {2025},
author = {Mac Aogáin, M},
title = {Beyond ORBIT: Mapping the Constellation of Pseudomonas Endotypes in Bronchiectasis Clinical Trials.},
journal = {American journal of respiratory and critical care medicine},
volume = {},
number = {},
pages = {},
doi = {10.1164/rccm.202506-1388ED},
pmid = {40664260},
issn = {1535-4970},
}
@article {pmid40664089,
year = {2025},
author = {Zhu, Y and Xi, Q and Liu, Y and Zhou, Y and Liao, J and Wu, Q},
title = {Recent advances in exosome-based nanodelivery systems for Parkinson's disease.},
journal = {Biomaterials},
volume = {325},
number = {},
pages = {123548},
doi = {10.1016/j.biomaterials.2025.123548},
pmid = {40664089},
issn = {1878-5905},
abstract = {Parkinson's disease (PD) is a progressive neurodegenerative disorder that primarily affects dopaminergic neurons in the substantia nigra. Its multifactorial pathogenic mechanisms include oxidative stress, mitochondrial dysfunction, α-synuclein aggregation, neuroinflammation, and alterations in the gut microbiome, ultimately leading to neuronal deficits and debilitating motor and nonmotor symptoms. Although conventional therapies provide temporary relief, their efficacy tends to wane over time or produce adverse effects. Exosome-based therapeutic strategies are a promising alternative, and we highlight the unique advantages of exosomes, including their biocompatibility, low immunogenicity, and ability to cross the blood-brain barrier, thereby facilitating the targeted delivery of neuroprotective and anti-inflammatory medications to affected regions. We also discuss recent advances in exosome engineering to improve cargo loading, enhance cell specificity and improve efficacy. However, large-scale exosome production, targeted delivery and long-term safety remain major challenges. Early-phase clinical trials of exosome-based therapies in other neurodegenerative conditions have demonstrated acceptable tolerability, and ongoing preclinical studies in PD models suggest potential efficacy, laying the groundwork for future clinical translation.},
}
@article {pmid40663917,
year = {2025},
author = {El-Keblawy, A and Jarrar, H and Manikandan, SK and Abideen, Z and Sheteiwy, MS},
title = {Rhizosheaths in desert plants: Natural mechanisms and bioinspired technologies for water harvesting and dryland restoration.},
journal = {The Science of the total environment},
volume = {994},
number = {},
pages = {180064},
doi = {10.1016/j.scitotenv.2025.180064},
pmid = {40663917},
issn = {1879-1026},
abstract = {Rhizosheaths, which are sand sheaths formed around plant roots, represent a critical adaptation in many desert species, enabling survival under arid conditions through enhanced water and nutrient retention. Although rhizosheaths also occur in crops such as wheat and maize, this review emphasizes desert-adapted grasses and sedges that exhibit highly specialized rhizosheath structures and functions. We synthesize current knowledge on rhizosheath formation, microbial and biochemical interactions, and mechanisms of soil and atmospheric water harvesting. Our analysis shows that rhizosheaths significantly enhance local moisture availability, support beneficial microbial communities, and contribute to nutrient cycling in sandy soils. We also highlight the key role of mucilage chemistry and root-microbe interactions in stabilizing rhizosheaths under drought. The review highlights their ecological functions as nutrient-rich microhabitats and their role in supporting drought-adapted microbial consortia. We further explore how rhizosheath biology inspires bioinspired technologies such as hydrogels, root-zone irrigation systems, and exopolysaccharide-based seed coatings. In conclusion, we identify key knowledge gaps-particularly in mucilage composition, microbiome specificity, and the scalability of synthetic rhizosheaths-and propose future directions for climate-resilient agriculture and dryland restoration.},
}
@article {pmid40663882,
year = {2025},
author = {Khattak, F and Galgano, S and Pearson, R and Houdijk, JGM and Short, F and Leigh, A},
title = {Enhancing key broiler welfare indicators, meat quality, and gut microbiome composition using oxygen-enriched drinking water under commercially relevant housing conditions.},
journal = {Poultry science},
volume = {104},
number = {10},
pages = {105550},
doi = {10.1016/j.psj.2025.105550},
pmid = {40663882},
issn = {1525-3171},
abstract = {Water is a critical nutrient in poultry production, yet its quality, particularly dissolved oxygen (DO) content, is often overlooked. This study is the first to comprehensively evaluate the impact of oxygen-enriched drinking water on broiler welfare, breast muscle myopathies, and gut microbiome composition under commercially relevant housing conditions. A total of 840 male Ross 308 broiler chicks were randomly assigned to two treatment groups (oxygenated water vs. tap water), with 12 replicate pens per treatment. Oxygenated water was enriched to a DO level of approximately 32 mg/L, compared to around 9.5 mg/L in tap water. Birds were reared to 36 days of age. The consistently high performance of both treatment groups under controlled experimental conditions is demonstrated by final body weights and feed conversion ratios surpassing Ross 308 breed standards by approximately 19-22 % from day 24 onward. Although growth performance remained unaffected under these optimal conditions, oxygenated water significantly improved welfare indicators, including feather condition, hock burn scores, and breast cleanliness (P< 0.05). Birds on oxygenated water also showed lower abdominal fat (-12 %) and higher thigh yield (+2.6 %) without compromising breast yield. Carcass fat deposition was significantly lower (abdominal fat pad reduced by ∼12 %), and thigh yield was higher in the oxygenated water treatment (P < 0.05), although overall carcass weight and breast yield were unchanged. No major differences were detected in breast meat nutrient composition (P > 0.05). The prevalence of white striping in breast fillets was markedly reduced in birds receiving oxygenated water, 32 mg/L indicating enhanced muscle integrity (P < 0.05). Metagenomic analysis revealed that some bacterial lipid metabolism pathways where differentially abundant in oxygenated-water birds. Following up on previous knowledge suggesting the interplay between lipid metabolism and broiler welfare, these findings suggest that supplementing broiler drinking water with 32 mg/L DO levels may offer a practical, non-pharmaceutical strategy to mitigate breast muscle myopathies and improve overall animal welfare and meat quality.},
}
@article {pmid40663629,
year = {2025},
author = {Kriete, AL and Scott, MJ},
title = {Direct and trans-generational effects of tetracyclines on the microbiome, transcriptome, and male mating behavior of the sheep blowfly Lucilia cuprina.},
journal = {G3 (Bethesda, Md.)},
volume = {},
number = {},
pages = {},
doi = {10.1093/g3journal/jkaf160},
pmid = {40663629},
issn = {2160-1836},
abstract = {Tetracyclines are broad-spectrum antibiotics widely used in agriculture, medicine, and research. However, they are associated with harmful side effects. In arthropods, parental exposure to tetracyclines has been linked to reduced health and fitness in untreated offspring. These trans-generational effects of tetracyclines could jeopardize the success of pest control programs that use tetracyclines to control gene expression. In this study, we investigated the transgenerational effects of two tetracyclines, doxycycline (DOX) and anhydrotetracycline (ATC), in the blowfly Lucilia cuprina, a significant pest of sheep. To simulate the rearing conditions of a transgenic male-only release program, blowflies were reared on standard diet alone, or on standard diet plus DOX or ATC, for three generations, then reared for an additional fourth generation on standard diet alone. We used behavioral assays, 16S amplicon sequencing, and mRNA sequencing to determine how DOX and ATC influenced male sexual competitiveness, microbiome composition and gene expression in the third and fourth generations. We found that three generations of DOX treatment led to lower sexual competitiveness in both third- and fourth-generation males. In addition, DOX and ATC shifted the composition of the blowfly microbiome and altered the expression of numerous mitochondria- and immunity-related genes in both generations. Our study supports an emerging body of evidence that tetracyclines exert not only direct but also trans-generational effects, and sheds light on the transcriptional and microbial responses to antibiotic exposure and removal. Our findings emphasize the need for pest control programs that use tetracyclines to evaluate the long-term effects of these antibiotics.},
}
@article {pmid40663456,
year = {2025},
author = {Novák, &#xc1; and Zajta, E and Csikós, M and Halmos, E and Horváth, M and Tildy, O and Szekeres, A and Svorenj, G and Gémes, N and Szebeni, GJ and Tóth, R and Gacser, A},
title = {Comprehensive analysis of human keratinocyte interactions with Candida albicans and Candida parapsilosis.},
journal = {Virulence},
volume = {},
number = {},
pages = {2532815},
doi = {10.1080/21505594.2025.2532815},
pmid = {40663456},
issn = {2150-5608},
abstract = {In recent years, microbiome studies revealed that Candida species are common colonisers of the human skin. The distribution of species however varies greatly. Although C. parapsilosis is more likely to resemble skin commensals, opinions are divided, and discrepancies are present regarding C. albicans, that is also often associated with cutaneous candidiasis. Therefore, we aimed to thoroughly assess the nature of skin epithelial cell - Candida interactions. To study species-specific host responses, we examined internalization, cytokine and metabolic responses in different keratinocytes (HaCaT, HPV-KER) along with host cell damage following fungal stimuli. To rigorously examine yeast-keratinocyte interactions, we applied two distinct isolates of both C. albicans (SC5314, WO-1) and C. parapsilosis (GA1, CLIB214). Comparison of the two fungi's virulence revealed that while C. albicans effectively adheres to human keratinocytes and causes subsequent damage, C. parapsilosis is unable to establish lasting physical contact and causes less harm. In terms of keratinocyte response, both cell lines showed significantly enhanced cellular (internalization), humoral (IL-6, IL-8) and metabolic responses (2-ketoglutaric acid, citric acid, threorine, hypotaurine) to C. albicans strains, while those towards C. parapsilosis remained relatively low or similar to the control condition. Under certain conditions strain preference was also detected. Of the two cell lines, HPV-KER was more sensitive, as besides interspecies differences, intraspecies differences were also measurable. These results suggest that C. albicans triggers an enhanced antifungal response, thus does not closely resemble skin commensals, like C. parapsilosis. Furthermore, HPV-KER might serve as a more applicable tool for studying keratinocyte antifungal responses.},
}
@article {pmid40663222,
year = {2025},
author = {Chen, Q and Wang, G and Shu, J and Zou, X and Miao, W and Nong, W and Li, M and Lan, G and Huang, W and Huang, X and Luo, H and Qu, S},
title = {Mendelian randomization analysis of gut microbiota-immune cell interactions in malignant neoplasm of nasopharynx.},
journal = {AMB Express},
volume = {15},
number = {1},
pages = {106},
pmid = {40663222},
issn = {2191-0855},
support = {2024GXNSFBA010070//Guangxi Natural Science Foundation/ ; },
abstract = {Observational studies have suggested associations among the gut microbiome, immune cells, and the risk of malignant neoplasms of nasopharynx. However, the causality of these relationships remains unclear. Thus, we conducted multiple Mendelian Randomization analyses to estimate the causal association of gut microbiota with the risk of malignant neoplasms of nasopharynx and to evaluate the mediating effect of immune cells on this causal pathway. Genetic variants extracted from genome-wide association studies of human gut microbiota compositions (n = 211), immune cell traits (n = 731) and malignant neoplasms of nasopharynx served as instrumental variables for calculating causal associations and mediating effects. Four gut microbiota compositions and eight immune cell traits exhibited detrimental causal effects, while three gut microbiota compositions and fifteen immune cell traits demonstrated protective effects. Interestingly, the causal association of genus Candidatus Soleaferrea id.11350 was no longer significant after adjusting for two established immune cell traits (HLA DR + + monocyte %leukocyte and HLA DR + + monocyte % monocyte). Moreover, HLA DR + + monocyte %leukocyte exhibited a mediating effect (OR 0.75, 95% CI 0.59-0.96) on the causal pathway of genus Candidatus Soleaferrea id.11350-malignant neoplasms of nasopharynx, with a mediating proportion of 21.59%. To our knowledge, this study is the first to identify potential therapeutic targets and elucidate mechanistic insights for malignant neoplasms of nasopharynx interventions involving gut microbiota and immune cell traits; however, these findings warrant further validation through adequately powered randomized clinical trials (RCTs).},
}
@article {pmid40662747,
year = {2025},
author = {Touceda-Suárez, M and Ponsero, AJ and Barberán, A},
title = {Differences in the genomic potential of soil bacterial and viral communities between urban greenspaces and natural arid soils.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0212424},
doi = {10.1128/aem.02124-24},
pmid = {40662747},
issn = {1098-5336},
abstract = {Urban green spaces provide essential ecosystem services that are ever more important in arid cities. However, the design and management of these greenspaces often require physicochemical transformations, whose effect in the balance of the arid urban ecosystems is normally not accounted for. In this project, we leverage metagenomic data from soil microbial communities of urban greenspaces and neighboring natural areas in a city from the arid Southwestern USA (Tucson, Arizona) to understand the differences in microbial (bacterial and viral) community structure, taxonomy, and function in urban greenspaces compared to natural arid soils. We found bacterial and viral communities to be distinct between urban greenspace and natural arid soils, with urban greenspace bacteria displaying reduced metabolic versatility and higher genetic potential for simple carbohydrate consumption and nitrogen reduction. Moreover, bacteria in urban greenspaces exhibit higher genetic potential for resistance to heavy metals and certain clinical antibiotics. Our results suggest that the conversion of arid natural land to urban greenspaces determines the soil microbiome structure and functioning, and potentially its ability to adapt to the changing environment.IMPORTANCEUrban green spaces are critical for the sustainability of arid cities. Nevertheless, they require deep soil physicochemical transformations. Soil bacterial and viral communities are responsible for soil functioning and provision of some ecosystem services, but they are also highly influenced by changes in the soil environment. The significance of our research is in illustrating the structural and functional changes that microbial and viral communities undergo in urban soils of arid cities and their potential impacts on urban greenspace soil processes.},
}
@article {pmid40662685,
year = {2025},
author = {Verstraete, W and Strubbe, L and Pikaar, I and Vinestock, TW and Lee, PH and Matassa, S and Chong, J and Zhou, J and Daigger, GT and Guo, M},
title = {Escaping Historical Lock-in─Redesigning Wastewater Treatment Plants and Their Microbiomes for the 21st Century.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c06208},
pmid = {40662685},
issn = {1520-5851},
abstract = {Wastewater treatment plants (WWTPs) have gradually, over the last hundred years, been designed and extended to deal with a sequence of problems, including a) odor, b) suspended solids, c) organics, d) ammonia, e) nitrate and phosphate, and f) recalcitrant pollutants. The line of historical developments was piecemeal rather than holistic and did not focus on sustainability, resource recovery, and water reuse. On the contrary, microbial processes that accelerated the removal of nitrogen were incorporated and heralded as a positive part of the "cleanup" agenda, despite their relatively large energy consumption and substantial production of nitrous oxide, a potent greenhouse gas. The time has come to examine the historical, technological, and microbiological lock-in present in today's WWTPs, so that a more coherent integrated system can be developed for future generations. Some disruptive strategies are outlined, and a categorization of processes in terms of their potential for the future is formulated.},
}
@article {pmid40662582,
year = {2025},
author = {Li, B and Fu, M and Jin, G and Liu, Z},
title = {Rare bacterial subcommunity drives nutrient cycling in phyllosphere habitat of evergreen conifers.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0051825},
doi = {10.1128/spectrum.00518-25},
pmid = {40662582},
issn = {2165-0497},
abstract = {UNLABELLED: Phyllosphere bacteria are crucial for pathogen resistance, stress tolerance, and productivity maintenance of host plants and further have potential effects on ecosystem functions. However, whether and how assembly patterns of both abundant and rare subcommunities changed across needle age cohorts, and their relative contributions to nutrient cycling in phyllosphere habitat of evergreen conifers are still unclear. Here, we examined both phyllosphere abundant and rare bacterial subcommunities in three needle age cohorts of the representative evergreen conifers in mixed broadleaved-Korean pine forests throughout Northeast China. We found that dispersal limitation and ecological drift dominated abundant and rare subcommunities, respectively. Deterministic assembly gradually increased with needle aging, which was mainly attributed to the increased needle chemical defense traits such as flavonoids. We further showed that multiple nutrient cycling in phyllosphere habitat was regulated by the rare subcommunity, closely related to the variations in diversity and composition. Collectively, our findings facilitate us in clarifying the mechanisms underlying the formation and succession of phyllosphere bacterial subcommunities across needle age cohorts and emphasize the vital role of rare subcommunities in promoting ecosystem functions.<br><br>IMPORTANCE: Host-associated microbial communities are critical for host health. However, the relative importance of abundant and rare subcommunities in driving nutrient cycling in phyllosphere habitat across needle age cohorts of evergreen conifers remains unknown. Here, we showed the different assembly mechanisms of abundant and rare subcommunities and emphasized the ecological role of rare subcommunities in promoting ecosystem functions. This is useful for understanding the formation and succession dynamics of plant microbiome to advance future applications with microbial agents to sustainable productivity and reduce diseases.},
}
@article {pmid40662533,
year = {2025},
author = {Jiang, J and Hu, D and Hu, S and Huang, K and Zheng, J and Pei, E},
title = {Age-Related Differences in Gut Microbiome and Fecal Metabolome of Captive African Penguins (Spheniscus demersus).},
journal = {Zoo biology},
volume = {},
number = {},
pages = {},
doi = {10.1002/zoo.70014},
pmid = {40662533},
issn = {1098-2361},
support = {//This study was supported by a Project of Shanghai Zoo (SZ220302) and Special Fund for Scientific Research of Shanghai Landscaping &amp; City Appearance Administrative Bureau (G250407)./ ; },
abstract = {The purpose of the present study was to characterize the profiles of gut microbiota and fecal metabolites in African penguins (Spheniscus demersus) of different ages. The combination of metagenome and metabolome was performed on the feces of captive African penguins of varying age groups, including juvenile (1-3 years old), adult (4-15 years old) and senior (16-20 years old) individuals. The results of the metagenome showed that microbial abundance was significantly different between groups. Adult penguins had higher abundances of Gallilactobacillus and Ligilactobacillus compared to juvenile penguins. Senior penguins exhibited higher abundances of Gammaproteobacteria and Escherichia coli than adult penguins. We further identified differentially expressed metabolites across the groups using liquid chromatography-mass spectrometry analysis. Correlation analysis showed that age was correlated significantly with certain differential microbial species and fecal metabolites. The results revealed that age is a key factor influencing gut microbiota and metabolism in African penguins. Our results provide baseline information on gut microbial structure and fecal metabolite characteristics in African penguins of different ages, which is vital for the management and ex situ conservation of this endangered species.},
}
@article {pmid40662501,
year = {2025},
author = {Bai, L and Wen, Y and Han, G and Tang, J and Xu, Z and Wang, Z and Jiang, L and Ren, H},
title = {Long-term climate warming and nitrogen deposition increase leaf epiphytic and endophytic bacterial diversity.},
journal = {Journal of integrative plant biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jipb.13965},
pmid = {40662501},
issn = {1744-7909},
support = {2022YFF1302300//National Key Research and Development Program of China/ ; YLXKZX-NND-002//First-Class Discipline Research Program/ ; 2023JQ09//Distinguished Young Scholars Program of Inner Mongolia/ ; BR230301//Distinguished Young Scholars Program of Inner Mongolia/ ; 32260301//National Natural Science Foundation of China/ ; NMGIRT2403//Program for Innovative Research Team in Universities of Inner Mongolia Autonomous Region/ ; },
abstract = {Plant microbiome plays a vital role in plant fitness and ecosystem functioning, yet its response to global environmental change remains poorly understood. Using an 18-year field experiment, we investigated the effects of climate warming and nitrogen deposition on the diversity of leaf epiphytic and endophytic bacterial communities in two dominant plant species (Stipa breviflora and Cleistogenes songorica) of a temperate desert steppe. We found that warming and nitrogen addition increased both epiphytic and endophytic bacterial diversity, but via different mechanisms. Specifically, epiphytic diversity increased with leaf temperature and transpiration rate, whereas greater endophyte diversity was linked to higher leaf carbon and nitrogen concentrations. Structural equation modeling revealed that both epiphytic and endophytic diversity were negatively associated with plant diversity. Our results demonstrate different mechanisms driving similar responses of leaf epiphytic and endophytic bacterial diversity to global change, and point to a negative feedback loop between phyllosphere bacterial and plant diversity.},
}
@article {pmid40662393,
year = {2025},
author = {Wilson, EJ and Lee, STM and Zeglin, LH and Arias Rodriguez, L and Tobler, M},
title = {Host-Microbiome Associations in Livebearing Fishes Adapted to Toxic Environments Rich in Hydrogen Sulfide.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {e70034},
doi = {10.1111/mec.70034},
pmid = {40662393},
issn = {1365-294X},
support = {//Friends of the Sunset Zoo Conservation Scholar Program/ ; IOS-1931657//National Science Foundation/ ; IOS-2423844//National Science Foundation/ ; //Des Lee Collaborative Vision in Zoological Studies/ ; W911NF-15-1-0175//Army Research Office/ ; W911NF-16-1-0225//Army Research Office/ ; },
abstract = {Organisms inhabiting extreme environments must tolerate a variety of physiochemical stressors. In some cases, host-associated microbial communities facilitate the survival of their hosts in extreme environments, but extremophile symbioses have not been identified in vertebrates. We used 16S rRNA amplicon sequencing to investigate commonalities and differences in the gut bacterial communities of livebearing fishes (Poecilia mexicana species complex, Poeciliidae) that have repeatedly colonised toxic sulfide streams in southern Mexico. We found shared gut microbial taxa across habitat types and drainages but also differences in the microbiomes between sulfidic and nonsulfidic populations, both in terms of patterns of diversity and community composition. Most importantly, we documented convergent changes in microbiome composition across evolutionarily independent sulfide spring lineages. These patterns were consistent when we analysed the gut microbiomes as well as primarily host-associated microbiomes that excluded taxa that are commonly found in the environment. Our analyses also revealed several microbial taxa associated with sulfide spring coloniation that have previously been implicated in symbioses and may influence the host's tolerance to the extreme environmental conditions. Our study sheds light on how shared environmental pressures can give rise to convergent host-microbiome associations in fishes, and it provides a foundation for investigating the role of host-microbiome interactions in vertebrate adaptation to extreme environments.},
}
@article {pmid40662304,
year = {2025},
author = {Byrne, K and Lisiecka, D and Moran, G and Daly, B and Fleischmann, I and McCallion, P and McCarron, M and Phadraig, CMG},
title = {Oral Health and Pneumonia in Adults With Intellectual and Developmental Disabilities: A Scoping Review.},
journal = {Journal of intellectual disability research : JIDR},
volume = {},
number = {},
pages = {},
doi = {10.1111/jir.70013},
pmid = {40662304},
issn = {1365-2788},
support = {//School of Dental Science PhD scholarship fund/ ; //Trinity College Dublin/ ; },
abstract = {INTRODUCTION: Pneumonia is a leading cause of death for people with intellectual and developmental disabilities (IDD), who also have increased risk of oral disease. Given the known relationship between oral disease and pneumonia in similar populations, this review aims to explore what is known about the association between oral health and pneumonia among people with IDD.<br><br>METHODS: This systematic scoping review was carried out in accordance with the Joanna Briggs Institute methods and the Preferred Reporting Items for Systematic Reviews and Meta-Analyses Extension for Scoping Reviews checklist (PRISMA-ScR). A systematic search of Medline (Ovid), Embase, Cochrane Trials, Cochrane Review, CINAHL and PubMed was conducted, guided by a registered protocol. The PCC framework informed the search and inclusion criteria. Titles and abstracts were independently screened by two reviewers, with full texts assessed for relevance to oral health and pneumonia in adults with IDD.<br><br>RESULTS: Following a protocol and defined criteria, (2544) articles were abstract screened; a further (31) reached full-text review, with (7) included in this review. Study designs included cross-sectional studies (2), retrospective cohorts (2), prospective cohorts (2) and one RCT pilot (1). Six studies reported oral carriage of respiratory pathogens such as Streptococcus pneumoniae, Pseudomonas aeruginosa and Klebsiella pneumoniae. Two studies reported predictive relationships between oral pathogens and pneumonia, with increased odds of respiratory illness associated with positive PCR results for specific pathogens (OR 9.0, 95% confidence interval [CI] 2.3-38.8). Two studies identified poor oral health as a predictor of pneumonia, using validated tools such as the ROAG (OR 1.6, 95% CI 1.1-2.5). Mediating factors included enteral feeding, level of IDD, and history of oral disease.<br><br>CONCLUSIONS: Research consistently finds carriage of potential respiratory pathogens in the oral microbiome of people with IDD. Despite this, there is a significant lack of research into the relationship between the oral microbiome, poor oral health, and pneumonia in this population, though the latter two are both prevalent and consequential. There is an urgent need for further research exploring the role that oral health and the oral microbiome play in pneumonia among people with IDD.},
}
@article {pmid40662048,
year = {2025},
author = {Pai, HD and Baid, R and Palshetkar, NP and Pai, R and Pai, A and Palshetkar, R},
title = {Role of Vaginal and Gut Microbiota in Human Papillomavirus (HPV) Progression and Cervical Cancer: A Systematic Review of Microbial Diversity and Probiotic Interventions.},
journal = {Cureus},
volume = {17},
number = {6},
pages = {e85880},
pmid = {40662048},
issn = {2168-8184},
abstract = {Cervical cancer remains a major global health concern, primarily associated with persistent infection by high-risk human papillomavirus (HrHPV) types. Both gut and vaginal microbiome may influence the progression from HPV infection to cervical intraepithelial neoplasia (CIN) and cervical cancer. We performed a systematic review to study the relevant literature on gut and cervical microbiota in patients with HPV infection, CIN, and cervical cancer, as well as the role of probiotics in managing these conditions. The protocol was registered in the PROSPERO database (#CRD42024584685). We searched PubMed, the Cochrane Library, Web of Science, and Google Scholar from their inception to September 2024. Two reviewers independently checked study eligibility. Both reviewers were responsible for data extraction. Disagreements were resolved by a third senior reviewer. The review was conducted in accordance with Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines for reporting systematic reviews. The Joanna Briggs Institute (JBI) checklist was used to assess the risk of bias of the included studies. In total, 82 papers were included in this review. Microbial dysbiosis plays a significant role in HPV infection, its progression, and clearance. The analysis of the microbiome reveals that the transition from HPV infection to CIN to cervical cancer involves a shift from a Lactobacillus-dominated, healthy microbiome to one dominated by pathogenic genera. Women with CIN and cervical cancer demonstrated increased microbial diversity compared to HPV-positive individuals. Pathogenic organisms such as Gardnerella, Prevotella, Sneathia, Streptococcus, and Porphyromonas were more prevalent in the patient population compared to controls. Probiotics were effective in restoring vaginal microbiota and managing HPV clearance, and were also associated with cytological and inflammatory improvement rates. Patients with HPV, CIN, and cervical cancer exhibited a microbial community characterised by an increased abundance of pathogenic genera and reduced levels of beneficial Lactobacillus species. Probiotics could be used as a prophylactic or an adjuvant therapy while treating HPV infection, CIN, and cervical cancer.},
}
@article {pmid40661986,
year = {2025},
author = {Wu, Z and Li, X and Wang, Y and Zhang, J and Ji, L and Gan, L},
title = {Microbiome analysis reveals gut bacterial alterations in adult Tibetan pigs with diarrhea.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1524727},
pmid = {40661986},
issn = {1664-302X},
abstract = {Diarrhea is a significant ailment that causes heavy economic losses in the pig industry. The Tibetan pig is a native Chinese breed that is unique to high-altitude regions and displays strong disease resistance. However, scientific research on the structural characteristics of the gut microbiota and key genera associated with diarrhea in Tibetan pigs is still scarce, especially those involving adult Tibetan pigs. In this study, fresh fecal samples from diarrheic (case, N = 9) and healthy adult Tibetan pigs (control, N = 10) were collected and sequenced using 16S rRNA gene sequencing. Our results revealed that the gut microbial community of the case pigs exhibited lower alpha diversities but higher intragroup variability in microbiota composition. The genera Treponema and Prevotellaceae_UCG-001 were underrepresented in the pigs, serving as hallmarks of diarrhea, while Lactobacillus, Escherichia-Shigella, and Muribaculaceae showed increased abundance. Moreover, the genera Lactobacillus and Ignatzschineria were significantly enriched biomarkers in the case pigs. Notably, these changes were not consistent with those observed in Tibetan piglets and other commercial pigs. Furthermore, the decreased abundance of Treponema in the diarrheic pigs indicated that this disease was associated with a high-fiber diet and environmental adaptability. The differentially enriched pathways in the case and control pigs further revealed that gut dysbiosis exacerbated immune and inflammatory responses to promote the development of diarrhea. In conclusion, this study characterized the distribution of gut microbiota composition in adult Tibetan pigs with different health status, which may enhance our understanding of the role of the gut microbiota in intestinal issues.},
}
@article {pmid40661978,
year = {2025},
author = {Rutkowska, N and Daroch, M and Marchut-Mikołajczyk, O},
title = {Exploring the diversity and genomics of cultivable Bacillus-related endophytic bacteria from the medicinal plant Galium aparine L.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1612860},
pmid = {40661978},
issn = {1664-302X},
abstract = {INTRODUCTION: Endophytes are crucial partners that contribute to the plants' health and overall wellbeing. Apart from the elucidation of the relationship between plants and their microbiota, the metabolic potential of endophytes is also of a special interest. Therefore, it is crucial to isolate and taxonomically identify endophytes, as well as to investigate their genomic potential to determine their significance in plant health and potential as bioactive metabolite producers for industrial application.<br><br>METHODS: In this study, we isolated ten endophytic bacterial strains from different tissues of medicinal plant Galium aparine L. and performed de novo assembly of their genomes using short and long reads. Comparative genomic analysis was conducted to assess the accurate taxonomic identification of the strains. The investigation also focused on the presence of mobile genetic elements and their significance concerning endophytic lifestyles. We performed functional annotation of coding sequences, particularly targeted genes that encode carbohydrate enzymes and secondary metabolites within gene clusters.<br><br>RESULTS: Through sequencing using two complementary methods, we obtained 10 bacterial genomes, ranging in size, coding density and number of mobile genetic elements. Our findings provide a first insight into the cultivable bacterial community of the medicinal plant Galium aparine L., their genome biology, and potential for producing valuable bioactive metabolites. Obtained whole genome sequences allowed for complete phylogenetic analysis, which revealed crucial insights into the taxonomic status of bacteria and resulted in the discovery of two putatively novel bacterial species from the Bacillus and Priestia genera, suggesting that plants are hiding a reservoir of novel species with potentially useful properties and unknown mechanisms related to their relationship with plant host.},
}
@article {pmid40661950,
year = {2025},
author = {Ma, Y and Suo, J and Sheng, S and Chen, L},
title = {PD-L1 deficiency exacerbates colitis severity by remodeling gut microbiota in inflammatory bowel disease.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1622744},
pmid = {40661950},
issn = {1664-3224},
mesh = {Animals ; *Gastrointestinal Microbiome/immunology ; *B7-H1 Antigen/genetics/deficiency ; Mice ; Mice, Knockout ; *Colitis/pathology/microbiology/chemically induced/genetics/immunology/metabolism ; *Inflammatory Bowel Diseases/microbiology/immunology/pathology/genetics/metabolism ; Dysbiosis ; Disease Models, Animal ; Severity of Illness Index ; Mice, Inbred C57BL ; Dextran Sulfate ; Male ; },
abstract = {BACKGROUND: Inflammatory bowel disease (IBD) is a chronic autoimmune disorder driven by gut microbiota dysbiosis. As an essential immune checkpoint, Programmed death-ligand 1 (PD-L1) has been implicated in modulating gut microbiota composition. However, the precise role of PD-L1 in shaping metagenomic profiles during IBD-associated colitis remains unexplored.<br><br>METHODS: DSS-induced colitis was established in both PD-L1 knockout (Pdcd1lg1-/-) mice and wild-type (wt) control mice. Clinical parameters, including disease activity index (DAI), body weight changes, colon length, and histopathological alterations, were systematically evaluated using non-parametric Kruskal-Wallis tests and ANOVA to compare colitis severity between genotypes.<br><br>RESULTS: PD-L1 knockout mice exhibited exacerbated colitis, manifesting significantly greater weight loss (p<0.05 vs. wt_DSS), colonic shortening (p<0.05), and DAI scores (p<0.05) and inflammatory changes. PD-L1 knockout mice showed distinct dysbiosis, with enriched pathobionts (Escherichia coli, p=0.006; Bacteroides thetaiotaomicron, p=0.015) and depletion of commensals (Tritrichomonas foetus, p<0.001; Ligilactobacillus murinus). Alpha diversity analysis using Chao1 index revealed statistically significant differences between experimental groups (p=0.05). The transporters downregulate anti-inflammatory SCFA metabolism. KEGG enrichment analysis of differentially expressed genes (DEGs) revealed significant associations with immune and inflammatory pathways in PD-L1 knockout mice.<br><br>CONCLUSION: PD-L1 deficiency aggravates colitis by driving pathogenic microbiota alterations and impairing microbial metabolic homeostasis, highlighting its dual regulatory roles in immune homeostasis and microbiome dynamics.},
}
@article {pmid40661942,
year = {2025},
author = {Yin, J and Kaakoush, NO and Massey, J and Danta, M},
title = {Understanding the microbiome in autologous haemopoietic stem cell transplant for multiple sclerosis.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1590601},
pmid = {40661942},
issn = {1664-3224},
mesh = {Humans ; *Hematopoietic Stem Cell Transplantation/methods ; Adult ; Female ; *Gastrointestinal Microbiome ; Male ; *Multiple Sclerosis/therapy/microbiology ; Middle Aged ; Transplantation, Autologous ; Natalizumab/therapeutic use ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; },
abstract = {BACKGROUND: MS is a chronic inflammatory and degenerative disease of the central nervous system (CNS) resulting in neurological deficits associated with physical and/or cognitive disability. The gut microbiome can interact with the CNS and immune system through various molecular pathways and has been previously implicated in MS. Autologous Haematopoietic Stem Cell Transplant (AHSCT) in MS arrests inflammatory disease and has evidence of long-term therapeutic benefit. To date, no study has explored the effect of AHSCT on the gut microbiome in people with MS.<br><br>METHOD: The microbiome of people with MS (pwMS) undergoing AHSCT was compared with pwMS on Natalizumab (NTZ). Longitudinal microbiome analysis was also conducted within the AHSCT cohort at two timepoints. Amplicon sequencing of the 16S ribosomal RNA V3-4 region (Illumina MiSeq) was used to evaluate alpha and beta diversity, oral-stool microbiota distances, and relative taxa abundances on both oral and stool microbiota.<br><br>RESULTS: The pre-transplant, baseline samples from the AHSCT cohort (n=8) was compared to the Natalizumab group (n=22). The AHSCT cohort had lower oral species richness compared to the NTZ cohort (p=0.026). There was a significant difference in oral beta diversity between the two cohorts (p=0.043). The oral taxa analysis of AHSCT subjects showed increased relative abundances of Porphyromonas and decreased Veillonella.<br><br>CONCLUSION: This pilot study identified specific microbiome changes, particularly in the oral alpha diversity and abundance of specific bacteria which may reflect treatment status or disease activity in MS.},
}
@article {pmid40661744,
year = {2025},
author = {Wang, X and Liu, X and Gong, F and Jiang, Y and Zhang, C and Zhou, W and Zhang, W},
title = {Targeting gut microbiota for diabetic nephropathy treatment: probiotics, dietary interventions, and fecal microbiota transplantation.},
journal = {Frontiers in endocrinology},
volume = {16},
number = {},
pages = {1621968},
pmid = {40661744},
issn = {1664-2392},
mesh = {Humans ; *Fecal Microbiota Transplantation/methods ; *Probiotics/therapeutic use ; *Gastrointestinal Microbiome/physiology ; *Diabetic Nephropathies/therapy/microbiology ; Animals ; Dysbiosis/therapy ; },
abstract = {Diabetic nephropathy (DN) stands as a prominent microvascular complication of diabetes mellitus and presents a significant global health challenge. Despite advancements in glycemic control and renin-angiotensin system inhibition, current treatments merely delay disease progression without targeting fundamental pathological processes. This review explores gut microbiota modulation as a promising treatment strategy for DN through probiotic supplementation, dietary interventions, and fecal microbiota transplantation(FMT) protocols. The gut microbiota, integral to the "gut-kidney axis," is critically implicated in DN pathogenesis. DN is associated with gut dysbiosis-characterized by reduced microbial diversity, depletion of beneficial short-chain fatty acid (SCFA)-producing bacteria, and proliferation of opportunistic pathogens. This dysbiosis impairs gut barrier integrity, fostering systemic inflammation and the accumulation of uremic toxins like indoxyl sulfate. Furthermore, translocated bacterial lipopolysaccharides activate Toll-like receptors and the NLRP3 inflammasome, exacerbating kidney damage and fibrosis. Interventions targeting the microbiota, including dietary strategies (e.g., enhancing fermentable fibers, low-protein diets) and FMT, show promise in preclinical and early clinical studies, though FMT requires stringent safety and donor screening protocols. Significant challenges persist, such as managing inter-individual microbiota variability for personalized therapies, fully elucidating molecular mechanisms like SCFA-GPR43 signaling, and leveraging multiomics for biomarker discovery. Advancing microbiota-focused interventions for DN towards microbiome-centered precision medicine necessitates addressing standardization, deepening mechanistic understanding, and validating combination therapies, heralding a potential shift from traditional nephroprotective approaches.},
}
@article {pmid40661523,
year = {2025},
author = {Siegel, SJ and Pomerantz, D and Heimburg-Molinaro, J and Mahmood, SD and Korzenik, JR and Cummings, RD and Rakoff-Nahoum, S},
title = {A glycan atlas of the mammalian intestine through ontogeny and inflammation.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.03.06.641959},
pmid = {40661523},
issn = {2692-8205},
abstract = {UNLABELLED: The muco-epithelial interface in the mammalian gut is composed of a mucus and epithelial lining fundamental to barrier function, microbe-host interactions, and intestinal homeostasis. This barrier is heavily glycosylated by O-linked sugars covalently linked to mucin glycoproteins, and N-linked sugars that coat epithelial surface proteins. Gut O- and N-glycans are thought to play central roles in barrier function, host defense, nutrition and attachment for commensals and pathogens, immunoregulation and cell-cell interactions. However, the precise nature of the glycans and how glycan composition changes through development, as a function of diet, and during inflammation, remains incompletely understood. Here, we apply O- and N-glycomic platforms to profile glycans on mucus and intestinal epithelium. By mapping individual glycan species spatially and temporally we identify 57 O- and 18 N-glycans in the mouse intestine, and observe that fucosylation and sialylation varies according to intestinal region and developmental stage. We identify a subset of glycans regulated by the gut microbiome, and observe a constriction of the glycan repertoire during inflammation in both mice and humans. Together, these results provide an atlas of individual intestinal glycans and their dynamic range through ontogeny and inflammation, and represent a significant resource for our understanding of the role of intestinal glycans in health and disease and glycan-focused therapies for intestinal inflammation and shaping the gut microbiome.<br><br>HIGHLIGHTS: - Individual glycans vary across gut region and developmental stage- Terminal fucose and sialic acid residues vary across space and time- The microbiome influences gut glycan composition early in life- Gut inflammation in mice and humans converge on a restricted glycan repertoire.<br><br>ETOC BLURB: Microbes colonizing the mammalian intestines encounter mucus and an epithelial layer highly decorated by glycans. Siegel et al. use glycomics to map these sugars in high resolution across gut region, microbial colonization, development and inflammation in both humans and mice.},
}
@article {pmid40661479,
year = {2025},
author = {Parajuli, B and Midya, V and Kiddle, R and De Jager, N and Eggers, S and Spakowicz, D and Hoyd, R and Salhia, B and Chan, CHF and Churchman, ML and Rounbehler, RJ and Yao, S and Rutkowski, MR and Tarhini, AA and Mudaranthakam, DP and Masood, A and Bocklage, TJ and Lentz, RW and Hatoum, H and Ilozumba, MN and Hardikar, S and Ulrich, CM and Round, JL and Riedlinger, G and Shriver, CD and Bosch, DE},
title = {Primary tumor microbiomes predict distant metastasis of colorectal cancer.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.06.02.654060},
pmid = {40661479},
issn = {2692-8205},
abstract = {Metastasis causes most cancer-related deaths in colorectal carcinoma (CRC), and microbiome markers may have prognostic value. We hypothesized that primary tumor microbiomes predict distant metastases. We analyzed 5-year metastasis-free survival (MFS) in a retrospective cohort of 900 ORIEN CRC tumor microbiomes (RNAseq). ORIEN findings were validated on an independent cohort using 16S rDNA sequencing and pathobiont-specific qPCR. Microbiome alpha diversity was higher in primary tumors than metastases and positively correlated with metastasis risk. Microbiome beta diversity distinguished primary vs. metastasis and predicted 5-year MFS. High primary tumor abundance of B. fragilis and low F. nucleatum were associated with short MFS. Enterobacteriaceae, including E. coli, were enriched in metastases. qPCR identified increased enterotoxigenic B. fragilis and pks+ E. coli detection in CRC metastasizers. Microbial co-occurrence analysis identified a 3-species clique that predicts metastasis (OR 1.9 [1.4-2.6]). Results suggest that primary tumor microbiomes and specific pathobionts are precision markers for metastasis risk.},
}
@article {pmid40661243,
year = {2025},
author = {Xing, H and Lin, WJ and Hu, WL and Cao, JS and Cui, LY and Lyu, W and Zhu, HK and Wu, AJ and Xu, QX and Zhao, Y and Bao, SY},
title = {Insights of acupuncture in modulating gut microbiota in stroke treatment.},
journal = {Frontiers in neurology},
volume = {16},
number = {},
pages = {1579585},
pmid = {40661243},
issn = {1664-2295},
abstract = {Stroke, an acute neurological disorder caused by the interruption of cerebral blood flow, is the second leading cause of death and a major contributor to long-term disability worldwide. Recent research has increasingly highlighted the role of gut microbiota in stroke recovery. Post-stroke gut microbiota dysbiosis, characterized by an imbalance in microbial composition, exacerbates neuroinflammation and neuronal injury. Restoring the balance of the gut microbiome may facilitate neurological recovery. Acupuncture, a traditional therapeutic modality, has shown potential in stroke rehabilitation. Evidence suggests that acupuncture modulates gut microbiota composition, restores gut barrier integrity, and reduces endotoxin translocation into the bloodstream, which collectively reduces systemic inflammation and alleviates neurological damage. Additionally, acupuncture may influence immune responses through the gut-brain axis, a bidirectional communication system between the gut and brain, thereby suppressing neuroinflammation and promoting neuronal repair. Despite these promising findings, current evidence is limited by methodological inconsistencies, including variability in acupuncture protocols and heterogeneous patient populations, which may confound result interpretation. The precise mechanisms underlying acupuncture's modulation of gut microbiota and its role in stroke recovery remain unclear. Future studies should adopt standardized protocols and larger sample sizes to improve reproducibility, validate these findings, explore the molecular pathways involved, and determine the clinical efficacy of acupuncture in stroke rehabilitation.},
}
@article {pmid40661167,
year = {2025},
author = {Oba, PM and Roberts, LJ and Geary, EL and Suchodolski, JS and Swanson, KS},
title = {Effects of diet type on the core fecal bacterial taxa and the dysbiosis index of healthy adult dogs.},
journal = {Frontiers in veterinary science},
volume = {12},
number = {},
pages = {1572875},
pmid = {40661167},
issn = {2297-1769},
abstract = {There is great interest in studying the canine gastrointestinal microbiome. In healthy dogs versus those with acute and chronic enteropathies, specific bacterial taxa have been identified that are consistently associated with shifts in the microbiome. A qPCR-based dysbiosis index (DI) that assesses microbiome shifts was developed based on a subset of these taxa. Because most dogs consume kibble diets, published data on core bacteria and the DI were largely derived from dogs consuming that diet form. Because dietary composition impacts the microbiome, it was unknown whether data from dogs consuming other diet types would adhere to reported core taxa abundance and DI guidelines. The study's aim was to determine the fecal abundance of core bacteria and DI of dogs fed commercially available kibble vs. mildly-cooked human-grade (fresh) diets. Fecal samples collected from adult dogs across four experiments were used (4 kibble diets, n = 10-12/treatment; 4 fresh diets, n = 10-24/treatment). Moderate correlations were observed between total dietary fiber (TDF) and Fusobacterium (positive correlation), Lactobacillus (negative), and DI (negative). Dietary protein was correlated with fecal Ruminococcus gnavus (negative), while dietary fat was correlated with fecal Bacteroides and C. perfringens abundance (both positive). Dogs fed fresh diets exhibited higher (p < 0.01) abundances of Streptococcus, Escherichia coli, and Clostridium perfringens, while those fed kibble diets had higher (p < 0.05) abundances of Fusobacterium, Clostridium hiranonis, and Bacteroides. Dogs fed fresh diets had a greater (p < 0.0001) DI, but the majority of scores remained within the normal range. Dogs fed animal protein-based kibble diets had higher (p < 0.05) fecal Faecalibacterium and Fusobacterium, while dogs fed animal protein-based fresh diets had higher (p < 0.05) Streptococcus, E. coli, and C. perfringens. Bifidobacterium and Bacteroides were more abundant (p < 0.01) in dogs fed animal protein-based kibble and plant protein-based fresh diets. Dogs fed animal protein-based fresh diets had a greater (p < 0.0001) DI. Even though microbiota populations were statistically different among diets, all mean DI were <0, with only a few individual dogs consuming fresh diets having DI >0 (5 dogs >0; 1 dog >2). Overall, these data demonstrate the utility of the DI across different diet types in healthy dogs.},
}
@article {pmid40660964,
year = {2025},
author = {Ng, HM and Wall, CL and Bayer, SB and Gearry, RB and Roy, NC},
title = {The interconnection between dietary fibre, gut microbiome and psychological well-being.},
journal = {The Proceedings of the Nutrition Society},
volume = {},
number = {},
pages = {1-10},
doi = {10.1017/S002966512510061X},
pmid = {40660964},
issn = {1475-2719},
abstract = {This review highlights the importance of dietary fibres (DF) intake and its interconnection with the gut microbiome and psychological well-being, while also exploring the effects of existing DF interventions on these aspects in adults. The gut microbiota is a complex and diverse ecosystem in which microbial species interact, influencing the human host. DF are heterogeneous, requiring different microbial species to degrade the complex DF structures. Emerging evidence suggests that microbial fermentation of DF produces short-chain fatty acids (SCFA), which may play a role in regulating psychological well-being by affecting neurotransmitter levels, including serotonin. The effectiveness of DF interventions depends on factors such as baseline gut microbiota composition, the dosage and the source of DF consumed. Although the gut microbiota of adults is relatively stable, studies have shown that the abundance of the species in the gut microbiota can change within 24 h of an intervention and may return to baseline following the termination of DF intervention. This review underscores the need for larger and well-powered dietary clinical trials incorporating longitudinal biological sample collections, advanced sequencing and omic techniques (including novel dietary biomarkers and microbial metabolites), validated subjective questionnaires and dietary records. Furthermore, mechanistic studies driven by clinical observations are crucial to understanding gut microbiota function and its underlying biological pathways, informing targeted dietary interventions.},
}
@article {pmid40660619,
year = {2025},
author = {Armstrong, R},
title = {Microbes as Teachers: Rethinking Knowledge in the Anthropocene.},
journal = {Microbial biotechnology},
volume = {18},
number = {7},
pages = {e70195},
doi = {10.1111/1751-7915.70195},
pmid = {40660619},
issn = {1751-7915},
support = {101114746//European Innovation Council (EIC), Pathfinder Challenges/ ; },
mesh = {Humans ; Ecosystem ; *Microbiology/education ; },
abstract = {This opinion piece proposes that the environmental crises of our time arise from a failure to recognise the vital role of microbes in sustaining life on Earth, where ecosystems have been shaped for billions of years by microbial processes, including oxygen production, nutrient cycling and climate regulation. Yet the idea that microbes can 'teach' us how to navigate complexity, adapt across scales, and sustain planetary systems is still marginalised in science, policy, and education. A paradigm shift is proposed: microbes must be reframed as active collaborators in solving global challenges. This perspective is grounded in microbial ecology, Indigenous knowledge, and ethical philosophy, advocating for 'learning' through and with microbial life. To institutionalise this transition, policy and educational reforms are urged, centring microbial literacy as a foundation for ecological understanding. By integrating microbial agency into human knowledge systems, societal actions could be realigned with the biochemical and evolutionary logics that have sustained life for millennia. Ultimately, a deeper engagement with microbial knowledge is called for-one that informs a more sustainable future.},
}
@article {pmid40660416,
year = {2025},
author = {Grosche, A and Selci, M and Smedile, F and Giovannelli, D and Borin, S and Le Bris, N and Vetriani, C},
title = {The chemosynthetic biofilm microbiome of deep-sea hydrothermal vents across space and time.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {88},
pmid = {40660416},
issn = {2524-6372},
support = {OCE 1948623//National Science Foundation/ ; },
abstract = {Microbial biofilms colonize mineral and biological substrates exposed to fluid circulation at deep-sea hydrothermal vents, providing a biologically active interface along redox boundaries. Since many biofilms at deep-sea vents are associated with invertebrates, microbial distribution and abundance are not only constrained by local fluid geochemistry, but also through host-microbe interactions. This study examined the spatial distribution and diversity of established microbial biofilm communities collected from three distinct biological regimes characteristic of the East Pacific Rise (9°50 N, 104°17 W) vent system, as well as newly established biofilms on experimental microbial colonization devices. Transcripts from 16S rRNA-based amplicon sequencing revealed that Campylobacterota of the Sulfurimonas and Sulfurovum genera dominated newly-formed biofilms across all biological regimes. Statistical analyses using environmental chemistry data from each sampling site suggest that community composition is significantly impacted by biofilm age, temperature and sulfide concentration ranges, and to a lesser extent, locality. Further, metatranscriptomic analyses were used to investigate changes in community gene expression between seafloor and subseafloor biofilms. Our findings revealed differences in the type and abundance of transcripts related to respiratory pathways, carbon fixation and reactive oxygen species (ROS) detoxification. Overall, this study provides a novel conceptual framework for evaluating biofilm structure and function at deep-sea vents by showing a transition from a niche-specific pioneer microbial community in newly-formed biofilms, to a complex population of increased diversity in established biofilms and by identifying key changes in gene expression in taxonomically similar biofilms during the transition from the shallow subseafloor to the seafloor.},
}
@article {pmid40660385,
year = {2025},
author = {Ji, X and Zhi, M and Gu, X and Han, Y and Lan, X and Song, L and Sun, P and Li, J and Qi, X and Feng, Q},
title = {DnaK of Parvimonas micra extracellular vesicles interacts with the host fibroblasts BAG3-IKK-γ axis to accelerate TNF-α secretion in oral lichen planus.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {164},
pmid = {40660385},
issn = {2049-2618},
support = {ZR2023MH045//Shandong Natural Science Foundation/ ; YJRC2021002//the start-up fund for introduction of talents to Jinan Central Hospital/ ; 2022-2-7//Science and Technology Development Program of Jinan Municipal Health Commission/ ; 82270980//National Natural Science Foundation of China/ ; 2019//he National Young Scientist Support Foundation/ ; ZR2021JQ29//Excellent Young Scientist Foundation of Shandong Province/ ; 2021SFGC0502//Major Innovation Projects in Shandong Province/ ; 2021GXRC021//the Periodontitis innovation team of Jinan City/ ; 2019//Taishan Young Scientist Project of Shandong Province/ ; 2020KJK001//Oral Microbiome Innovation Team of Shandong Province/ ; 2021ZDSYS18//Shandong Province Key Research and Development Program/ ; },
mesh = {Humans ; *Fibroblasts/metabolism/microbiology ; *Extracellular Vesicles/metabolism ; *Tumor Necrosis Factor-alpha/metabolism ; *Lichen Planus, Oral/microbiology/metabolism/pathology ; *Adaptor Proteins, Signal Transducing/metabolism/genetics ; Mouth Mucosa/microbiology ; *I-kappa B Kinase/metabolism/genetics ; Male ; Signal Transduction ; Female ; NF-kappa B/metabolism ; Middle Aged ; *Bacterial Proteins/metabolism/genetics ; *HSP70 Heat-Shock Proteins/metabolism/genetics ; Apoptosis Regulatory Proteins ; },
abstract = {BACKGROUND: Oral lichen planus (OLP) is one of the most frequent oral mucosal diseases associated with chronic inflammation, despite a profoundly limited understanding of its underlying pathogenic mechanisms.<br><br>RESULTS: The microbiome analysis was conducted on buccal and lip mucosae, tongue dorsum, and saliva in nonerosive/erosive OLP patients and healthy individuals. Significant variations were observed in the oral microbiome of OLP patients, particularly in the buccal mucosa. Network, random forest, and NetShift analysis collectively indicated that Parvimonas micra (P. micra) emerged as a crucial bacterium in OLP. In vivo analysis further demonstrated that P. micra was abundant at the junction of epithelial and connective tissue layers in OLP lesions. Single-cell RNA sequencing data implicated fibroblasts as potential targets, characterized by upregulation of the NF-&#x3ba;B pathway linked to TNF-&#x3b1;. Co-culturing of P. micra or its extracellular vesicles (EVs) with fibroblasts showed that P. micra and EVs could activate the NF-&#x3ba;B signaling pathway and suppress autophagy in buccal mucosal fibroblasts. Among the pathogenic effectors, DnaK from P. micra EVs was identified to interact with BAG3 in fibroblasts. The interaction of DnaK with BAG3 subsequently activated the NF-&#x3ba;B pathway and decreased autophagy flux. Additionally, we identified that IKK-&#x3b3; was the key downstream protein that could bind with DnaK-BAG3, thereby inhibiting autophagy and promoting TNF-&#x3b1; secretion.<br><br>CONCLUSIONS: We initially revealed that P. micra was a crucial pathogen in the development of OLP and demonstrated that P. micra's EVs induce the inhibition of autophagy and enhanced TNF-&#x3b1; secretion in OLP fibroblasts via the DnaK-BAG3-IKK-&#x3b3; axis. This study offers novel insights into the pathogenic mechanisms underlying OLP. Video Abstract.},
}
@article {pmid40660333,
year = {2025},
author = {Yang, Z and Zhang, Y and Ran, S and Zhang, J and Gao, Y and Zhang, Y and Li, X and Ai, B and Wei, S and Tian, F and Jia, G and Lin, H and Chen, Z and Zhang, Z},
title = {Exposure to ambient air pollution over developmental stages induced neurodevelopmental impairment in mice offspring via microbiome-gut-brain axis.},
journal = {Particle and fibre toxicology},
volume = {22},
number = {1},
pages = {20},
pmid = {40660333},
issn = {1743-8977},
support = {2024A1515010465//Basic and Applied Basic Research Foundation of Guangdong Province/ ; 2022A1515010695//Basic and Applied Basic Research Foundation of Guangdong Province/ ; 82203988//National Natural Science Foundation of China/ ; 2023A04J2071//Guangzhou Municipal Science and Technology Project/ ; 23qnpy107//Fundamental Research Funds for the Central Universities of Sun Yat-sen University/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Female ; *Air Pollution/adverse effects ; Mice ; Male ; *Neurodevelopmental Disorders/chemically induced/microbiology ; Pregnancy ; *Prenatal Exposure Delayed Effects/chemically induced ; *Brain/drug effects/growth &amp; development ; *Air Pollutants/toxicity ; Mice, Inbred C57BL ; Behavior, Animal/drug effects ; *Brain-Gut Axis/drug effects ; },
abstract = {Exposure to air pollution has been increasingly recognized as a risk factor for neurodevelopmental disorders, and gut microbiome may play a critical role. However, current evidence still remains scarce. In the present study, mice were exposed to real-time ambient air pollution from conception through young adulthood, with neurobehavioral performance and gut microbiome being assessed across different developmental stages. Neurodevelopmental changes including emotional and cognitive impairments were observed in behavioral tests, accompanied by pathological and inflammation changes in brain, which were more pronounced in adolescence than in young adulthood. Alterations in the compositions and functions of gut microbiome were also revealed by fecal metagenomic sequencing. Mediation analysis showed that gut microbiome alterations significantly contributed to the observed neurodevelopmental changes induced by air pollution. Furthermore, after antibiotic (ABX) intervention, the observed neurobehavioral, pathological and inflammatory differences between the exposed and control groups diminished. These findings indicate that the gut microbiome mediates the neurodevelopmental damage caused by exposure to air pollution during developmental stages, adding novel insights on the underlying mechanisms linking air pollution and neurodevelopmental disorders.},
}
@article {pmid40660288,
year = {2025},
author = {Qin, W and Yin, N and Xu, B and Mei, Q and Fu, Y and Fan, J and Lu, Y and Wang, G and Ai, L and Lu, Z and Zeng, Y and Huang, C},
title = {Faecalibacterium prausnitzii enhances intestinal IgA response by host-microbe derived inecalcitol in colitis.},
journal = {BMC medicine},
volume = {23},
number = {1},
pages = {425},
pmid = {40660288},
issn = {1741-7015},
support = {No. 81970555//National Natural Science Foundation of China/ ; No.CCTR-2022B02//Shanghai General Hospital/ ; 202440170//Shanghai Municipal Health Commission/ ; No.22SJKGGG28//Science and Technology Commission of Songjiang District/ ; No.KY-2023-03-02//Shanghai Jiao Tong University School of Medicine, Digestive Institute/ ; },
mesh = {Animals ; Mice ; *Gastrointestinal Microbiome/immunology ; Humans ; *Faecalibacterium prausnitzii/immunology ; Mice, Knockout ; Mice, Inbred C57BL ; *Colitis, Ulcerative/microbiology/immunology ; Male ; *Immunoglobulin A/metabolism/immunology ; Dextran Sulfate ; Disease Models, Animal ; *Colitis/microbiology/immunology ; *Immunoglobulin A, Secretory ; Female ; Feces/microbiology ; },
abstract = {BACKGROUND: Faecalibacterium prausnitzii plays a crucial role in ulcerative colitis (UC) remission, but its action mechanism is unknown. Here, we aimed to explore the potential mechanisms focusing on the interaction of F. prausnitzii with host immune response and its potential modulation on gut microbiome.<br><br>METHODS: RNA-seq analysis together with 16S rRNA sequencing and metabolomics were performed in a dextran sodium sulfate (DSS)-induced colitis mouse model followed by F. prausnitzii gavage. To present evidence of sIgA involved in the anti-inflammatory effects of F. prausnitzii, we further applied immunoglobulin A (IgA) knockout mice and secretory IgA (sIgA) depletion mouse models using polymeric immunoglobulin receptor (pIgR) neutralizing antibody. Colonic immune cells were characterized by flow cytometry. The fecal relative abundance of F. prausnitzii, inecalcitol, and colonic IgA expression were assessed in UC patients.<br><br>RESULTS: F. prausnitzii markedly ameliorated colitis by alleviating intestinal inflammation and barrier dysfunction, with significantly decreased abundance of pro-inflammatory taxa (Enterococcus, Desulfovibrio, Escherichia-Shigella, and Enterorhabdus) and increased abundance of Lachnospiraceae NK4A136_group. Functions related to intestinal immune network for IgA production pathway were up-regulated shown by transcriptomics and KEGG pathway analysis. Increased expression of IgA production associated genes including MHCII-related genes, Aicda, and Tnfrsfl3c were verified, accompanied by up-regulated colonic IgA and pIgR. The IgA knockout mice and sIgA depletion model weakened the anti-inflammation and microbiota-modulation effects of F. prausnitzii, which was further proved by fecal microbiota transplantation (FMT). The shift profile of fecal metabolites after F. prausnitzii supplement was characterized by increased production of inecalcitol, which may account for the enhanced IgA response. In a cohort of UC patients, the relative abundance of F. prausnitzii was decreased and positively correlated with colonic IgA expression and negatively correlated with disease severity.<br><br>CONCLUSIONS: F. prausnitzii effectively alleviated colonic inflammation and modulated dysbiosis via enhancing colonic IgA response, thus showing promise as a UC treatment.},
}
@article {pmid40660153,
year = {2025},
author = {Cui, X and Wang, Y and Yu, G and He, B and Huang, L and Liu, Y and Zhan, Z},
title = {Integrated morphological observation, metabolomics, and transcriptomics to investigate the effect of growth years on the quality of Atractylodes macrocephala Koidz.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {912},
pmid = {40660153},
issn = {1471-2229},
support = {CI2023E002//Scientific and Technological Innovation Project of China Academy of Chinese Medical Sciences/ ; CI2023E002//Scientific and Technological Innovation Project of China Academy of Chinese Medical Sciences/ ; CI2023E002//Scientific and Technological Innovation Project of China Academy of Chinese Medical Sciences/ ; CI2023E002//Scientific and Technological Innovation Project of China Academy of Chinese Medical Sciences/ ; CI2023E002//Scientific and Technological Innovation Project of China Academy of Chinese Medical Sciences/ ; 2060302//Ministry of Finance Central Level of the Special/ ; 2060302//Ministry of Finance Central Level of the Special/ ; 2060302//Ministry of Finance Central Level of the Special/ ; 2060302//Ministry of Finance Central Level of the Special/ ; 2060302//Ministry of Finance Central Level of the Special/ ; },
mesh = {*Atractylodes/growth &amp; development/genetics/metabolism/anatomy &amp; histology ; *Transcriptome ; Metabolomics ; Gene Expression Profiling ; Rhizome/growth &amp; development/metabolism ; Metabolome ; Gene Expression Regulation, Plant ; Plants, Medicinal/growth &amp; development/metabolism/genetics ; },
abstract = {BACKGROUND: Atractylodes macrocephala Koidz. is a medicinal plant in high clinical demand due to its pharmacological efficacy. However, research on its quality dynamics across different growth years remains limited, primarily focusing on transcriptomics, microbiome analysis, and photosynthetic capacity, with studies only extending to three-year-old plants.<br><br>RESULTS: This study examines A. macrocephala over a broader growth span (1, 2, 3, 5, and 10 years), integrating morphological, microstructural, metabolomic, spatial metabolite distribution, and transcriptomic analyses. Morphologically, rhizome weight and length increased with age, and the characteristic "Hejing" structure became more pronounced. Microstructural analysis revealed progressively developed xylem. Metabolomic profiling indicated a decline in sucrose content, alongside increased accumulation of bioactive sesquiterpenoids and phenolic acids over time. Transcriptomic analysis showed that genes involved in the biosynthesis of these active compounds-terpenoid backbone (HMGR, DXS, idi, GPS, and GGPS), phenylpropanoid (PAL, 4CL, and HCT), and sucrose metabolism (SPS and SPP)-were upregulated in older plants. Desorption electrospray ionisation mass spectrometry imaging (DESI-MSI) revealed an expanded distribution of key metabolites with increasing growth years.<br><br>CONCLUSION: The findings suggest that A. macrocephala aged 5 and 10 years exhibit superior quality, with a more distinct "Hejing" morphology and higher levels of bioactive compounds. The quality stabilises after five years, indicating that older plants may possess enhanced medicinal value.},
}
@article {pmid40659807,
year = {2025},
author = {Ledford, H},
title = {Found: a human gut microbe that makes cancer therapy more effective in mice.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {40659807},
issn = {1476-4687},
}
@article {pmid40659728,
year = {2025},
author = {Rehner, J and Molano, LG and Christodoulou, C and Holländer, S and Förster, MO and Keller, V and Jäger, J and Volz-Willems, S and Becker, SL and Glanemann, M and Jelden, M},
title = {Examining spatial microbiome variations across gastrointestinal tract regions in obesity.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {25423},
pmid = {40659728},
issn = {2045-2322},
mesh = {Humans ; *Obesity/microbiology/surgery ; *Gastrointestinal Microbiome/genetics ; Male ; Female ; *Gastrointestinal Tract/microbiology ; Adult ; RNA, Ribosomal, 16S/genetics ; Middle Aged ; Bariatric Surgery ; Feces/microbiology ; Bacteria/genetics/classification ; },
abstract = {Obesity, a global health concern, is associated with alterations in the gut microbiome, yet its spatial dynamics across the gastrointestinal (GI) tract remain poorly understood. This study provides the first comprehensive analysis of the spatial microbiome in individuals with obesity, encompassing samples from the stomach, peritoneum, jejunum (50 cm and 150 cm post-Treitz), and feces before and after bariatric surgery. Using 16 S rRNA sequencing, we analyzed microbial composition and diversity after computational decontamination in 172 high-quality samples from 51 participants. Our results reveal significant differences in alpha diversity across GI sites, with stool samples exhibiting the highest diversity, which decreased post-surgery. The presence of microbial DNA in traditionally sterile compartments, such as the peritoneum and stomach, suggests potential microbial-host interactions warranting further exploration. Contaminants, including Nitrotoga sp., were identified in low-biomass samples and excluded using computational decontamination, emphasizing the need for rigorous controls. This study establishes a foundation for spatial microbiome analysis in obesity, highlighting the impact of bariatric surgery and the importance of advanced multi-omics approaches to unravel host-microbiome dynamics.},
}
@article {pmid40659339,
year = {2025},
author = {Singh, A and Juyal, G and Gacesa, R and Joshi, MC and Midha, V and Thelma, BK and Weersma, RK and Sood, A},
title = {Cross-ethnic evaluation of gut microbial signatures reveal increased colonization with oral pathobionts in the north Indian inflammatory bowel disease cohort.},
journal = {Intestinal research},
volume = {},
number = {},
pages = {},
doi = {10.5217/ir.2024.00216},
pmid = {40659339},
issn = {1598-9100},
abstract = {BACKGROUND/AIMS: Inflammatory bowel disease (IBD) has become a global health concern. With the growing evidence of the gut microbiota's role in IBD, studying microbial compositions across ethnic cohorts is essential to identify unique, populationspecific microbial signatures.<br><br>METHODS: We analyzed stool samples and clinical data from 254 IBD patients (226 ulcerative colitis, 28 Crohn's disease) and 66 controls in northern India using metagenomic shotgun sequencing to assess microbiota diversity, composition, and function. Results were replicated in 436 IBD patients and 903 controls from the Netherlands using identical workflows. Using machine learning, we evaluated the generalizability of Indian IBD signals to the Dutch cohort, and vice versa.<br><br>RESULTS: Indian IBD patients exhibited reduced bacterial diversity and an abundance of opportunistic pathogens, including Clostridium, Streptococcus, and oral bacteria like Streptococcus oralis and Bifidobacterium dentium. There was a significant loss of energy metabolic pathways and distinct co-occurrence patterns among microbial species. Notably, 39% of these signals replicated in the Dutch cohort. Unique to the Indian cohort were oral pathobionts such as Scardovia, Oribacterium, Actinomyces dentalis, and Klebsiella pneumoniae. Both Indian and Dutch IBD patients shared reduced butyrate producers. Machine-learning diagnostic models trained on the Indian cohort achieved high predictive accuracy (sensitivity 0.84, specificity 0.95) and moderately generalized to the Dutch cohort (sensitivity 0.77, specificity 0.69).<br><br>CONCLUSIONS: IBD patients across populations exhibit shared and unique microbial signatures, suggesting a role for the oral-gut microbiome axis in IBD. Crossethnic diagnostic models show promise for broader applications in identifying IBD.},
}
@article {pmid40659293,
year = {2025},
author = {Laguna-Marín, C and Escolà-Casas, M and Subirats, J and Matamoros, V},
title = {Biochar enhanced floating root mats to reduce recalcitrant contaminants of emerging concern from wastewater effluents.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {132960},
doi = {10.1016/j.biortech.2025.132960},
pmid = {40659293},
issn = {1873-2976},
abstract = {This bench-scale study assessed a novel biochar-intensified floating root mat (FRM) system to reduce contaminants of emerging concern (CEC) from secondary-treated wastewater. Three configurations were evaluated: (1) FRM with plants (Cyperus alternifolius) and biochar, (2) FRM with plants only, and (3) unplanted control reactors, under two hydraulic loading rates (12 and 24 mm/day) over six months. The planted FRM enhanced CEC removal by 15 and 28 %, while the addition of biochar further increased removal by 35 % and 41 %, achieving CEC attenuation ranging from 41-99 %. Untargeted analysis corroborated this performance, and microbiological analysis linked CEC reduction to increased abundance of genera such as Exiguobacterium, Nocardia, Rodobacter and Amaricoccus, associated with biodegradation processes. This work therefore demonstrates that integrating biochar into FRMs enhances the attenuation of CEC and, for the first time, links biochar addition to microbial community shifts, offering a new strategy to tackle CEC pollution in wastewater treatment plants.},
}
@article {pmid40659121,
year = {2025},
author = {Eapen, AA and Shankhwar, S and von Mutius, E and Johnson, CC},
title = {Environmental Risk Factors and Asthma Primary Prevention: from Birth Cohort Studies to Clinical Trials.},
journal = {The Journal of allergy and clinical immunology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jaci.2025.07.002},
pmid = {40659121},
issn = {1097-6825},
abstract = {With the prevalence of pediatric asthma and allergy rising substantially since last mid-century, birth cohort studies starting in pregnancy have been pivotal in identifying prenatal and early life environmental factors that influence risk of these diseases. With these findings, researchers have been able to identify biological mechanisms at play with the eventual goal of engineering tailored interventions to optimize immune system development and decrease the risk of allergic disorders. In this review, we describe the critical role birth cohort studies have played in starting to disentangle the environmental epidemiology and etiology of childhood-onset asthma and other allergic diseases, and how these studies have guided ongoing clinical trials for asthma and allergy prevention. Lastly, we highlight important questions that remain unanswered and potential approaches to help fill these gaps in knowledge.},
}
@article {pmid40659087,
year = {2025},
author = {Wang, Y and Zhao, D and Li, Z and Yang, Y and Peng, Z and Meng, C and Ma, S and Xu, K and Li, Y and Ding, G and Zheng, Y and Zhang, CS},
title = {Kaempferol drives genotype-specific microbiota Bacillaceae to enhance nitrogen acquisition in rapeseed.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2025.07.018},
pmid = {40659087},
issn = {2090-1224},
abstract = {INTRODUCTION: Host genotype is a key driver in shaping plant microbiome in response to dynamic changes in soil nitrogen (N) availability. However, the effects of rapeseed (Brassica napus) genotypes with different N use efficiency characteristics on microbiome assembly, as well as the underlying plant-microbe interaction mechanisms, remain poorly understood.<br><br>OBJECTIVES: This study aims to: (1) assess microbial assembly differences between N-use efficient and inefficient genotypes; (2) identify specific microbiota associated with plant N acquisition; and (3) reveal the molecular mechanisms driving plant-microbe interactions.<br><br>METHODS: We conducted comparative microbiome profiling of N-use efficient and inefficient genotypes, followed by functional validation of microbial roles in plant N uptake. Multi-omics approaches, including RNA-seq and metabolomics, were used to uncover the regulatory interactions between the host and rhizosphere microbiota.<br><br>RESULTS: The N-use efficient genotype constructed more diverse root-associated microbes than the inefficient genotype, with Bacillaceae emerging as the most enriched taxon. A representative isolate, Bacillus sp. 41S2 from the N-use efficient genotype, markedly enhanced root biomass and N uptake in the N-use inefficient genotype, as confirmed by [15]N tracer assays. RNA-Seq analysis further demonstrated that genes involved in jasmonic acid and ethylene signaling pathways were upregulated in strain 41S2-inoculated plants, likely contributing to enhanced root development. Metabolomic profiling identified kaempferol, a flavonol with the highest fold-change between genotypes, as a key root exudate promoting the growth and biofilm formation of strain 41S2. Furthermore, the fls1 mutant (deficient in kaempferol biosynthesis) failed to recruit Bacillaceae, confirming the role of kaempferol in mediating genotype-specific microbial enrichment.<br><br>CONCLUSIONS: Our findings reveal a novel, microbe-dependent N acquisition pathway in N-use efficient rapeseed genotypes, driven by kaempferol-mediated recruitment of Bacillaceae. This work highlights the potential of host genotype and metabolite signaling to shape beneficial microbiota for improved nutrient efficiency and sustainable crop production.},
}
@article {pmid40659044,
year = {2025},
author = {Nolan, M and Chan, B and Loc-Carrillo, C and Parker, A and France, D and Grubb, PH and Drews, F},
title = {Increased Caregiver Interaction with the NICU Environment during Medication Administration May Contribute to Higher Infection Rates: A Pilot Observational Study.},
journal = {American journal of perinatology},
volume = {},
number = {},
pages = {},
doi = {10.1055/a-2641-9863},
pmid = {40659044},
issn = {1098-8785},
abstract = {After nearly 3 years without a single central line-associated bloodstream infection (CLABSI), our neonatal intensive care unit (NICU) experienced a significant rise in CLABSI rates beginning in 2019. The increase coincided with changes made to the intravenous (IV) medication pump integration process, which added more safety checks and procedural steps. This study aimed to investigate the potential association between these process changes and increased CLABSI and non-CLABSI (bloodstream infection, BSI) rates prior to inclusion in a future QI project Key Driver Diagram.This observational pilot study used a mixed-methods approach, including statistical process control analysis to confirm a special-cause increase in CLABSI rate, human factors observations, and environmental microbiome sampling focusing on the equipment involved in the IV pump integration. We compared these findings to the CLABSI and BSI rates to identify temporal and geographic associations.Following the 2019 implementation of IV pump integration, statistically significant increases in CLABSI and BSI rates were observed. The enhanced safety checks added steps to IV medication administrations, with timestamp observation indicating up to 14 location changes around the bed spaces and a mean of 5.5 minutes for any IV medication administration. Environmental microbial sampling showed a 27% positivity rate. The highest microbial burden was found on patient-specific mobile equipment (30%) used during IV medication administration, including isolettes, IV hubs, and glove boxes, compared with other equipment (26%) like nursing computers or ventilators (p = 0.093). A strong overlap was observed between the microorganisms found in the NICU environment and those responsible for positive patient blood cultures, particularly coagulase-negative Staphylococcus (CONS).Though not statistically significant, the findings suggest that the added complexity and extended duration of the modified IV pump integration process may have increased the frequency of caregiver interactions with the NICU environment, exposing immune-vulnerable NICU patients to a higher risk of infection. Further human factors analysis and quality improvement efforts are necessary to simplify the IV medication administration process, reduce environmental microbial loads, and decrease infection rates. · Increased CLABSI/BSI rates post-IV pump integration.. · High microbial load on equipment related to the IV medication administration process.. · Process changes with IV pump integration to enhance patient safety may have unintended consequences, like increasing caregiver-environment interaction and patient infection rates..},
}
@article {pmid40658810,
year = {2025},
author = {Allegretti, AS and Levitsky, J and Sharma, P and Ouyang, T and Jamil, K and Silvey, S and Bajaj, JS},
title = {Predictors of response to terlipressin therapy in hepatorenal syndrome: Metabolomic and proteomic analysis from the CONFIRM trial.},
journal = {Hepatology communications},
volume = {9},
number = {8},
pages = {},
pmid = {40658810},
issn = {2471-254X},
mesh = {Humans ; *Hepatorenal Syndrome/drug therapy/blood/urine/metabolism ; *Terlipressin/therapeutic use ; Male ; Female ; Middle Aged ; *Vasoconstrictor Agents/therapeutic use ; Proteomics ; Metabolomics ; Treatment Outcome ; Biomarkers/blood/urine ; Aged ; Creatinine/blood ; Adult ; },
abstract = {BACKGROUND: Terlipressin is the only FDA-approved vasoconstrictor for hepatorenal syndrome (HRS). The CONFIRM study is the largest trial of terlipressin versus placebo. Novel predictors of HRS response are required to enrich patient selection and optimize outcomes.<br><br>METHODS: Samples at treatment initiation were tested using (a) liquid chromatography-mass spectrometry of 1594 plasma/1420 urine metabolites (Metabolon Inc.), (b) aptamer-based array of 7289 plasma proteins (SomaScan), and (c) 14 plasma/urine pre-specified assays. The CONFIRM trial's original definition of HRS response [2 serum creatinine (SCr) <1.5&#xa0;mg/dL separated by >2&#xa0;h] was used as the primary outcome.<br><br>RESULTS: In all, 115 patients [79 terlipressin-treated (TT) and 36 placebo-treated (PT)] provided samples. Baseline characteristics, outcomes, and 2:1 TT:PT allocation were preserved from the original 300-patient trial. A total of 36 out of 116 (31.0%) patients achieved HRS reversal. HRS reversal was associated with lower SCr (p=0.001), cystatin C (p=0.005), angiopoietin-2 (p=0.04), and beta-2 microglobulin (p=0.006). In metabolite analysis, PT had the most significant differences in HRS reversal [n=26 plasma, n=50 urine, including lower urine levels of those centered on sulfated secondary bile acids (microbiome-derived), N-acetylated amino acids, catechols (both uremic toxins), and phosphocholines (cell membrane integrity)], with fewer in TT (n=1 plasma, n=2 urine), and in all patients (n=3 plasma, n=7 urine). There were no significant aptamers associated with HRS reversal after false-discovery correction.<br><br>CONCLUSIONS: SCr, cystatin C, angiopoietin-2, and beta-2 microglobulin were associated with HRS reversal. Protein and metabolite signals centered on microbiome function and uremic toxins appeared more robust in PT patients, likely selecting a subgroup that may recover without terlipressin. Use of novel biomarkers may enrich for terlipressin response.},
}
@article {pmid40658737,
year = {2025},
author = {Lundberg, DS and Kersten, S and Mehmetoğlu Boz, E and Pramoj Na Ayutthaya, P and Zhu, W and Poersch, K and Yuan, W and Swartz, S and Müller, D and Bezrukov, I and , and Weigel, D},
title = {A major trade-off between growth and defense in Arabidopsis thaliana can vanish in field conditions.},
journal = {PLoS biology},
volume = {23},
number = {7},
pages = {e3003237},
doi = {10.1371/journal.pbio.3003237},
pmid = {40658737},
issn = {1545-7885},
abstract = {When wild plants defend themselves from pathogens, this often comes with a trade-off: the same genes that protect a plant from disease can also reduce its growth and fecundity in the absence of pathogens. One protein implicated in a major growth-defense trade-off is ACCELERATED CELL DEATH 6 (ACD6), an ion channel that modulates salicylic acid (SA) synthesis to potentiate a wide range of defenses. Wild Arabidopsis thaliana populations maintain significant functional variation at the ACD6 locus, with some alleles making the protein hyperactive. In the greenhouse, plants with hyperactive ACD6 alleles are resistant to diverse pathogens, yet they are of smaller stature, their leaves senesce earlier, and they set fewer seeds compared to plants with the standard allele. We hypothesized that ACD6 hyperactivity would not only affect the growth of microbial pathogens but also more generally change leaf microbiome assembly. To test this in an ecologically meaningful context, we compared plants with hyperactive, standard, and defective ACD6 alleles in the same field-collected soil, both outdoors and in naturally lit and climate-controlled indoor conditions, taking advantage of near-isogenic lines as well as a natural accession and a CRISPR-edited derivative. We surveyed visual phenotypes, gene expression, hormone levels, seed production, and the microbiome in each environment. The genetic precision of CRISPR-edited plants allowed us to conclude that ACD6 genotype had no effect on mature field plants in our setting, despite reproducibly dramatic effects on greenhouse plants. We conclude that additional abiotic and/or microbial signals present outdoors-but not in the greenhouse-greatly modulate ACD6 activity. This raises the possibility that the fitness costs of other commonly studied immune system genes may be grossly misjudged without field studies.},
}
@article {pmid40658721,
year = {2025},
author = {Mahajan, T and Maslov, S},
title = {Coarse-grained model of serial dilution dynamics in synthetic human gut microbiome.},
journal = {PLoS computational biology},
volume = {21},
number = {7},
pages = {e1013222},
doi = {10.1371/journal.pcbi.1013222},
pmid = {40658721},
issn = {1553-7358},
abstract = {Many microbial communities in nature are complex, with hundreds of coexisting strains and the resources they consume. We currently lack the ability to assemble and manipulate such communities in a predictable manner in the lab. Here, we take a first step in this direction by introducing and studying a simplified consumer resource model of such complex communities in serial dilution experiments. The main assumption of our model is that during the growth phase of the cycle, strains share resources and produce metabolic byproducts in proportion to their average abundances and strain-specific consumption/production fluxes. We fit the model to describe serial dilution experiments in hCom2, a defined synthetic human gut microbiome with a steady-state diversity of 63 species growing on a rich media, using consumption and production fluxes inferred from metabolomics experiments. The model predicts serial dilution dynamics reasonably well, with a correlation coefficient between predicted and observed strain abundances as high as 0.8. We applied our model to: (i) calculate steady-state abundances of leave-one-out communities and use these results to infer the interaction network between strains; (ii) explore direct and indirect interactions between strains and resources by increasing concentrations of individual resources and monitoring changes in strain abundances; (iii) construct a resource supplementation protocol to maximally equalize steady-state strain abundances.},
}
@article {pmid40658705,
year = {2025},
author = {Cui, X and Martinez Luna, AA and Gillone, A and Wu, Q and Serag, M and Murata, RM},
title = {Correlation between pre-extraction periodontal diagnosis and peri-implant microbiome for patients treated with implant-retained overdenture - A retrospective cohort pilot study.},
journal = {PloS one},
volume = {20},
number = {7},
pages = {e0325711},
pmid = {40658705},
issn = {1932-6203},
mesh = {Humans ; Female ; Male ; Aged ; Pilot Projects ; *Microbiota ; Middle Aged ; *Denture, Overlay/microbiology ; Retrospective Studies ; *Dental Implants/microbiology ; RNA, Ribosomal, 16S/genetics ; *Periodontitis/diagnosis/microbiology ; Aged, 80 and over ; Peri-Implantitis/diagnosis/microbiology ; },
abstract = {Limited clinical data exists on the peri-implant microbiome in edentulous patients with implant-retained overdentures (IRO). This study aimed to examine the peri-implant microbiome and its correlation with pre-treatment periodontal diagnosis. A total of twenty-five patients with 50 implants were included, with demographic information and pre-treatment periodontal diagnosis collected. Clinical measurements and subgingival plaque samples were obtained from each implant, followed by 16S rRNA gene-targeted sequencing. Peri-implant parameters and microbiome were analyzed in relation to gender, remaining teeth prior to treatment, IRO function time, implant system, bone graft at implant placement, and peri-implant diagnosis. The mean age of patients was 71 years, with pre-extraction diagnoses including clinical healthy gingiva on a reduced periodontium (4 patients), localized periodontitis (4 patients), generalized periodontitis (7 patients), and generalized Stage IV Grade C periodontitis (10 patients). Nineteen implants were diagnosed with peri-implant mucositis, while 31 were healthy. The predominant genera detected were Streptococcus, Rothia, Veillonella, Actinomyces, and Schaalia. No significant correlation was found between pre-treatment periodontal diagnosis and peri-implant diagnosis. The findings suggest that while pre-extraction periodontal diagnosis might influence the peri-implant subgingival microbiome in IRO patients, it may not correlate with the clinical peri-implant diagnosis.},
}
@article {pmid40658627,
year = {2025},
author = {Ma, T and Wang, W and Li, S and Li, D and Shen, L and Qu, G and Chiang, VL and Zhang, Q and Wu, D and Niu, B},
title = {A Workflow for the Quantitative Assessment of the Endophytic and Epiphytic Bacterial Microbiomes of the Bark of Populus trichocarpa.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {220},
pages = {},
doi = {10.3791/66318},
pmid = {40658627},
issn = {1940-087X},
mesh = {*Populus/microbiology ; *Plant Bark/microbiology ; *Microbiota ; *Bacteria/genetics/classification/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Workflow ; DNA, Bacterial/genetics ; Polymerase Chain Reaction/methods ; Endophytes/genetics/isolation &amp; purification ; },
abstract = {Microorganisms colonizing plant surfaces and internal tissues may possess beneficial functions in promoting plant growth and health. However, information on the microbiome of bark tissues of woody plants remains limited, especially regarding the endophytic and epiphytic bacterial microbiota of the bark of Populus. To overcome this limitation, we established a workflow to quantify the composition and diversity of the endophytic and epiphytic bacterial microbiota colonizing the bark of Populus trichocarpa. Briefly, the epidermis of the stem of P. trichocarpa was repeatedly wiped with a cotton ball dipped in 0.1% Tween 20 to acquire epiphytic bacterial samples. The stripped epidermis was sterilized and then repeatedly frozen and crushed using liquid nitrogen and a bead beater, respectively, to collect endophytic bacterial samples. Genomic DNA was extracted from the cotton-adhered epiphytic bacterial communities and the crushed bark of P. trichocarpa, and underwent ploymerase chain reaction (PCR) amplification with primers targeting the hypervariable V5-V7 and V4 regions of the bacterial 16S rRNA gene. Three replicates of the obtained PCR products of each endophytic or epiphytic sample were mixed in equal concentrations to build the amplicon library, which was then sequenced. The obtained sequences were analyzed by sequence splicing, quality filtering, chimera removal, and taxonomic annotations. In summary, we established a reliable and efficient workflow from sample collection to data analysis for determining the endophytic and epiphytic bacterial microbiomes of the bark of P. trichocarpa through 16S rRNA gene profiling. Together with the methods for exploring microbiota colonizing barks established in the previous study, our methodology may serve as a blueprint for designing protocols for investigating the bark microbiome of other woody plant species, particularly economically important trees of forests.},
}
@article {pmid40658318,
year = {2025},
author = {Yu, S and Li, J and Ye, Z and Zhang, M and Guo, X and Wang, X and Liu, L and Wang, Y and Zhou, X and Fu, W and Zhang, MQ and Chen, YG},
title = {Identification of a 10-species microbial signature of inflammatory bowel disease by machine learning and external validation.},
journal = {Cell regeneration (London, England)},
volume = {14},
number = {1},
pages = {32},
pmid = {40658318},
issn = {2045-9769},
support = {2023YFA1800603//National Key Research and Development Program of China/ ; 31988101//Natural Science Foundation of China/ ; 92354306//Natural Science Foundation of China/ ; Z231100007223006//Beijing Science and Technology Plan/ ; B2302022//Shenzhen Medical Research Fund/ ; 20224ACB209001//Natural Science Foundation of Jiangxi Province/ ; O0390302//Guangdong Provincial Postdoctoral Science Foundation/ ; },
abstract = {Genetic and microbial factors influence inflammatory bowel disease (IBD), prompting our study on non-invasive biomarkers for enhanced diagnostic precision. Using the XGBoost algorithm and variable analysis and the published metadata, we developed the 10-species signature XGBoost classification model (XGB-IBD10). By using distinct species signatures and prior machine and deep learning models and employing standardization methods to ensure comparability between metagenomic and 16S sequencing data, we constructed classification models to assess the XGB-IBD10 precision and effectiveness. XGB-IBD10 achieved a notable accuracy of 0.8722 in testing samples. In addition, we generated metagenomic sequencing data from collected 181 stool samples to validate our findings, and the model reached an accuracy of 0.8066. The model's performance significantly improved when trained on high-quality data from the Chinese population. Furthermore, the microbiome-based model showed promise in predicting active IBD. Overall, this study identifies promising non-invasive biomarkers associated with IBD, which could greatly enhance diagnostic accuracy.},
}
@article {pmid40658295,
year = {2025},
author = {Li, B and Lin, W and Hu, R and Bai, S and Ruan, Y and Fan, Y and Qiao, S and Wen, X and Liu, R and Chen, H and Cui, W and Cai, Z and Zhang, G},
title = {Crosstalk between lung and extrapulmonary organs in sepsis-related acute lung injury/acute respiratory distress syndrome.},
journal = {Annals of intensive care},
volume = {15},
number = {1},
pages = {97},
pmid = {40658295},
issn = {2110-5820},
support = {No. 82470068, No. 82270086//National Natural Science Foundation of China/ ; LZ25H150001//Natural Science Foundation of Zhejiang Province/ ; WKJ-ZJ-2526//National Health Commission Scientific Research Fund/ ; },
abstract = {Sepsis-related acute lung injury/acute respiratory distress syndrome (ALI/ARDS) is associated with considerable morbidity and mortality, yet the efficacy of current treatments is limited. Previous studies have predominantly focused on the lung itself as an isolated organ, whereas the role of organ crosstalk in the pathogenesis of sepsis-related ALI/ARDS cannot be overlooked. Meanwhile, neglecting the discussion of heterogeneity in sepsis caused by different sources of infection may be another important obstacle to translating previous studies into clinical efficacy. In this review, we initially delineated the distinctions in pathogenesis between pulmonary and extrapulmonary sepsis-related ALI/ARDS in microbial species, pathogenesis, host response, and clinical manifestations. Additionally, systemic organ crosstalk mechanisms are summarized, including the commonality and specificity of systemic inflammation, lung and gut microbiome, as well as cascade cell injury and death in distant organs. Subsequently, organ crosstalk between lung and extrapulmonary in pulmonary sepsis and extrapulmonary sepsis-related ALI/ARDS are discussed by organs, including immunity, neuroendocrine, metabolism, and so forth. Furthermore, extracellular vesicles represent a promising avenue of research as potential players and targets in organ-lung crosstalk in sepsis. While the complexity of multi-organ interactions and the heterogeneity of septic patients present significant challenges, these issues are expected to be addressed by the emergence of organ-on-a-chip platforms, 3D organoid cultures, and multi-omics techniques.},
}
@article {pmid40658186,
year = {2025},
author = {You, L and Huang, W and Chen, S},
title = {Unveiling the anticancer potential of flavonoids in hepatocellular carcinoma through microbiome and spatially resolved metabolomics analysis.},
journal = {Discover oncology},
volume = {16},
number = {1},
pages = {1327},
pmid = {40658186},
issn = {2730-6011},
abstract = {BACKGROUND: Hepatocellular carcinoma (HCC) causes a large worldwide health burden, needing novel ways to prevention and treatment. Traditional Chinese medicine, which is rich in bioactive substances, has emerged as a viable approach to tackling HCC difficulties. Artemisia rupestris L. (AR), a perennial plant, has received interest for its immunoregulatory qualities and potential protection against viral influenza and hepatocellular cancer.<br><br>METHODS: In this work, we looked at the pharmacological effects of Artemisia rupestris L. extract (ARE) on HCC mice. We used 16&#xa0;S rRNA sequencing and computational biology approaches to investigate ARE-induced changes in bacterial composition inside HCC mouse tissues. Furthermore, we used liquid chromatography tandem mass spectrometry (UPLC-MS/MS) to identify metabolic changes caused by ARE.<br><br>RESULTS: Our data indicate that ARE affects hepatocellular cancer via several pathways. AR offers a multi-faceted strategy to combating HCC by influencing critical metabolic pathways such &#x3b1;-linolenic acid and glycerophospholipid metabolism.<br><br>CONCLUSIONS: This research sheds new light on Artemisia rupestris L.'s anticancer potential, setting the platform for a more in-depth knowledge of its influence on hepatocellular carcinoma using a multi-omics approach.},
}
@article {pmid40658106,
year = {2025},
author = {Chen, G and Wang, Y and Zhang, X and Jiang, K and Yu, M and Fang, L and Li, F},
title = {Periphyton-Driven Arsenic Methylation in Paddy Soils: The Crucial Role of Trophic Interactions.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c06047},
pmid = {40658106},
issn = {1520-5851},
abstract = {Arsenic (As) methylation facilitated by periphyton in paddy soils is crucial for its biogeochemical cycling and thus its bioavailability. However, the key functional taxa and underlying interactive metabolisms remain unclear due to the high complexity of the periphytic microbiome. Here, we employ DNA-stable isotope probing with metagenomic binning analysis to uncover the critical role of intrinsic trophic interactions in stimulating As methylation within the periphyton in association with soil inorganic carbon. Abundance of As-methylating microorganisms in the periphyton increases by 2.1-fold after bicarbonate addition. Members of phototrophs are predominantly responsible for regulating the stability of the periphytic microbiome, of which photoautotrophs (e.g., Oscillatoriales) initiate carbon fixation and constitute a major portion of As-methylating populations. These phototrophs further offer requisite organic substrates such as polysaccharides for heterotrophic bacteria (e.g., Chitinophagales) that in return foster the growth of the periphytic community, while these taxa simultaneously detoxify As through biomethylation to secure their ecological niches in periphyton. Such a symbiotic metabolism between phototrophs and heterotrophs facilitates carbon sequestration and shapes the functional community, collaboratively determining methylated As production in paddy soils. These findings offer new insights into the influence of trophic interactions within the periphyton on As speciation with potential implications for element cycling and soil remediation in paddy soils.},
}
@article {pmid40657987,
year = {2025},
author = {Van Dyke, TE and Baima, G and Romandini, M},
title = {Periodontitis: Microbial Dysbiosis, Non-Resolving Inflammation, or Both?.},
journal = {Journal of periodontal research},
volume = {},
number = {},
pages = {},
doi = {10.1111/jre.13424},
pmid = {40657987},
issn = {1600-0765},
support = {DE025020/DE/NIDCR NIH HHS/United States ; DE032406/DE/NIDCR NIH HHS/United States ; },
abstract = {The central question addressed in this review revisits the historical chicken-and-egg debate: "In periodontitis, does microbial dysbiosis drive inflammation, or does inflammation shape the subgingival microbiome?" This question is reframed through the lens of inflammation resolution. Specialized pro-resolving mediators (SPMs) provide a mechanistic framework for understanding how inflammation intersects with microbial dysbiosis. Derived from omega-3 and omega-6 fatty acids, SPMs actively promote the resolution of inflammation through binding of specific cell surface receptors rather than nonspecifically suppressing it, highlighting their therapeutic potential as side-effect-free host modulators, with implications beyond periodontitis to other chronic inflammatory diseases. The evidence reviewed shows how SPMs can: (1) control inflammation by resolution rather than inhibition, (2) reverse microbial dysbiosis as a consequence of inflammation control, and (3) promote tissue regeneration through diverse biological pathways. Whether the primary dysregulation in periodontitis lies solely in resolution failure or involves additional-possibly still unidentified-mechanisms, remains unclear. All individuals harbor periodontal pathobionts, yet only a subset develop severe disease. Why do some individuals with significant biofilm accumulation maintain attachment levels, while others with reasonable plaque control become edentulous? This remains one of the most significant unanswered questions in periodontology. What is evident, however, is the need for a paradigm shift. While bacteria initiate the inflammatory process in all individuals, it is the host response that ultimately determines the progression to periodontitis.},
}
@article {pmid40657968,
year = {2025},
author = {Morandi, SC and Uldry, AC and Eldridge, N and Kreuzer, M and Herzog, EL and Zinkernagel, M and Zysset-Burri, DC},
title = {Toward the Characterization of the Human Core Ocular Surface Microbiome.},
journal = {Investigative ophthalmology &amp; visual science},
volume = {66},
number = {9},
pages = {40},
doi = {10.1167/iovs.66.9.40},
pmid = {40657968},
issn = {1552-5783},
mesh = {Humans ; *Microbiota/genetics ; Middle Aged ; Adult ; *Tears/microbiology/metabolism ; *Conjunctiva/microbiology ; Female ; Male ; Tandem Mass Spectrometry ; *Eyelids/microbiology ; *Bacteria/genetics/isolation &amp; purification ; Chromatography, Liquid ; Eye Proteins/metabolism ; },
abstract = {PURPOSE: The field of ocular surface microbiome (OSM) research suggests its involvement in ocular surface (OS) health and disease. However, existing OSM data are heterogeneous. This study aims to provide a whole-metagenome shotgun sequencing-based description of the healthy core ocular surface microbiome (COSM), encompassing all taxonomic kingdoms at species-level resolution.<br><br>METHODS: Swabs from the conjunctiva and lower lid margin, and tear fluid of 27 individuals without OS disease aged 40 to 60&#xa0;years were collected at 3 time points. The OSM was sequenced and taxonomically and functionally profiled using Kraken2 and HUMAnN3, respectively. To validate sequencing results, human and microbial proteins of the tear fluid, termed the tear proteome (TP), were characterized by nano liquid chromatography-tandem mass spectrometry (nLC-MS/MS) and profiled by gene ontology. The COSM was defined as the microbiome present in most of the study population over time. Therefore, species present in > 50% of all samples across the three time points were considered to form the COSM.<br><br>RESULTS: At species level, Cutibacterium acnes, Malassezia restricta, and Staphylococcus epidermidis formed the COSM, with Corynebacterium segmentosum additionally being part of the core lid microbiome (LM). No significant differences in the OSM and human TP were observed between the left and right eyes on individual levels. However, the variance between subjects mostly exceeded that between eyes within subjects, suggesting an individual-specific COSM and TP.<br><br>CONCLUSIONS: The description of the COSM provides the basis for future OSM research and potential targets for preventive and therapeutic interventions of the OS and associated diseases.},
}
@article {pmid40657928,
year = {2025},
author = {Knotek, AAU and Kristich, CJ},
title = {Phosphorylation of the cell wall hydrolase MltG in response to cell wall stress modulates resistance toward cephalosporins in Enterococcus faecalis.},
journal = {Journal of bacteriology},
volume = {},
number = {},
pages = {e0009925},
doi = {10.1128/jb.00099-25},
pmid = {40657928},
issn = {1098-5530},
abstract = {Enterococcus faecalis is an opportunistic pathogen that colonizes the human gut microbiome. E. faecalis commonly establishes infection subsequent to antibiotic therapy in patients due to intrinsic resistance exhibited by E. faecalis toward cephalosporins and acquired resistance to many clinically used antibiotics. Intrinsic resistance toward cephalosporins in E. faecalis depends on the kinase activity of IreK, a transmembrane serine/threonine PASTA kinase that mediates responses to cell wall stress, including stress caused by cephalosporins, by phosphorylating downstream effector proteins. Our previous phosphoproteomics analysis identified MltG, a transmembrane protein with an extracellular catalytic domain that cleaves nascent peptidoglycan strands, as a putative substrate for phosphorylation by IreK in E. faecalis, suggesting the hypothesis that IreK-mediated phosphorylation of MltG might regulate cell wall homeostasis and possibly intrinsic cephalosporin resistance. Here we report that MltG is a bona fide direct substrate of IreK in E. faecalis. We found that MltG phosphorylation in vivo is enhanced in response to cell wall stress in an IreK-dependent manner, requiring a specific residue in the MltG cytoplasmic domain for phosphorylation by IreK both in vivo and in vitro. Finally, phosphoablative and phosphomimetic substitutions of MltG reciprocally influence resistance of E. faecalis to ceftriaxone, pointing to functional consequences of MltG phosphorylation. Collectively, our results reveal a novel pathway by which IreK senses antibiotic-mediated cell wall stress and responds by phosphorylating the cytoplasmic segment of MltG to enhance antibiotic resistance.IMPORTANCEInfections caused by Enterococcus faecalis are increasingly prevalent and difficult to treat due to the multi-drug resistance exhibited toward common antibiotics. A greater understanding of the mechanisms underlying antibiotic resistance can enable the development of new drugs or strategies to overcome antibiotic-resistant infections. E. faecalis exhibits intrinsic resistance toward cephalosporins. This intrinsic resistance requires activity of the PASTA kinase IreK; however, few substrates for phosphorylation by IreK have been rigorously identified. Here, we report that MltG is directly phosphorylated by IreK in response to cell wall stress. This phosphorylation event acts to promote cephalosporin resistance as part of the IreK signaling network. Our results thereby validate a new substrate and expand knowledge of the IreK signaling pathway contributing to cephalosporin resistance.},
}
@article {pmid40657927,
year = {2025},
author = {Robinson, JM and Crino, OL and Camargo, A and Breed, MF},
title = {Does a microbial-endocrine interplay shape love-associated emotions in humans? A hypothesis.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0041525},
doi = {10.1128/msystems.00415-25},
pmid = {40657927},
issn = {2379-5077},
abstract = {Emerging evidence suggests that the human gut microbiome plays a regulatory role in the endocrine system, influencing hormone activity and potentially shaping the emotional and physiological dimensions of behaviors such as aggression and emotional states, including love. Here, we review the hypothesis that microbial-endocrine interactions shape love-associated emotions by modulating hormone levels and activity. While the division of love into discrete components such as lust, attraction, and attachment is somewhat artificial and may not fully capture the complexity of human experience, the associated emotions nevertheless correspond to well-characterized neuroendocrine processes. Psycho-endocrinological theory proposes that the complex and nonlinear interplay between testosterone, estradiol, and other hormones drives emotions associated with lust; serotonin and dopamine play a role in emotions linked to attraction; and oxytocin and vasopressin influence the modulation of attachment and social bonds. Microbial communities may influence emotions and relationship dynamics through effects on the hormonal pathways linked to love-associated emotions. While non-human animal studies suggest microbiota can impact social bonding, sexual preferences, and stress-related behaviors, direct evidence in humans remains limited. Investigating the evolutionary underpinnings of microbial-endocrine interactions could provide insights into how microbes influence emotions beyond love, including hate and aggression-with important societal implications. Indeed, understanding these mechanisms could have profound implications for human relationships, mental health, and even therapeutic interventions targeting the microbiota-gut-brain axis. Future research is needed to unravel the extent to which microbiomes contribute to the neurobiology of love (and other emotions) and whether manipulating microbial communities could modulate emotional and social behaviors.IMPORTANCELove is often considered an abstract emotion, but emerging science suggests that it may be shaped by the microscopic inhabitants of our bodies: microbes. This paper explores the intriguing hypothesis that microbes can influence the hormonal and neural systems linked to love-associated emotions-via the microbiota-gut-brain axis. Drawing on animal studies and early human microbiome and endocrine research, we highlight how microbes modulate neurohormones like oxytocin, dopamine, and testosterone, which play key roles in social bonding. By regulating these systems, microbes may also shape emotional and behavioral responses. This research opens new avenues for understanding not just the (micro)biology of love but also the potential for microbiome-targeted therapies to support relational well-being. By linking microbiome and emotion science, the article raises the important question of whether love is a phenomenon influenced by our resident symbionts, adding an intriguing and potentially impactful dimension to our understanding of human connection and behavior.},
}
@article {pmid40657876,
year = {2025},
author = {Strachan, CR and Bowers, CM and Kim, BC and Movsesijan, T and Neubauer, V and Mueller, AJ and Yu, XA and Pereira, FC and Nagl, V and Faas, J and Wagner, M and Zebeli, Q and Weimer, PJ and Candry, P and Polz, MF and Lawson, CE and Selberherr, E},
title = {Distinct lactate utilization strategies drive niche differentiation between two co-existing Megasphaera species in the rumen microbiome.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf147},
pmid = {40657876},
issn = {1751-7370},
abstract = {Lactate utilization mitigates rumen acidosis and is associated with decreased methane production in the rumen. While several lactate utilization pathways exist across different microbial species in the rumen, how they are metabolically differentiated remains unclear. Here, we show that the key lactate-utilizing species Megasphaera hexanoica and Megasphaera elsdenii display distinct growth strategies based on their fermentative end products. This allows them to co-exist and play distinct metabolic roles, which appear particularly relevant in the early stages of rumen development, as both species are highly enriched in the calf. Specifically, M. hexanoica is more strongly associated with rumen microbiome states that involve increased lactate utilization and preferentially runs reverse beta-oxidation (termed chain elongation) to produce butyrate and medium-chain fatty acids from lactate. As M. elsdenii instead utilizes lactate via the acrylate pathway to produce propionate, we leverage Enzyme Cost Minimization to predict how this pathway relates to a distinct growth strategy. We find that M. elsdenii maximizes growth rate when lactate transiently accumulates, which contrasts M. hexanoica's invariably high-yield strategy. This trade-off, which is supported by the analysis of growth kinetics, metabolic flux, and bioreactors simulating the rumen microbiome, ultimately contributes to co-existence on lactate and may have driven niche differentiation. Lastly, we demonstrate how lactate utilization in the Megasphaera is threatened by toxins widespread in feed, which points to dietary interventions to support calf health.},
}
@article {pmid40657740,
year = {2025},
author = {Miyako, E},
title = {Reply to "Exploring Bacteria-Based Cancer Immunotherapy"-Comment on "Discovery of Intratumoral Oncolytic Bacteria Toward Targeted Anticancer Theranostics".},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e11325},
doi = {10.1002/advs.202511325},
pmid = {40657740},
issn = {2198-3844},
support = {23H00551//Japan Society for the Promotion of Science/ ; 25K21827//Japan Society for the Promotion of Science/ ; JPMJSF2318//Japan Science and Technology Agency/ ; },
abstract = {This manuscript is a formal response to the commentary by A/Prof. Dr. Chen-xi Li and colleagues regarding our previous publication in Advanced Science. We clarify the rationale, methods, and outcomes of our original study and highlight ongoing work in the field of bacterial cancer immunotherapy.},
}
@article {pmid40657642,
year = {2025},
author = {Wu, W and Meng, T and Han, L and Jin, F and Han, P and Zhou, Y},
title = {Bridging traditional Chinese medicine and Alzheimer's disease: the pivotal role of gut microbiota in multitarget therapeutic mechanisms.},
journal = {Frontiers in pharmacology},
volume = {16},
number = {},
pages = {1630205},
pmid = {40657642},
issn = {1663-9812},
abstract = {Microbiota-gut-brain axis communication represents another crucial pathway in the pathogenesis of Alzheimer's disease (AD), whereby gut microbiota significantly impacts AD pathology by modulating immune, metabolic, digestive, and neurological functions. Although research on treating AD through gut microbiota interventions is advancing, substantial breakthroughs remain limited. Given AD's complex pathological mechanisms, Traditional Chinese Medicine (TCM) presents a clear advantage with its multi-target effects. During the processes of TCM intake, absorption, and therapeutic action, the gut microbiota serves both as a mediator and as a therapeutic target. However, the mechanisms by which TCM interacts with gut microbiota to exert beneficial effects on AD remain largely unclarified. Here, we review the mechanisms through which TCM may intervene in AD from the perspective of gut microbiota, examining the potential mechanisms and clinical application prospects of Chinese herbal medicine in regulating the gut microbiome. This provides a novel theoretical foundation and methodological support for further research into herbal therapies for AD.},
}
@article {pmid40657495,
year = {2025},
author = {Bruins-van Sonsbeek, LGR and Verschuren, MCM and Kaal, S and Lindenburg, PW and Rodenburg, KCW and Clauss, M and Speksnijder, AGCL and Rutten, VPMG and Bonnet, BFJ and Wittink, F},
title = {Correction: Rhinoceromics: a multi-amplicon study with clinical markers to transferrin saturation levels in ex-situ black rhinoceros (Diceros bicornis michaeli).},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1644681},
doi = {10.3389/fmicb.2025.1644681},
pmid = {40657495},
issn = {1664-302X},
abstract = {[This corrects the article DOI: 10.3389/fmicb.2025.1515939.].},
}
@article {pmid40656962,
year = {2025},
author = {Gunawan, SP and Huang, SY and Hsu, JW and Lin, CY and Nguyen, NN and Tung, TH and Liang, SL and Lee, GA and Su, CT and Chen, YC},
title = {Chronic sleep deprivation is associated with delayed puberty onset in rats, activation of proinflammatory cytokines and gut dysbiosis.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e19668},
pmid = {40656962},
issn = {2167-8359},
mesh = {Animals ; *Sleep Deprivation/complications/physiopathology ; *Gastrointestinal Microbiome ; Male ; Rats ; *Cytokines/metabolism/blood ; *Dysbiosis ; Female ; Rats, Sprague-Dawley ; *Sexual Maturation ; *Puberty, Delayed/etiology ; Inflammation ; },
abstract = {Chronic sleep deprivation (CSD) in adolescents has become a trend with adverse health outcomes. Previous studies have demonstrated that sleep deprivation causes inflammation, alters puberty onset, and changes the gut microbiome composition; however, the relationship between these is still unknown. Therefore, we hypothesized that CSD delays the onset of puberty via elevating proinflammatory cytokines and alter ation of gut microbiome composition. Using the modified multiple platform method, we conducted a 4-week CSD experiment in juvenile rats and assessed pubertal markers, antioxidant activity, cytokine levels, and gut microbiome profiles. CSD significantly reduces body weight, delays onset of puberty, and elevated antioxidant enzyme activities in both sexes. In the sleep-deprivation female (SDF) rats, plasma levels of lipopolysaccharide-binding protein (LBP), interleukin-1β (IL-1β), interleukin-6 (IL-6), and tumor necrosis factor-α (TNF-α) were significantly elevated; mRNA levels of TNF-α and IL-1β were also significantly elevated in the colon and reproductive organs, respectively. In the sleep-deprivation male (SDM) rats, only plasma levels of IL-6 were elevated considerably; in addition, mRNA levels of IL-1β and TNF-α were also significantly elevated in the colon and reproductive organs, respectively. Gut microbiome analysis revealed that the predominant bacteria at the genus level were Muribaculaceae, Prevotellaceae UCG-001, and Ruminococcaceae UCG-005 in the SDF rats; Prevotellaceae NK3B31, Ruminococcaceae UCG-010, Eubacterium coprostanoligenes, and Shuttleworthia in the SDM rats. CSD rats with abundant genera were positively correlated with antioxidant enzyme activities and mRNA levels of proinflammatory cytokines. Overall, CSD is associated with delayed puberty onset, possibly via an increase in the expression levels of proinflammatory cytokines and altering the gut microbiome composition, indicating proinflammatory cytokines and gut microbiome play an important role in pubertal timing change. These findings may guide the future studies to intervene sleep deprivation-related delays in the onset of puberty.},
}
@article {pmid40656088,
year = {2024},
author = {Schneider, E and Leigh, SJ and Lynch, CMK and Hilbert, A and Clarke, G and Higgs, S and Cryan, JF},
title = {Microbiota-gut-brain axis in binge-eating disorder: Towards microbiome-based therapies.},
journal = {Neuroscience applied..},
volume = {3},
number = {},
pages = {104088},
pmid = {40656088},
issn = {2772-4085},
abstract = {Binge-eating disorder (BED) is the most common eating disorder, but the mechanisms that underlie this disorder are still largely unknown. There is tentative evidence to suggest that the gut microbiota, which communicates to the brain via the gut-brain axis, plays a role in the pathogenesis of BED. However, more mechanistic research is urgently required to gain greater clarity and inform the development of superior management strategies. In this review, we sought to develop a new conceptual model that incorporates the gut microbiota to provide valuable guidance for future research in this area. In BED, the large quantities of hyper-palatable, energy-dense foods rapidly consumed reduces microbial diversity and their associated metabolites alongside promotions in microbial volatility and inflammation. These dietary-induced effects on the microbiota alter pathways implicated in BED including satiety, reward, impulsivity, and mood. The biological mechanisms underpinning the psychological effects include actions of microbial components and metabolites, alongside effects on the hypothalamic-pituitary-adrenal axis and the dopaminergic and serotonergic systems. Importantly, individual baseline characteristics such as genetics and environmental stressors can moderate the relationship between one's diet, the gut microbiota, and BED. A growing body of evidence suggests that microbiota-targeted interventions, so called psychobiotics, may affect these pathways to modulate brain and behaviour. While further research is necessary to test this hypothesis, the gut microbiota represents a novel avenue for future BED therapeutics.},
}
@article {pmid40655582,
year = {2025},
author = {Patel, SP and Bhoraniya, SJ and Kalola, SD and Rukadikar, A and Ravi, R and Farooqui, S and Rukadikar, C},
title = {Gut Microbiota and its Impact on Chronic Diseases: A Comprehensive Review.},
journal = {Journal of pharmacy &amp; bioallied sciences},
volume = {17},
number = {Suppl 2},
pages = {S1080-S1082},
pmid = {40655582},
issn = {0976-4879},
abstract = {The intricate community of bacteria that live in the gastrointestinal system, known as the gut microbiota, is essential to preserving human health and equilibrium. The pathophysiology of several chronic illnesses, including as neurological, cardiovascular, immunological, and metabolic disorders, has been progressively associated with its dysbiosis. This thorough analysis looks at the complex relationships that exist between gut microbiota and host physiology, examining processes including metabolic signaling, immunological regulation, and gut-brain axis communication. We discuss current developments in the study of the microbiome, with an emphasis on the role that the variety and makeup of gut microbes play in the development of chronic diseases. In order to restore microbial balance and lessen the severity of the condition, the study also covers new treatment approaches such as dietary changes, probiotics, prebiotics, and fecal microbiota transplantation. The development of novel, microbiome-based diagnostic and therapeutic strategies is made possible by an understanding of the complex link between the gut microbiota and chronic illnesses, highlighting the vital role that personalized medicine plays in enhancing health outcomes.},
}
@article {pmid40655378,
year = {2025},
author = {Sreehari, OK and Jose, RM and Menon, DB and Saranya, MK and Anilkumar, TR},
title = {Comparative Analysis of Faecal Bacteria in Captive Asian Elephants of Various Age Groups and Musth.},
journal = {Indian journal of microbiology},
volume = {65},
number = {2},
pages = {1225-1233},
pmid = {40655378},
issn = {0046-8991},
abstract = {UNLABELLED: Study of gut microbiome is an emerging area in modern research with over one trillion population is known to inhabit the gut of organisms. The gut microbiome constitutes bacteria, viruses, protozoa and fungi and their collective genetic material present in the gastrointestinal tract. It is an essential part of a species' ecology and influenced by the diet and phylogeny of the host. Most studies on the significance of gut microbiota and its association with physiology were done in humans than animals, and even fewer in elephants. Here in this study, we ventured to study the diversity of faecal bacteria of elephants of various age groups and musth. Bacteriological analysis of faecal samples from elephants of various age groups and musth were done and a total viable count was determined. Bacterial colonies obtained from elephant faecal samples of various age groups and musth were identified employing 16S rDNA sequencing. Here we evolved a PCR based strategy to amplify partial gene which encodes 16S rRNA was sequenced and the sequence obtained was analyzed by NCBI BLAST to identify these bacterial strains. Stenotrophomonas maltophilia, Lactococcus lactis and Staphylococcus arlettae were the major species of bacteria identified from the samples of captive elephants, of which, Stenotrophomonas maltophilia is an opportunistic pathogen that dominates in all the age groups. Lactococcus lactis is the major bacteria in the fecal samples of four years old elephant (Juvenile) and found to constitute nearly 68%. Fecal samples collected from 25 years old constitute Stenotrophomonas maltophilia as the major bacteria (73%) followed by Lactococcus lactis while 45 years old showed the higher occurrence of Staphylococcus arlettae followed by Lactococcus lactis. Elephant of the very old age group (84 years) showed high diversity in the fecal bacteria with Stenotrophomonas maltophilia dominating in this group (72%). Elephant in musth, a condition characterized by the high level of testosterone, temporal secretion and high gastric acidity was shown the dominance of acidophilic Stenotrophomonas maltophilia in the gut while alkalophilic Lactococcus lactis which was prevalent in other groups was not detected in musth condition.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12088-024-01391-7.},
}
@article {pmid40655373,
year = {2025},
author = {Sabarish, S and Dhanasekaran, D},
title = {Bacterial Community Profile of Bovine Mastitis Infected Dairy Cow Milk by 16S rRNA Amplicon Sequencing.},
journal = {Indian journal of microbiology},
volume = {65},
number = {2},
pages = {1142-1151},
pmid = {40655373},
issn = {0046-8991},
abstract = {UNLABELLED: The prevalence of Bovine mastitis, an important disease of cow, causing huge economic loss in dairy industries, was tested in cows and other types of breeds reared at Salem and Trichirappalli district. It was interesting to note that the country breed cow was free from disease. The presence of mastitis microbes was identified by culture dependent method. Staphylococcus aureus, Staphylococcus agalactiae, Klebsiella sp. and Pseudomonas sp. were the most common bacteria found in mastitis-infected milk. Opportunistic anaerobic bacteria such as Fusobacterium necrophorum and Porphyromonas levii were found in abundance in mastitis milk samples, but not in non-mastitis milk samples. Milk samples from a mastitis-infected Jersey cow and healthy cow as a control cow were utilized to construct V3-V4 sections of 16S rRNA gene profiles, which were compared to bacterial diversity and abundance. A total of 16,000 sequence numbers were acquired from the 16S rRNA dataset, with a cumulative length of base pairs (bp) of 250. About 321 OTUs were created from these readings. Among these, 190 OTUs are similar in milk from both uninfected healthy and infected Jersey cow. A total of 70 OTUs and 61 OTUs were unique to milk obtained from healthy milk and mastitis infected milk respectively. The hierarchically clustered heat map depicted the overall perspective of the found relationships of bacterial populations among milk samples. The relative abundance of the Ochrobactrum, Pseudomonas and Stenotrophomonas (Kamilari) were associated in the milk. The Shannon index of a healthy cow milk sample was greater (4.136), suggesting the quantity and evenness of the microbial species present. The Simpson index also revealed that during a cow infection, the species richness and evenness declined. Metagenomic analysis can help us better understanding the pathophysiology of bovine mastitis, and it has the potential to be employed as a diagnostic tool as well.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12088-024-01310-w.},
}
@article {pmid40655369,
year = {2025},
author = {Hoda, S and Aggarwal, KK},
title = {Impact of Organophosphates on Diversity and Functional Characteristics of Phyllosphere Bacterial Communities of Solanum melongena.},
journal = {Indian journal of microbiology},
volume = {65},
number = {2},
pages = {1161-1172},
pmid = {40655369},
issn = {0046-8991},
abstract = {UNLABELLED: The phyllosphere harbours a distinctive microbial community that is influenced by plant species, geological locations, and biotic and abiotic environmental factors. Organophosphates represent a significant category of pesticides that are applied to plant surfaces for pest management. Despite substantial research into phyllosphere microorganisms, little is known about the influence of pesticides on the phyllosphere bacterial ecosystem. In the present study, the effect of chlorpyrifos, monocrotophos, and malathion was studied on the phyllosphere bacterial community of Solanum melongena. The plant-inhabitant bacterial population was explored using culturable and high-throughput 16S rRNA gene amplicon sequencing, with and without pesticide application. A total of 165 genera belonging to 14 phyla were observed in the control and 108 genera belonging to 11 phyla in the treated sample. In total, 28 morphologically distinct bacteria were isolated from the abaxial and adaxial surfaces of leaf, and 4 bacteria were found tolerant to pesticides. An increased abundance of Psychrobacter, Janthinobacterium, Sphingomonas, Flavobacterium, and Pedobacter were observed from the pesticide-treated phyllosphere. Overall pesticide impacted the evenness and diversity of the bacterial communities colonizing the S. melongena phyllosphere.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12088-024-01322-6.},
}
@article {pmid40655366,
year = {2025},
author = {Yadav, S and Kapley, A},
title = {Profiling of Pharmaceutical Sludge Microbiome, Resistome and Secondary Metabolites Using Metagenomics.},
journal = {Indian journal of microbiology},
volume = {65},
number = {2},
pages = {1181-1200},
pmid = {40655366},
issn = {0046-8991},
abstract = {UNLABELLED: Antibiotic manufacturing sites act as the hotspot for the dissemination of antibiotic resistance. The present study explores the resistome and secondary metabolites profile associated with the sludge of two pharmaceutical industries located in Delhi and Mysore, India. It confirmed that the pharma sludge contains complex microbiome and resistome. The presence of antibiotic-resistant genes (ARGs), class I integrons, and secondary metabolite genes (NRPs and PKs) was confirmed using PCR. Metagenomic tools like ResFinder 3.2, DeepARG, BusyBee, MG-RAST, and CoMET universe were used to analyze pharmaceutical sludge metagenome. Proteobacteria was found abundant in both metagenomes, followed by firmicutes &amp; bacteriodetes. KEGG analysis predicted the expression of vancomycin, Pandrug, antifolate resistance pathway in both metagenomes. Resfinder predicted the presence of aminoglycoside, macrolide, and sulphonamide resistance genes in both metagenomes. DeepARG analysis classified ARGs in 28 (Arbro) &amp; 27 (Mysore) ARG category and 431 &amp; 368 ARG class. Further, CoMET universe indicated the presence of biosynthetic gene clusters like type II polyketide biosynthesis, Nonribosomal polypeptide biosynthesis, vancomycin &amp; tetracycline, and macrolide biosynthesis. The present study provides primary insight about the diversity of secondary metabolites clusters present in pharmaceutical sludge. Microbes residing in such environment grows under higher selection pressure and produce various secondary metabolites. These metabolites could be exploited for the discovery of novel metabolites with antimicrobial potential and combating AMR. In future, the author aims to clone metagenome in expression vector (BAC/YAC vectors) for the discovery of novel secondary metabolites.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12088-024-01349-9.},
}
@article {pmid40655336,
year = {2025},
author = {Yata, VK},
title = {From Bioreactors to Organoids: Tools for Culturing and Understanding Microbiota.},
journal = {Indian journal of microbiology},
volume = {65},
number = {2},
pages = {623-644},
pmid = {40655336},
issn = {0046-8991},
abstract = {Emerging evidence on the role of gut microbiota on human health necessitated the investigations on gut microbial composition and functions. The diet, drug and disease are the major factors that influence the gut microbial composition and subsequent changes in gut physiology. The consequences of external factors on gut microbiota leads to immunological and neurological disorders. The in vivo studies and animal models are associated with difficulties such as surgical procedures, differences in animal and human tissue responses and ethical issues. Microbiota culture outside the in vivo systems provides mechanistic insights on the effect of external factors on gut microbiota function. In order to provide more information on gut microbiota, researchers have developed intestinal gut models that allow the culture of microbiota under controlled conditions. The multistage, dynamic in vitro fermenters have been developed to simulate the stomach, intestine and colon conditions to culture microbiota. The co-culture of host and microbiome is difficult in in vitro models due to differences in the culture media and oxygen requirements for both the cultures. Microfluidics based gut on chip models demonstrated co-culture of host and microbiota in separate channels connected by semipermeable membranes. Host-microbiota interactions play an important role in deciphering the mechanisms of microbiota related human diseases. The ex-vivo systems show more resemblance to the host signaling as these systems use the individual's explants or host tissues. This review discusses the design considerations, pros and cons of the existing in vitro, microfluidic and ex-vivo intestinal microbiota culture models. The collective information provided in this review would be helpful to design novel in vitro microbiota culture models or methods.},
}
@article {pmid40654961,
year = {2025},
author = {Medeiros, MJ and Schoville, S and Price, D and Yew, JY},
title = {Abiotic factors are the primary determinants of endemic Hawaiian Drosophila microbiome assembly.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.05.06.652154},
pmid = {40654961},
issn = {2692-8205},
abstract = {The Hawaiian Drosophila radiation exemplifies rapid adaptation and species diversification. Many factors have been attributed to these phenomena, including allopatry, sexual selection, and ecological specialization. In recent years, the microbiome has come to the forefront as an important driver of adaptation that is capable of facilitating host survivorship, enhancing resilience to local environmental challenges, and enabling the use of different dietary resources. To determine how microbial communities assemble in natural populations and potentially contribute to the rapid adaptation of Hawaiian drosophilids, we conducted a survey of bacterial and fungal communities from over 500 wild flies collected from across six islands of the Hawaiian archipelago. These samples represent a breadth of host plant specializations, habitats, lifestyles, and endemicity. Our findings reveal that microbiome assembly is largely driven by abiotic factors including elevation, temperature, rainfall, and evapotranspiration, but is not strongly constrained by phylogenetic relatedness. Identical species inhabiting two separate locations exhibited different microbiomes. By contrast, distantly related species inhabiting the same site had more similar microbiomes. The microbiomes of native species also differ from recently introduced, non-native Drosophila in terms of diversity, composition, and function. Given the myriad roles of the microbiome in nutrition, reproduction, and mate choice, these results support a role for the microbiome in the remarkable ecological divergence of Hawaiian Drosophila .},
}
@article {pmid40654884,
year = {2025},
author = {Wirbel, J and Hickey, AS and Chang, D and Enright, NJ and Dvorak, M and Chanin, RB and Schmidtke, DT and Bhatt, AS},
title = {Discovering Broader Host Ranges and an IS-bound Prophage Class Through Long-Read Metagenomics.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.05.09.652943},
pmid = {40654884},
issn = {2692-8205},
abstract = {Gut bacteriophages profoundly impact microbial ecology and human health, yet they are greatly understudied. Using deep, long-read bulk metagenomic sequencing, a technique that overcomes fundamental limitations of short-read approaches, we tracked prophage integration dynamics in 12 longitudinal stool samples from six healthy individuals, spanning a two-year timescale. While most prophages remain stably integrated into their host over two years, we discover that ∼5% of phages are dynamically gained or lost from persistent bacterial hosts. Within the same sample, we find evidence of population heterogeneity in which identical bacterial hosts with and without a given integrated prophage coexist simultaneously. Furthermore, we demonstrate that phage induction, when detected, occurs predominantly at low levels (1-3x coverage compared to the host region). Interestingly, we identify multiple instances of integration of the same phage into bacteria of different taxonomic families, challenging the dogma that phage are specific to a host of a given species or strain. Lastly, we describe a new class of phages, which we name "IScream phages". These phages co-opt bacterial IS30 transposases to mediate their integration, representing a previously unrecognized form of phage domestication of selfish bacterial elements. Taken together, these findings illuminate fundamental aspects of phage-bacterial dynamics in the human gut microbiome and expand our understanding of the evolutionary mechanisms that drive horizontal gene transfer and microbial genome plasticity in this ecosystem.},
}
@article {pmid40654877,
year = {2025},
author = {Graversen, KB and Bjarnov-Nicolau, B and Kløve, S and Halajová, K and Andersen, SB},
title = {Neonatal infection with Helicobacter pylori affects stomach and colon microbiome composition and gene expression in mice.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.04.30.650706},
pmid = {40654877},
issn = {2692-8205},
abstract = {The stomach bacterium Helicobacter pylori is estimated to infect half of the world's population, and the health implications are affected by the age at infection. Neonatal H. pylori infection of mice is a relevant model to investigate metabolic and immunological effects. We performed an explorative study at the dynamic first month of life, to compare the composition of the gastrointestinal tract microbiome and stomach gene expression of mice neonatally infected with H. pylori with that of uninfected mice. We found that H. pylori was present only in the stomach, and that H. pylori loads increase with age from one week after infection and onwards, especially after weaning. Stomach and colon microbiome composition was strikingly similar between sites at the same sampling time, but changed significantly over one week, with increased diversity at both sites. Despite that the relative abundance of H. pylori in the stomach was low and never exceeded 3%, the composition and alpha diversity of the gastrointestinal microbiome was significantly affected by infection. In a pathway enrichment analysis we found that stomach gene expression related to the extracellular matrix, muscle contraction, and metabolism was affected by infection. Expression of these key processes was, in infected mice, shifted away from that of control mice, towards that of all mice sampled the subsequent week, which we speculate represents accelerated development in infected mice.},
}
@article {pmid40654848,
year = {2025},
author = {Fuentes, JJ and Singh, S and Pudlo, NA and Heaver, SL and Ley, RE and Martens, EC},
title = {Carbohydrates and the oxidative branch of the pentose phosphate pathway modify Bacteroides thetaiotaomicron phage resistance by phase variable S-layers.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.05.01.651756},
pmid = {40654848},
issn = {2692-8205},
abstract = {UNLABELLED: The human gut microbiota consists of hundreds of bacterial species, some of which persist in the presence of lytic phage that infect them. Bacteroides employ numerous phase-variable strategies to survive in the presence of phage, including capsular polysaccharides (CPS) and S-layer lipoproteins. We previously reported that a Bacteroides thetaiotaomicron strain lacking CPS exhibits almost complete resistance to multiple phages when forced to express the S-layer protein BT1927. However, this strain was only resistant after certain growth conditions, suggesting nutritional variables alter infection and resistance. We grew this strain on various simple sugars and polysaccharides finding that some substrates (fructose, glucose) promote strong resistance to a single phage (ARB25) while others like N -acetylgalactosamine (GalNAC) and mucin O -glycans increase susceptibility. Mixing fructose and GalNAc indicates the effects of GalNAc are dominant. Despite increasing ARB25 susceptibility, GalNAc did not reduce BT1927 transcript or protein levels. Instead, GalNAc reduced the amount of BT1927 displayed on the cell surface and increased outer membrane vesiculation. Mutants in any of the 3 steps of the oxidative branch of the pentose phosphate pathway-grown in fructose-behaved similarly to wild-type cells grown in GalNAc, illuminating this pathway in regulation of sugar-mediated phage-resistance. Despite promoting strong resistance, cells grown in glucose/fructose sometimes displayed sub-populations that appeared to completely lack surface BT1927, suggesting another checkpoint exists to control whether this phage defense is deployed. Finally, we show the mucin sugar GalNAc increases susceptibility to several other phage, which has implications for B. thetaiotaiomicron persistence in niches like the mucus layer.<br><br>IMPORTANCE: The persistence of viruses that infect bacteria (bacteriophages or phages) in the human gut microbiome and their effects on bacterial physiology and host health are active areas of investigation. Our study investigates how various sugars and polysaccharides alter phage susceptibility and resistance in the model gut symbiont Bacteroides thetaiotaomicron to lytic phages that are capable of infecting it. Our finding that the mucin sugar, N -acetylgalactosamine, and mucin O -glycans that contain this sugar reduce B. thetaiotaomicron resistance to multiple phages has implications for how this symbiont persists in different gut microhabitats, such as the mucus layer, and which defense mechanisms it can deploy to survive in these niches.},
}
@article {pmid40654794,
year = {2025},
author = {Newman, KL and Standke, AK and James, G and Vendrov, KC and Inohara, N and Bergin, IL and Higgins, PDR and Rao, K and Young, VB and Kamada, N},
title = {Miniature bioreactor arrays for modeling functional and structural dysbiosis in inflammatory bowel disease.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.05.09.653173},
pmid = {40654794},
issn = {2692-8205},
abstract = {Alterations in the gut microbiota, known as gut dysbiosis, are associated with inflammatory bowel disease (IBD). There is a need for model systems that can recapitulate the IBD gut microbiome to better understand the mechanistic impact of differences in microbiota composition and its functional consequences in a controlled laboratory setting. To this end, we introduced fecal samples from patients with Crohn's disease (CD) and ulcerative colitis (UC), as well as from healthy control subjects, to miniature bioreactor arrays (MBRAs) and analyzed the microbial communities over time. We then performed two functional assessments. First, we evaluated the colitogenic potential of the CD microbiotas in genetically susceptible germ-free IL-10-deficient mice and found that colitogenic capacity was preserved in a bioreactor-cultivated CD microbiota. Second, we tested impaired colonization resistance against Clostridioides difficile in UC microbiotas using the MBRA system and found that UC microbiotas were innately susceptible to C. difficile colonization while healthy microbiotas were resistant, consistent with what is seen clinically. Overall, our results demonstrate that IBD microbiotas perform comparably to healthy donor microbiotas in the MBRA system, successfully recapitulating microbial structure while preserving IBD-specific functional characteristics. These findings establish a foundation for further mechanistic research into the IBD microbiota using MBRAs.},
}
@article {pmid40654784,
year = {2025},
author = {Wanyama, JW and Okyere, L and Duan, L and Gaulke, CA},
title = {Influence of Housing, Sex, and Sampling Location on Taxonomy and Function of Adult Zebrafish Microbiomes.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.05.08.652836},
pmid = {40654784},
issn = {2692-8205},
abstract = {The zebrafish (Danio rerio) has emerged as an important animal model for the study of host-microbiome interactions. However, information on how variation in experimental parameters contribute to microbiome structure and function in adult zebrafish is limited which complicates experimental design, interpretation of results, and may reduce reproducibility. Here we quantified the impact of two potential sources of microbiome variation - housing strategy and sampling location - on microbial diversity of adult zebrafish using 16S rRNA amplicon sequencing. Our findings indicate that housing strategy significantly impacts gut microbiome diversity in adult fish with the highest similarity between individuals co-housed on recirculating water systems. Microbiome acclimation after housing transfer took between 14- and 21-days. Significant variation in microbiome composition was also observed across sampling sites. As in humans, fecal and intestinal microbial communities were similar and varied by sex, however each body site sampled possessed a small site-specific microbial community signature. Consistently, imputed function of these communities showed that gene family diversity is also predicted to vary by body site particularly between gut and non-gut locations. Together our work demonstrates that housing, sex, and sampling strategy all significantly impact microbial community composition and highlight the need for community wide discussions on best practices and reporting standards for adult zebrafish microbiome studies.},
}
@article {pmid40654714,
year = {2025},
author = {Carmichael, MM and Valls, RA and Soucy, S and Sanville, J and Madan, J and Surve, SV and Sundrud, MS and O'Toole, GA},
title = {Profiling Bile Acids in the Stools of Humans and Animal Models of Cystic Fibrosis.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.05.08.651222},
pmid = {40654714},
issn = {2692-8205},
abstract = {UNLABELLED: Cystic fibrosis (CF) is associated with dysbiosis of the gut microbiome, alterations in intestinal mucus production, aberrant bile acid (BA) metabolism, fat malabsorption, and chronic inflammation. As little is known about BAs in CF, we performed both comprehensive and targeted BA profiling in stool of children with or without CF. Our results reveal that select BA species and metabolites are significantly different between children with CF (cwCF) and healthy controls. There is also a trend towards higher primary cBA and total BA levels for cwCF. Matched bacterial metagenomic analyses showed no change in alpha-diversity between groups in our small cohort, at odds with previous studies, whereas changes in relative abundance of Bacteroides (lower) and E. coli (increased) species is consistent with prior reports. A robust trend was noted toward reduced abundance of bsh gene families (Wilcox test, p = 0.052), a key rate-limiting enzyme required for bacterial synthesis of secondary BAs, in cwCF. Modest changes in both BAs and microbial BA metabolism-related gene abundances may be attributable to small sample sizes, but also suggest likely combination defects in both host and microbial BA metabolic pathways in cwCF. Importantly, although fecal BA profiles from both ferret and mouse CF models showed significant differences from human BA profiles, only the ferret model reproduced significant differences between CF and nonCF animals, highlighting ferrets as a potentially more appropriate model for studying BA in stool in the context of CF. Together, these results provide new insights into CF-related BA dysmetabolism in cwCF, and highlight limitations of CF animal models for BA functional studies.<br><br>IMPORTANCE: Changes in the abundance and/or composition of intestinal bile acids (BAs) may contribute to dysbiosis and altered gastrointestinal physiology in CF. Here, we report shifts in select fecal BA classes and species for children with CF (cwCF). Matched metagenomic analysis suggest possible defects in both host intestinal BA absorption and gut microbial BA metabolism. Additional analyses of mouse and ferret CF stool for BA composition suggest great care must be taken when interpreting BA functional studies using these animal models. Together, this work lays technical and conceptual foundations for interrogating BA-microbe interactions in cwCF.},
}
@article {pmid40654689,
year = {2025},
author = {Zhang, J and Thomas Backet, RV and Sekela, JJ and Zeller, MJ and Sellers, RS and Redinbo, MR and Gulati, AS and Bhatt, AP},
title = {Commercially Purchased and In-House Bred C57BL/6 Mice with Different Gut Microbiota Exhibit Distinct Indomethacin-Induced Toxicities.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.05.01.651704},
pmid = {40654689},
issn = {2692-8205},
abstract = {Non-steroidal anti-inflammatory drug (NSAID)-induced toxicities are a significant clinical problem, yet the factors influencing these outcomes remain incompletely understood. Here, we investigated the impact of mouse vendor on indomethacin-induced injury using C57BL/6 mice from different breeding facilities (in-house "Tar Heel" and commercial Charles River). We found that Tar Heel mice exhibited significantly enhanced susceptibility to indomethacin toxicity, characterized by greater body weight loss, increased ileal ulceration, elevated fecal lipocalin-2 levels, and higher goblet cell numbers in ileum compared to Charles River mice. Importantly, whole genome metagenomic analysis revealed distinct baseline gut microbiomes between the two types of mice. Notably, Tar Heel mice showed higher abundances of β-glucuronidase (GUS)-producing bacteria, particularly those expressing Loop-1 GUS enzymes, and elevated levels of mucolytic enzyme-encoding bacteria. These differences suggest that enhanced indomethacin toxicity observed in Tar Heel mice may be related to functional changes in their gut microbiome, which may predispose to an exaggerated response to NSAID exposure. Together, our findings demonstrate that vendor-specific differences significantly influence NSAID-induced intestinal toxicity and highlight the importance of considering mouse sources and gut microbial compositions in experimental design. Moreover, we highlight potential functional roles that gut microbes play in host-indomethacin interactions.},
}
@article {pmid40654602,
year = {2025},
author = {Cole, CG and Zhang, ZJ and Dommaraju, SR and Dong, Q and Pope, RL and Son, SS and McSpadden, EJ and Woodson, CK and Lin, H and Dylla, NP and Sidebottom, AM and Sundararajan, A and Mitchell, DA and Pamer, EG},
title = {Lantibiotic-producing bacteria impact microbiome resilience and colonization resistance.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.05.06.652565},
pmid = {40654602},
issn = {2692-8205},
abstract = {A subset of commensal bacterial strains secrete bacteriocins, such as lantibiotics, to establish and protect their niche in the gut. Because the antimicrobial spectrum of lantibiotics includes opportunistic pathogens, such as vancomycin-resistant Enterococcus faecium (VRE), they may provide an approach to reduce antibiotic-resistant infections. The impact of lantibiotic-producing bacteria on the complex microbial populations constituting the microbiome, however, remains poorly defined. We find that genes encoding lanthipeptides, including lantibiotics, are commonly present in the microbiomes of healthy humans and in dysbiotic microbiomes of hospitalized patients. In fecal samples collected from hospitalized patients, bacterial species encoding lantibiotic genes are present in greater abundance than lantibiotic-deficient strains of the same species. We demonstrate that the lantibiotic-producing bacterium, Blautia pseudococcoides SCSK, prevents intestinal recolonization of mice by a wide range of commensal species following antibiotic-induced dysbiosis and markedly reduces fecal concentrations of microbiota-derived metabolites associated with mucosal immune defenses. Lantibiotic-mediated dysbiosis results in sustained loss of colonization resistance against Klebsiella pneumoniae and Clostrioides difficile infection. Our findings reveal the potential impact of lantibiotic-producing bacterial species on microbiome resilience and susceptibility to infection following antibiotic treatment.},
}
@article {pmid40654575,
year = {2025},
author = {Du, Y and Fan, C and Song, X and Teng, C and Zhang, Z and Zhang, J and Zhao, T and Xin, T},
title = {Gut microbiota and metabolite features in NSCLC nude mouse models of subcutaneous tumor and leptomeningeal metastasis: a microbiome-metabolome combined analysis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1616695},
pmid = {40654575},
issn = {2235-2988},
mesh = {Animals ; *Gastrointestinal Microbiome ; Mice ; *Metabolome ; Disease Models, Animal ; *Lung Neoplasms/pathology/microbiology/metabolism ; RNA, Ribosomal, 16S/genetics ; *Carcinoma, Non-Small-Cell Lung/pathology/microbiology/metabolism ; Mice, Nude ; Feces/microbiology ; Chromatography, Liquid ; *Meningeal Neoplasms/secondary ; Metabolomics ; Female ; Humans ; },
abstract = {BACKGROUND: The incidence and mortality rates of lung cancer are both elevated. In lung cancer, leptomeningeal metastasis (LM) is a serious consequence. Patients suffering from LM have severe symptoms and a short survival time. Numerous studies have shown a connection between the prognosis of lung cancer and the composition of the gut microbiota. However, Current knowledge regarding the gut microbiota and metabolites in lung cancer patients with LM, as well as their potential impacts on LM pathogenesis, remains remarkably limited.<br><br>METHOD: We established a mouse model of LM from lung cancer and a subcutaneous metastatic model, using wild-type mice as controls. Each of the three groups above contained six mice. We examined the fecal microbiota and metabolites of three groups of mice utilizing 16S rRNA gene sequencing and liquid chromatography-mass spectrometry (LC-MS) technologies. Conducting correlation analysis on microbiome and metabolome data concurrently to identify significant relationships.<br><br>RESULT: Mice with LM had a different gut microbiota and metabolite composition than wild-type and subcutaneous metastatic mice; the LM group had a higher ratio of Firmicutes to Bacteroidetes. Differential metabolites are primarily seen in pathways such as Nicotinate and nicotinamide metabolism, Tryptophan metabolism; Association analysis reveals that some changes in gut microbiota are linked to metabolites, such as a positive association between Eubacteria and N-Acetylsorotonin.<br><br>CONCLUSION: Some microbiota and metabolites may act as biomarkers for LM, controlling gut microbiota and metabolites or giving a novel option for research into lung cancer leptomeningeal metastases.},
}
@article {pmid40654462,
year = {2025},
author = {Yu, JJ and Hernandez-Kapila, Y and Wang, CW},
title = {Probiotics to reduce microbiota-related dental stains: A potential approach.},
journal = {Journal of dental sciences},
volume = {20},
number = {3},
pages = {1890-1893},
pmid = {40654462},
issn = {2213-8862},
abstract = {Adult extrinsic black stains on teeth, caused by bacterial colonization, impact aesthetics and confidence. Conventional treatments can be abrasive and have a high recurrence rate. This pilot case study explores probiotics as an adjunctive approach. Direct application of probiotic powder over the black stains of the teeth was carried out prior to routine home care. Results showed black stain removal was possible with tooth brush and dental floss. Saliva and biofilm samples were analyzed via 16S rRNA sequencing. Microbiome revealed a noticeable reduction in Corynebacterium, a key black stain-associated bacterium, with slight shifts in major phyla like Actinobacteriota and Firmicutes. This case study aimed to evaluate the potential of probiotics in reducing black stains on teeth and assess the associated microbiome changes.},
}
@article {pmid40654456,
year = {2025},
author = {Wen, CC and Lin, JCY and Salamanca, E and Teng, NC and Lin, YJ and Wu, YF and Chang, HM and Chang, WJ},
title = {Full-length 16S rRNA sequencing reveals microbial characteristics in supragingival plaque of periodontitis patients.},
journal = {Journal of dental sciences},
volume = {20},
number = {3},
pages = {1739-1748},
pmid = {40654456},
issn = {2213-8862},
abstract = {BACKGROUND/PURPOSE: Periodontitis is a chronic inflammatory disease that disrupts oral microbial homeostasis and contributes to systemic inflammation. While previous studies have focused on subgingival microbiota, the role of supragingival plaque as an early microbial reservoir remains underexplored. Most previous studies have relied on short-read 16S rRNA sequencing but limited detailed classification. This study uses Third-Generation Sequencing (TGS) with full-length 16S rRNA sequencing and DADA2-based error correction to better characterize the supragingival microbiome in periodontitis.<br><br>MATERIALS AND METHODS: A total of 30 participants (15 periodontitis patients and 15 healthy controls) were recruited. Supragingival plaque samples were collected, and full-length 16S rRNA sequencing was performed using a TGS platform. Sequencing data were processed with DADA2 for error correction and taxonomic classification using the Human Oral Microbiome Database (HOMD), including diversity indices and Principal Component Analysis (PCA), which were conducted to compare microbial compositions between groups.<br><br>RESULTS: The periodontitis group exhibited significantly higher microbial diversity (P < 0.05) and enrichment of key periodontal pathogens, including Porphyromonas, Prevotella, Fusobacterium, and Treponema. On the other hand, commensal bacteria such as Streptococcus and Neisseria were more abundant in the healthy group. PCA demonstrated distinct clustering patterns, indicating supragingival microbial shifts associated with disease progression.<br><br>CONCLUSION: This study provides the high-resolution microbial profiling of supragingival plaque in periodontitis using full-length 16S rRNA sequencing. The findings suggest that supragingival plaque may serve as an early-stage reservoir for periodontal pathogens, which leads to subgingival colonization and disease progression. It highlights the potential of microbial biomarkers in early diagnosis and suggests that targeted microbiome-based therapies could be developed to restore microbial balance in periodontal disease. This method offers greater precision in bacterial identification and future translational potential for personalized periodontal care.},
}
@article {pmid40654436,
year = {2025},
author = {Xu, X and He, L and Huo, P and Jin, D and Zhu, Y and Lu, H and Meng, H},
title = {Potential short-term shift in oral microbiota of patients with stage III-IV periodontitis and type 2 diabetes treated by non-surgical periodontal therapy.},
journal = {Journal of dental sciences},
volume = {20},
number = {3},
pages = {1470-1479},
pmid = {40654436},
issn = {2213-8862},
abstract = {BACKGROUND/PURPOSE: Adjunctive use of systemic antibiotics has more clinical improvement than scaling and root planing alone in stage III-IV periodontitis patients with type 2 diabetes mellitus (T2DM). There is still no study that concentrate on dynamic changes in oral microbiota by high throughput sequencing technique with the treatment regimen including adjunctive antibiotics.<br><br>MATERIALS AND METHODS: Thirty-two periodontitis patients with T2DM who received non-surgical periodontal treatment (NSPT) in the previously published randomized trial were selected for microbiological analysis. Seventeen subjects in the test group received scaling and root planing (SRP) and antibiotics (500 mg of amoxicillin [AMX], and 200 mg of metronidazole [MTZ], three times daily for seven days). Fifteen subjects in the control group received SRP only. Examination of periodontal and hematological parameters, cytokines in serum and gingival crevicular fluid, and collection of subgingival plaque was taken at baseline and three months after treatment. The V3-V4 region of 16S DNA was sequenced, and taxonomic assignment was based on the Human Oral Microbiome database.<br><br>RESULTS: Both the test and the control group showed lower richness and diversity for subgingival microbiota after treatment. The distribution of subgingival microbial composition was different between the baseline and 3 months in both groups. The subgingival microbial dysbiosis index decreased significantly in both groups at 3 months, and 8 out of 12 dysbiotic discriminatory genera decreased significantly in the test group. The relative abundance of the red complex, Porphyromonas gingivalis and T. forsythus decreased more in the test group than that in the control group. The decrease of clinical periodontal parameters was positively correlated with the decline of Treponema, Porphyromonas, Capnocytophaga and PeptostreptococcaceaeXIG-6, and negatively correlated with the increase of Neisseria and Pseudomonas. HbA1c level decrease was positively related to the changes of Leptotrichia, Veillonella, Saccharibacteria TM7 G-5 and Actinomyces.<br><br>CONCLUSION: NSPT could significantly change the oral microbiome towards healthy status in patients with stage III-IV periodontitis and diabetes. AMX + MTZ had more advantages in the decrease of periodontal pathogens. Periodontists should cautiously use the antibiotics to treat such patients.},
}
@article {pmid40654342,
year = {2025},
author = {Madamanchi, K and Zhang, J and Melkani, GC},
title = {Linkage of circadian rhythm disruptions with Alzheimer's disease and therapeutic interventions.},
journal = {Acta pharmaceutica Sinica. B},
volume = {15},
number = {6},
pages = {2945-2965},
pmid = {40654342},
issn = {2211-3835},
abstract = {Alzheimer's disease (AD) is a progressive neurodegenerative disorder characterized by cognitive decline and pathological brain changes. While aging is the primary risk factor, circadian rhythm disruption (CRD) is increasingly recognized as a central driver of AD pathology. CRD exacerbates oxidative stress, systemic inflammation, and gut microbiome dysbiosis, impairing sleep-wake cycles, disrupting metabolic homeostasis, and promoting neuroinflammation, ultimately accelerating disease progression. Oxidative stress, a key factor in neuronal damage, is both a cause and consequence of circadian misalignment, while mitochondrial dysfunction further amplifies oxidative damage, impairing synaptic function and cognitive stability. Additionally, gut microbiome dysbiosis contributes to neuroinflammatory processes, worsening neurodegeneration. Given these complex interactions, this review aims to elucidate the role of CRD in AD pathology and explore potential therapeutic interventions targeting circadian dysfunction. Specifically, it examines the efficacy of time-restricted feeding (TRF), a dietary strategy that aligns food intake with circadian rhythms. TRF has shown promise in restoring circadian function, reducing oxidative stress, improving mitochondrial health, and promoting gut microbiome diversity. By addressing CRD, TRF may offer a novel approach to mitigating AD pathologies. This review also identifies current research gaps and future directions for developing circadian-based interventions in AD prevention and treatment.},
}
@article {pmid40654338,
year = {2025},
author = {Rakib, A and Mamun, MAA and Mandal, M and Sinha, P and Singh, UP},
title = {Obesity-cancer axis crosstalk: Molecular insights and therapeutic approaches.},
journal = {Acta pharmaceutica Sinica. B},
volume = {15},
number = {6},
pages = {2930-2944},
pmid = {40654338},
issn = {2211-3835},
abstract = {Now recognized as a global health crisis, obesity has been linked to an increased risk of many types of cancer, including those of the breast, colon, rectum, uterus, gallbladder, and ovary. Obesity and cancer share several characteristics at the cellular, molecular, and epigenetic levels. Obesity is characterized by chronic inflammation of the adipose tissue (AT), resulting in genotoxic stress that further induces metabolic complications and contributes to the initiation and progression of cancer. The excessive accumulation of AT provides adipokines and lipids to engage tumor cells with stromal and immune cells to infiltrate carcinomas and secrete a plethora of cytokines, chemokines, and growth factors within the tumor microenvironment (TME) that contribute to carcinogenesis. Obesity also alters the metabolic reprogramming of immune cells, including macrophages, neutrophils, and T cells, thereby providing a suitable environment for the growth and progression of cancer. Obesity-associated metabolic dysregulation also perturbs the gut microbiome, which produces metabolites that can further increase the risk of cancer progression. This review will discuss links between obesity and cancer progression, including several crucial pathways that bridge the crosstalk between obesity-associated changes in AT inflammation, immune cells, adipokines, chemokines, and tumor cells to support cancer progression. We will also discuss our insights into the mechanisms by which obesity-driven factors influence metabolic reprogramming and touch base on how obesity mediates microbiome dysbiosis to alter metabolite and affect cancer progression. Altogether, this review highlights the crossroads of the obesity-cancer axis, describes its salient features, and presents possible therapeutic approaches for obesity-related cancers.},
}
@article {pmid40654331,
year = {2025},
author = {Schumacher, SM and Doyle, WJ and Hill, K and Ochoa-Repáraz, J},
title = {PICRUSt2 Analysis of Fecal Microbiome Associated With a Murine Model of Multiple Sclerosis.},
journal = {FASEB bioAdvances},
volume = {7},
number = {7},
pages = {e70029},
pmid = {40654331},
issn = {2573-9832},
abstract = {Multiple sclerosis (MS) is a debilitating neuroinflammatory disease of the central nervous system (CNS). Approximately 2-3 million people globally are believed to have MS. There is growing interest in the mechanistic link between MS and gut microbiome composition. Experimental autoimmune encephalomyelitis (EAE) is a murine model of inflammatory demyelination of the CNS commonly used to investigate the pathology of MS in relation to the microbiome. Previous research has shown that EAE affects the gut microbiome, and the improvement of EAE can promote microbiome homeostasis. Microbiome homeostasis is crucial for host health, as it contributes to immune regulation and produces bioavailable metabolic products in the digestive tract. Several factors, including diet, genetics, and environment, influence microbiome homeostasis apart from disease state. Our lab previously demonstrated that mice of the same genetic line, sourced from different manufacturers, exhibit differences in microbiome composition despite being housed under similar conditions. Furthermore, these mice showed variations in EAE progression and severity, indicating that differences in the microbiome may contribute to the discrepancies in EAE. Here, we employ PICRUSt2 to estimate functional differences in the microbiomes of EAE mice from various sources at key time points during the EAE disease course. The reanalysis of our microbiome data reveals distinct differences in predicted gene expression of microbiomes that are disproportionately related to the metabolism of amino acids, carbohydrates, lipids, and other metabolites. Our findings support previous observations regarding microbiome alterations in the context of EAE and suggest that evaluating microbiome dynamics would benefit from both taxonomic assessment and metabolic activity, allowing for more effective and comprehensive research strategies.},
}
@article {pmid40654283,
year = {2025},
author = {Chai, Y and Li, M and Deng, X and Ma, C and Zhou, N and Chen, Y and Yao, Y and Li, K and Gong, W and Lei, H},
title = {Gut microbiota and tuberculosis infection: interaction and therapeutic potential.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2531201},
doi = {10.1080/19490976.2025.2531201},
pmid = {40654283},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome ; Mycobacterium tuberculosis/physiology ; *Tuberculosis, Pulmonary/microbiology/immunology/therapy ; Lung/microbiology/immunology ; Animals ; },
abstract = {Pulmonary tuberculosis (PTB), caused by Mycobacterium tuberculosis (MTB), is a serious chronic infectious disease. Although significant progress has been made in the prevention and treatment of MTB, current anti-tuberculosis therapies still face numerous challenges. The human gut microbiota, a complex ecosystem, plays a role in host metabolism, immune regulation, and health maintenance. Recent studies have increasingly highlighted a close relationship between gut microbiota and PTB. The gut microbiota, through the gut-lung axis, mediates the immune processes of PTB, while MTB infection can disrupt the ecological balance of the gut microbiome. This review aims to summarize the changes in gut microbiota among PTB patients and their relationship with clinical manifestations, explore the role of gut microbiota in PTB immunity, and further analyze the potential application of gut microbiota therapy in PTB treatment. The goal is to provide clear direction for future research on gut microbiota and lung diseases and propose new strategies for MTB treatment.},
}
@article {pmid40653861,
year = {2025},
author = {Li, B and Tang, Y and Huang, Z and Ma, L and Song, J and Xue, L},
title = {Synergistic innovation in organ-on-a-chip and organoid technologies: Reshaping the future of disease modeling, drug development and precision medicine.},
journal = {Protein &amp; cell},
volume = {},
number = {},
pages = {},
doi = {10.1093/procel/pwaf058},
pmid = {40653861},
issn = {1674-8018},
abstract = {FDA issued guidance on April 10th, 2025 to phase out animal trials in favor of organoids and organ-on-a-chip systems. This pivotal move was swiftly followed by National Institutes of Health (NIH) on April 29th, when it inaugurated the Office of Research Innovation, Validation, and Application (ORIVA). The establishment of ORIVA aims to spearhead the advancement of human-centric organ-on-a-chip technologies, marking a major stride toward more accurate, ethical, and efficient research methods in the biomedical field. Compared to traditional 2D cell cultures and animal models, organ-on-a-chip systems enable precise control of hydrodynamic parameters and biomechanical microenvironments. This review systematically elaborates on applications of single-organ, multi-organ, and organoid-on-a-chip technologies in modeling complex diseases, host-microbiome interactions, inter-organ physiological networks, and quantitative prediction of pharmacokinetics, toxicity responses, and personalized therapies. Furthermore, the core challenges in translating these technologies to pharmaceutical development and clinical practice are critically analyzed. With interdisciplinary integration of materials engineering, biosensing, and artificial intelligence, organ-on-a-chip technologies are transcending the limitations of conventional preclinical research. Their strategic value as 'patient surrogates' is poised to accelerate breakthroughs in precision medicine and rare disease treatments.},
}
@article {pmid40653681,
year = {2025},
author = {Cheng, Y and Yan, DM and Wu, ZE and Zhu, WF and Li, F},
title = {Integrated Metabolomics and Gut Microbiome Analysis Reveal the Role of Demethylzeylasteral in Alleviating Ulcerative Colitis in Mice.},
journal = {Journal of proteome research},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jproteome.5c00035},
pmid = {40653681},
issn = {1535-3907},
abstract = {Demethylzeylasteral (DMLL) is a natural compound isolated from the root of the herbal plant Tripterygium wilfordii Hook. F. It exhibits various pharmacological activities, yet the therapeutic effects against ulcerative colitis (UC) remain poorly understood. In this study, multiomics analysis revealed that DMLL alleviated DSS-induced experimental colitis by reconstructing gut microbiota and improving metabolic dysbiosis. The Bacteroidota phylum and genera of norank_f_Muribaculaceae and Ruminococcus with beneficial potential for UC were the major gut flora influenced by DMLL treatment. In terms of microbiota-derived metabolites, DMLL primarily enriched tryptophan metabolites, secondary bile acids, and nicotinamide. These compounds possess anti-inflammatory activity and protective effects for intestinal epithelial barrier, subsequently altered metabolic pathways, and improved impaired host gut homeostasis. In addition, we found significantly elevated levels of indolelactic acid (ILA) in the cecum of colitis mice and showed a strong positive correlation with UC symptoms, whereas serum levels of ILA were remarkably reduced and exhibited a negative association with UC, suggesting its dual role in colitis. Importantly, DMLL treatment effectively restored ILA levels in both the cecum and the systemic circulation. These findings provide novel mechanistic insights into the anticolitis effect of DMLL in mice, highlighting the crucial role of gut microbiota in its therapeutic action.},
}
@article {pmid40653476,
year = {2025},
author = {Bi, BY and Lin, L and Huang, L and Zhou, J and Yan, WJ and Huang, L and Wang, J and Li, XB},
title = {Effects of arabinoxylan on BDNF/TrkB/p-CREB signaling pathway in the prefrontal cortex and intestinal microbiome in post-stroke depressed rats.},
journal = {BMC neuroscience},
volume = {26},
number = {1},
pages = {40},
pmid = {40653476},
issn = {1471-2202},
support = {No. S2018073,No. S2021003//Guangxi Medical and Health Appropriate Technology Development and Promotion Application/ ; No. S2018073,No. S2021003//Guangxi Medical and Health Appropriate Technology Development and Promotion Application/ ; No. S2018073,No. S2021003//Guangxi Medical and Health Appropriate Technology Development and Promotion Application/ ; No. S2018073,No. S2021003//Guangxi Medical and Health Appropriate Technology Development and Promotion Application/ ; No. S2018073,No. S2021003//Guangxi Medical and Health Appropriate Technology Development and Promotion Application/ ; No. S2018073,No. S2021003//Guangxi Medical and Health Appropriate Technology Development and Promotion Application/ ; No. S2018073,No. S2021003//Guangxi Medical and Health Appropriate Technology Development and Promotion Application/ ; No. S2018073,No. S2021003//Guangxi Medical and Health Appropriate Technology Development and Promotion Application/ ; },
mesh = {Animals ; *Prefrontal Cortex/metabolism/drug effects ; *Brain-Derived Neurotrophic Factor/metabolism ; *Gastrointestinal Microbiome/drug effects ; Male ; Signal Transduction/drug effects ; Rats ; Receptor, trkB/metabolism ; *Depression/metabolism/drug therapy/etiology ; *Xylans/pharmacology ; Rats, Sprague-Dawley ; *Stroke/complications/metabolism ; Cyclic AMP Response Element-Binding Protein/metabolism ; },
abstract = {AIM: To explore the effects of arabinoxylan on the BDNF/TrkB/p-CREB signaling pathway in the prefrontal cortex of post-stroke depressed rats, and to explore its neuronal protective effects through the microbial-gut-brain axis in the regulation of this pathway.<br><br>METHODS: The rat model of post-stroke depression (PSD) was established by middle cerebral artery occlusion (MCAO) combined with chronic unpredictable mild stimulation (CUMS). They were randomly divided into 5 groups (blank control, post-stroke depression, arabinoxylan, fluoxetine hydrochloride, fluoxetine hydrochloride combined arabinoxylan). The rats were treated differently for 28 days according to their grouping. Body mass, sugar and water consumption experiments and open-field experiments were used to evaluate the behavior of rats. The pathological changes were observed by H&amp;E staining. The expression levels of amine neurotransmitters were detected by ELISA. The expression levels of BDNF mRNA and BDNF, TrkB and p-CREB were detected by RT-PCR and Western blot. The analysis of intestinal metagenomics was conducted by 16&#xa0;S rDNA sequencing.<br><br>RESULTS: Compared with the post-stroke depression group, the body weight, activity and sugar water consumption rate of the arabinoxylan group were increased. The expression levels of 5-HT in the prefrontal cortex, colon and serum levels of 5-HT, DA and NE were increased. The expression levels of BDNF mRNA and BDNF, TrkB and P-CREB in the prefrontal cortex were also upregulated. The number of neurons in the prefrontal cortex increased; Colon mucosal injury and inflammatory cell infiltration decreased, the intestinal microbial diversity increased; The relative abundance of probiotics such as bifidobacterium, Christensenia, Dubosiella New York and ruminococcus increased. The relative abundance of Prevotella NK3B31 group was reduced. The level of 5-HT in the prefrontal cortex was negatively correlated with the abundance of Prevotellaceae NK3B31 group.<br><br>CONCLUSION: Arabinoxylan improved depressive-like behavior in rats and its neuroprotective role was achieved by promoting the growth of intestinal probiotics, improving the intestinal barrier, affecting the BDNF/TrkB/p-CREB signaling pathway, and increasing the expression levels of monoamine neurotransmitters 5-HT, DA and NE.},
}
@article {pmid40653357,
year = {2025},
author = {Meena, AS and Singh, P and Shukla, PK},
title = {Cancer and microbiome-targeted therapies.},
journal = {International review of cell and molecular biology},
volume = {395},
number = {},
pages = {99-132},
doi = {10.1016/bs.ircmb.2024.12.006},
pmid = {40653357},
issn = {1937-6448},
mesh = {Humans ; *Neoplasms/therapy/microbiology ; *Microbiota/drug effects ; Animals ; Probiotics/therapeutic use ; Tumor Microenvironment ; Fecal Microbiota Transplantation ; },
abstract = {Emerging research highlights the profound interplay between the microbiome and cancer, offering novel avenues for therapeutic interventions. This review explores the burgeoning field of microbiome-targeted therapies in oncology, focusing on how microbial communities influence cancer development, progression, and response to treatment. The microbiome's role in modulating immune responses, drug metabolism, and tumor microenvironment is examined, revealing its potential to both inhibit and promote tumorigenesis. We discuss current strategies that leverage microbiome modulation, including probiotics, prebiotics, and fecal microbiota transplantation, to enhance the efficacy of conventional cancer therapies and mitigate side effects. Additionally, the review addresses the challenges and future directions in integrating microbiome-based approaches into clinical practice. By elucidating the mechanisms through which the microbiome affects cancer and therapy outcomes, this work aims to pave the way for innovative, personalized treatment strategies that harness the power of microbial communities to improve cancer care.},
}
@article {pmid40653356,
year = {2025},
author = {Sarath Krishnan, MP and Goyal, B and Nampui, L and Gupta, SC},
title = {The role of microbiome in gastrointestinal cancer.},
journal = {International review of cell and molecular biology},
volume = {395},
number = {},
pages = {67-98},
doi = {10.1016/bs.ircmb.2024.12.009},
pmid = {40653356},
issn = {1937-6448},
mesh = {Humans ; *Gastrointestinal Neoplasms/microbiology/pathology/therapy ; *Gastrointestinal Microbiome ; Animals ; },
abstract = {The human microbiome consists of the diverse microorganisms with their equally diverse functional abilities that have evolved over millions of years with humans. This microbiome creates a mutually beneficial symbiotic relationship with their host. Through their varied functions, the human gut microbiota is crucial for preserving health and homeostasis. Any imbalance in this microbial population can lead to an array of diseased states, including cancer especially of the gastrointestinal system. The focus of this chapter is to discuss the mechanisms through which the gut microbiome creates a conducive environment for initiation and progression of cancer. In addition, the effect of microbial products such as short chain fatty acids, bile acids and Trimethylamine N-oxide on the formation of gastrointestinal cancer is also discussed. The various experimental methods and new molecular techniques that have facilitated the characterization and study of microorganisms is also discussed. The developments in microbiome research have shed light on the potential role of gut microbiota for novel biomarker discovery and therapeutic interventions in gastrointestinal cancer, like fecal microbiota transplantation. The prospects of these areas for further exploration are discussed.},
}
@article {pmid40653355,
year = {2025},
author = {Murakonda, SP and Balusu, S and Chava, H and Murakonda, AB and Polneedi, R and Bodduluri, S and Gupta, SC and Challagundla, KB},
title = {Influence of gut microbiota on systemic immune responses and cancer immunotherapy.},
journal = {International review of cell and molecular biology},
volume = {395},
number = {},
pages = {23-66},
doi = {10.1016/bs.ircmb.2024.12.005},
pmid = {40653355},
issn = {1937-6448},
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; *Immunotherapy/methods ; *Neoplasms/therapy/immunology/microbiology ; Animals ; *Immunity ; },
abstract = {The gut microbiota is increasingly being recognized as a key player in the onset and progression of several human diseases, including malignancies. Recent research has shed light on the complex relationships between the gut microbiome and the effectiveness of cancer immunotherapy. Gaining a thorough understanding of how the gut microbiota influences immune responses during cancer treatments is critical for medical advancements. This review aims to delve into the intricate interactions between gut microbiota, the systemic immune system, and cancer immunotherapy. Additionally, as the gut microbiota can contribute to immune-related adverse effects, we explored possible interventions to alleviate these side effects and reviewed microbiota-targeted strategies that could enhance the success of cancer immunotherapies.},
}
@article {pmid40653354,
year = {2025},
author = {Gupta, R and Gaur, S},
title = {Effect of diet and lifestyle on microbiome composition.},
journal = {International review of cell and molecular biology},
volume = {395},
number = {},
pages = {157-174},
doi = {10.1016/bs.ircmb.2024.12.008},
pmid = {40653354},
issn = {1937-6448},
mesh = {Humans ; *Life Style ; *Diet ; *Microbiota ; Animals ; },
abstract = {Microbes are major drivers of many important physiological pathways in the human body. A well-adapted and established microbial community at key body sites performs a wide range of functions, including digestive and immunological roles. However, the structure of these microbial communities depends on numerous factors, both genetic and external. Diet and lifestyle are the most common external factors influencing microbiome composition. A healthy diet and lifestyle promote the growth of beneficial microbes, while disturbances in these factors can alter the entire microbial dynamics, potentially leading to pathogenesis. These perturbations can occur at any stage of life, from birth to old age, and may result in serious clinical conditions such as obesity, diabetes, cancers, metabolic syndromes, and many others. Therefore, it is essential to identify the dietary and lifestyle factors that support a healthy microbiome and prevent dysbiosis. This chapter aims to discuss the role of various component of diet and life style that can ultimately shape the human microbiome.},
}
@article {pmid40653353,
year = {2025},
author = {Jain, P and Joshi, N and Sahu, V and Dominic, A and Aggarwal, S},
title = {Autoimmune diseases and microbiome targeted therapies.},
journal = {International review of cell and molecular biology},
volume = {395},
number = {},
pages = {133-156},
doi = {10.1016/bs.ircmb.2024.12.007},
pmid = {40653353},
issn = {1937-6448},
mesh = {Humans ; *Autoimmune Diseases/microbiology/therapy/immunology ; *Gastrointestinal Microbiome/drug effects ; Animals ; },
abstract = {Previously regarded solely as a digestive entity, the human gut has been revealed to harbor a rich diversity of microbial flora, pivotal in maintaining overall health and organ functionality. Contrary to conventional wisdom, certain microbes confer notable benefits rather than posing threats. The gut microbiota, consisting of Firmicutes, Bacteroidetes, Actinobacteria, Proteobacteria, Fusobacteria, and Verrucomicrobia, plays a crucial role in health maintenance, and dysbiosis can precipitate disease onset. Autoimmune disorders stem from immune system dysregulation, resulting in self-cell attacks. Recent microbiome research underscores a correlation between altered gut microbiota and autoimmune diseases. This chapter delves into the impact of the gut microbiome in autoimmune diseases and presents gut microbiome targeting therapy as a possible treatment alternative.},
}
@article {pmid40653352,
year = {2025},
author = {Singh, K and Bhadauriya, AS},
title = {Effect of microbial dysbiosis on autoimmune associated inflammation.},
journal = {International review of cell and molecular biology},
volume = {395},
number = {},
pages = {1-22},
doi = {10.1016/bs.ircmb.2024.12.016},
pmid = {40653352},
issn = {1937-6448},
mesh = {Humans ; *Dysbiosis/complications/microbiology/immunology ; *Autoimmune Diseases/microbiology/immunology ; *Inflammation/microbiology/immunology/complications ; Animals ; *Gastrointestinal Microbiome/immunology ; },
abstract = {Trillions of microorganisms inhabit the human body, playing crucial roles in the development of the immune system, maintaining balance within the gut's immune system, and overall well-being. When these microbial communities experience imbalance, known as dysbiosis, it can lead to localized inflammatory conditions such as colitis and inflammatory bowel diseases, as well as systemic autoimmune disorders like type 1 diabetes, rheumatoid arthritis, and multiple sclerosis. Gut microbes engage with the immune system through various means, including influencing host microRNAs to regulate gene expression and generating metabolites that interact with cellular receptors such as TLRs and GPCRs. These interactions impact critical immune processes like the differentiation of lymphocytes, the production of interleukins, and the maintenance of gut barrier function. Looking into, how gut microbes contribute to or defend against systemic autoimmune diseases is crucial for developing strategies to manage or prevent these conditions. These approaches may include dietary or lifestyle modifications, microbiome-targeted therapies such as prebiotics or probiotics, the identification of diagnostic biomarkers for predicting disease risk, and monitoring and intervening in shifts in microbial populations during autoimmune flare-ups. Recognizing the microbiome's significance in systemic autoimmune diseases offers promise for transforming these presently challenging-to-treat conditions into more controllable or preventable ones.},
}
@article {pmid40653335,
year = {2025},
author = {Kramer, A and Dahl, MB and Bengtsson, MM and Boyce, JM and Heckmann, M and Meister, M and Papke, R and Pittet, D and Reinhard, A and Slevogt, H and Wang, H and Zwicker, P and Urich, T and Seifert, U},
title = {Response to the comment on the article "No detrimental effect on the hand microbiome of health care staff by frequent alcohol-based antisepsis".},
journal = {American journal of infection control},
volume = {53},
number = {8},
pages = {916-917},
doi = {10.1016/j.ajic.2025.04.013},
pmid = {40653335},
issn = {1527-3296},
}
@article {pmid40653334,
year = {2025},
author = {Huda, NU and Javed, R and Ibrahim, H},
title = {Letter to editor: No detrimental effect on the hand microbiome of health care staff by frequent alcohol-based antisepsis.},
journal = {American journal of infection control},
volume = {53},
number = {8},
pages = {915},
doi = {10.1016/j.ajic.2025.04.007},
pmid = {40653334},
issn = {1527-3296},
}
@article {pmid40653216,
year = {2025},
author = {Ren, F and Wu, F and Jie, Y and Wu, X and Gao, L},
title = {Carbon-nitrogen metabolic coupling for optimized protein production of corn stover polysaccharides: From molecular mechanisms to buffalo rumen microbiome.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {145901},
doi = {10.1016/j.ijbiomac.2025.145901},
pmid = {40653216},
issn = {1879-0003},
abstract = {The efficient bioconversion of polysaccharide-rich lignocellulosic agricultural residues into high-value products remains a significant challenge in sustainable agriculture. We investigated the molecular mechanisms of carbon‑nitrogen metabolic coupling during corn stover bioconversion through solid-state fermentation with Trichoderma longibrachiatum. Statistical optimization of fermentation conditions enhanced substrate nutritional value, achieving 17.57 % true protein content (53.45 % increase) and substantial lignocellulose degradation (cellulose 24.89 %, hemicellulose 23.54 %, lignin 22.28 %). Transcriptomic analysis revealed key metabolic coupling mechanisms, with cysteine supplementation significantly enhancing cellulolytic enzyme activities and protein accumulation. The optimized fermented corn stover increased dry matter intake and nutrient digestibility in buffalo feeding trials, while rumen microbiome analysis demonstrated shifts towards beneficial taxa and metabolic pathways. This study reveals the molecular interplay between polysaccharide metabolism and protein synthesis, providing a comprehensive strategy with dual benefits: environmental sustainability through efficient agricultural waste valorization and enhanced animal production through improved feed digestibility and nutrient utilization. This approach simultaneously addresses global food security concerns and environmental challenges associated with agricultural waste management.},
}
@article {pmid40653001,
year = {2025},
author = {Pudipeddi, A and Bijle, MN and Yiu, C},
title = {Effect of arginine-based synbiotics on multispecies biofilm.},
journal = {Journal of dentistry},
volume = {},
number = {},
pages = {105974},
doi = {10.1016/j.jdent.2025.105974},
pmid = {40653001},
issn = {1879-176X},
abstract = {OBJECTIVE: To examine the effect of arginine (Arg)-based synbiotics on multispecies biofilm.<br><br>METHODS: In vitro biofilms (Streptococcus mutans UA159, S. gordonii DL1, S. sanguinis DSS-10) were grown on HA discs under anaerobic conditions (37&#xb0;C, 5% CO&#x2082;, 24 h) and treated with: (1) Arg (0.25%, 0.5% w/v.), (2) Lacticaseibacillus rhamnosus GG (LRG) at 10&#x2077; CFU/mL, or (3) their combinations, 2&#xd7; daily for 3 days. At 96 h, biofilm matrix components (exoproteins, eDNA, and carbohydrates) and microbial viability (confocal microscopy and PMA-qPCR) were quantified. Relative gene expression analysis was also conducted with species-specific genes (gtfB, sagP, arcA, argG, argH).<br><br>RESULTS: For carbohydrates, no significant difference was identified among treatment groups (p>0.05). Protein content for 0.5% Arg+LRG was significantly lower than LRG (p<0.05). The lowest eDNA content was observed in LRG (p<0.05); while eDNA content of 0.5% Arg+LRG, was similar to 0.5% Arg and control (p>0.05). Using confocal imaging, the highest proportion of live cell was found in 0.5% Arg+LRG (p<0.05), followed by 0.25% Arg+LRG, 3-D biofilm imaging demonstrated increased biomass with smoother architecture in biofilms treated with 0.5% Arg+LRG (p<0.05). 0.5% Arg+LRG significantly enhanced growth of commensal streptococci (S. gordonii, S. sanguinis) compared to monotherapies and control, while also reducing viability of S. mutans compared to control (p<0.05). Gene expression analysis revealed downregulation of S. mutans virulence (gtfB) and upregulation of commensal metabolism (sagP, arcA) for 0.5% Arg+LRG (p<0.05).<br><br>CONCLUSION: The 0.5% Arg+LRG synbiotics uniquely integrates ecological modulation by regulating biochemical matrix components, promoting commensal enrichment and suppressing cariogenic pathogens.<br><br>CLINICAL SIGNIFICANCE: A deliverable Arg-LRG synbiotics for caries prevention addresses a global public health priority. This strategy aligns with microbial homeostasis principles, presenting a novel paradigm for caries prevention. The Arg-LRG synbiotics can counter the limitations of fluorides to establish a diverse oral microbiome, imparting an ecologically driven approach to caries prevention.},
}
@article {pmid40652984,
year = {2025},
author = {Wu, S and Huang, M},
title = {Letter to the editor: "Association between oral microbiome and depression: A population-based study".},
journal = {Journal of affective disorders},
volume = {},
number = {},
pages = {119897},
doi = {10.1016/j.jad.2025.119897},
pmid = {40652984},
issn = {1573-2517},
}
@article {pmid40652765,
year = {2025},
author = {Chen, C and Qin, J and Li, G and Gu, Y and Gao, C and Meng, X and Yang, L},
title = {Effects of plant essential oils on intestinal microflora and growth performance of Lingshan native hens.},
journal = {Poultry science},
volume = {104},
number = {10},
pages = {105539},
doi = {10.1016/j.psj.2025.105539},
pmid = {40652765},
issn = {1525-3171},
abstract = {This study examined the effects of dietary supplementation with citronella oil and cinnamon oil on the abundance and diversity of the intestinal microbiome in Lingshan native hens and explored how these changes may enhance chicken quality by influencing metabolic pathways. After three months of supplementation, the relative abundance of Firmicutes decreased, whereas Bacteroidota and Proteobacteria increased significantly in the experimental group. Correspondingly, the fatty acid content decreased, whereas the levels of free amino acids and inosine monophosphate (IMP) increased. Correlation analysis revealed a significant positive correlation between IMP content and Proteobacteria, whereas the abundances of Erysipelatoclostridium, Barnesiella, and Faecalitalea were significantly negatively correlated with IMP variation. The abundance of Rikenellaceae_RC9_intestine_group differed across all experimental groups and was strongly correlated with IMP content, suggesting that it is a key microbial factor influencing community composition and chicken traits.},
}
@article {pmid40652649,
year = {2025},
author = {Kong, T and Sun, X and Gao, P and Huang, W and Guan, X and Xu, Z and Li, B and Sun, W},
title = {Investigation of the ecological roles of the plastisphere microbiome in metal-contaminated river sediments: elucidation of their metabolic versatilities for plastics mineralization and metal resistance.},
journal = {Water research},
volume = {286},
number = {},
pages = {124170},
doi = {10.1016/j.watres.2025.124170},
pmid = {40652649},
issn = {1879-2448},
abstract = {Both plastics and heavy metal(loid)s (HMs) are ubiquitous environmental contaminants, and their frequent interactions in aquatic environments are observed globally. These interactions could result in adsorption of HMs onto plastics, thereby altering the environmental behavior of both contaminants. The change of physicochemical property of plastics surfaces, due to HM adsorption, inevitably impacts the plastisphere microbiome, as well as the fate of plastics in the environment. However, our understanding of how plastisphere microbiomes respond to HMs stress, and the subsequent impacts on the fate of plastics and HMs, remain in its infancy. The current study identified keystone taxa of the plastisphere microbiome and identified their ecological roles in HM metabolism. Members of Mycobacterium were identified as the keystone taxa in the HM contaminated plastisphere. Metagenomic binning and pangenome analysis demonstrated that Mycobacterium encoded essential genes for plastics biodegradation and HM resistance. Pure isolates of Mycobacterium further confirmed that the bacteria can mineralize plastics under arsenic exposure, with plastics biodegradation rates remaining unaffected by environmentally relevant As concentrations (up to 0.5 mM). In summary, the metabolic potentials of HM detoxification as well as the mineralization of plastics by the keystone taxa of the plastisphere microbiome may play important environmental service to promote the bioremediation of the co-contamination of HMs and plastics.},
}
@article {pmid40652256,
year = {2025},
author = {Tang, Y and Zhan, P and Wu, Y and Zhang, T and Yin, D and Gao, Y and Yu, Y and Qiu, S and Zhao, J and Zhang, X and Ma, Z and Chen, Y and Zhao, L and Mao, S and Huang, J and Chen, WH and Liu, J},
title = {Landscape of mobile genetic elements and their functional cargo across the gastrointestinal tract microbiomes in ruminants.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {162},
pmid = {40652256},
issn = {2049-2618},
mesh = {Animals ; *Ruminants/microbiology ; *Gastrointestinal Microbiome/genetics ; *Interspersed Repetitive Sequences ; Metagenomics/methods ; *Bacteria/genetics/classification/isolation &amp; purification ; Plasmids/genetics ; Gene Transfer, Horizontal ; *Gastrointestinal Tract/microbiology ; Metagenome ; },
abstract = {BACKGROUND: Mobile genetic elements (MGEs) drive horizontal gene transfer and microbial evolution, spreading adaptive genes across microbial communities. While extensively studied in other ecosystems, the role of MGEs in shaping ruminant gastrointestinal microbiomes-especially their impact on diversity, adaptation, and dietary responsiveness-remains largely unexplored. This study systematically profiles MGE distribution and functionality across gastrointestinal regions in multiple ruminant species to advance our understanding of microbial adaptation.<br><br>RESULTS: Across 2458 metagenomic samples from eight ruminant species, we identified 4,764,110 MGEs-a&#x2009;~&#x2009;216-fold increase over existing MGE databases. These elements included integrative and conjugative elements, integrons, insertion sequences, phages, and plasmids, with mobilization patterns largely confined to closely related microbial lineages. The distribution of MGEs varied by GIT regions, often reflecting nutritional gradients. In a validation cohort, GH1-carrying plasmids enriched in carbohydrate-active enzymes were found to predominate in the stomach, showing notable responsiveness to forage-based diets. All annotated MGEs have been compiled into a publicly accessible database, rumMGE (https://rummge.liulab-njau.com), to support further research.<br><br>CONCLUSIONS: This study substantially expands the catalog of known MGEs in ruminants, revealing their diverse roles in microbial evolution and functional adaptation to dietary changes. The findings provide a valuable resource for advancing research on microbial functionality and offer insights with potential applications for enhancing ruminant health and productivity, through strategies aimed at modulating the microbiome in agricultural contexts. Video Abstract.},
}
@article {pmid40652165,
year = {2025},
author = {Guzmán-Guzmán, P and Etesami, H and Santoyo, G},
title = {Trichoderma: a multifunctional agent in plant health and microbiome interactions.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {434},
pmid = {40652165},
issn = {1471-2180},
mesh = {*Trichoderma/physiology ; *Microbiota ; Soil Microbiology ; *Plants/microbiology ; Rhizosphere ; Plant Diseases/microbiology ; Microbial Interactions ; Plant Development ; Crops, Agricultural/microbiology ; },
abstract = {The beneficial fungus Trichoderma is a key component of agricultural soils, contributing to sustainable crop production through multiple mechanisms. Among its major roles are the suppression of plant pathogens, promotion of plant growth, and activation of plant immune responses. This study reviews recent advances in understanding the modes of action of Trichoderma spp. related to pathogen control and plant growth promotion, using comparative analysis of its interactions across different plant-associated habitats. In recent years, considerable progress has been made in elucidating how Trichoderma interacts with plants in the rhizosphere, endosphere, and phyllosphere, where it exhibits distinct colonization patterns and functional traits. Additionally, this review explores emerging but less-studied topics, such as the involvement of Trichoderma in the pathobiome concept. Finally, we discuss the synergistic interactions between Trichoderma and other plant-associated microorganisms, highlighting their importance in shaping complex microbial networks within agroecosystems.},
}
@article {pmid40652088,
year = {2025},
author = {Venkatraman, A and Jacobs, K and Binns, J and An, R and Rey, F and Thibeault, SL},
title = {Effects of psychosocial stress on laryngeal microbiology and epithelial barrier integrity.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {25278},
pmid = {40652088},
issn = {2045-2322},
support = {F32DC021367/NH/NIH HHS/United States ; R01DC004336/NH/NIH HHS/United States ; 2023//AshFoundation New Investigator Grant/ ; 2023//American Bronchoesphagological Association Young Investigator Award/ ; },
mesh = {*Stress, Psychological/microbiology ; Female ; Male ; Animals ; *Microbiota ; Mice ; RNA, Ribosomal, 16S/genetics ; *Larynx/microbiology ; Vocal Cords/microbiology ; },
abstract = {Psychosocial stress and laryngeal physiology are linked. However, the biological mechanisms of psychosocial stress on voice have not been studied. This study delineated the effects of psychosocial stress on laryngeal microbiota composition and vocal fold epithelial integrity. We hypothesized that stress would result in reduced microbial diversity and abundance in laryngeal microbiota, and reduced vocal fold epithelial barrier integrity, with more pronounced differences in females and with increased duration of stress. One hundred and eight, conventionally-raised, C56BL/7 mice (8-10 weeks of age, 54 males, 54 females) were allocated to short stress, prolonged stress or control groups. Psychosocial stress involved restraint stress for 7 days (short stress) and 14 days (prolonged stress). Laryngeal microbiota profiles were compared across stress groups using 16S rRNA sequencing (N = 66). Outcome measures of alpha and beta diversity, differentially abundant taxa were obtained. Independently, stress-altered epithelial targets were delineated using RT-qPCR (N = 24) and immunofluorescence (N = 18).We found that prolonged stress, but not short stress, altered measures of alpha, beta diversity, indicating distinct laryngeal microbiota composition compared to control samples. Prolonged stress samples were dominated by Firmicutes phyla, whereas, short stress and control groups by Actinobacteria, and Proteobacteria phyla. Within genera, prolonged psychosocial stress decreased relative abundance of Corynebacterium and increased Streptococcus. Laryngeal microbial differences were more pronounced in females following psychosocial stress, as hypothesized. In addition, short and prolonged psychosocial stress downregulated gene and/or protein expression of inflammatory cytokines, sensory receptors, adherens and tight junction (E cadherin, Zo-1), TLRs and mucins (MUC2) within the larynx, with more severe effects in the prolonged stress group. Short and prolonged psychosocial stress alters laryngeal microbiota composition and vocal fold epithelial barrier integrity. Future studies should delineate causal host epithelial-microbiome interactions in the larynx in response to stress.},
}
@article {pmid40652009,
year = {2025},
author = {Wang, J and Cong, Y and Tang, B and Liu, J and Pu, K},
title = {Integrative analysis of multi-omics data and gut microbiota composition reveals prognostic subtypes and predicts immunotherapy response in colorectal cancer using machine learning.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {25268},
pmid = {40652009},
issn = {2045-2322},
support = {CBY21-QD31//The Intramural Fund of North Sichuan Medical College/ ; CBY23-NCR06//Nanchong City Talent Development Fund/ ; 23JCYJPT0056//Fund of Bureau of Science&amp;Technology Nanchong City/ ; },
mesh = {Humans ; *Colorectal Neoplasms/therapy/microbiology/genetics/mortality/immunology ; *Gastrointestinal Microbiome ; *Machine Learning ; Prognosis ; *Immunotherapy/methods ; Female ; Male ; Tumor Microenvironment ; Middle Aged ; Aged ; Multiomics ; },
abstract = {Colorectal cancer (CRC) exhibits substantial heterogeneity in molecular subtypes and clinical outcomes. We performed an integrative analysis of multi-omics data from 274 CRC patients to investigate the impact of gut microbiota composition on prognosis, identify novel subtypes, and develop a machine learning-based prognostic model. Our microbiome analysis revealed significant differences between CRC and normal tissues. Multi-omics clustering identified two major CRC subtypes, CS1 and CS2, with distinct molecular characteristics and survival outcomes. We developed the Multi-Omics Integrative Clustering and Machine Learning Score (MCMLS) model, which demonstrated strong prognostic value in predicting patient survival and outperformed existing models. The MCMLS low-score group exhibited higher immune cell infiltration, increased metabolic pathway activity, and potentially better immunotherapy response. In contrast, the MCMLS high-score group showed higher mutation burden, fibroblast infiltration, and enrichment of cell adhesion and migration pathways. Bacterial analysis revealed differentially abundant bacteria associated with prognosis. Importantly, MCMLS consistently predicted immunotherapy response across six independent datasets. Our findings highlight the complex interplay between the gut microbiome, tumor microenvironment, and immune landscape in CRC, providing valuable insights for improving patient stratification and personalized treatment strategies.},
}
@article {pmid40651630,
year = {2025},
author = {Wu, Q and Gao, G and Kwok, LY and Lv, H and Sun, Z},
title = {Insomnia: the gut microbiome connection, prospects for probiotic and postbiotic therapies, and future directions.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2025.07.005},
pmid = {40651630},
issn = {2090-1224},
abstract = {BACKGROUND: The gut microbiota is influenced by a complex interplay of factors including the host's genetics, diet, and lifestyle. It plays a crucial role in regulating metabolic processes and is linked to various diseases. Growing evidence suggests that the gut-brain axis, which involves bidirectional communication between the gut microbiota and the brain, plays a crucial role in regulating sleep patterns and has significant implications in the development of sleep disorders.<br><br>AIM OF REVIEW: This comprehensive review aims to summarize the current knowledge on the mechanisms underlying insomnia and its association with the gut microbiota and metabolome. Probiotics and postbiotics are beneficial microorganisms and their components and metabolites, which offer potential in modulating the gut microbiota of the host and alleviating insomnia. We present an overview of recent progress in probiotic and postbiotic intervention trials for managing insomnia, highlighting both the potential benefits and limitations of existing research in this domain. Additionally, we offer suggestions for future directions in this field. Probiotics can regulate sleep-wake behavior by modulating gut microbiota and its metabolites, influencing endocrine, neuronal, and immune responses. In addition, to understand the role of probiotics in improving insomnia, a standardized sleep behavior index and sleep monitoring method are needed.},
}
@article {pmid40651395,
year = {2025},
author = {Gustafsson, F and Hansen, AE and Fuursted, K and Andersen, N and Riley, CH and Lebech, AM and Ørbæk, M},
title = {Borrelia afzelii-associated seronegative Lyme neuroborreliosis in an immunocompromised patient.},
journal = {Diagnostic microbiology and infectious disease},
volume = {113},
number = {3},
pages = {116999},
doi = {10.1016/j.diagmicrobio.2025.116999},
pmid = {40651395},
issn = {1879-0070},
abstract = {This case highlights the diagnostic complexity of Lyme neuroborreliosis (LNB) in immunosuppressed patients. A 62-year-old man with a history of follicular lymphoma, previously treated with R-Bendamustine and currently rituximab, presented with generalized symptoms and systemic inflammation. Lymphoma relapse was excluded and diagnostic evaluations for infectious, metabolic, and autoimmune etiologies yielded unremarkable results. Several antibiotic treatments were without effect. An amplicon-based microbiome blood analysis using next-generation sequencing identified Borrelia afzelii, confirmed by specific PCR. Cerebrospinal fluid analysis revealed pleocytosis and elevated CXCL13. Blood serology and intrathecal Borrelia burgdorferi antibodies were negative. Treatment with doxycycline led to clinical and laboratory improvement corroborating LNB diagnosis. The case underscores that B-cell-depleting therapy can impair antibody responses, resulting in false-negative serology and LNB may present atypically. In cases like this advanced diagnostics like PCR and CXCL13 measurement can be valuable tools. Clinicians must consider the impact of immunosuppression on both disease presentation and diagnostic reliability.},
}
@article {pmid40651297,
year = {2025},
author = {Chen, LJ and Liu, Y and Liu, JL and Chen, ZJ and Zhao, W and Li, JH and Hsu, C and Chen, L and Zeng, JH and Li, XW and Yang, JZ and Li, JH and Xie, XL and Tao, SH and Wang, Q},
title = {Lycopene ameliorates Di-(2-ethylhexyl) phthalate-induced neurotoxicity in mice via the gut-brain axis.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {145},
number = {},
pages = {157057},
doi = {10.1016/j.phymed.2025.157057},
pmid = {40651297},
issn = {1618-095X},
abstract = {BACKGROUND: Di(2-ethylhexyl) phthalate (DEHP), a ubiquitous plasticizer present in numerous consumer products, poses a substantial neurotoxic risk through environmental and dietary exposure. Growing evidence highlights a critical association between DEHP-induced neurotoxicity and gut microbiota dysbiosis. Renowned for its potent antioxidant and anti-inflammatory capabilities, the natural carotenoid lycopene (Lyc) demonstrates therapeutic promise in treating various neurological disorders.<br><br>PURPOSE: The potential neuroprotective mechanisms of Lyc against DEHP-induced neurotoxicity in mice were investigated in this study, with a specific focus on its interaction with the gut-brain axis.<br><br>METHODS: For 35 consecutive days, mice received daily intragastric administrations of DEHP or Lyc. A comprehensive approach involving integrated transcriptome, microbiome, and molecular biology analyses, in conjunction with bacteriotherapy, was utilized to thoroughly investigate the underlying mechanisms.<br><br>RESULTS: Our findings demonstrated that Lyc administration or fecal microbiota transplantation (FMT) from Lyc-treated mice effectively ameliorated DEHP-induced anxiety- and depression-like behaviors. At the molecular level, Lyc mitigated neuroinflammation in the hippocampus, potentially through modulation of the NOD-like receptor signaling pathway. Furthermore, Lyc treatment improved gut microbiota composition by promoting the growth of beneficial bacteria, such as Akkermansiaceae, and enhanced intestinal barrier integrity via increased expression of tight junction proteins. Lyc also regulated the LPS-TLR4/MyD88 signaling pathway in the colon, thereby reducing local inflammation.<br><br>CONCLUSION: These results provide compelling evidence that Lyc confers protection against DEHP-induced neurotoxicity through a multifaceted strategy involving modulation of gut-brain axis, suppression of neuroinflammation, and restoration of gut homeostasis. We propose a novel therapeutic strategy to alleviate the risks posed by DEHP to both neurological and intestinal health. This approach involves either supplementation with Lyc or the application of bacteriotherapy.},
}
@article {pmid40651180,
year = {2025},
author = {Gorczyca, A and Przemieniecki, SW and Bednarz, S and Niemiec, M and Szerement, J and Kula-Maximenko, M and Guzik, M},
title = {Closing the loop: Agricultural applications of hydrolyzed polyhydroxyalkanoates production waste.},
journal = {Waste management (New York, N.Y.)},
volume = {205},
number = {},
pages = {115006},
doi = {10.1016/j.wasman.2025.115006},
pmid = {40651180},
issn = {1879-2456},
abstract = {The increasing global demand for sustainable materials and circular economy solutions has driven research into innovative applications of polyhydroxyalkanoates (PHA) and their by-products. While PHAs are well-recognized biodegradable bioplastics, the potential reuse of waste streams generated during their production remains largely unexplored. This study investigates the feasibility of utilizing hydrolysates derived from PHA post-fermentation biomass as biostimulants for rapeseed (Brassica napus L.) growth. Waste biomass from two bacterial fermentation processes - Zobellella denitrificans and Pseudomonas putida CA-3 - was subjected to acid hydrolysis to generate liquid formulations suitable for soil application. Their effects on plant growth, photosynthetic efficiency, phytohormone profiles, soil chemical composition, and microbiome dynamics were evaluated through microbiotests and pot experiments. Results indicated that hydrolysate application enhanced biomass accumulation and improved soil nutrient content, while also modulating key physiological responses, including chlorophyll fluorescence dynamics and hormone levels, suggesting a role in stress resilience. Additionally, hydrolysates induced a shift in the rhizosphere microbiome, decreasing bacterial dominance while enhancing diversity, particularly through the promotion of plant growth-associated microbial taxa. These findings support the integration of PHA production residues into agriculture, aligning with circular bioeconomy principles by converting industrial by-products into value-added biostimulants. Future research should focus on optimizing hydrolysate formulations, assessing their long-term agronomic impact, and evaluating their commercial feasibility for sustainable crop production.},
}
@article {pmid40651111,
year = {2025},
author = {Špulák, M and Nelic, D and Randáková, A and Konečná, K and Janďourek, O and Smutná, L and Kubíček, V and Gathergood, N and Pourová, J and Pávek, P and Pour, M and Svoboda, D and Ďurinová, A and Jakubík, J and Trejtnar, F},
title = {Evaluation of pharmacokinetics, pharmacodynamics, and toxicity of potential quinazoline bronchodilators derived from vasicinone.},
journal = {The Journal of pharmacology and experimental therapeutics},
volume = {392},
number = {8},
pages = {103636},
doi = {10.1016/j.jpet.2025.103636},
pmid = {40651111},
issn = {1521-0103},
abstract = {Various synthetic modifications of the alkaloid (-)-vasicinone are known to exhibit a remarkable bronchodilatory effect. This study aimed to examine selected pharmacological and toxicological properties of 2 quinazolines derived from vasicinone with previously proven bronchodilatory action to consider their potential applicability for further preclinical development. Both compounds were found to have relatively low in vitro toxicity in a standard hepatic cell model. Pharmacokinetic studies in rats using oral and intravenous administration showed significant differences in oral availability (0.66 ± 0.11% vs 0.36 ± 0.18%), distribution volume, and elimination parameters of the 2 tested agents (for all parameters, P < .05). The different pharmacokinetic properties offer the possibility to select more convenient compounds for inhalation or systemic administration in further stages of development. The performed pharmacodynamic studies using an in vitro model showed that the tested quinazolines bind to the allosteric site on muscarinic acetylcholine receptors with micromolar affinity (pKB higher than pKI for M1 and M3 receptors, P < .05) and exert functional antagonism of carbachol-induced response. The main effect is not accompanied by a concomitant antibiotic effect. The proven inhibition of muscarinic receptors including the M3 subtype is analogous to the effects of clinically used anticholinergic bronchodilators. Therefore, the findings suggest that the bronchodilating effect of the tested compounds is likely mediated by a similar mechanism. The muscarinic receptor blocking effect based on allosteric binding to the receptors may potentially allow the development of a new group of highly selective M3 antagonists. SIGNIFICANCE STATEMENT: Two tested synthetic quinazoline derivatives with proven bronchodilator action exhibit allosteric binding to muscarinic receptors. Since the extracellular domain at which allosteric modulators commonly bind varies among subtypes of muscarinic receptors, this characteristic may allow further development of highly selective M3 antagonists. The examined compounds exhibit low toxicity as well as no concomitant antimicrobial effect that would potentially affect the bronchial microbiome.},
}
@article {pmid40651052,
year = {2025},
author = {Arutselvan, R and Kumar, S and Akash, AU and Greeshma, K and Sinha, SS and Khan, AS and Pati, K and Chauhan, VBS and Gowda, KH and Pradhan, S and Jeeva, ML and Veena, SS and Makeshkumar, T and Meena, M and Sangeetha, BG and Laxminarayana, K and Nedunchezhiyan, M},
title = {Deciphering the complex signaling networks in phytophthora infected plants: Insights into microbiome interactions and plant defense mechanisms.},
journal = {Plant physiology and biochemistry : PPB},
volume = {228},
number = {},
pages = {110222},
doi = {10.1016/j.plaphy.2025.110222},
pmid = {40651052},
issn = {1873-2690},
abstract = {Phytophthora species are destructive plant pathogens that cause severe economic losses in agriculture and natural ecosystems, known for their rapid spread through soil and water and resistance to conventional control methods. Understanding the complex signaling networks activated in plants during Phytophthora infection is crucial for developing effective management strategies. This review summarizes research findings on Phytophthora-plant interactions, with special emphasis on Phytophthora-plant microbiome interactions. Initially, molecular mechanisms involved in the plant response to Phytophthora infection are discussed, further emphasizing key signaling pathways activated by Phytophthora in host plants. The role of phytohormones in imparting resistance to Phytophthora infections is explored in depth. Additionally, the interaction and effects of Phytophthora and the plant immune system with the plant microbiome are examined, highlighting how these interactions facilitate disease and/or aid in plant defense. Various biotechnological approaches for enhancing plant resistance to Phytophthora, including recent technologies like CRISPR-Cas systems, are also reviewed. The conclusion addresses the need for further research into signaling networks within Phytophthora-plant-microbiome interactions and their future implications for crop protection.},
}
@article {pmid40650586,
year = {2025},
author = {Xu, S and Wang, C and Zhou, Q and Wang, Y and Yan, H and Tang, J and Zhang, R and Li, H and Zhao, X and Jiang, X and Liu, G and Luo, H and Wu, D and Che, L},
title = {Effects of 25-hydroxycholecalciferol supplementation during gestation on sow performance, offspring development and intestinal microbiota in sows and piglets.},
journal = {Journal of animal science},
volume = {},
number = {},
pages = {},
doi = {10.1093/jas/skaf228},
pmid = {40650586},
issn = {1525-3163},
abstract = {The 25-hydroxycholecalciferol (25OHD3) is a metabolite of vitamin D (VD) and status biomarker of VD in blood. We investigate the effect of dietary 25OHD3 supplementation on gestation sow litter performance, milk composition, nutrient metabolism, the growth performance of offspring, and intestinal microbiota. A total of 60 sows were randomly allocated to receive VD3 diet (CON, 50 µg·kg-1, n = 30) or 25OHD3 diet (50 µg·kg-1, n = 30). All sows had the same diet during lactation. No difference was observed in litter size at farrowing and piglet performance at weaning between treatments. Sows fed 25OHD3 diet had increased plasma concentrations of prolactin (P = 0.05) and tended to have increased estradiol concentrations (P = 0.09) at farrowing. Sows fed 25OHD3 diet tended to have higher dry matter and fat contents in milk on day 10 of lactation (P = 0.08), increased plasma calcium concentration in newborn piglets (P < 0.05), and proportions of tibia and femur to body weights (P < 0.05) in weaning piglets. Newborn piglets from sows fed 25OHD3 diet had increased crypt depth (P < 0.05), and decreased ratio of villus height to crypt depth (P < 0.05). Compared with the VD3 diet, sows fed the 25OHD3 diet tended to have more fecal Firmicutes (P = 0.09) and fewer Campylobacterota (P < 0.05) at farrowing, and had fewer Bacteroidota and Spirochaetota (P < 0.05) at the end of lactation. Moreover, the weaning piglets from sows fed 25OHD3 diet had a higher abundance of Pseudomonas (P < 0.05), and a lower abundance of Bacteroides, Megasphaera, CAG-873, and Olsenella (P < 0.05) in colonic chyme. We conclude that 25OHD3 supplementation in gestation sows improves milk composition, increases the blood calcium concentration of newborn piglets, the tibia and femur weight of weaned piglets, and alters the intestinal microbiota of both sows and piglets.},
}
@article {pmid40650585,
year = {2025},
author = {Shin, YH and Bang, S and Xavier, R and Clardy, J},
title = {Eggerthella lenta Produces a Cryptic Pro-inflammatory Lipid.},
journal = {Journal of the American Chemical Society},
volume = {},
number = {},
pages = {},
doi = {10.1021/jacs.5c08613},
pmid = {40650585},
issn = {1520-5126},
abstract = {Eggerthella lenta is both one of the most studied and least understood members of the human gut microbiome. Most of the interest in this Gram-positive anaerobe originates from multiple robust associations of its population with a variety of autoimmune diseases, perhaps most notably inflammatory bowel disease (IBD). The links between bacteria and inflammation are only partially known. Inflammation is driven by Th17 cells and their inflammatory cytokine IL-17, and the population of these cells is promoted by a transcription factor, RORγt. Bacterial metabolites appear to activate RORγt in a cell- and antigen-independent fashion, but the metabolites and their activating mechanism are unknown. This report describes an assay-driven search for pro-inflammatory metabolites from E. lenta that revealed a plasmalogen-triggered plasmalogen pair that forms a single molecule signal transduction device. Small electrophiles characteristic of inflammatory environments react with the plasmalogen's sensitive vinyl ether moiety to create a lipid signal, a lysoglycoglycerolipid that upregulates the inflammatory cytokines TNF-α and IL-6 through a TLR receptor. This provides a molecular mechanism that allows E. lenta to upregulate inflammatory responses in a cell- and antigen-independent fashion. This molecular mechanism is similar to an endogenous signaling system that upregulates RORγt through a triggered mammalian plasmalogen signal, 1-18:0-lysophosphatidylethanolamine.},
}
@article {pmid40650575,
year = {2025},
author = {Guigard, L and Nazaret, F and Almario, J and Bertolla, F and Boubakri, H and Cantarel, AAM and Cournoyer, B and Favre-Bonté, S and Florio, A and Galia, W and Hazard, C and Henry, G and Belaroussi, AH and Chong, SKTF and Lavire, C and Lobreau, C and Luis, P and Maréchal, M and Meyer, T and Pozzi, ACM and Minard, G and Nazaret, S and Nicol, GW and Prigent-Combaret, C and Richaume, A and Rodriguez, V and Sanchez-Cid, C and Moro, CV and Vial, L and Vigneron, A and Wisniewski-Dye, F and Shade, A},
title = {The connections of climate change with microbial ecology and their consequences for ecosystem, human, and plant health.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxaf168},
pmid = {40650575},
issn = {1365-2672},
abstract = {The climate crisis presents an urgent challenge for Earth's living creatures and the habitats in which they have been adapted to thrive. Climate-related stress presents risks to microorganisms, the stability of the functions they provide, and their maintenance of beneficial interactions with their hosts and ecosystems. Microbes move across the continuum of anthropogenic influence on Earth's ecosystems, from pristine to human-managed to fully urbanized environments. Because microbial feedback within and across this continuum exists at multiple, connected scales from molecules to ecosystem-level processes, predicting microbial responses to climate stress and their potentially wide-ranging consequences remains difficult. Here, we discuss the broad implications of microbial and microbiome responses to climate change as they interface with human, plant, and ecosystem health. For each section on human, plant and ecosystem health, we briefly discuss the state of knowledge for each and follow with proposed future research, including some directions that are promising but require more work to evaluate. We end by considering overarching microbial ecology research needs across these systems and microbial solutions under investigation as possible climate-resilient interventions to maintain human, plant, and ecosystem health. This work draws on diverse expertise to identify broad research directions across typically separated disciplines and builds a holistic framework for considering their interrelationships.},
}
@article {pmid40650475,
year = {2025},
author = {Zhai, T and Zou, X and Zhang, Z and Wang, Y and Shi, L and Ren, W and Huang, J},
title = {Circadian rhythms of gut microbiota and plaque vulnerability: mechanisms and chrono-microbiota modulation interventions.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2532703},
doi = {10.1080/19490976.2025.2532703},
pmid = {40650475},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Circadian Rhythm/physiology ; *Plaque, Atherosclerotic/microbiology/physiopathology ; Animals ; Probiotics/administration &amp; dosage ; Circadian Clocks ; Chronotherapy ; },
abstract = {The stability of atherosclerotic plaques constitutes the fundamental pathological basis for acute cardiovascular events, and their circadian rhythm characteristics highlight the essential role of dynamic interactions between the host and microorganisms. This review systematically elucidates the multifaceted mechanisms by which disruptions in the circadian rhythm of the gut microbiota contribute to plaque destabilization. Specifically, the microbiota modulates endothelial function, immune homeostasis, and vascular inflammation via rhythmic variations in metabolites. Perturbations in this rhythm compromise the structural integrity of plaques through a synergistic "metabolic-immune-vascular" network. Furthermore, the review unveils the bidirectional regulation between the host's circadian clock and the microbiota's rhythm. Innovatively, we propose "Chronotherapy-based Microbiome Modulation (CMM)," a strategy that reestablishes synchrony between the host and microbiota rhythms through time-restricted feeding, time-specific probiotics, and drugs targeting the circadian clock, thereby, it is possible to improve plaque stability by regulating the host's gut microbiota. The clinical translation of these findings requires overcoming technical challenges, such as personalized time window prediction and microbiota ecological risk assessment, and integrating multi-omics dynamic monitoring with AI modeling and optimization strategies. This review presents a novel perspective on the regulation of plaque stability.},
}
@article {pmid40650267,
year = {2025},
author = {Borowik, A and Wyszkowska, J and Zaborowska, M and Kucharski, J},
title = {Regulation of the Microbiome in Soil Contaminated with Diesel Oil and Gasoline.},
journal = {International journal of molecular sciences},
volume = {26},
number = {13},
pages = {},
pmid = {40650267},
issn = {1422-0067},
support = {30.610.006-110//University of Warmia and Mazury in Olsztyn, Faculty of Agriculture and Forestry, Department of Soil Science and Microbiology/ ; Regional Initiative of Excellence Program//Minister of Education and Science in the range of the program entitled Funded by the Minister of Science/ ; },
mesh = {*Soil Microbiology ; *Gasoline/analysis ; *Microbiota/drug effects ; *Soil Pollutants ; Fungi/drug effects/genetics/classification ; Bacteria/genetics/classification/drug effects ; Biodegradation, Environmental ; Zea mays/growth &amp; development ; Soil/chemistry ; },
abstract = {Petroleum-derived contaminants pose a significant threat to the soil microbiome. Therefore, it is essential to explore materials and techniques that can restore homeostasis in disturbed environments. The aim of the study was to assess the response of the soil microbiome to contamination with diesel oil (DO) and gasoline (G) and to determine the capacity of sorbents, vermiculite (V), dolomite (D), perlite (P) and agrobasalt (A), to enhance the activity of microorganisms under Zea mays cultivation conditions in pot experiments. The restoration and activity of the soil microbiome were evaluated based on the abundance and diversity of bacteria and fungi, using both classical microbiological methods and Next Generation Sequencing (NGS). Bioinformatic tools were employed to calculate the physicochemical properties of proteins. DO increased the abundance of cultured microorganisms, whereas G significantly reduced it. Both DO and G increased the number of ASVs of Proteobacteria and decreased the relative abundance of Gemmatimonadetes, Chloroflexi, Acidobacteria, Verrucomicrobia, Planctomycetes, and fungal OTUs. These contaminants stimulated the growth of bacteria from the genera Rhodanobacter, Sphingomonas, Burkholderia, Sphingobium, and Mycobacterium, as well as fungi belonging to the Penicillium genus. Conversely, they had a negative effect on Kaistobacter, Rhodoplanes, and Ralstonia, as well as the fungi Chaetomium, Pseudaleuria, and Mortierella. DO caused greater changes in microbial alpha diversity than G. The stability of microbial proteins was higher at 17 °C than at -1 °C. The most stable proteins were found in bacteria and fungi identified within the core soil microbiome. These organisms exhibited greater diversity and more compact RNA secondary structures. The application of sorbents to contaminated soil altered the composition of bacterial and fungal communities. All sorbents enhanced the growth of organotrophic bacteria (Org) and fungi (Fun) in DO-contaminated soils, and actinobacteria (Act) and fungi in G-contaminated soils. V and A had the most beneficial effects on cultured microorganisms. In DO-contaminated soils, all sorbents inhibited the growth of Rhodanobacter, Parvibaculum, Sphingomonas, and Burkholderia, while stimulating Salinibacterium and Penicillium. In G-contaminated but otherwise unamended soils, all sorbents negatively affected the growth of Burkholderia, Sphingomonas, Kaistobacter, Rhodoplanes, Pseudonocardia, and Ralstonia and increased the abundance of Gymnostellatospora. The results of this study provide a valuable foundation for developing effective strategies to remediate soils contaminated with petroleum-derived compounds.},
}
@article {pmid40650181,
year = {2025},
author = {Udawatte, NS and Liu, C and Staples, R and Han, P and Kumar, PS and Arumugam, TV and Ivanovski, S and Seneviratne, CJ},
title = {Short-Term Probiotic Colonization Alters Molecular Dynamics of 3D Oral Biofilms.},
journal = {International journal of molecular sciences},
volume = {26},
number = {13},
pages = {},
pmid = {40650181},
issn = {1422-0067},
support = {HREC No. 2023000467//Australian Dental Association/ ; },
mesh = {*Biofilms/growth &amp; development/drug effects ; *Probiotics/pharmacology/administration &amp; dosage ; Humans ; RNA, Ribosomal, 16S/genetics ; *Streptococcus salivarius/physiology/growth &amp; development/genetics ; Microbiota ; Saliva/microbiology ; Bifidobacterium/genetics ; Mouth Mucosa/microbiology ; Pilot Projects ; *Mouth/microbiology ; In Situ Hybridization, Fluorescence ; },
abstract = {Three-dimensional (3D) scaffold systems have proven instrumental in advancing our understanding of polymicrobial biofilm dynamics and probiotic interactions within the oral environment. Among oral probiotics, Streptococcus salivarius K12 (Ssk12) has shown considerable promise in modulating microbial homeostasis; however, its long-term therapeutic benefits are contingent upon successful and sustained colonization of the oral mucosa. Despite its clinical relevance, the molecular mechanisms underlying the adhesion, persistence, and integration of Ssk12 into the native oral microbiome/biofilm remain inadequately characterized. In this pilot study, we explored the temporal colonization dynamics of Ssk12 and its impact on the structure and functional profiles of salivary-derived biofilms cultivated on melt-electrowritten poly(ε-caprolactone) (MEW-mPCL) scaffolds, which emulate the native oral niche. Colonization was monitored via fluorescence in situ hybridization (smFISH), confocal microscopy, and RT-qPCR, while shifts in community composition and function were assessed using 16S rRNA sequencing and meta-transcriptomics. A single administration of Ssk12 exhibited transient colonization lasting up to 7 days, with detectable presence diminishing by day 10. This was accompanied by short-term increases in Lactobacillus and Bifidobacterium populations. Functional analyses revealed increased transcriptional signatures linked to oxidative stress resistance and metabolic adaptation. These findings suggest that even short-term probiotic colonization induces significant functional changes, underscoring the need for strategies to enhance probiotic persistence.},
}
@article {pmid40650144,
year = {2025},
author = {Gáspár, Z and Lakatos, B},
title = {Mapping the Gut Microbiota Composition in the Context of Raltegravir, Dolutegravir, and Bictegravir-A Scoping Review.},
journal = {International journal of molecular sciences},
volume = {26},
number = {13},
pages = {},
pmid = {40650144},
issn = {1422-0067},
mesh = {*Gastrointestinal Microbiome/drug effects ; Pyridones/pharmacology ; Humans ; *Heterocyclic Compounds, 3-Ring/pharmacology/therapeutic use ; Piperazines/pharmacology ; Oxazines/pharmacology ; *Raltegravir Potassium/pharmacology/therapeutic use ; *HIV Integrase Inhibitors/pharmacology/therapeutic use ; *HIV Infections/drug therapy/microbiology ; Amides ; *Heterocyclic Compounds, 4 or More Rings/pharmacology/therapeutic use ; },
abstract = {(1) Background: Second-generation integrase strand transfer inhibitors (INSTIs) are now the preferred first-line therapies for human immunodeficiency virus (HIV). However, concerns regarding their side effects, such as weight gain and metabolic disturbances, have emerged. This scoping review aims to assess the effects of INSTIs on the gut microbiota, with a focus on differences between agents and their clinical implications. (2) Methods: A scoping review was conducted using PubMed, Web of Science, and Embase, with reports collected following PRISMA for Scoping Reviews (PRISMA-ScR). (3) Results: The majority of available evidence focused on dolutegravir, which demonstrated beneficial effects on microbiota diversity and composition. However, factors such as younger age, lower CD4+ counts, and extreme BMI were associated with proinflammatory changes. Limited data on bictegravir also suggested favorable alterations in the gut microbiota. Raltegravir, a first-generation INSTI, was associated with improvements in alpha diversity and microbial composition, although these changes were not consistently beneficial. Moreover, associated changes in inflammatory and microbial translocation markers suggested unfavorable alterations. (4) Conclusions: Based on the evidence mapped, second-generation INSTIs may generally induce favorable changes in the gut microbiota. However, further research is needed to explore the clinical implications of these microbiota alterations, particularly in specific patient groups.},
}
@article {pmid40650070,
year = {2025},
author = {Bai, Y and Li, Z and Chen, Z and Luo, L and Wang, J and Yao, S and Yun, K and Gao, C and Guo, X},
title = {Integrated Metabolomic and Gut Microbiome Profiles Reveal Postmortem Biomarkers of Fatal Anaphylaxis.},
journal = {International journal of molecular sciences},
volume = {26},
number = {13},
pages = {},
pmid = {40650070},
issn = {1422-0067},
support = {82271925//National Natural Science Foundation of China/ ; 81971790//National Natural Science Foundation of China/ ; 2024KY364//the Postgraduate Education Innovation Project of Shanxi/ ; },
mesh = {*Anaphylaxis/metabolism/microbiology/diagnosis/blood/mortality ; *Biomarkers/blood/metabolism ; Animals ; *Gastrointestinal Microbiome ; Rats ; *Metabolomics/methods ; Male ; RNA, Ribosomal, 16S/genetics ; Rats, Sprague-Dawley ; Humans ; Immunoglobulin E/blood ; *Metabolome ; Disease Models, Animal ; Myocardial Infarction/diagnosis/metabolism ; Tryptophan/blood ; Feces/microbiology ; },
abstract = {The incidence of fatal anaphylaxis is increasing, but there is still no recognized "golden standard" for forensic diagnosis. Due to its non-specific symptoms, especially cardiovascular symptoms without cutaneous changes, it can easily be misdiagnosed as acute myocardial infarction. Here, we established rat models (n = 12) of fatal anaphylaxis (FA), acute myocardial infarction (AMI), and coronary atherosclerosis with anaphylaxis (CAA). The untargeted metabolomics of plasma and 16S rRNA sequencing of fecal matter was performed, and a random forest was used to identify potential biomarkers. Three metabolites (tryptophan, trans-3-indole acrylic acid, and imidazole acetic acid) and three microbial genera (g_Prevotellaceae_Ga6A1_group, g_UCG_008, and g_Eubacterium_hallii_group) were identified as potential biomarkers for distinguishing anaphylaxis and non-anaphylaxis. The classification model of plasma metabolites showed a much better discriminatory performance than that of microbial genus, serum IgE, and tryptase. The performance of the microbial genera was superior to the serum IgE but inferior to the serum tryptase. Forensic samples of fatal anaphylaxis and non-anaphylaxis deaths (n = 12) were collected for untargeted metabolomics detection. The results showed that among the three identified metabolic biomarkers, tryptophan has better stability in cadaveric blood samples. Its diagnostic performance (AUC = 87.1528) was superior to serum IgE and tryptase, making it more suitable as a postmortem biomarker of fatal anaphylaxis.},
}
@article {pmid40650060,
year = {2025},
author = {Baek, KR and Singh, S and Hwang, HS and Seo, SO},
title = {Using Gut Microbiota Modulation as a Precision Strategy Against Obesity.},
journal = {International journal of molecular sciences},
volume = {26},
number = {13},
pages = {},
doi = {10.3390/ijms26136282},
pmid = {40650060},
issn = {1422-0067},
support = {Research Program//SeoulTech (Seoul National University of Science and Technology)./ ; },
mesh = {*Obesity/microbiology/therapy/metabolism/prevention &amp; control ; *Gastrointestinal Microbiome/physiology ; Humans ; Probiotics/therapeutic use ; Animals ; Prebiotics/administration &amp; dosage ; Energy Metabolism ; },
abstract = {Obesity is a complex metabolic disorder with high global prevalence. Recent studies have highlighted the crucial role of gut microbiota in obesity's onset and progression. This review explores the relationship between gut microbiota composition and obesity, emphasizing how changes in microbial communities can influence host metabolism, energy balance, and fat storage. By reviewing current evidence regarding the interactions between specific microbial taxa; their metabolic byproducts, such as short-chain fatty acids; and host signaling pathways, we aim to clarify the mechanisms through which the gut microbiome contributes to obesity. Furthermore, we discuss the potential of microbiota engineering through precision strategies such as the use of probiotics, prebiotics, and genetically engineered microbial strains. Collectively, this review highlights the targeted modulation of the gut microbiome as a promising and innovative approach to the prevention and treatment of obesity.},
}
@article {pmid40650015,
year = {2025},
author = {Yang, L and Cui, R and Li, Z and Xue, M and Chan, S and Xue, P and Yang, X and Zhang, L and Lv, F and Fang, M},
title = {Gut Microbiota-Bile Acid Crosstalk Contributes to Meat Quality and Carcass Traits of Tan and Dorper Sheep.},
journal = {International journal of molecular sciences},
volume = {26},
number = {13},
pages = {},
doi = {10.3390/ijms26136224},
pmid = {40650015},
issn = {1422-0067},
support = {U21A20246//the National Natural Science Foundation of China/ ; 2021YFD1200900//the National Key Research and Development Program-Key Projects/ ; },
mesh = {Animals ; *Bile Acids and Salts/metabolism ; *Gastrointestinal Microbiome/physiology ; Sheep/metabolism ; *Meat/analysis ; Transcriptome ; Colon/metabolism ; },
abstract = {Tan sheep outperform Dorper sheep in meat-quality traits, including muscle fiber characteristics and fatty acid composition, while Dorper sheep excel in carcass weight. However, the molecular mechanisms underlying these breed-specific traits, especially gut microbiota-bile acid (BA) interactions, remain poorly understood. As host-microbiota co-metabolites, BAs are converted by colonic microbiota via bile salt hydrolase (BSH) and dehydroxylases into secondary BAs, which activate BA receptors to regulate host lipid and glucose metabolism. This study analyzed colonic BA profiles in 8-month-old Tan and Dorper sheep, integrating microbiome and longissimus dorsi muscle transcriptome data to investigate the gut-muscle axis in meat-quality and carcass trait regulation. Results showed that Tan sheep had 1.6-fold higher secondary BA deoxycholic acid (DHCA) levels than Dorper sheep (p < 0.05), whereas Dorper sheep accumulated conjugated primary BAs glycocholic acid (GCA) and tauro-α-muricholic acid (p < 0.05). Tan sheep exhibited downregulated hepatic BA synthesis genes, including cholesterol 7α-hydroxylase (CYP7A1) and 27-hydroxylase (CYP27A1), alongside upregulated transport genes such as bile salt export pump (BSEP), sodium taurocholate cotransporting polypeptide (NTCP), and ATP-binding cassette subfamily B member 4 (ABCB4), with elevated gut BSH activity (p < 0.05). DHCA was strongly correlated with g_Ruminococcaceae_UCG-014, ENSOARG00000001393, and ENSOARG00000016726, muscle fiber density, diameter, and linoleic acid (C18:2n6t) (|r| > 0.5, p < 0.05). In contrast, GCA was significantly associated with g_Lachnoclostridium_10, g_Rikenellaceae_RC9_gut_group, ENSOARG0000001232, carcass weight, and net meat weight (|r| > 0.5, p < 0.05). In conclusion, breed-specific colonic BA profiles were shaped by host-microbiota interactions, with DHCA potentially promoting meat quality in Tan sheep via regulation of muscle fiber development and fatty acid deposition, and GCA influencing carcass traits in Dorper sheep. This study provides novel insights into the gut microbiota-bile acid axis in modulating ruminant phenotypic traits.},
}
@article {pmid40649958,
year = {2025},
author = {Roznovan, CN and Măruțescu, LG and Gradisteanu Pircalabioru, G},
title = {Immuno-Oncology at the Crossroads: Confronting Challenges in the Quest for Effective Cancer Therapies.},
journal = {International journal of molecular sciences},
volume = {26},
number = {13},
pages = {},
doi = {10.3390/ijms26136177},
pmid = {40649958},
issn = {1422-0067},
mesh = {Humans ; *Neoplasms/therapy/immunology ; Tumor Microenvironment/immunology ; *Immunotherapy/methods ; Precision Medicine ; Cancer Vaccines/therapeutic use/immunology ; Animals ; Immune Checkpoint Inhibitors/therapeutic use ; *Medical Oncology/methods ; },
abstract = {Immuno-oncology has rapidly evolved into a cornerstone of modern cancer therapy, offering promising avenues for durable responses and personalized treatment strategies. This narrative review provides a thorough overview of the mechanisms underlying tumor-immune system interactions and the therapeutic innovations emerging from this knowledge. Central to this discussion is the tumor microenvironment (TME), a complex ecosystem of immune and stromal cells that supports tumor growth and shapes therapeutic outcomes. Key cellular and molecular factors within the TME are examined, along with diverse immune escape strategies. We further analyze the landscape of immunotherapeutic approaches, including immune checkpoint inhibitors, cancer vaccines, adoptive cell therapies such as CAR-T cells, and cytokine-based interventions. This review also addresses the increasing importance of predictive biomarkers in immuno-oncology, particularly in patient stratification, monitoring resistance, and managing immunotherapy-related toxicity. Finally, we explore the emerging role of the microbiome as a modulator of immunotherapy efficacy, shedding light on host-microbe-immune interactions that may influence clinical outcomes. By integrating current biological insights with therapeutic innovation, this review outlines the challenges and opportunities ahead in immuno-oncology and emphasizes the need for translational research and cross-disciplinary collaboration to optimize cancer immunotherapy in the era of precision medicine.},
}
@article {pmid40649947,
year = {2025},
author = {Pinheiro, I and Bolca, S and Van den Bossche, L and Vanhove, W and Van Ryckeghem, S and Gottardi, D and Laukens, D and Possemiers, S},
title = {MH002, a Novel Butyrate-Producing Consortium of Six Commensal Bacterial Strains Has Immune-Modulatory and Mucosal-Healing Properties.},
journal = {International journal of molecular sciences},
volume = {26},
number = {13},
pages = {},
doi = {10.3390/ijms26136167},
pmid = {40649947},
issn = {1422-0067},
mesh = {Animals ; Humans ; *Butyrates/metabolism ; *Gastrointestinal Microbiome ; Mice ; Caco-2 Cells ; *Inflammatory Bowel Diseases/microbiology/immunology/therapy ; Rats ; *Intestinal Mucosa/microbiology/immunology/metabolism ; Male ; Colitis/chemically induced/microbiology ; Leukocytes, Mononuclear/metabolism ; Mice, Inbred C57BL ; *Bacteria/metabolism ; Wound Healing ; },
abstract = {Inflammatory bowel disease (IBD) is a chronic relapsing inflammatory condition of the gastrointestinal tract. It is generally accepted that IBD is characterized by an inappropriate immune response to the intestinal microbiome in genetically susceptible individuals. Despite the available treatment options ranging from salicylates and corticosteroids, to immunosuppressants and biologics, there is still a high unmet medical need for patients who respond poorly to drugs or are not able to tolerate them. Microbiome-based therapeutics offer a valid treatment strategy for IBD with enhanced safety. A butyrate-producing consortium of six commensal strains (MH002) was evaluated in a series of in vitro, ex vivo, and in vivo experiments mimicking multiple IBD-related dysfunctions, namely disrupted intestinal permeability and immune activation. MH002 rapidly produced high levels of butyrate in fed-batch cultures, and significantly increased butyrate levels within one day after administration to IBD-derived gut microbial communities in vitro. Both in Caco-2/peripheral blood mononuclear cells (PBMCs) co-cultures, and IBD patients-derived organoids and colonic explants, MH002 reduced inflammation and restored epithelial barrier integrity. In addition, MH002 promoted wound repair in vitro. Finally, MH002 protected mice and rats from chemically induced colitis. Altogether, results showed that MH002 presents a novel therapeutic avenue for the treatment of IBD.},
}
@article {pmid40649930,
year = {2025},
author = {Lin, SH and Lin, RJ and Chu, CL and Chen, YL and Fu, SC},
title = {Associations Between Gut Microbiota Composition and Impulse Control Disorders in Parkinson's Disease.},
journal = {International journal of molecular sciences},
volume = {26},
number = {13},
pages = {},
doi = {10.3390/ijms26136146},
pmid = {40649930},
issn = {1422-0067},
support = {MOST 111-2628-M-A49-004-MY3//National Science and Technology Council/ ; NSTC 113-2314-B-259 -001 -MY3//National Science and Technology Council/ ; },
mesh = {*Parkinson Disease/microbiology/complications ; Humans ; *Gastrointestinal Microbiome/genetics ; Male ; RNA, Ribosomal, 16S/genetics ; Female ; Middle Aged ; *Disruptive, Impulse Control, and Conduct Disorders/microbiology/etiology ; Aged ; Bacteria/genetics/classification ; },
abstract = {Impulse control disorders (ICDs) are a debilitating non-motor symptom of Parkinson's disease (PD), often associated with dopaminergic therapy. However, their occurrence in some patients but not others suggests additional biological mechanisms, including the gut microbiome. In this study, we analyzed 191 PD patients (14 with ICDs, 177 without) using 16S rRNA gene sequencing to explore the association between gut microbiota and ICDs. No significant differences were observed in alpha or beta diversity between groups, but several bacterial taxa showed differential abundances. Notably, Methanobrevibacter and Intestinimonas butyriciproducens were enriched in ICD patients. Functional pathway analysis revealed differences in metabolic pathways, including enrichment of xenobiotic degradation and nicotinate metabolism in the ICD group. These findings suggest that specific gut microbial taxa and their associated metabolic functions may contribute to ICDs in PD, highlighting a potential non-dopaminergic mechanism and opening new avenues for microbiome-targeted intervention.},
}
@article {pmid40649842,
year = {2025},
author = {Muttiah, B and Wahid, W and Sukri, A and Hanafiah, A},
title = {Towards Effective Helicobacter pylori Eradication: Emerging Therapies in the Wake of Antibiotic Resistance.},
journal = {International journal of molecular sciences},
volume = {26},
number = {13},
pages = {},
doi = {10.3390/ijms26136064},
pmid = {40649842},
issn = {1422-0067},
support = {DIP-2024-005//National University of Malaysia/ ; },
mesh = {Humans ; *Helicobacter pylori/drug effects ; *Helicobacter Infections/drug therapy/microbiology ; *Anti-Bacterial Agents/therapeutic use/pharmacology ; *Drug Resistance, Bacterial/drug effects ; Probiotics/therapeutic use ; Antimicrobial Peptides/therapeutic use/pharmacology ; Animals ; },
abstract = {Helicobacter pylori (H. pylori) infection is a leading cause of gastritis, peptic ulcers, and gastric cancer, affecting more than half of the global population. Its persistence in the acidic gastric environment and its ability to evade host immunity present major treatment challenges. Although antibiotics remain the standard therapy, rising antimicrobial resistance has reduced treatment efficacy, prompting the search for alternative and adjunct approaches. Emerging therapies include probiotics, antimicrobial peptides (AMPs), and plant-derived compounds, which target H. pylori through membrane disruption, immunomodulation, or direct antimicrobial activity. Novel drug delivery systems and microbiota-sparing interventions are also being investigated. Additionally, vaccine development offers a promising strategy for long-term protection, though challenges related to antigenic variability and host-specific responses remain. Despite these advances, treatment variability and the limited clinical validation of alternatives hinder progress. A multifaceted approach integrating microbiome research, host-pathogen interactions, and new therapeutic agents is essential for future success.},
}
@article {pmid40649705,
year = {2025},
author = {Borbélyová, V and Szabó, J and Sušienková, P and Potvin, J and Belvončíková, P and Groß, T and Jančovičová, A and Bačová, Z and Rašková, B and Szadvári, I and Antal, M and Pirník, Z and Karhánek, M and Šoltys, K and Gardlík, R and Celec, P and Ostatníková, D and Tomova, A},
title = {The Effect of Parental Faecal Microbiome Transplantation from Children with Autism Spectrum Disorder on Behavior and Gastrointestinal Manifestations in the Male Offspring of Shank3 Mice.},
journal = {International journal of molecular sciences},
volume = {26},
number = {13},
pages = {},
doi = {10.3390/ijms26135927},
pmid = {40649705},
issn = {1422-0067},
support = {APVV-20-0114//Slovak Research and Development Agency/ ; VEGA 1/0062/21//Ministry of Education, Science, Research, and Sport of the Slovak Republic/ ; },
mesh = {Animals ; *Autism Spectrum Disorder/therapy/microbiology/genetics ; *Fecal Microbiota Transplantation ; Mice ; Male ; Female ; *Nerve Tissue Proteins/genetics/metabolism ; Humans ; Behavior, Animal ; Pregnancy ; Gastrointestinal Microbiome ; Mice, Knockout ; Disease Models, Animal ; Child ; Prenatal Exposure Delayed Effects ; Microfilament Proteins ; },
abstract = {The increasing incidence of autism spectrum disorder (ASD) increases the urgency of establishing the mechanism of its development for effective prevention and treatment. ASD's etiology includes genetic predisposition and environmental triggers, both of which can play a role in the changed microbiota. Recent research has proved the impact of maternal microbiota on the neurodevelopment of the child. To investigate the co-play of genetic and microbiota factors in ASD development, we performed fecal microbiota transplantation (FMT) from children with ASD to female Shank3b[+/-] mice and studied the autism-like symptoms in the male Shank3b[-/-] and wild-type (WT) offspring. WT animals with prenatal exposure to ASD microbiota had delayed neurodevelopment and impaired food intake behavior, but also elevated plasma leptin concentration and body weight. Shank3b[-/-] mice after FMT ASD exhibited impaired learning and exacerbated anxiety-like behavior in adulthood. Interestingly, FMT ASD improved learning in adolescent Shank3b[-/-] mice. Prenatal exposure to ASD microbiota decreased the activity of hypocretin neurons of the lateral hypothalamic area in both genotypes. The combination of genetic predisposition and FMT ASD led to an increased colon permeability, evaluated by zonula occludens (ZO1, ZO3) and claudin factors. These results suggest the effect of parental FMT exposure on shaping offspring behavior in Shank3b[-/-] mice and the potential of microbiota in the modulation of ASD.},
}
@article {pmid40649157,
year = {2025},
author = {Cannizzaro, R and Maiero, S and Pelizzo, P and Gulotta, M and Facchin, S and Tessarolo, G and Zucchetto, A and Matrone, F and Realdon, S and Bortolus, R},
title = {Microencapsulated Sodium Butyrate in the Prevention of Acute Radiotherapy Proctitis: Single-Center Prospective Study.},
journal = {Journal of clinical medicine},
volume = {14},
number = {13},
pages = {},
pmid = {40649157},
issn = {2077-0383},
abstract = {Background/Objectives: Prostate cancer is the most frequent cancer in men, for which Radiotherapy (RT) is used as a radical or post-surgical treatment. Actinic proctitis is one of the most disabling side effects of RT. Intestinal microbiome studies have highlighted the importance of short-chain fatty acids, in particular butyric acid, for their beneficial effects over intestinal epithelial cells. The aim of this prospective study is to evaluate if treatment with micro-encapsulated sodium butyrate (MESB) can reduce the incidence of actinic proctitis during RT in prostate cancer patients. Methods: In total, 122 consecutive patients with prostate cancer treated in Radiotherapy Unit, Centro di Riferimento Oncologico, IRCCS Aviano, were enrolled. Patients received MESB (3 tablets/day) from one week before until four weeks after RT. They completed a diary, tracking daily bowel movements, rectal bleeding, abdominal pain, and perceived health status before, at the end, and one month after RT. Results: Although an improvement in symptoms was observed, when comparing interpatient data before RT vs. one month after the end of RT, statistically significant differences emerged only regarding abdominal pain (94.2% vs. 81.6% vs. 81.6%) (McNemar's test p < 0.002). Conclusions: MESB appears effective in reducing radiation-induced bowel toxicity during RT, minimizing stool changes, incontinence, and abdominal pain. Although patients' health perception declined at RT completion, it improved after one month, suggesting MESB may support clinical recovery post-treatment.},
}
@article {pmid40649085,
year = {2025},
author = {Adames, SM and Naz, S and Dai, J and Wang, Y and Shirwaikar Thomas, A},
title = {The Impact of Fecal Diversion on Immune Checkpoint Inhibitor Adverse Gastrointestinal Toxicities.},
journal = {Journal of clinical medicine},
volume = {14},
number = {13},
pages = {},
pmid = {40649085},
issn = {2077-0383},
abstract = {Background/Objective: Immune checkpoint inhibitors (ICIs) are highly effective cancer therapies used across a broad spectrum of malignancies. They function by disrupting immune inhibitory pathways, resulting in an amplified immune response against tumors. However, this heightened immune activity can predispose patients to immune-mediated colitis (IMC), which is graded using the Common Terminology Criteria for Adverse Events (CTCAE) and can range from mild diarrhea to severe colitis. Prior studies have shown that fecal stream diversion can modify the gut microbiome and influence the severity of intestinal inflammation. This study investigates the impact of fecal stream diversion on IMC outcomes in cancer patients receiving ICIs. Methods: We conducted a retrospective cohort study of patients treated with ICIs from 2016 to 2023 who had a history of fecal stream diversion. Demographic, oncologic, and toxicity-related data were collected. Patients with active gastrointestinal infections, autoimmune GI diseases, or graft-versus-host disease were excluded. Descriptive statistics and univariate and multivariate logistic regression analyses were performed using SAS version 9.4. Results: A total of 44 patients were included and categorized into two groups based on the timing of bowel stoma creation relative to the IMC event. CTCAE grade for diarrhea was used to assess GI toxicity. While overall CTCAE grade distribution for diarrhea did not differ significantly between groups (p = 0.22), Hispanic ethnicity was significantly associated with a lower CTCAE grade compared to non-Hispanic or Latino individuals (OR [95% CI] = 0.12 [0.02, 0.62], p = 0.011). In contrast, higher CTCAE grades were significantly associated with ileostomy versus colostomy (OR [95% CI] = 3.21 [1.01, 10.18], p = 0.048) and in patients without an ostomy at the time of diarrhea onset compared to those with an ostomy (OR [95% CI] = 8.87 [2.51, 31.31], p = 0.0007). Conclusions: Our findings suggest that the CTCAE diarrhea grade is significantly associated with ethnicity, type of stoma, and presence of ostomy at the time of diarrhea. Limitations include the retrospective study design and small sample size. These results contribute to understanding potential strategies for mitigating the serious gastrointestinal toxicities of ICIs.},
}
@article {pmid40648949,
year = {2025},
author = {Shiina, N and Shimpo, Y and Kikuchi, K and Sekiya, T and Tomonari, H},
title = {Effects of 0.05% Cetylpyridinium Chloride Mouthwash on Halitosis and Tongue Microbiota in Patients Undergoing Orthodontic Treatment: A Double-Blind Randomized Clinical Trial.},
journal = {Journal of clinical medicine},
volume = {14},
number = {13},
pages = {},
pmid = {40648949},
issn = {2077-0383},
abstract = {Background: Halitosis is frequently observed in patients undergoing orthodontic treatment with multibracket appliances, primarily due to volatile sulfur compounds (VSCs) produced by oral anaerobic bacteria. Cetylpyridinium chloride (CPC) is a widely used antimicrobial agent in oral care products and may help alleviate halitosis.This study aimed to evaluate the effects of 0.05% CPC mouthwash on halitosis, oral hygiene indices, and the tongue microbiota in orthodontic patients with elevated VSC levels. Methods: In this randomized, double-blind, placebo-controlled clinical trial, 30 orthodontic patients with elevated VSCs (≥150 ppb) were assigned to a CPC mouthwash group or a placebo group. Participants used the assigned mouthwash three times daily for 1 month. Halitosis was quantitatively assessed by gas chromatography (Oral Chroma™), and oral hygiene parameters including Plaque Index (PI), Gingival Index (GI), Tongue Coating Index (TCI), and unstimulated salivary flow rate were evaluated at baseline and after the intervention. The tongue microbiota was analyzed by 16S rRNA sequencing. Results: The CPC mouthwash group showed significant reductions in total VSCs, hydrogen sulfide, methyl mercaptan, PI, GI, and TCI (p < 0.05), while salivary flow rate and dimethyl sulfide remained unchanged. Microbiome analysis revealed decreases in halitosis-associated genera (Actinomyces, Corynebacterium, Tannerella) and increases in beneficial species such as Streptococcus salivarius. Conclusions: CPC mouthwash (0.05%) effectively reduced halitosis and improved oral hygiene parameters in orthodontic patients, likely through modulation of the tongue microbiota. This mouthwash may serve as a safe and practical adjunct to conventional oral hygiene practices during orthodontic treatment.},
}
@article {pmid40648819,
year = {2025},
author = {Hoying, D and Sangwan, N and Chaaban, MR},
title = {Investigating the Role of the Sinus Microbiome and Cytokine Profile in the SNOT-22 Response After Functional Endoscopic Sinus Surgery in Chronic Rhinosinusitis Patients.},
journal = {Journal of clinical medicine},
volume = {14},
number = {13},
pages = {},
pmid = {40648819},
issn = {2077-0383},
abstract = {Background: Functional endoscopic sinus surgery (FESS) is the treatment of choice for medically refractory CRS. However, the success rate of FESS is dependent on both baseline medical and demographic characteristics. Consequently, we performed an analysis of systemic/nasal cytokines and the sinus microbiome to assess their impact on the SNOT-22 response after functional endoscopic sinus surgery (FESS). Methods: A prospective observational study was performed on 44 patients with chronic rhinosinusitis undergoing FESS between December 2021 and September 2022. Diseased sinus tissue from 25 patients was subjected to whole-exome sequencing (WES) for taxonomical profiling of the sinus bacterial composition. Additional data collection included demographics, comorbidities, baseline sinonasal outcome test scores, post-operative sinonasal outcome test scores (at 3-4 months), and nasal/systemic cytokines. Results: Our analysis demonstrated that CRSwNP patients in the surgical responder cohort had statistically significantly higher median [P25, P75] levels of intra-nasal IL-5, indicating type 2 sinonasal disease (63 pg/μL [28, 118] versus 17 pg/μL [16.6, 18], p = 0.04). At the genus level, the relative abundance of Staphylococcus was significantly higher in the surgical non-responder cohort compared to the responder group. An ROC curve was highly accurate at distinguishing responders versus non-responders to FESS based on a microbiota-based random forest model (AUC = 0.92). Conclusions: Intra-nasal IL-5 levels and the bacterial composition of the sinus microbiome may be important predictors of symptomatic response after sinus surgery.},
}
@article {pmid40647985,
year = {2025},
author = {Perelló, A and Romero-Munar, A and Martinez, SI and Busquets, A and Cañellas, M and Quetglas, BM and Bosch, R and Vadell, J and Cabot, C and Gomila, M},
title = {Xylem Sap Mycobiota in Grapevine Naturally Infected with Xylella fastidiosa: A Case Study: Interaction of Xylella fastidiosa with Sclerotinia sclerotiorum.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {13},
pages = {},
pmid = {40647985},
issn = {2223-7747},
abstract = {Grapevine (Vitis vinifera) is a key crop in Mediterranean agriculture, now increasingly threatened by Xylella fastidiosa subsp. Fastidiosa (Xff), the causal agent of Pierce's disease. This study investigated: (1) the diversity of culturable fungal endophytes in the xylem sap of naturally Xff-infected grapevines, and (2) the interaction between Xff and the pathogenic fungus Sclerotinia sclerotiorum identified in the sap. The xylem sap was collected from Cabernet Sauvignon vines in Mallorca, Spain, and fungal communities were characterized using culture-dependent methods. Both beneficial fungi (e.g., Aureobasidium pullulans, Rhodotorula mucilaginosa) and pathogenic species (e.g., S. sclerotiorum, Cladosporium sp., Alternaria alternata, and the Phoma complex) were isolated from both Xff-positive and Xff-negative plants, indicating similar community profiles. Although limited by small sample size, these findings offer preliminary evidence of complex ecological interactions between Xff and the xylem-associated mycobiota, with potential implications for grapevine health and disease development under varying environmental and management conditions. Further experiments under controlled conditions revealed that grapevines co-inoculated with Xff and S. sclerotiorum showed increased disease severity, suggesting a synergistic interaction. These preliminary results highlight the complex interplay between Xff and the fungal endophytic microbiome, which may modulate grapevine susceptibility depending on environmental and management conditions.},
}
@article {pmid40647668,
year = {2025},
author = {Chudzicka-Strugała, I and Gołębiewska, I and Brudecki, G and Elamin, W and Banaszewska, B and Chudzicka-Adamczak, M and Strugała, D and Zwoździak, B},
title = {Proinflammatory Cytokines in Women with PCOS in Atypical Pathogen Infections.},
journal = {Diagnostics (Basel, Switzerland)},
volume = {15},
number = {13},
pages = {},
pmid = {40647668},
issn = {2075-4418},
abstract = {Background/Objectives: Polycystic ovary syndrome (PCOS) is one of the most frequently diagnosed endocrine and metabolic disorders in women of reproductive age before menopause. It is associated with excess androgens and ovarian dysfunction, reduced fertility, the presence of obstetric disorders, but also metabolic disorders, and, among others, insulin resistance, obesity and type II diabetes. Its close relationship with changes in the diversity of the vaginal microbiome, vaginal inflammation and changes in the vaginal microenvironment, which can pave the way for pathogenic microorganisms, is emphasized. Methods: The research in the presented paper focuses on a group of women with PCOS (n = 490) of reproductive age (26-43 years), in whom the frequency of infections of the reproductive system caused by atypical pathogens, Chlamydia trachomatis, Mycoplasma hominis and Ureaplasma spp., were analyzed, and then the immune system response was assessed in terms of the level of serum proinflammatory cytokines, IL-1β, IL-6 and TNF-α. Results: Our results showed a 40% infection rate in the studied group of patients with PCOS, with C. trachomatis being the most common pathogen (17.7%), followed by Ureaplasma spp. (10%) and M. hominis (4.9%). In some cases, co-infections such as Mycoplasma and Ureaplasma were also observed in 3.1% or all three atypical bacteria, M. hominis, Ureaplasma spp. and C. trachomatis, in 4.3% of patients with PCOS. In our study, in women with PCOS and confirmed infection with any atypical pathogen (n = 196), we analyzed the levels of proinflammatory cytokines, IL-1 β a, IL-6 and TNF-α. The results were compared with a control group (control group A) consisting of patients with the same underlying disease, i.e., PCOS (n = 39), who did not experience infection with atypical pathogens or symptoms of gynecological infection. Additionally, a control group B (n = 28) consisting of healthy women (without PCOS and without infection) was introduced. The results regarding the levels of cytokines studied in this work (IL-1β, IL-6, TNF-α) may suggest that the presence of intracellular C. trachomatis in the infection will play a dominant role in the immune system response. In the infections with atypical pathogens analyzed in this study in patients with PCOS, no characteristic clinical features were observed, apart from indications in the form of an increase in the number of leukocytes in the assessment of the vaginal biocenosis, suggesting cervicitis and reported reproductive failure or lower abdominal pain. An additional problem is the inability to detect the presence of atypical pathogens in routine microbiological tests; therefore, confirmation of such etiology requires referral of the patient for targeted tests. Conclusions: Invasion of host cells by atypical pathogens such as C. trachomatis and infections with "genital mycoplasmas" can disrupt the function of these cells and lead to many complications, including infertility. The immune response with the production of proinflammatory cytokines such as TNF-α, IL-1β, and IL-6, observed in response to infection with C. trachomatis, M. hominis, and Ureaplasma spp., induces or amplifies inflammation by activating immune cells or controlling infection, but may lead to the facilitation of the survival of pathogenic microorganisms and irreversible damage to fallopian tube tissues. Especially in the case of the proinflammatory cytosine TNF-α, there seems to be a close correlation with infections with atypical pathogens and a marked immune response, as well as with increased IL-1β and IL-6 values compared with the absence of infection (both in the presence and absence of PCOS). The presented study may suggest the importance of extended diagnostics to include atypical pathogens in the case of PCOS and the importance of research in this area also from the point of view of the immune response.},
}
@article {pmid40647560,
year = {2025},
author = {Unrug-Bielawska, K and Sandowska-Markiewicz, Z and Piątkowska, M and Czarnowski, P and Goryca, K and Zeber-Lubecka, N and Dąbrowska, M and Kaniuga, E and Cybulska-Lubak, M and Bałabas, A and Statkiewicz, M and Rumieńczyk, I and Pyśniak, K and Mikula, M and Ostrowski, J},
title = {Comparative Analysis of Gut Microbiota Responses to New SN-38 Derivatives, Irinotecan, and FOLFOX in Mice Bearing Colorectal Cancer Patient-Derived Xenografts.},
journal = {Cancers},
volume = {17},
number = {13},
pages = {},
doi = {10.3390/cancers17132263},
pmid = {40647560},
issn = {2072-6694},
support = {2018/31/B/NZ7/02675//National Science Center/ ; },
abstract = {BACKGROUND: Symbiotic gut microbiota can enhance cancer therapy efficacy, while treatment-induced dysbiosis may reduce effectiveness or increase toxicity. Our preclinical study compared the anticancer effects and impact on fecal microbiota and metabolites of two water-soluble SN-38 derivatives (BN-MePPR and BN-MOA), with those observed after treatment with Irinotecan, and the FOLFOX regimen in NOD scid gamma mice bearing patient-derived colon adenocarcinoma xenografts (CRC PDX).<br><br>METHODS: Five individual experiments with Irinotecan and its derivatives and eight individual experiments with FOLFOX were conducted using eight CRC PDX models. Chemotherapeutics were administered intraperitoneally 4-5 times at 5-day intervals. Fecal samples were collected before and after treatment. Microbiota composition was analyzed by 16S rRNA gene (V3-V4 regions) sequencing. Mass spectrometry was used to quantify short-chain fatty acids (SCFAs) and amino acids (AAs).<br><br>RESULTS: All treatments significantly inhibited tumor growth versus controls. However, no significant changes were observed in gut microbiota &#x3b1;- and &#x3b2;-diversity between treated and untreated groups. Tumor progression in controls was associated with increased abundance of Marvinbryantia, Lactobacillus, Ruminococcus, and [Eubacterium] nodatum group. FOLFOX-treated mice showed increased Marvinbryantia, Bacteroides, and Candidatus Arthromitus, and decreased Akkermansia. No distinct taxa changes were found in the Irinotecan or derivative groups. SCFA levels remained unchanged across groups, while BN-MePPR, BN-MOA, and Irinotecan all increased AA concentrations.<br><br>CONCLUSIONS: Contrary to earlier toxicological data, these findings indicate a relatively limited impact of the tested chemotherapeutics on the gut microbiome and metabolome, emphasizing the importance of research method selection in preclinical studies.},
}
@article {pmid40647535,
year = {2025},
author = {Palkovsky, M and Modrackova, N and Neuzil-Bunesova, V and Liberko, M and Hlodakova, A and Soumarova, R},
title = {Role of Human Microbiome in Development and Management of Head and Neck Squamous Cell Carcinoma.},
journal = {Cancers},
volume = {17},
number = {13},
pages = {},
doi = {10.3390/cancers17132238},
pmid = {40647535},
issn = {2072-6694},
abstract = {Despite decades of research, cancer remains a major global health problem [...].},
}
@article {pmid40647494,
year = {2025},
author = {Fajkić, A and Lepara, O and Jahić, R and Hadžović-Džuvo, A and Belančić, A and Chupin, A and Pavković, D and Sher, EK},
title = {Ultra-Processed Diets and Endocrine Disruption, Explanation of Missing Link in Rising Cancer Incidence Among Young Adults.},
journal = {Cancers},
volume = {17},
number = {13},
pages = {},
doi = {10.3390/cancers17132196},
pmid = {40647494},
issn = {2072-6694},
abstract = {The global increase in early-onset cancers among adolescents and young adults has happened at the same time as the rise in the consumption of ultra-processed foods (UPFs). Far beyond their poor nutritional quality, UPFs are increasingly seen as Trojan horses, complex biological agents that interfere with many functions of the human organism. In this review, we utilise the Trojan horse model to explain the quiet and building health risks from UPFs as foods that seem harmless, convenient, and affordable while secretly delivering endocrine-disrupting chemicals (EDCs), causing chronic low-grade inflammation, altering the microbiome, and producing epigenetic alterations. We bring together new proof showing that UPFs mess up hormonal signals, harm the body's ability to fight off harmful germs, lead to an imbalance of microbes, and cause detrimental changes linked to cancer. Important components, such as bisphenols and phthalates, can migrate from containers into food, while additional ingredients and effects from cooking disrupt the normal balance of cells. These exposures are especially harmful during vulnerable developmental periods and may lay the groundwork for disease many years later. The Trojan horse model illustrates the hidden nature of UPF-related damage, not through a sudden toxin but via chronic dysregulation of metabolic, hormonal, and genetic control. This model changes focus from usual diet worries to a bigger-picture view of UPFs as causes of life-disrupting damage. Ultimately, this review aims to identify gaps in current knowledge and epidemiological approaches and highlight the need for multi-omics, long-term studies and personalised nutrition plans to assess and reduce the cancer risk associated with UPFs. Recognising UPFs as a silent disruptor is crucial in shaping public health policies and cancer prevention programs targeting younger people.},
}
@article {pmid40647355,
year = {2025},
author = {Chu, J and No, CW and Joung, H and Kim, KH and Shin, CH and Lee, J and Ha, JH},
title = {Modulation of Gut Microbial Composition by Lactobacillus delbrueckii subsp. lactis CKDB001 Supplementation in a High-Fat-Diet-Induced Obese Mice.},
journal = {Nutrients},
volume = {17},
number = {13},
pages = {},
doi = {10.3390/nu17132251},
pmid = {40647355},
issn = {2072-6643},
support = {RS-2023-00227274//National Research Foundation of Korea/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; *Diet, High-Fat/adverse effects ; Male ; Mice, Inbred C57BL ; *Obesity/microbiology/etiology/therapy ; *Lactobacillus delbrueckii/physiology ; *Probiotics/administration &amp; dosage/pharmacology ; Mice ; *Dietary Supplements ; Feces/microbiology ; Mice, Obese ; Disease Models, Animal ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Background/Objectives:Lactobacillus delbrueckii subsp. lactis CKDB001 (LL) has demonstrated anti-inflammatory, antioxidant, and lipid-regulatory effects in vitro and in vivo, including attenuation of hepatic steatosis and modulation of lipid metabolism. Given the known interactions between host metabolism and gut microbiota, these findings suggest a potential role for LL in modulating microbial composition under conditions of diet-induced obesity. This study aimed to investigate the microbiome-related effects of LL using an established murine model. To evaluate the effect of LL supplementation on gut microbial composition and predict microbial metabolic functions in mice with high-fat diet-induced obesity. Methods: Male C57BL/6J mice were fed a high-fat diet and administered LL orally for 12 weeks. Fecal samples were collected and analyzed using 16S rRNA gene sequencing. Microbial taxonomic profiles were assessed using linear discriminant analysis effect size, and functional predictions were performed using PICRUSt2. Results: LL supplementation significantly altered the gut microbiota by increasing the relative abundance of Lactobacillus and other commensal taxa while reducing the prevalence of pro-inflammatory genera such as Alistipes and Bilophila. Functional prediction analysis revealed a downregulation of lipopolysaccharide and ADP-L-glycero-β-D-manno-heptose biosynthesis pathways. Microbial functions associated with carbohydrate metabolism and short-chain fatty acid production were enriched in the LL-treated group. Conclusions: LL modulated gut microbial composition and suppressed pro-inflammatory microbial pathways while enhancing beneficial metabolic functions in high-fat diet-fed mice. These findings support the potential of LL as a safe and effective microbiota-targeted probiotic for managing obesity-related metabolic disorders.},
}
@article {pmid40647335,
year = {2025},
author = {Chojnacki, M and Błońska, A and Kaczka, A and Chojnacki, J and Walecka-Kapica, E and Romanowska, N and Przybylowska-Sygut, K and Popławski, T},
title = {Assessment of the Gut Microbiome in Patients with Coexisting Irritable Bowel Syndrome and Chronic Fatigue Syndrome.},
journal = {Nutrients},
volume = {17},
number = {13},
pages = {},
doi = {10.3390/nu17132232},
pmid = {40647335},
issn = {2072-6643},
support = {503/6-006-05//UMED/ ; UK/US/06/2022/01/00004//ALAB/ ; },
mesh = {Humans ; *Irritable Bowel Syndrome/microbiology/complications/urine ; Female ; *Fatigue Syndrome, Chronic/microbiology/complications/urine ; *Gastrointestinal Microbiome/physiology ; Adult ; Middle Aged ; Tryptophan/metabolism ; Dysbiosis/microbiology ; },
abstract = {Background: The gut microbiome is a key modulator of the gut-brain axis and may contribute to the pathophysiology of both gastrointestinal and systemic disorders. This study aimed to evaluate gut microbiota composition and tryptophan/phenylalanine metabolism in women with unclassified irritable bowel syndrome (IBS-U), with or without coexisting chronic fatigue syndrome (CFS). Methods: Eighty women were enrolled and divided into two groups: IBS-U without CFS (Group I, n = 40) and IBS-U with coexisting CFS (Group II, n = 40). Microbial composition and diversity were assessed using the GA-map™ Dysbiosis Test, including the dysbiosis index (DI) and Shannon Diversity Index (SDI). Hydrogen and methane levels were measured in breath samples. Urinary concentrations of selected microbial and neuroactive metabolites-homovanillic acid (HVA), 5-hydroxyindoleacetic acid (5-HIAA), kynurenine (KYN), kynurenic acid (KYNA), xanthurenic acid (XA), quinolinic acid (QA), hydroxyphenylacetic acid (HPA), and 3-indoxyl sulfate (3-IS)-were quantified using LC-MS/MS. Fatigue severity was assessed using the Chalder Fatigue Questionnaire (CFQ-11) and the fatigue severity scale (FSS). Results: Compared to Group I, patients with IBS-CFS showed significantly greater microbial diversity, higher breath methane levels, and elevated urinary concentrations of QA, XA, 3-IS, and HVA, alongside lower concentrations of 5-HIAA and KYN. Fatigue severity was positively correlated with urinary XA and QA levels. Conclusions: Women with IBS and coexisting CFS exhibit distinct gut microbiota and tryptophan metabolite profiles compared to those without fatigue. The observed metabolite-symptom associations, particularly involving neuroactive kynurenine derivatives, warrant further investigation. These preliminary findings should be interpreted as hypothesis-generating and require validation through high-resolution microbiome analyses, functional pathway profiling, and longitudinal or interventional studies to clarify causality and clinical significance.},
}
@article {pmid40647334,
year = {2025},
author = {Szudzik, M and Zajdel, M and Samborowska, E and Perlejewski, K and Radkowski, M and Ufnal, M},
title = {High-Fat Diet with Normal Caloric Intake Elevates TMA and TMAO Production and Reduces Microbial Diversity in Rats.},
journal = {Nutrients},
volume = {17},
number = {13},
pages = {},
doi = {10.3390/nu17132230},
pmid = {40647334},
issn = {2072-6643},
support = {2020/37/B/NZ5/00366//National Science Center/ ; },
mesh = {Animals ; *Methylamines/metabolism/urine ; *Gastrointestinal Microbiome ; *Diet, High-Fat/adverse effects ; Rats, Sprague-Dawley ; Male ; Rats ; *Energy Intake ; RNA, Ribosomal, 16S/genetics ; Bacteria/classification ; },
abstract = {Background/Objectives: Trimethylamine (TMA), produced by gut microbiota, and its derivative trimethylamine N-oxide (TMAO) are both associated with cardiometabolic diseases. While the effects of high-fat diets (HFDs) and high-disaccharide diets (HDDs) on gut microbiota in the context of obesity have been well studied, their impact on TMA/TMAO production, particularly alongside physiological caloric intake, remains obscure. This study investigates how standard HFDs and HDDs alongside physiological caloric intake influence gut microbiota composition and TMA/TMAO production in rats. Methods: Sprague Dawley rats were fed one of three diets a standard diet, an HFD, or an HDD for 12 weeks, with chow availability adjusted by age to maintain physiological caloric intake. Gut bacterial diversity was analyzed using 16S rRNA gene sequencing, and metabolites were quantified via High-Performance Liquid Chromatography-Mass Spectrometry (HPLC-MS) in urine and plasma. Results: The HFD group had significantly higher urinary levels of TMA and TMAO compared to the control and HDD groups. Gut bacterial diversity in the HFD group was markedly reduced, displaying the lowest species richness and phylogenetic diversity among all the groups. Notably, Pasteurellaceae (within the order Pasteurellales) and S24-7 (within the order Bacteroidales) were positively correlated with TMAO levels. The demonstrated HDD group increased microbial diversity compared to both the control and HFD groups. Conclusions: A high-fat diet during controlled and physiological caloric intake increases TMA/TMAO production and reduces gut microbial diversity. This underscores the role of diet composition, beyond caloric excess, in shaping gut microbiota and the related cardiometabolic biomarkers.},
}
@article {pmid40647305,
year = {2025},
author = {Almatani, MF and Rompato, G and Stewart, EC and Hayden, M and Case, J and Rice, S and Hintze, KJ and Benninghoff, AD},
title = {Dynamic Microbiome Responses to Structurally Diverse Anthocyanin-Rich Foods in a Western Diet Context.},
journal = {Nutrients},
volume = {17},
number = {13},
pages = {},
doi = {10.3390/nu17132201},
pmid = {40647305},
issn = {2072-6643},
support = {2021-67018-33938//United States Department of Agriculture/ ; UTA-01456//Utah Agricultural Experiment Station/ ; },
mesh = {Animals ; *Anthocyanins/pharmacology/chemistry/administration &amp; dosage ; *Gastrointestinal Microbiome/drug effects ; Mice, Inbred C57BL ; *Fruit/chemistry ; *Diet, Western/adverse effects ; Male ; Mice ; Feces/microbiology ; Dietary Supplements ; RNA, Ribosomal, 16S/genetics ; Ribes/chemistry ; Vaccinium myrtillus/chemistry ; Polyphenols ; Rubus/chemistry ; },
abstract = {Background/Objectives: Anthocyanin (ACN)-rich foods are known to influence the gut microbiota composition, but the temporal dynamics and structural specificity of these effects remain poorly understood. This study investigated how distinct ACN-rich fruit supplements impact the gut microbiome over time in the context of a Western-style diet. We hypothesized that ACN-induced microbial shifts would occur rapidly, differ by ACN source, and require continued intake to persist. Methods: C57BL/6J mice were fed the total Western diet (TWD) supplemented with freeze-dried powders from bilberry (BB), tart cherry (TC), chokeberry (CB), elderberry (EB), black currant (BC), or black raspberry (BRB) for 0, 1, 3, or 7 days. Cocoa polyphenols (CPs) were included as a comparator with a distinct polyphenol profile. Fecal microbiota were collected at 0, 1, 3, and 7 days post exposure and analyzed by 16S rRNA sequencing. Results: ACN-rich supplements induced rapid microbial shifts detectable within one day of exposure. However, most changes reverted toward the baseline within days of supplement withdrawal, indicating limited persistence. Among the ACNs, BRB produced the most sustained microbiome alterations. Microbial responses varied by ACN source, suggesting that differences in glycoside and aglycone structures influence the community composition. Conclusions: ACN-rich foods can induce rapid but largely transient alterations in the gut microbiome, with variability linked to the polyphenol structure. These findings highlight the ecological sensitivity of the microbiome to specific dietary components and underscore the importance of sustained intake for maintaining microbial shifts.},
}
@article {pmid40647290,
year = {2025},
author = {Zdybel, K and Śliwka, A and Polak-Berecka, M and Polak, P and Waśko, A},
title = {Postbiotics Formulation and Therapeutic Effect in Inflammation: A Systematic Review.},
journal = {Nutrients},
volume = {17},
number = {13},
pages = {},
doi = {10.3390/nu17132187},
pmid = {40647290},
issn = {2072-6643},
mesh = {Humans ; *Probiotics/therapeutic use/administration &amp; dosage ; *Inflammation/therapy ; *Anti-Inflammatory Agents ; Inflammatory Bowel Diseases ; },
abstract = {Background: Postbiotics are bioactive compounds derived from inactivated probiotic microorganisms that show potential for preventing and treating inflammatory diseases. This review aimed to evaluate the evidence on their therapeutic effects in inflammatory conditions. Methods: A search of PubMed, Scopus, and Web of Science databases from 2014 to 2024 identified 39 eligible studies. Article selection was conducted using the Rayyan platform, risk of bias was assessed with the Cochrane ROB 2 tool, and results were visualized with ROBVIS. Bibliometric networks were constructed using VOSviewer. Due to data heterogeneity, a meta-analysis was not performed; therefore, results were described and presented graphically. Results: The most commonly used microorganisms belonged to the Lactobacillaceae and Bifidobacteriaceae families, with heat inactivation as the predominant method. Postbiotics exert multifaceted anti-inflammatory effects by modulating cytokine expression, influencing immune cell signaling pathways, and strengthening epithelial barrier integrity. They regulate immune mechanisms such as the Th1/Th2 and Treg/Th17 balance, indicating their potential in treating inflammatory bowel diseases, autoimmune diseases, and metabolic syndrome. However, the heterogeneity of studies, their limitations, and risk of bias require cautious interpretation. Conclusions: Future research should focus on standardizing postbiotic preparations, conducting long-term clinical trials, and analyzing synergistic effects of different strains. Postbiotics offer a promising approach to managing inflammation, with potential applications in functional foods and nutraceuticals.},
}
@article {pmid40647269,
year = {2025},
author = {Lamichhane, G and Godsey, TJ and Liu, J and Franks, R and Zhang, G and Emerson, SR and Kim, Y},
title = {Twelve-Week Curcumin Supplementation Improves Glucose Homeostasis and Gut Health in Prediabetic Older Adults: A Pilot, Double-Blind, Placebo-Controlled Trial.},
journal = {Nutrients},
volume = {17},
number = {13},
pages = {},
doi = {10.3390/nu17132164},
pmid = {40647269},
issn = {2072-6643},
support = {Barbara K. Pass//Oklahoma State University/ ; 1-503351//Ottogi Ham Taiho Foundation/ ; },
mesh = {Humans ; *Curcumin/administration &amp; dosage/pharmacology ; Double-Blind Method ; *Prediabetic State/drug therapy/blood ; Aged ; Male ; Female ; Pilot Projects ; *Blood Glucose/drug effects/metabolism ; Glycated Hemoglobin/metabolism ; Gastrointestinal Microbiome/drug effects ; Middle Aged ; *Homeostasis/drug effects ; *Dietary Supplements ; Diabetes Mellitus, Type 2/prevention &amp; control ; Insulin/blood ; Overweight ; Body Mass Index ; },
abstract = {Background: The prevalence of diabetes increases with age, and food bioactive compounds have shown potential in mitigating its development. This study aimed to evaluate the efficacy of curcumin in preventing type 2 diabetes mellitus (T2DM) in older adults with prediabetes. We hypothesized that curcumin, due to its insulin-sensitizing effects, would help maintain glucose homeostasis, metabolic health, and gut health. Methods: This randomized, double-blind, placebo-controlled trial included 28 older adults (aged 60 years or older) with prediabetes or overweight/obesity. Participants were randomly assigned to receive either curcumin (80 mg) or placebo capsules for 12 weeks. The primary outcome measures were glucose homeostasis markers, including hemoglobin A1c (HbA1c), blood glucose, and insulin levels. Secondary outcomes included body composition, body mass index (BMI), body weight, lipid profiles, and gut microbiome composition. Data normality was assessed using the Shapiro-Wilk test, and two-way repeated-measures ANOVA with multiple comparisons was used to find differences between groups and over time. Results: A total of 23 participants (age = 66.52 ± 5.76 years; 14 in the curcumin group and 9 in the placebo group) completed the 12-week intervention. HbA1c levels significantly decreased in the curcumin group, whereas levels remained stable in the placebo group. While the curcumin group observed an increase in AST levels, the ALT level was reduced in the placebo group. Both the curcumin and placebo groups showed a reduced ALT/AST ratio by the end of the intervention. Body mass index, lipid profiles, and body composition showed no significant changes over the study period. Gut microbiome analysis revealed no significant changes in alpha diversity or beta diversity of microbiome; however, there was marginal enrichment of beneficial bacteria such as Bacteroidota (phylum), Bacteroidaceae (family), Agathobacter, Bacteroides, and Roseburia (genera) in the curcumin-supplemented group over time. Conclusions: Curcumin supplementation improved or favorably maintained glucose homeostasis and showed modest improvements in beneficial gut microbiota in older adults with prediabetes, potentially reducing the risk of developing diabetes. Long-term studies with larger sample sizes are needed to confirm these findings and determine the clinical relevance of curcumin supplementation for prediabetes prevention.},
}
@article {pmid40647261,
year = {2025},
author = {Ding, Q and Xue, D and Ren, Y and Xue, Y and Shi, J and Xu, Z and Geng, Y},
title = {Apple Cider Vinegar Powder Mitigates Liver Injury in High-Fat-Diet Mice via Gut Microbiota and Metabolome Remodeling.},
journal = {Nutrients},
volume = {17},
number = {13},
pages = {},
doi = {10.3390/nu17132157},
pmid = {40647261},
issn = {2072-6643},
support = {32372302//National Natural Science Foundation of China/ ; 32101964//National Natural Science Foundation of China/ ; 31970746//National Natural Science Foundation of China/ ; 2024YFF0619500//National Key Research and Development Program of China/ ; 2023M731346//China Postdoctoral Science Foundation/ ; BK20241755//Natural Science Foundation of Jiangsu Province/ ; BJ2023046//Top Talent Support Program for young and middle-aged people of Wuxi Health Committee/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Diet, High-Fat/adverse effects ; Mice, Inbred C57BL ; Male ; Mice ; *Acetic Acid/pharmacology ; *Metabolome/drug effects ; Powders ; *Malus/chemistry ; Liver/drug effects/metabolism/pathology ; Dysbiosis ; },
abstract = {Background/Objectives: High-fat-diet (HFD) consumption drives chronic liver injury via gut dysbiosis and metabolic disturban. Apple cider vinegar, rich in polyphenols and organic acids, shows potential in metabolic regulation. This study aimed to investigate whether apple cider vinegar powder (ACVP) alleviates HFD-induced liver injury by modulating the gut-liver axis. Methods: For 12 weeks, C57BL/6 J mice received daily ACVP gavage while being fed a HFD. A series of biological assessments were conducted, including systemic metabolic evaluations (body weight, serum alanine aminotransferase (ALT)/aspartate aminotransferase (AST), and lipid/glucose levels), hepatic steatosis (hematoxylin and eosin (H&amp;E) staining), intestinal microbiome characterization (16S rRNA gene genomic analysis), and comprehensive metabolite profiling of cecal contents (non-targeted metabolomics). Pearson correlation networks integrated multi-omics data. Results: ACVP attenuated HFD-induced weight gain by 26.3%, hepatomegaly and dyslipidemia, as well as reduced hepatic lipid vacuoles and serum ALT (48%)/AST (21.5%). ACVP restored gut microbiota diversity, enriching Muribaculaceae. Cecal metabolomics identified 38 HFD-perturbed metabolites reversed by ACVP, including indolelactate, hyocholate, and taurocholic acid. the Kyoto encyclopedia of genes and genomes (KEGG) analysis revealed ACVP-mediated recovery of linoleic acid metabolism. Correlation networks linked Akkermansia to anti-inflammatory metabolites (e.g., trans-ferulic), while Desulfobacterota correlated with pro-inflammatory oxylipins (e.g., 12,13-dihydroxy-9Z-octadecenoic acid (DHOME)). Conclusions: ACVP mitigates HFD-induced liver injury by remodeling gut microbiota, restoring microbial metabolites, and enhancing gut-liver crosstalk.},
}
@article {pmid40647258,
year = {2025},
author = {Fekete, M and Lehoczki, A and Kryczyk-Poprawa, A and Zábó, V and Varga, JT and Bálint, M and Fazekas-Pongor, V and Csípő, T and Rząsa-Duran, E and Varga, P},
title = {Functional Foods in Modern Nutrition Science: Mechanisms, Evidence, and Public Health Implications.},
journal = {Nutrients},
volume = {17},
number = {13},
pages = {},
doi = {10.3390/nu17132153},
pmid = {40647258},
issn = {2072-6643},
support = {TKP2021-NKTA-47//Ministry of Innovation and Technology of Hungary/ ; RRF-2.3.1-21-2022-00003//National Cardiovascular Laboratory Program/ ; },
mesh = {Humans ; *Functional Food ; *Public Health ; *Nutritional Sciences ; Gastrointestinal Microbiome ; Nutrigenomics ; Nutritive Value ; Cardiovascular Diseases/prevention &amp; control ; Prebiotics ; },
abstract = {In recent years, functional foods have garnered increasing scientific and public health interest due to their potential to confer physiological benefits beyond basic nutritional value. International bodies such as EFSA, FDA, and WHO define functional foods as those containing bioactive components that may contribute to the prevention and management of chronic non-communicable diseases, including cardiovascular disease, type 2 diabetes, and certain cancers. The evolving paradigm of "food as medicine" reflects a broader shift in nutritional science towards proactive, health-oriented dietary strategies. This article provides a comprehensive, interdisciplinary overview of functional foods by examining their biological mechanisms, clinical evidence, public health significance, regulatory frameworks, and future prospects-particularly in the context of advances in personalized nutrition and nutrigenomics. A thorough literature review was conducted, drawing from recent peer-reviewed studies and guidelines from key health authorities. The review highlights the roles of specific compounds such as probiotics and prebiotics in modulating the gut microbiome, flavonoids and polyphenols in anti-inflammatory processes, omega-3 fatty acids in cardiometabolic regulation, and vitamins and minerals in supporting immune function. While an expanding body of clinical trials and meta-analyses supports the health benefits of these compounds-including reductions in LDL cholesterol, improved insulin sensitivity, and mitigation of oxidative stress-the integration of functional foods into everyday diets remains challenging. Socioeconomic disparities and limited health literacy often impede their accessibility and widespread adoption in public health practice. Functional foods represent a promising component of prevention-focused modern healthcare. To maximize their impact, a coordinated, evidence-based approach is essential, involving collaboration among healthcare professionals, nutrition scientists, policymakers, and the food industry. Looking forward, innovations in artificial intelligence, microbiome research, and genomic technologies may unlock novel opportunities for the targeted and effective application of functional foods in population health.},
}
@article {pmid40647253,
year = {2025},
author = {Zhang, D and Leitman, M and Pawar, S and Shera, S and Hernandez, L and Jacobs, JP and Dong, TS},
title = {The Association Between Prevotella copri and Advanced Fibrosis in the Progression of Metabolic Dysfunction-Associated Steatotic Liver Disease.},
journal = {Nutrients},
volume = {17},
number = {13},
pages = {},
doi = {10.3390/nu17132145},
pmid = {40647253},
issn = {2072-6643},
mesh = {Animals ; Gastrointestinal Microbiome ; Humans ; Disease Progression ; *Liver Cirrhosis/microbiology ; Mice ; *Prevotella/genetics ; Male ; *Fatty Liver/microbiology ; Diet, High-Fat/adverse effects ; Disease Models, Animal ; Mice, Inbred C57BL ; Lipid Metabolism/genetics ; RNA, Ribosomal, 16S/genetics ; Liver/pathology/metabolism ; Female ; Obesity/microbiology/complications ; Middle Aged ; *Non-alcoholic Fatty Liver Disease/microbiology ; Metabolic Syndrome/microbiology/complications ; },
abstract = {Background/Objectives: Metabolic dysfunction-associated steatotic liver disease (MASLD), driven by obesity and metabolic syndrome, is increasingly prevalent and a significant contributor to liver fibrosis, cirrhosis, and liver-related mortality. Emerging research implicates the gut microbiome as a critical player in MASLD progression, yet specific microbial drivers remain poorly understood. Here, we explore the role of Prevotella copri (P. copri) in MASLD progression through both human patient cohorts and a mouse model of diet-induced obesity. Methods/Results: Using 16S rRNA sequencing, we identified elevated P. copri abundance in MASLD patients with advanced fibrosis, linked with significant shifts in microbial diversity and bacterial network connectivity. To investigate causality, experimental colonization of P. copri in mice on a high-fat diet worsened MASLD progression, with P. copri-colonized mice showing significant increases in hepatic steatosis, liver triglyceride accumulation, and body weight, independent of caloric intake. At the molecular level, P. copri colonization downregulated key lipid metabolism genes, such as carnitine palmitoyltransferase 1 and adipose triglyceride lipase, and impaired tight intestinal junction integrity through the downregulation of occludin. Collectively, our findings position P. copri as a possible driver of MASLD progression by promoting hepatic steatosis through lipid and triglyceride accumulation and fibrosis through decreased tight junction integrity. These insights suggest a promising therapeutic avenue to target specific microbial signatures like P. copri to curb MASLD progression and mitigate the associated risk of advanced fibrosis.},
}
@article {pmid40647243,
year = {2025},
author = {Lei, O and Yang, J and Kang, HH and Li, Z},
title = {Impact of a 12-Week Hypocaloric Weight Loss Diet with Mixed Tree Nuts vs. Pretzels on Trimethylamine-N-Oxide (TMAO) Levels in Overweight Adults.},
journal = {Nutrients},
volume = {17},
number = {13},
pages = {},
doi = {10.3390/nu17132137},
pmid = {40647243},
issn = {2072-6643},
support = {NCT03159689//Center for Human Nutrition and the International Tree Nut Council Nutrition Research and Education Foundation/ ; },
mesh = {Humans ; Female ; Male ; *Methylamines/blood ; *Overweight/diet therapy/blood ; *Nuts ; Middle Aged ; Adult ; *Diet, Reducing/methods ; Weight Loss ; Choline/administration &amp; dosage ; },
abstract = {UNLABELLED: Trimethylamine N-oxide (TMAO), a gut microbiome metabolite linked to cardiovascular health, can be influenced by dietary factors like choline intake and diet quality. This study compared the effects of mixed tree nuts (MTNs) and pretzels, as part of a 12-week hypocaloric weight loss diet, on TMAO levels and identified dietary predictors.<br><br>METHODS: Plasma samples from 95 overweight individuals consuming either 1.5 oz. of mixed tree nuts (MTNs, n = 56) or isocaloric pretzels (n = 39) daily for 12 weeks were analyzed. Nutritional data were collected at baseline and week 12 through dietary recall using the Automated Self-Administered 24 h Dietary Assessment Tool (ASA24), and the overall diet quality was assessed via the Healthy Eating Index (HEI) score. TMAO levels were determined and analyzed using linear mixed-effect models, adjusting for covariates. Wilcoxon signed-rank tests compared baseline and week 12 TMAO and weight. Multiple linear regression identified baseline predictors of TMAO.<br><br>RESULTS: Baseline demographics, anthropometric measures, HEI scores, and dietary choline intake were similar between the MTN and pretzel groups. A significant positive association was observed between baseline dietary choline and plasma TMAO levels (p = 0.012). The 12-week hypocaloric diet led to significant weight reduction in both groups (p < 0.01), but the magnitude of weight loss did not differ significantly between the MTN (-3.47 lbs) and pretzel (-4.25 lbs) groups (p = 0.18). Plasma TMAO levels decreased significantly in both groups (p < 0.01), but the between-group difference in reduction was not significant. (MTNs: -0.34 vs. pretzels: -0.37; p = 0.43). HEI scores and dietary choline intake remained unchanged, with no significant time-intervention interaction. Participants with low baseline HEI scores (&#x2264;53.72) had a more pronounced reduction in TMAO levels in the MTN group compared to the pretzel group (MTN: -0.54 vs. pretzel: -0.23; p = 0.045) over 12 weeks, despite similar weight loss. This difference was not observed in participants with higher HEI scores.<br><br>CONCLUSIONS: The 12-week hypocaloric diet reduced body weight and plasma TMAO levels similarly in both MTN and pretzel groups. Participants with lower dietary quality saw a greater reduction in TMAO levels in the MTN group, suggesting MTNs may better modulate TMAO levels, especially for those with poorer baseline diets.},
}
@article {pmid40647237,
year = {2025},
author = {Kalman, D and Hewlings, S and Madelyn-Adjei, A and Ebersole, B},
title = {Dietary Heme Iron: A Review of Efficacy, Safety and Tolerability.},
journal = {Nutrients},
volume = {17},
number = {13},
pages = {},
doi = {10.3390/nu17132132},
pmid = {40647237},
issn = {2072-6643},
mesh = {Humans ; *Heme/administration &amp; dosage/adverse effects/pharmacokinetics ; *Iron, Dietary/adverse effects/administration &amp; dosage/pharmacokinetics ; *Anemia, Iron-Deficiency/prevention &amp; control ; Dietary Supplements ; Biological Availability ; Intestinal Absorption ; *Iron/adverse effects ; Animals ; },
abstract = {Iron is a fundamental micronutrient essential for oxygen transport, enzymatic activity, and metabolic homeostasis. Yet it remains the most deficient nutrient in the world, with more than 2 billion people estimated with iron deficiency anemia. In the diet, animal foods provide iron primarily as heme iron. Dietary heme iron is absorbed through the active transport pathways catalyzed by heme oxygenase in the intestinal enterocyte. This form of heme differs in its bioavailability, absorption mechanisms, and tolerability compared to non-heme forms of iron, including iron salts and chelates. Adding more heme iron to a diet, including through iron supplements, may help to reduce the prevalence of iron deficiency. Future research should focus on research of heme iron supplementation strategies to enhance absorption efficiency, gut microbiome health, and safety, ensuring optimal iron status across diverse populations.},
}
@article {pmid40647225,
year = {2025},
author = {Shakhman, S and Pfeffer-Gik, T and Elial-Fatal, S and Broitman, Y and Yanai, H and Gophna, U and Dotan, I and Godny, L},
title = {Industrial Bread Composition: Potential Implications for Patients with Inflammatory Bowel Disease.},
journal = {Nutrients},
volume = {17},
number = {13},
pages = {},
doi = {10.3390/nu17132120},
pmid = {40647225},
issn = {2072-6643},
support = {G-2203-05892//Leona M. and Harry B. Helmsley Charitable Trust/ ; },
mesh = {*Bread/analysis ; Humans ; *Inflammatory Bowel Diseases/etiology/microbiology ; *Food Additives/analysis/adverse effects ; Food Handling ; Emulsifying Agents/analysis/adverse effects ; Gastrointestinal Microbiome ; Israel ; Food Preservatives/analysis/adverse effects ; },
abstract = {Background: Ultra-processed food (UPF) intake, particularly that of industrial breads rich in food additives (FAs) like emulsifiers, has been linked to higher risk of inflammatory bowel diseases (IBD). Here, we screened the ingredients and FAs used in the bread industry and reviewed their potential biological effects. Methods: We consecutively screened breads available at supermarket and health food store chains in Israel. Bread products were analyzed by dietitians and categorized into three categories based on their composition: low processed (traditional ingredients), medium processed (additives like malt and fibers), and highly processed (FAs like emulsifiers and preservatives). We conducted a literature review to explore the links between the identified FAs, microbial composition and intestinal inflammation. Results: Of the 233 breads screened, 195 (84%) were highly processed, 9 (4%) medium-processed and 29 (12%) low-processed. We identified 37 different FAs and ingredients used. Most breads contained preservatives-189 (81%), and emulsifiers-178 (76%). Calcium propionate (E-282) was the most prevalent preservative present in 112 (48%) breads, while sodium-stearoyl-2-lactylate (SSL-E-481) was the most prevalent emulsifier present in 86 (37%) breads. The literature review revealed that 19 (51%) FAs used in the bread industry were associated with the exacerbation of inflammation or gut microbiome dysbiosis by increasing cytokine production and adversely affecting microbial composition. Conclusions: Most of the available breads in Israel are highly processed, containing FAs that may mediate intestinal inflammation. Low-processed breads are available and may be more recommended to patients with IBD. Further understanding of the role of FAs in IBD etiology may guide dietary recommendations.},
}
@article {pmid40647222,
year = {2025},
author = {Braszczyńska-Sochacka, J and Sochacki, J and Mik, M},
title = {The Gut's Secret Code: Bowel Microbiota as a Biomarker for Adaptation.},
journal = {Nutrients},
volume = {17},
number = {13},
pages = {},
doi = {10.3390/nu17132117},
pmid = {40647222},
issn = {2072-6643},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Short Bowel Syndrome/microbiology/physiopathology/therapy ; Biomarkers/metabolism ; *Adaptation, Physiological ; Dysbiosis ; *Intestinal Failure/microbiology/therapy/physiopathology ; Intestine, Small/microbiology/surgery ; Parenteral Nutrition ; },
abstract = {Background: Chronic intestinal failure (CIF), most commonly caused by short bowel syndrome (SBS), necessitates complex care. This review explores the gut microbiota's role in intestinal adaptation in SBS, examining its potential as both a biomarker and therapeutic target. SBS results from extensive small bowel resection, leading to malabsorption and dependence on parenteral nutrition (PN). Post-resection, the gut microbiota undergoes significant alterations. While the small bowel microbiome typically comprises Streptococcus, Veillonella, and others, SBS patients often exhibit increased Gram-negative Proteobacteria. Dysbiosis is linked to adverse outcomes like liver disease and impaired growth, but beneficial effects such as energy salvage also occur. Intestinal adaptation, a process of increasing absorptive surface area in the remaining bowel, involves acute, remodeling, and maintenance phases. Preservation of ileum and stimulation with the oral diet are crucial. Biomarkers are needed to predict success, with gut microbiota composition emerging as a promising non-invasive option. The precise mechanisms driving adaptation remain incompletely understood. Conclusions: GLP-1 and GLP-2 analogues show promise in enhancing adaptation and reducing PN dependence. Surgical rehabilitation aims to maximize intestinal absorptive capacity, while transplantation remains a last resort due to high complication risks. Further research is needed to fully elucidate the microbiota's role and harness its potential in managing SBS.},
}
@article {pmid40647165,
year = {2025},
author = {Sultan, N and Tuck, CJ and Cheng, E and Kellow, NJ and Biesiekierski, JR},
title = {The Impact of Egg Consumption on Gastrointestinal Health: A Systematic Literature Review and Meta-Analysis.},
journal = {Nutrients},
volume = {17},
number = {13},
pages = {},
doi = {10.3390/nu17132059},
pmid = {40647165},
issn = {2072-6643},
support = {APP2025943//National Health and Medical Research Council/ ; GROW005//Australian Eggs/ ; },
mesh = {Humans ; *Eggs ; *Gastrointestinal Microbiome/physiology ; Methylamines/blood ; *Gastrointestinal Tract/microbiology/physiology ; Choline/blood ; C-Reactive Protein/metabolism ; Adult ; Female ; *Diet ; Biomarkers/blood ; Male ; },
abstract = {OBJECTIVE: Eggs are a valuable source of nutrients and bioactive compounds that may influence the gastrointestinal tract by modulating the microbiome, promoting the production of gastrointestinal-related metabolites, and mediating inflammation. Limited human studies have explored the effects of whole egg intake on indices of gastrointestinal health. This systematic literature review aimed to synthesise research investigating the impact of whole egg consumption on markers of gastrointestinal health.<br><br>METHODS: Five databases were searched from inception until July 2024. Studies were included if they examined the link between whole egg consumption and gastrointestinal markers, including symptoms, gut microbiome composition, inflammation, colonic fermentation, and egg-derived metabolites such as trimethylamine N-oxide (TMAO) in healthy adults. Two reviewers independently conducted title and abstract and full-text screening, with conflicts resolved by a third reviewer. Similarly, two authors conducted data extraction, which was verified by a third. A risk of bias assessment was conducted using validated tools. Random effects meta-analyses were performed to summarise the effect of egg consumption on TMAO, choline, and C-reactive protein (CRP).<br><br>RESULTS: Twenty-two studies were included in a narrative synthesis and ten in the meta-analyses. Nine were randomised controlled trials (RCTs), three were non-randomised intervention trials, eight were cross-sectional, and two were prospective cohort studies. Meta-analyses indicated that egg consumption did not impact plasma TMAO (n = 6, p = 0.22) or CRP (n = 3, p = 0.45) concentrations but did increase plasma choline (n = 5, p < 0.001) in the short term (&#x2264;4 weeks). Four studies found correlations between habitual egg consumption and specific gut bacteria, although results varied as egg consumption was both positively and negatively associated with butyrate-producing genera.<br><br>CONCLUSIONS: This review found conflicting results regarding egg consumption and most gastrointestinal outcomes, highlighting that future studies are needed to explore links between habitual egg intake and plasma TMAO, microbial diversity, and inflammation (PROSPERO registration: 408532).},
}
@article {pmid40647144,
year = {2025},
author = {Sreenesh, B and Varghese, E and Kubatka, P and Samuel, SM and Büsselberg, D},
title = {Prebiotic Potential of Dietary Polyphenols in Colorectal Cancer Immunomodulation.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {13},
pages = {},
pmid = {40647144},
issn = {2304-8158},
support = {NPRP14S-0311-210033//Qatar National Research Fund/ ; },
abstract = {Molecular crosstalk between the gut microbiome and human diet represent a potential therapeutic avenue requiring further investigation as it can be applied to human health management and treatment. Colon cancer, the third leading cause of cancer mortality, is often linked to the gut microbiome. In vitro and in vivo studies and metagenomic research have revealed alterations in gut microbial flora among diseased individuals. The human diet is connected to these changes in microbial inhabitants related to the pathophysiology underlying colorectal cancer (CRC). Polyphenols are well-studied, naturally occurring plant secondary metabolites recognized for their anti-inflammatory and antioxidant properties. The anticancer activities of these compounds are increasingly reported, offering insights into the administration of these natural molecules for managing various types of cancer and developing novel medications from them. Recent investigations have highlighted the prebiotic-like effects of these compounds on gut microbial dysbiosis and their metabolism concerning colorectal cancer, influencing colon cancer by interfering with multiple signaling pathways. This review will focus on the existing literature regarding the prebiotic potential of dietary polyphenols, and further research in this area would be valuable, as the integration of artificial intelligence (AI) and machine learning (ML) can enable analysis of the connections between unique gut microbiome profiles and other dependent factors such as physiological and genetic variables, paving the way for personalized treatment strategies in gut microbiome-based health management and precision medicine.},
}
@article {pmid40647126,
year = {2025},
author = {Zhou, B and Xing, Z and Wang, Y and Guan, X and Wang, F and Yin, J and Li, Z and Zhao, Q and Hou, H and Sang, X},
title = {Apple Juice Fermented with Lactiplantibacillus plantarum Improves Its Flavor Profile and Probiotic Potential.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {13},
pages = {},
pmid = {40647126},
issn = {2304-8158},
support = {2024YFD2401904//National Key Research and Development Program Project of China/ ; 2024-MSLH-049//Liaoning Provincial Natural Science Foundation Program Project/ ; HDYJ202201//Dalian Ocean University Doctoral Initiation Project/ ; },
abstract = {Fermented apple juice (FAJ), a nutrient-dense beverage rich in vitamins, offers multiple health benefits, including improved digestion, enhanced fat metabolism, and sustained energy provision with reduced caloric intake. To advance the development of probiotic-enriched flavored and functional juices, this study establishes Lactiplantibacillus plantarum (L. plantarum) as a safe and effective starter culture for apple juice fermentation. The selected strain exhibited minimal biogenic amine synthesis, producing only 30.55 ± 1.2 mg/L of putrescine and 0.59 ± 0.55 mg/L of cadaverine, while histamine and tyramine were undetectable. Furthermore, the strain demonstrated no hemolytic activity and exhibited robust biofilm-forming capacity, reinforcing its suitability for fermentation applications. An electronic nose analysis revealed that L. plantarum significantly enriched the volatile compound profile of FAJ, leading to an improved flavor profile. The strain also displayed excellent growth adaptability in the apple juice matrix, further optimizing fermentation efficiency and sensory quality. Crucially, 16S rRNA sequencing demonstrated that FAJ specifically restructures the gut microbiota in obese individuals, significantly elevating the relative abundance of beneficial genera, including Enterococcus, Parabacteroides, and Bifidobacterium (p < 0.05). Concurrently, FAJ enhanced glycolytic activity, suggesting a potential role in metabolic regulation. Collectively, these findings confirm that L. plantarum-fermented FAJ combines favorable sensory properties and safety with promising anti-obesity effects mediated through gut microbiome modulation and metabolic pathway activation. This study provides a critical scientific foundation for designing next-generation functional fermented beverages with targeted health benefits.},
}
@article {pmid40647113,
year = {2025},
author = {Terpou, A and Dahiya, D and Nigam, PS},
title = {Evolving Dynamics of Fermented Food Microbiota and the Gut Microenvironment: Strategic Pathways to Enhance Human Health.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {13},
pages = {},
pmid = {40647113},
issn = {2304-8158},
abstract = {The growing interest in health-promoting diets has brought fermented foods into the spotlight due to their unique microbial compositions and bioactive metabolites. Fermented foods and their beneficial microbiota are expected to stimulate the overall industry's expansion over the next few years as their beneficial health effects become established. This narrative review explores the evolving dynamics of fermented food microbiota and their interactions with the gut microenvironment, emphasizing strategic pathways to enhance human health. Fermented foods, both industrially produced and traditionally prepared, serve as carriers of beneficial microorganisms such as lactic acid bacteria, yeasts, and certain fungi that transform food substrates into bioactive compounds including short-chain fatty acids (SCFAs), exopolysaccharides, and bioactive peptides. Simultaneously, their bioactive metabolites are the subject of passionate investigation by the scientific community, uncovering novel beneficial aspects that have not been elucidated until now. These metabolites contribute to improved gut barrier function, modulation of immune responses, and overall metabolic health. Notably, microbial fermentation can reshape the intrinsic properties of food, offering therapeutic potential beyond basic nutrition. The interactions between food-derived microbes and the host gut microbiota suggest a synergistic mechanism influencing gastrointestinal and systemic health outcomes. Nevertheless, there remains a significant gap in the comprehensive evaluation of the existing literature in this specific research area. Further research is needed to standardize fermented food formulations, validate the effects of individual microbial strains, and optimize their application in personalized nutrition and functional food development. Accordingly, this review highlights the association between the microbiota of fermented foods and their metabolites with the gut microenvironment, emphasizing their potential health-promoting properties.},
}
@article {pmid40647075,
year = {2025},
author = {Sun, C and Zhang, Z and Sun, Y and Sun, X and Jin, Y and Zhu, J and Yu, J and Wu, T},
title = {Enteric Delivery of Probiotics: Challenges, Techniques, and Activity Assays.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {13},
pages = {},
pmid = {40647075},
issn = {2304-8158},
support = {23ZYCGSN00970//Tianjin Science and Technology Plan Project/ ; },
abstract = {Probiotics, as live microbial agents, play a pivotal role in modulating host microbiota balance, enhancing immunity, and improving gastrointestinal health. However, their application is hindered by critical challenges, such as inactivation during processing, storage, and gastrointestinal delivery, as well as low colonization efficiency. This article comprehensively reviews recent advances in probiotic delivery systems, focusing on innovative technologies, including hydrogels, nanocoatings, emulsions, and core-shell microgels. It provides an in-depth analysis of natural polyphenol-based nanocoatings and metal-phenolic network (MPN) single-cell encapsulation strategies for enhancing bacterial survival rates while highlighting the unique potential of microalgae-based bio-carriers in targeted delivery. Research demonstrates that well-designed edible delivery systems can effectively preserve probiotic viability and enable controlled intestinal release, offering novel strategies to reshape a healthy gut microbiome. While these systems show promise in maintaining probiotic activity and gut colonization, challenges remain in safety, scalable production, and clinical translation. Overcoming these barriers is crucial to fully harnessing probiotics for human health.},
}
@article {pmid40647044,
year = {2025},
author = {Park, I and Mannaa, M},
title = {Fermented Foods as Functional Systems: Microbial Communities and Metabolites Influencing Gut Health and Systemic Outcomes.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {13},
pages = {},
pmid = {40647044},
issn = {2304-8158},
support = {2024//This work was supported by Youngsan University research fund of/ ; },
abstract = {Fermented foods represent an intricate ecosystem that delivers live microbes and numerous metabolites, influencing gut health. In this review, we explore how complex microbial communities and metabolites generated during food fermentation modulate the gut microbiome and affect human health. We discuss fermentation-induced biochemical transformations, including enhanced fiber fermentability; nutrient availability; and the synthesis of bioactive metabolites such as short-chain fatty acids, exopolysaccharides, bacteriocins, and modified polyphenols. We describe the dynamic microbial ecology of fermented foods, influenced by ingredient variations, highlighting its effect on health-related metabolic outcomes. Fermented products when consumed transiently introduce beneficial microbes and bioactive compounds into the gut, thereby boosting microbial diversity, resilience, and barrier function. We review clinical and preclinical studies to substantiate the roles of fermented foods in immune regulation, metabolic homeostasis, cognitive function, and inflammation mitigation. Individual variability in response to fermented foods has been emphasized, underscoring the potential for personalized nutrition strategies informed by advanced omics technologies. By integrating microbial ecology, metabolomics, and clinical evidence, this review positions fermented food intake as a strategic dietary intervention for microbiome modulation and health promotion.},
}
@article {pmid40646988,
year = {2025},
author = {Shi, L and Yang, L and You, J and Wu, W and Xiong, G and Wang, L and Yin, T},
title = {Integrated Microbiome and Metabolomics Insights into Meat Quality Changes in Rice-Field Eel Slices During Refrigeration Storage: Effects of ε-Polylysine, Vitamin C, Epigallocatechin Gallate, and Phloretin.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {13},
pages = {},
pmid = {40646988},
issn = {2304-8158},
support = {2024BBB079, 2024BBB078//Hubei Provincial Technology Innovation Program Project/ ; CARS-46//China Agriculture Research System/ ; },
abstract = {Rice-field eel (Monopterus albus) slices, an important aquatic product in Southeast Asia, are prone to spoilage and deterioration during cold chain storage. In this study, the effects of a composite preservative (ε-polylysine, Vitamin C (Vc), epigallocatechin gallate (EGCG), and phloretin) on the muscle quality (color, texture, water holding capacity (WHC)) of rice-field eel slices during refrigeration storage at 4 °C for up to 7 days was investigated, and the underlying mechanism was elucidated by the integrated microbiome and metabolomics, in addition to Elisa and Low-Field Nuclear Magnetic Resonance (LF-NMR). After 7 days of storage, the WHC, shear force, and a* decreased by 11.39%, 34.37%, and 49.20% in treated samples, and by 19.18%, 38.38%, and 54.87% in control samples, respectively. The addition of the composite preservative significantly increased Hexokinase, Pyruvate kinase, and Creatine kinase, while it decreased the total viable count (TVC), total volatile basic nitrogen (TVB-N), thiobarbituric acid reactive substance (TBARS), and Lactic acid. Preservative treatment maintained the moisture content of the eel slices during storage and prevented bright red oxymyoglobin from transforming into brown metmyoglobin. Microbiota composition (especially Pseudomonas) and metabolic pathways (including amino acid and its metabolites, nucleotide and its metabolite, and organic acid and its derivatives, etc.) were obviously altered by the preservative treatment. Pseudomonas, tryptophan-aspartic acid (Trp-Asp), D-Glucose 6-phosphate, Succinic Acid, Biliverdin 1, 5-Diaminopentane, and Tyramine, etc., are potential biomarkers for the quality changes of eel slices during refrigeration. These findings provide an in-depth understanding of the improvement of the eel slice quality during refrigeration storage by the composite preservative.},
}
@article {pmid40646874,
year = {2025},
author = {Longshaw, M and Quest, B and Miller, W and Oba, PM and Swanson, OR and Swanson, KS and Miller, K},
title = {The Safety of FeedKind Pet[®] (Methylococcus capsulatus, Bath) as a Cultured Protein Source in the Diet of Adult Dogs and Its Effect on Feed Digestibility, Fecal Microbiome, and Health Status.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {13},
pages = {},
pmid = {40646874},
issn = {2076-2615},
support = {N/A - internal funding//Calysta (Inc)/ ; N/A - internal funding//Calysta (Inc)/ ; },
abstract = {Thirty-two healthy adult dogs (16 males and 16 females) were fed control kibble diets for one month, followed by six months (Weeks 0 to 25) of diets containing either 0, 4, 6, or 8% cultured protein derived from Methylococcus capsulatus (FeedKind Pet[®], FK), then they were fed control diets (0% FK) for a further two months (Weeks 25 to 34). The diets were isonitrogenous, isolipidic, and isocaloric and stage- and age-specific. The dogs were assessed for overall health, weight gain, and body condition score (BCS). Blood samples were collected 1 week prior to randomization, during acclimation, then in Weeks 5, 13, 25, 30, 32, and 34 for hematology, coagulation, and clinical chemistry; urine was collected according to the same time schedule for urinalysis. Feces were assessed for parasite load and presence of occult blood during Weeks 5, 9, 13, 17, 21, and 25. Fecal samples were collected during acclimation and Weeks 25 and 34 for fecal microbiome analysis and in Week 25 for apparent total gastrointestinal tract digestibility (ATTD). All dogs maintained a healthy weight and BCS throughout the study. Hematology parameters were within normal limits at the end of each phase of the study. With the exception of a decrease in serum phosphorus level and in urine pH in all groups at the end of the study, urine and serum chemistry results were within normal limits at the end of each phase. ATTD values for organic matter, protein, and energy exceeded 80%, whilst digestibility values for copper were around 20%. The fecal microbiome was dominated by Firmicutes. Alpha diversity increased during the safety phase before returning to baseline levels during the washout phase. The dominant genera in all groups were Megamonas, Peptoclostridium, Turicibacter, Catenibacterium, Fusobacterium, Romboutsia, and Blautia. The study has shown that the inclusion of cultured protein at up to 8% of the total diet of adult dogs can provide sufficient nutrition and is safe with no long-term effects on a range of health parameters.},
}
@article {pmid40646872,
year = {2025},
author = {Yu, SS and Xiang, JW and Zhang, L and Guo, XH and Wang, Y and Ding, GH and Hu, HL},
title = {Integrated Microbiome-Metabolome Analysis Reveals Intestine-Liver Metabolic Associations in the Moustache Toad.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {13},
pages = {},
pmid = {40646872},
issn = {2076-2615},
support = {2024-HZ12//County-School Cooperation Project in Suichang County, China/ ; N/A//Ecological Discipline Construction Fund of Lishui University, China/ ; },
abstract = {The intestinal microbiota regulates host metabolic homeostasis through production of bioactive microbial metabolites. These microorganisms facilitate digestion, enhance immune function, maintain osmoregulation, and support physiological balance via these bioactive compounds, thereby enhancing environmental adaptation. Our study investigated intestinal microbiota-liver metabolic interactions in Leptobrachium liui using 16S rRNA gene sequencing and non-targeted liquid chromatography-tandem mass spectrometry metabolomics. Key findings include (1) comparable alpha diversity but distinct microbial community structures between the small intestine (SI) and large intestine (LI), with the SI dominated by Enterobacteriaceae (72.14%) and the LI by Chitinophagaceae (55.16%); (2) segment-specific microbe-metabolite correlations, with predominantly positive correlations in the SI and complex patterns in the LI involving fatty acids, amino acids, and energy metabolites; and (3) significant correlations between specific bacterial families (Aeromonadaceae, Enterobacteriaceae, Chitinophagaceae) and hepatic metabolites related to fatty acid metabolism, amino acid synthesis, and energy pathways, indicating potential gut-liver axis associations. These findings provide insights into amphibian intestinal microbiota-hepatic metabolite associations and may inform future studies of host-microbe interactions.},
}
@article {pmid40646853,
year = {2025},
author = {Liu, H and Xiao, L and Liu, Z and Deng, Y and Zhu, J and Yang, C and Liu, Q and Tian, D and Cui, X and Peng, J},
title = {Impacts of Captive Domestication and Geographical Divergence on the Gut Microbiome of Endangered Forest Musk Deer.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {13},
pages = {},
pmid = {40646853},
issn = {2076-2615},
support = {No. 31470570//The People's Republic of China Wildlife Protection Program of the Central Forestry Reform and Development Fund of the State Forestry Administration, and the National Natural Science Foundation of China/ ; },
abstract = {Forest musk deer (Moschus berezovskii Flerov), a critically endangered ruminant species, faces extinction risks, with captive populations further threatened by prevalent digestive and immune disorders. This study utilized comparative metagenomic sequencing to assess intestinal microbiota structure and functional profiles between wild populations in Chongqing and Hunan and captive individuals. Wild populations exhibited a Pseudomonadota-dominated gut microbiota (significantly more abundant than in captive counterparts), enriched with lignin-degrading genera Novosphingobium and Acinetobacter. In contrast, the captive group demonstrated increased abundances of Bacillota/Bacteroidota, alongside abnormal proliferation of Escherichia and Clostridium. Both alpha and beta diversity analyses confirmed significant compositional divergences among the three groups, with wild populations maintaining higher diversity than captive populations. Notably, while substantial disparities in microbial abundance existed between wild populations (attributed to habitat vegetation differences), core microbial diversity and carbohydrate metabolic functions exhibited convergence. Functional analyses marked divergences in metabolic pathways: Captive microbiota showed enrichment in translation and glycan metabolism pathways, whereas wild populations displayed pronounced enrichment in immune regulation and environmental sensing pathways. These findings establish a theoretical foundation for optimizing wild population conservation strategies and developing science-based captive management protocols.},
}
@article {pmid40646851,
year = {2025},
author = {Mrenoshki, S and Temerario, L and Mastrorocco, A and Visci, G and Notario, E and Marzano, M and Martino, NA and Mrenoshki, D and Lacalandra, GM and Pesole, G and Dell'Aquila, ME},
title = {Taxonomic Profile of Cultivable Microbiota from Adult Sheep Follicular Fluid and Its Effects on In Vitro Development of Prepubertal Lamb Oocytes.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {13},
pages = {},
pmid = {40646851},
issn = {2076-2615},
abstract = {The aims of the present study were to analyze the taxonomic profile and to evaluate the functional effects of sheep FF cultivable microbiota on prepubertal lamb oocytes PLOs developmental potential. Ovarian FFs were recovered from slaughtered adult sheep via the aspiration of developing follicles and used for microbiota propagation. Bacterial pellets underwent 16S rRNA gene sequencing and targeted culturomics, whereas cell-free supernatants were used as supplements for the in vitro maturation (IVM) of slaughtered PLOs. For the first time, bacteria presence in adult sheep FF was detected, with the first report of Streptococcus infantarius subsp. infantarius (as a species) and Burkholderia cepacia (as a genus and species) in either animal or human FF. The short- and long-term effects of bacterial metabolites on PLO maturation and embryonic development were demonstrated. As short-term effects, the addition of FF microbiota metabolites did not affect the oocyte nuclear maturation and mitochondria distribution pattern, except in one of the examined supernatants, which reduced all quantitative bioenergetic/oxidative parameters. As long-term effects, one of them reduced the total cleavage rate after in vitro embryo culture (IVC). In conclusion, microbiota/bacteria are present in adult sheep FF and may influence reproductive outcomes in vitro. Future studies may reveal the beneficial in vitro effects using the microbiome from preovulatory follicles.},
}
@article {pmid40646844,
year = {2025},
author = {Kerek, &#xc1; and Szabó, &#xc1; and Jerzsele, &#xc1;},
title = {Amoxicillin Resistance: An In Vivo Study on the Effects of an Approved Formulation on Antibiotic Resistance in Broiler Chickens.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {13},
pages = {},
pmid = {40646844},
issn = {2076-2615},
support = {RRF-2.3.1-21-2022-00001//National Research, Development and Innovation Office/ ; },
abstract = {Background: Antimicrobial resistance (AMR) is a growing global concern in poultry production, where antibiotic use can disrupt gut microbiota and enrich antimicrobial resistance genes (ARGs). Objectives: This study aimed to assess the in vivo effects of a veterinary-approved amoxicillin formulation on gut microbiome composition and ARG profiles in broiler chickens. Methods: A total of 120 Ross-308 broiler chickens were randomly allocated into 12 experimental groups (n = 10 per group), with three replicates per treatment. Birds received either full-dose (1×), a subtherapeutic quarter-dose (¼×) of amoxicillin, a placebo (starch), or no treatment. Cloacal swabs were collected on days 0, 14, and 28 for shotgun metagenomic sequencing. One-way ANOVA was used to evaluate treatment effects on body weight, with significant differences observed from day 14 onward (p < 0.0001). Results: The ¼× dose caused a more pronounced microbiome shift than the 1× dose, with a marked reduction in Pseudomonadota and increase in Bacillota and Bacteroidota. ARG abundance declined in the ¼× group (from 1386 to 1012). While TEM-type ESBL genes were ubiquitous, CTX-M-1 emerged only after ¼× treatment. Worryingly, 20 types of vancomycin resistance genes were detected across all samples. Plasmid-borne ARGs and mobile genetic elements decreased in the ¼× group. Conclusions: Even subtherapeutic antibiotic exposure significantly reshapes the gut microbiota composition and ARG landscape, highlighting the need for refined risk assessments and microbiome-conscious antimicrobial policies in poultry farming.},
}
@article {pmid40646835,
year = {2025},
author = {Kyrtsoudis, D and Alvanou, MV and Loukovitis, D and Gourdouvelis, D and Bampidis, VA and Chatziplis, D and Mitsopoulos, IK},
title = {Influence of Oregano Essential Oil on the Rumen Microbiome of Organically Reared Alpine Goats: Implications for Methanobacteria Abundance.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {13},
pages = {},
pmid = {40646835},
issn = {2076-2615},
support = {20957//Rural Development Project (RDP) 2014-2020, project code M16&#x3a3;&#x3a5;&#x39d;2-00144, Agricultural European Innovation Partnership (EIP AGRI)/ ; },
abstract = {The present study aimed to evaluate the effects of dietary supplementation with organic oregano (Origanum vulgare) essential oil (OEO) on the rumen microbial population, with a focus on methanogenic archaea, in lactating dairy goats. A total of nine age-matched goats (mean body weight 49 ± 1.8 kg) were assigned to three experimental groups (n = 3 per group) in a completely randomized design. All animals were fed a basal diet consisting of a corn-based concentrate and a forage mix composed of alfalfa hay, wheat straw and corn silage. Group 1 was the control group while Groups 2 and 3 received an OEO supplement at dosages of 1 mL/day and 2 mL/day per animal, respectively, incorporated into the concentrate feed. Rumen fluid samples were collected on days 15, 30 and 45 of the feeding trial and their microbial profile was assessed using NGS analysis. The results demonstrated a reduction in the relative abundance of methanobacteria in both OEO-supplemented groups compared to the control group. Statistical analysis revealed significant differences between feeding groups and days of sampling. These findings suggest that OEO has the potential to modulate the rumen microbiome by reducing methane-producing archaeal populations. In conclusion, dietary supplementation with OEO may serve as a natural strategy to mitigate enteric methane emissions in Alpine dairy goats.},
}
@article {pmid40646827,
year = {2025},
author = {Hu, X and Zhu, S and Chen, Y and Zhang, L and Tan, H and Wu, C and Zhang, X and Deng, X and Li, Y},
title = {Bioaccumulation, Ecotoxicity, and Microbial Responses in Hoplobatrachus rugulosus Tadpoles Following Co-Exposure to Imidacloprid and Microplastics.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {13},
pages = {},
pmid = {40646827},
issn = {2076-2615},
support = {221CXTD1015//Hainan Provincial Natural Science Foundation of China/ ; 42107501//National Natural Science Foundation of China/ ; 1630042025002//Central Public-interest Scientific Institution Basal Research Fund/ ; },
abstract = {Agricultural organic pollutants have been identified as a key factor contributing to amphibian population decline, particularly during early developmental stages when tadpoles are frequently exposed to neonicotinoids (NEOs) and microplastics (MPs). In this study, Hoplobatrachus rugulosus tadpoles were exposed to imidacloprid (IMI: 0.045, 0.45, and 4.5 mg L[-1]) and polyethylene-derived MPs (10 mg L[-1]) from agricultural mulch films, both individually and in combination. We systematically evaluated acute toxicity, bioaccumulation, developmental and oxidative stress responses, and changes in the skin and gut microbiota. The results showed that the 96 h median lethal concentration (LC50) of IMI was 44.8 mg L[-1] in the IMI-only group and was 40.5 mg L[-1] in the IMI + MPs group, indicating the negligible impact of MPs on acute toxicity. However, in the highest co-exposure group (IMI4.5 + MPs), tadpole body length and weight decreased by 14.7% and 22.6%, respectively, alongside marked changes in oxidative stress, whereby catalase (CAT) and superoxide dismutase (SOD) activities were suppressed, while malondialdehyde (MDA) levels increased by 35%, indicating elevated lipid peroxidation. Furthermore, the micronucleus frequency in erythrocytes was significantly elevated, suggesting genotoxic effects. Microbial community analysis revealed significant shifts in the relative abundance of gut and skin microbiota under IMI + MPs exposure, with a notable enrichment of Proteobacteria, Fusarium, Actinomycetota, and Bacteroidota, indicating the disruption of host-microbiome interactions. This study proposes a comprehensive multi-tiered assessment framework encompassing environmental exposure, bioaccumulation, toxicological endpoints, oxidative stress biomarkers, and microbiome shifts. Our findings provide new mechanistic insights and quantitative evidence on the compound threats posed by IMI and MPs to amphibians in aquatic environments.},
}
@article {pmid40646826,
year = {2025},
author = {Rey, AI and Higueras, C and Olmeda, P and Sainz, A and Gálvez, BG and Larrosa, M},
title = {Markers of Gut Health in Small Animals: Focus on Fatty Acids and Amino Acids as Indicators of Intestinal Functionality and Microbiome Activity.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {13},
pages = {},
pmid = {40646826},
issn = {2076-2615},
abstract = {Chronic inflammatory enteropathies (CIEs) in companion animals represent a group of idiopathic, immune-mediated gastrointestinal disorders in which the intestinal epithelium can be altered, affecting intestinal functionality, nutrient absorption, and microbiota composition. This review presents an overview of markers that could be used for the assessment of intestinal health, focusing extensively on functional biomarkers, with particular attention to fatty acids (including short-chain fatty acids, SCFAs) and amino acids. Studies have consistently shown reduced concentrations of SCFAs in companion animals with CIEs compared to healthy groups. These alterations occur with varying intensity depending on the type of enteropathy. Alterations in saturated, monounsaturated, and long-chain polyunsaturated fatty acids have also been reported in blood and feces, particularly in omega-3 and omega-6 derivatives, as well as in the elongase and desaturase indices responsible for endogenous synthesis. In addition, amino acids serve as precursors to key metabolites involved in mucosal immunity, oxidative stress regulation, and microbial homeostasis. In CIEs, alterations in systemic and fecal amino acid profiles have been observed, reflecting both host metabolic adaptation and microbial dysbiosis. Integrating fatty acid and amino acid profiles can help distinguish different types of enteropathies, providing additional discriminatory power for determining response to dietary treatment. Future research should aim to elucidate the causal relationships between metabolic alterations and disease pathogenesis, which could lead to novel dietary interventions targeting metabolic interactions between the microbiota and the host.},
}
@article {pmid40646806,
year = {2025},
author = {Irving, J and Pineau, V and Shultz, S and Ter Woort, F and Julien, F and Lambey, S and van Erck-Westergren, E},
title = {Impact of Low-Starch Dietary Modifications on Faecal Microbiota Composition and Gastric Disease Scores in Performance Horses.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {13},
pages = {},
pmid = {40646806},
issn = {2076-2615},
support = {2625299/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; NA//Lambey SAS/ ; },
abstract = {Equine gastric disease (EGD) is a common condition in performance horses (Equus caballus), potentially compromising behaviour, performance, and welfare. EGD is often attributed to high-starch, high-sugar feeds and limited forage. Evidence for diet-induced changes on digestive microbiota is lacking. Nine elite showjumping horses were housed at the same performance yard with standardised diet and management throughout the study. Horses were transitioned from a high-sugar and -starch (31%) feed to a low-starch and -sugar (16.5%) concentrate feed. Gastroscopies, blood, and faecal samples were taken pre- and 12 weeks post-diet change. Squamous and glandular ulceration was blindly graded a posteriori using 0-4 scores and faecal microbiota profiled using 16S rRNA gene amplicon sequencing. Total (t(1,8) = -6.17, p < 0.001; Pre: 4 [0-5], Post: 1 [0-2]), squamous (t(1,8) = -5.32, p < 0.001; Pre: 1 [0-3], Post: 0 [0-1]), and glandular (t(1,8) = -2.53, p = 0.04; Pre: 2.5 [0-4], Post: 0 [0-2]) disease improved following the introduction of a low-starch diet. Diet change did not impact microbiota communities (PERMANOVA: F(1,16) = 1.37, p = 0.15, r[2] = 0.08), but Firmicute to Bacteroidota (F/B) ratio reduced (t(1,8) = -3.13, p = 0.01; Pre: 2.07 ± 0.21 vs. Post: 1.29 ± 0.14). Lower F/B ratios were associated with reduced total EGD scores (ChiSq(1,17) = 3.83, p = 0.05). Low-starch diets did not influence faecal microbiota diversity but aided gastric disease healing and reduced F/B ratios in elite showjumpers during a competition season without medication.},
}
@article {pmid40646733,
year = {2025},
author = {Pettett, L and Ebrahimie, E and Chinkangsadarn, T and Mohammadi Dehcheshmeh, M and Trott, DJ and Bird, PS},
title = {The Oral Microbiome in Queensland Free-Ranging Koalas (Phascolarctos cinereus) and Its Association with Age and Periodontal Disease.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {13},
pages = {},
pmid = {40646733},
issn = {2076-2615},
abstract = {This study was developed to profile the oral microbiome of free-ranging Queensland koalas and its association with age, gingivitis and periodontitis. Using next-generation sequencing of 16S rRNA genes, the microbiota of oral plaque samples from eight koalas across different age groups (joey, juvenile, adult and old) were compared. The findings revealed significant shifts in microbiota composition with age and disease presence. At the phylum level, Proteobacteria were the most dominant phylum, especially in younger koalas. Proteobacteria abundance decreased with age, while Bacteroidetes, Fusobacteria and Actinobacteria increased. At the genus level, Acinetobacter declined with age. Fusobacterium and Porphyromonas became more prominent genera in older koalas and those with periodontal disease. The beneficial genus Lactobacillus was detected only in the joey, suggesting a potential loss of protective microbes with age. Alpha diversity analysis showed high variability within individuals based on age. Alpha diversity was remarkably lower in younger koalas and increased with periodontal disease. Beta diversity suggested distinct microbiota composition differences between younger (joey and juvenile) and older (adult and old) koalas, although statistical significance was limited by sample size. This is the first detailed characterization of the oral microbiome in Queensland's free-ranging koalas and highlights its association with age and oral health status. Findings may contribute to better understanding of oral disease progression in koalas and support conservation and health management efforts.},
}
@article {pmid40646729,
year = {2025},
author = {Lawless, C and Kovacs, K and Mohammadi Dehcheshmeh, M and Ebrahimie, E and Messele, YE and Snowball, M and Trott, DJ and McLelland, DJ},
title = {Higher Dietary Fibre Increases the Faecal Microbiome Diversity of Golden Lion Tamarins (Leontopithecus rosalia).},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {13},
pages = {},
pmid = {40646729},
issn = {2076-2615},
support = {Donation//This research was in part funded by a generous donation to The University of Adelaide by As-sociate Professor Phil Bird./ ; },
abstract = {Gut microbiota influences host energetics, metabolic rate, and overall health. Optimising the diet, such as by increasing dietary fibre, is a key strategy for promoting a healthy microbiome and improving host energy balance. In this study, we compared the faecal microbiome of five zoo-housed golden lion tamarins (Leontopithecus rosalia) before and after a dietary fibre increase using 16S rRNA gene sequencing. Prevotella, the most abundant genus, declined significantly (FDR-corrected p < 0.05) following the introduction of a higher-fibre diet. The dietary change also significantly altered the overall gut microbial composition, including the emergence of Eisenbergiella (FDR-adjusted p < 0.05), a butyrate-producing genus whose relative abundance increased from 0% to 0.005% (FDR-adjusted p < 0.05). Given the role of Eisenbergiella in butyrate synthesis, this shift may enhance host energy metabolism and microbial interactions. Additionally, both alpha and beta diversity increased significantly (p < 0.05) after the dietary fibre intervention. A significant reduction in Desulfobacterota (FDR-adjusted p < 0.05) following dietary fibre enrichment was observed, suggesting a shift away from microbial groups that may be associated with pathogenicity or pro-inflammatory effects. Collectively, these changes represent a positive shift in the microbiome, supporting improved host energetics and metabolic health.},
}
@article {pmid40646691,
year = {2025},
author = {Zhou, D and Wu, C and Li, C and Li, M and Li, Z and Li, J and Zhang, Y and Zhao, H and Wang, Y and Liang, L and Xu, L and Li, Y and Zhong, LL and Feng, S and Tian, GB},
title = {SLAMF7 regulates goblet cell mucus production and negatively impacts gut homeostasis and commensalism.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2527857},
doi = {10.1080/19490976.2025.2527857},
pmid = {40646691},
issn = {1949-0984},
mesh = {Animals ; Homeostasis ; *Goblet Cells/metabolism ; *Gastrointestinal Microbiome ; Mice ; Intestinal Mucosa/microbiology/metabolism ; Macrophages/metabolism/immunology ; *Signaling Lymphocytic Activation Molecule Family/genetics/metabolism ; Mice, Inbred C57BL ; *Mucus/metabolism ; Symbiosis ; Mice, Knockout ; Inflammatory Bowel Diseases/microbiology ; Male ; Akkermansia ; },
abstract = {Crosstalk between the intestinal mucosal barrier and the gut microbiota contributes to maintaining intestinal homeostasis. Accumulating evidence suggests that diverse mechanisms are involved in maintaining intestinal homeostasis. Any disturbance in these pathways can compromise gut homeostasis and trigger chronic inflammatory diseases such as inflammatory bowel disease (IBD). However, how host factors regulate the intestinal mucosal barrier and change the gut microbiome has not been well defined. Here, we discovered that disruption of SLAMF7 protects against intestinal inflammation. SLAMF7 deficiency significantly altered the intestinal microbiota composition, specifically the expansion of the mucus-specific bacterium Akkermansia muciniphila. Moreover, SLAMF7 deficiency resulted in goblet cell generation by increasing the number of M2-like C1q+ macrophages, which may contribute to a thicker mucosal barrier. Mechanistically, SLAMF7 deficiency increased goblet cell generation through C1q+ M2-like macrophage polarization, which partly led to a thicker mucosal barrier. Depletion of SLAMF7 in intestinal macrophages upregulated C1q via activation of the STAT6-MafB pathway. The upregulation of C1q in macrophages resulted in a bias toward the M2 phenotype in response to damage-associated molecular patterns (DAMPs) stimulation. Accordingly, SLAMF7 activation induced a shift in macrophage polarization and reduced mucus secretion, which partially aggravated intestinal inflammation. Conversely, SLAMF7 knockdown mitigated DSS-induced intestinal inflammation to some extent. This work reveals the previously unrecognized functions of SLAMF7 in regulating intestinal inflammation and tissue homeostasis.},
}
@article {pmid40646653,
year = {2025},
author = {Wu, W and Cheng, J and Hou, Z and Yan, Q and Wang, X and He, J and Zhu, Y and Li, J},
title = {Association between the dietary index for gut microbiota and all-cause/cardiovascular mortality in patients with metabolic dysfunction-associated steatotic liver disease.},
journal = {Diabetology &amp; metabolic syndrome},
volume = {17},
number = {1},
pages = {263},
pmid = {40646653},
issn = {1758-5996},
support = {82270915//the National Natural Science Foundation of China/ ; 202304051001021//Special Fund for Science and Technology Innovation Teams of Shanxi Province/ ; 2022//Shanxi Funding for High Level Overseas Returns/ ; 202103021224425//Basic Research Program of Shanxi/ ; BYJL010//Shanxi Province Higher Education "Billion Project" Science and Technology Guidance Project/ ; },
abstract = {BACKGROUND: Nutrient interactions with the gut microbiome modulate the development of metabolic dysfunction-associated steatotic liver disease (MASLD) and cardiovascular disease. The dietary index for gut microbiota (DI-GM) is an innovative and comprehensive diet index to assess quality for health of gut microbiota.<br><br>METHOD: This is a cohort study from the interview date to the date of death or the end of follow-up (December 31, 2019). Involving 13,390 participants in National Health and Nutrition Examination Survey (NHANES), including 3538 with MASLD and 9852 without MASLD. DI-GM was calculated using 14 foods and nutrients with clear positive or negative impacts on gut microbiota, and MASLD was assessed based on liver steatosis and cardiometabolic risk factors, with all-cause and cardiovascular mortality determined through probabilistic matching and death certificate review. Restricted Cubic Spline (RCS) analysis and Cox regression were palyed for the DI-GM-mortality correlation. Subgroup analyses to identify the interactive factors that influence their relationship in MASLD. Six sensitivity analyses reinforced findings.<br><br>RESULTS: MASLD participants exhibited lower DI-GM levels, which were statistically associated with higher mortality. Each DI-GM unit increase in MASLD was associated with a 13% lower all-cause mortality (HR&#x2009;=&#x2009;0.87, 95% CI 0.78-0.98) and a 19.5% lower cardiovascular mortality (HR&#x2009;=&#x2009;0.805, 95% CI 0.690-0.938). In advanced fibrosis MASLD, this increase was linked to a 20% lower cardiovascular mortality risk (HR&#x2009;=&#x2009;0.800, 95% CI 0.691-0.927). Age and prediabetes significantly modified DI-GM's effect on mortality risk.<br><br>CONCLUSIONS: The study revealed a significant inverse correlation between the DI-GM and all-cause/cardiovascular mortality in patients with MASLD, which provide dietary suggestions and guidance for MASLD patients in preventing early mortality. However, limitations such as the cross-sectional design, potential residual confounding, and population-specific generalizability should be considered when interpreting these findings.},
}
@article {pmid40646642,
year = {2025},
author = {Peng, Q and Sun, S and Ma, J and Chen, S and Gao, L and Du, X and Liu, X and Zhu, F and Peng, W and Liu, Y and Su, P and Cernava, T and Zhang, D},
title = {The effect of developmental stages on microbiome assembly in the phyllosphere and rhizosphere of rice grown in urban area soil.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {86},
pmid = {40646642},
issn = {2524-6372},
support = {32302316//Natural Science Foundation of China/ ; 32302316//Natural Science Foundation of China/ ; 32302316//Natural Science Foundation of China/ ; 2023YFD1400200//National Key R&amp;D Program of China/ ; },
abstract = {BACKGROUND: The plant microbiome can support plant health and fitness in the face of biotic and abiotic stress. Research has mostly focused on plant growth in natural and agricultural soils. However, as urban areas continue to expand and soils change in the Anthropocene, microbiome assembly during development of plants grown in urban area soil remains largely elusive. Here, we examined the effect of developmental stages on the phyllosphere and rhizosphere microbiomes of rice grown in soil from an urban area during the vegetative growth stages.<br><br>RESULTS: We found that the microbial alpha and beta diversity, networks, and functions of the phyllosphere and rhizosphere microbiomes significantly differed among rice seedling, tillering, and elongation stages. Notably, we observed that bacteria assigned to potential animal parasites or symbionts not only exhibited significantly higher relative abundances in the phyllosphere compared to the rhizosphere but are also influenced by the developmental stages. Plants grown in the urban area soil had a higher relative abundance of Bacteroidales and enriched bacteria assigned to potential animal parasites or symbionts in the phyllosphere in contrast to plants grown in field. Some of these bacteria were shown to significantly influence the assembly of the phyllosphere microbiome and to prevalently engage in negative interactions with other microbes.<br><br>CONCLUSION: Our study provides new insights into developmental stage-resolved microbiome assembly of plants grown in urban areas. The insights could help in the development of strategies for promoting 'One Health' by highlighting the role of plants as alternative host for bacterial groups that are prevalently associated with animals.},
}
@article {pmid40646631,
year = {2025},
author = {Wang, N and Ping, L and Mei, X and Zhang, Y and Zhang, Y and Yang, X and Guo, Y and Gao, Y and Xu, Y and Shen, Q and Yang, T and Wei, Z},
title = {Succinic acid reduces tomato bacterial wilt disease by recruiting Sphingomonas sp.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {85},
pmid = {40646631},
issn = {2524-6372},
support = {2022YFD1500202//the National Key Research and Development Program of China/ ; 2022YFD1500202//the National Key Research and Development Program of China/ ; 2022YFD1500202//the National Key Research and Development Program of China/ ; 2022YFD1500202//the National Key Research and Development Program of China/ ; 2022YFD1500202//the National Key Research and Development Program of China/ ; 2022YFD1500202//the National Key Research and Development Program of China/ ; 2022YFD1500202//the National Key Research and Development Program of China/ ; 2022YFD1500202//the National Key Research and Development Program of China/ ; 2022YFD1500202//the National Key Research and Development Program of China/ ; 2022YFD1500202//the National Key Research and Development Program of China/ ; 2022YFD1500202//the National Key Research and Development Program of China/ ; 2022YFD1500202//the National Key Research and Development Program of China/ ; GuiKe AA24010003//Guangxi&#x2002;Science and Technology Program/ ; },
abstract = {BACKGROUND: Root exudates are key mediators in maintaining plant health by mediating interactions with the rhizosphere microbiome. Plants release specific exudates to defend against pathogens, either directly by inhibiting pathogen growth or indirectly through alterations in the microbial community. However, the mechanisms by which root exudates influence the rhizosphere microbiome to enhance plant resistance remain poorly understood. In this study, we evaluated the effects of 23 root exudates on the growth of the pathogen Ralstonia solanacearum and tomato bacterial wilt.<br><br>RESULTS: Seventeen of the exudates reduced the disease index, with most having neutral or even promotive effects on R. solanacearum growth. Notably, succinic acid (SA) completely suppressed bacterial wilt without directly affecting the pathogen or tomato plants in the absence of the rhizosphere microbiome. We further explored the impact of SA on the rhizosphere bacterial community in both tomato rhizosphere and bulk soil. Only the bacterial community in the rhizosphere responded significantly to SA addition, with indicator species and network analyses identifying Sphingomonas sp. WX113 as the key taxa associated with this response. A subsequent greenhouse experiment showed that co-applying Sphingomonas sp. WX113 with SA achieved 100% biocontrol efficiency, outperforming either treatment alone. In vitro assays further demonstrated that SA enhanced the antagonistic activity of Sphingomonas sp. WX113 against R. solanacearum.<br><br>CONCLUSIONS: Our findings emphasize the host-mediated role of root exudates, such as succinic acid, in selectively promoting beneficial Sphingomonas sp., thereby enhancing plant resistance to bacterial wilt. These results offer new perspectives on the combination of beneficial microbes and their matching compounds for soil-borne diseases management.},
}
@article {pmid40646629,
year = {2025},
author = {Koutromanos, I and Legaki, E and Dovrolis, N and Vassilopoulos, E and Stem, A and Vasiliou, V and Tzavellas, E and Gazouli, M},
title = {Integrating gut microbiome and neuroplasticity genomics in alcohol use disorder therapy.},
journal = {Human genomics},
volume = {19},
number = {1},
pages = {78},
pmid = {40646629},
issn = {1479-7364},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Alcoholism/genetics/therapy/microbiology ; *Neuronal Plasticity/genetics ; Male ; Female ; Adult ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; *Genomics/methods ; Prospective Studies ; Dysbiosis/genetics/microbiology ; },
abstract = {BACKGROUND: Alcohol Use Disorder (AUD) is a chronic neuropsychiatric condition with substantial public health impact. The interplay between gut microbiota and neuroplasticity-related genes presents a novel approach to understand AUD pathophysiology and treatment response. While microbial dysbiosis has been implicated in AUD, its correlation with gene expression changes in neuroplasticity pathways remains unexplored. This study investigates microbiome composition, microbial metabolic pathways, and their correlation with neuroplasticity-related genes in AUD patients undergoing treatment.<br><br>METHODS: We conducted a prospective observational study integrating gut microbiome 16S rRNA sequencing and host neuroplasticity-related gene expression profiling in AUD patients undergoing treatment which combines psychotherapeutic intervention along with oral diazepam administration followed by Pythagorean Self Awareness Intervention. Patients were classified as responders or non-responders, and microbial composition, functional pathways, and host-microbiota interactions were analyzed using multi-omic correlation frameworks.<br><br>RESULTS: Responders exhibited a microbiome enriched in short-chain fatty acid (SCFA)-producing bacteria (e.g., Lachnospiraceae), linked to gut barrier integrity and neurotransmitter synthesis. In contrast, non-responders demonstrated enrichment of inflammation-associated taxa (Succinivibrionaceae) and oxidative stress-related metabolic pathways. Correlation analysis revealed microbiome-mediated modulation of neuroplasticity-related genes measured from peripheral blood, including BDNF, GRIA1, CAMK2G, and EGR family genes, suggesting a gut-brain-genomic axis in AUD treatment response.<br><br>CONCLUSIONS: This study highlights the role of gut microbiota as a modulator of neuroplasticity-related gene expression in AUD patients. Integrating microbiome and host genomic signatures could improve biomarker-based prediction of treatment response and inform precision medicine approaches for AUD. Future studies should expand these findings by incorporating multi-omic approaches, including epigenomics and exposomics, to refine microbiome-targeted interventions for addiction therapy.},
}
@article {pmid40646012,
year = {2025},
author = {Soler, Z and Serrano-Gómez, G and Pons-Tarín, M and Vega-Abellaneda, S and Xie, Z and Manjón, I and Cognard, C and Varela, E and Yañez, F and Noguera-Segura, A and Roca-Bosch, M and Manichanh, C},
title = {A contributory citizen science project reveals the impact of dietary keys to microbiome health in Spain.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {131},
pmid = {40646012},
issn = {2055-5008},
support = {FI21/00262//Instituto de Salud Carlos III/ ; FI21/00262//Instituto de Salud Carlos III/ ; SGR 00459//Ag&#xe8;ncia de Gesti&#xf3; d'Ajuts Universitaris i de Recerca/ ; SGR 00459//Ag&#xe8;ncia de Gesti&#xf3; d'Ajuts Universitaris i de Recerca/ ; SGR 00459//Ag&#xe8;ncia de Gesti&#xf3; d'Ajuts Universitaris i de Recerca/ ; 72190278//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; PI20/00130//Instituto de Salud Carlos III (ISCIII), Spain/ ; },
mesh = {Humans ; Spain/epidemiology ; Male ; Female ; Adult ; *Gastrointestinal Microbiome ; *Diet ; Middle Aged ; *Inflammatory Bowel Diseases/microbiology ; Dysbiosis/microbiology ; Young Adult ; Vegetables ; Fruit ; Aged ; *Bacteria/classification/genetics/isolation &amp; purification ; Adolescent ; Feces/microbiology ; },
abstract = {Low consumption of whole grains, fruits, and vegetables has been identified as dietary risks for non-communicable diseases such as inflammatory bowel diseases (IBDs). We explore how individual and lifestyle factors influence these risks by shaping gut microbiome composition. 1001 healthy participants from all Spanish regions provided personal and dietary data at baseline, six, and twelve months, yielding 2475 responses. Gut microbiome data were analyzed for 500 healthy participants and 321 IBD patients. Our findings reveal that adherence to national dietary guidelines-characterized by diets rich in nuts, seeds, fruits, and vegetables-was associated with greater microbial diversity and reduced IBD-related dysbiosis. Finally, we observed variations in dietary patterns and microbiome diversity and composition across age groups, genders, regions, seasons, and transit time. This study is among the first to uncover dietary intake associated with IBD-related dysbiosis and to propose an interactive website for participants (https://manichanh.vhir.org/POP/en).},
}
@article {pmid40645765,
year = {2025},
author = {Fusco, W and Adolph, T and Cammarota, G and Gasbarrini, A and Ianiro, G and Tilg, H},
title = {Gut microbiota and atherosclerosis.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2025-335610},
pmid = {40645765},
issn = {1468-3288},
abstract = {Atherosclerosis reflects a chronic inflammatory process of arteries. The origin of chronic vascular inflammation has been associated over a long time primarily with lipid disorders, but evidence from the past years has suggested that lipid-independent pathways are also involved. Recent research has demonstrated that the gastrointestinal microbiota has an impact on the development of atherosclerosis. Many clinical studies have revealed that there exist altered gut microbiota and increased intestinal abundance of bacteria from the oral cavity in atherosclerosis-related disorders such as cardiovascular disease or stroke, while several studies have demonstrated insights into underlying mechanisms. Various microbial-derived metabolites, such as the pathogen-associated molecular pattern endotoxin, trimethylamine N-oxide or imidazole propionate, contribute to atherosclerosis, while other bacterial metabolites, such as some tryptophan derivatives, might be protective. Furthermore, gut microbiota and lipid pathways are highly interactive, and the gut microbiota affects lipid absorption and storage, and the gut microbiota also contributes to vascular ageing. Interference with the gut microbiota by prebiotics, probiotics and antibiotics has demonstrated beneficial effects on atherosclerosis mainly in preclinical models. Overall, the gut microbiota has appeared as an important rheostat for vascular inflammation in atherosclerosis, which is controlled by host-microbe interactions that may be therapeutically exploited in the future.},
}
@article {pmid40645672,
year = {2025},
author = {Li, H and Leaman, AA and Zheng, Q},
title = {The cancer microbiome.},
journal = {Advances in clinical chemistry},
volume = {127},
number = {},
pages = {1-61},
doi = {10.1016/bs.acc.2025.04.001},
pmid = {40645672},
issn = {2162-9471},
mesh = {Humans ; *Neoplasms/microbiology ; *Microbiota ; Tumor Microenvironment ; Animals ; },
abstract = {The cancer microbiome is an emerging concept that is referred to as the microorganism communities associated with cancer. There has been controversy in terms of the bona fide functions of the microbiome in carcinogenesis and cancer development, since the microorganisms were first observed within tumor tissues. Recently, there has been growing evidence showing that the microbiome indeed plays a role in cancer initiation, development, diagnosis, and treatment through diverse mechanisms and interactions between host cells and microbes. Rather than contaminants or artifacts, the cancer microbiome has been proven to be alive in the tumor microenvironment and possess significantly differential physiological and morphological properties compared to the corresponding environmental microorganisms. However, due to the low abundance of microbes within cancer tissues (especially the intratumoral microbiota) and lack of efficient analytical tools (e.g., sensitive antibodies, sensors, and probes), there are still a number of challenges and question marks in this fast-growing field. In this chapter, we made a systematic summary of the cancer microbiome, specifically focusing on its discovery and the recent research advances with respect to the studies on its functions and corresponding technology development.},
}
@article {pmid40645376,
year = {2025},
author = {Zemko, P and Canevelli, M and Pavanello, S and Cesari, M and Bonsembiante, F and Campisi, M and Cannella, L and Buscarnera, S and Zotti, A and Banzato, T},
title = {Markers of biological age in dogs.},
journal = {Ageing research reviews},
volume = {111},
number = {},
pages = {102814},
doi = {10.1016/j.arr.2025.102814},
pmid = {40645376},
issn = {1872-9649},
abstract = {As human life expectancy continues to rise, ageing and age-related diseases have become critical societal challenges, driving extensive research across genetics, molecular biology, biochemistry, and behavioral sciences. In this context, domestic dogs (Canis lupus familiaris) offer a unique model for ageing research due to their shared environmental exposures with humans, diverse genetic profiles, and relatively short lifespans. This review aims to identify potential biomarkers of ageing in dogs, facilitating a deeper understanding of age-related mechanisms and supporting the evaluation of interventions designed to promote healthy ageing. We present a research of peer-reviewed literature on age-related variations of various parameters across multiple biological systems, including epigenetic, telomere, immune, metabolic, and cognitive markers in dogs. Our findings highlight several robust biomarkers, such as DNA methylation-based epigenetic clocks, telomere attrition, CD4+/CD8+ T-cell ratio, hematological markers (e.g., globulin levels), and cognitive function scores. These biomarkers demonstrate strong parallels with human ageing processes, particularly concerning genomic and epigenetic alterations. However, challenges remain, including breed-specific variability, body size differences, and inconsistent evidence regarding inflammageing markers, such as pro-inflammatory cytokines. Despite these limitations, indicators of chronic inflammation (e.g., anemia of chronic disease and elevated globulins) are evident in older dogs. Future research directions include the standardization of biomarker protocols for dogs, the development of longitudinal studies to track dynamic age-related changes, and further exploration of emerging biomarkers, such as those related to microbiome composition and oxidative stress.},
}
@article {pmid40645338,
year = {2025},
author = {Gudi, CR and Wannemuehler, MJ and Mansell, TJ},
title = {Gut-brain-immune interactions: exploring probiotics as a drug delivery platform for neurological disease.},
journal = {Advanced drug delivery reviews},
volume = {},
number = {},
pages = {115650},
doi = {10.1016/j.addr.2025.115650},
pmid = {40645338},
issn = {1872-8294},
abstract = {The gut-brain-immune (GBI) axis, connecting gut microbes, neural tissue, and the cells of the immune system, plays a critical role in human health, particularly in relation to neurological diseases. Research in this field over the last few decades shows that disruptions in the microbiome have been linked to chronic inflammation, which may contribute to neurological conditions, including Parkinson's disease, Alzheimer's disease, and other mental health disorders. As we gain a greater understanding of the links between these systems, novel therapeutic strategies are being explored to treat disease by modulation of the GBI axis. One of the most promising approaches is the use of live biotherapeutics, such as engineered probiotics, as next-generation drug delivery systems. These live microorganisms can be designed to deliver specific therapeutic compounds to the gut and brain in order to modulate immune responses and reduce inflammation at the source. Probiotics and live biotherapeutics can offer a targeted approach to treating neurological diseases by influencing both the microbiome and immune system. In this review, we outline the research and mechanisms that have been implicated in GBI interactions and highlight the potential of these innovative therapies in treating neurological disorders, emphasizing their role in improving precision medicine through targeted, microbiome-based interventions.},
}
@article {pmid40645337,
year = {2025},
author = {du Toit-Thompson, T and Leck, L and Gillson, J and Pavlakis, N and Gill, AJ and Samra, JS and Mittal, A and Sahni, S},
title = {Overcoming therapy resistance in pancreatic cancer: challenges and emerging strategies.},
journal = {Advanced drug delivery reviews},
volume = {},
number = {},
pages = {115647},
doi = {10.1016/j.addr.2025.115647},
pmid = {40645337},
issn = {1872-8294},
abstract = {Pancreatic cancer (PC) is one of the deadliest types of cancer, with a 5-year survival rate of ∼12.5 %. It is expected to become the second leading cause of cancer-related deaths by 2030. Despite recent advances in treatment options by advent of various targeted and immunotherapies, their benefits have not been actualized for PC patients and chemotherapy remains the mainstay systemic therapeutic option for these patients. However, the majority of PC tumours have a highly chemo-resistant phenotype, leading to therapeutic failure. This review provides a comprehensive overview of the established mechanisms related to chemoresistance in PC and provides insight into emerging theories, including the potential role of the microbiome in modulating therapeutic responsiveness. It further discusses potential opportunities to explore to overcome this critical clinical problem.},
}
@article {pmid40645301,
year = {2025},
author = {Melamed, E and Rungratanawanich, W and Liangpunsakul, S and Maki, KA and McCullough, RL and Llorente, C},
title = {Alcohol, Aging, and the Gut Microbiome: Intersections of Immunity, Barrier Dysfunction, and Disease.},
journal = {Alcohol (Fayetteville, N.Y.)},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.alcohol.2025.07.001},
pmid = {40645301},
issn = {1873-6823},
abstract = {Alcohol consumption exerts complex, dose- and context-dependent effects on human health, particularly by influencing the gut microbiome, intestinal barrier integrity, immune regulation, and aging processes. Genetic variation and advancing age are two major, and often interacting, factors that modify the risk of alcohol-related diseases. Among genetic factors, the prevalent aldehyde dehydrogenase 2 polymorphism (ALDH2*2) compromises acetaldehyde clearance, driving toxic metabolite accumulation, oxidative stress, and increased intestinal permeability that disrupts gut microbial communities, even at low levels of alcohol consumption. Heavy and chronic alcohol use further disrupts gut microbial communities, erodes mucosal integrity, and drives systemic inflammation, contributing to alcohol-associated liver disease (ALD), neuroinflammation, and multi-organ injury. Aging independently worsens these effects by promoting chronic low-grade inflammation and impaired immune responses, heightening susceptibility to alcohol-induced pathology. In specific contexts, such as certain autoimmune diseases, low to moderate alcohol intake may exert immunomodulatory effects and influence the gut microbiome, potentially contributing to reduced inflammation and alterations in microbial composition. This review synthesizes current mechanistic insights into how alcohol, host genetics, the gut microbiome, immune regulatory pathways, and aging intersect to influence disease risk. As global populations age and the burden of alcohol-related health issues rises, there is an urgent need for integrated, systems-level approaches. Future research should prioritize precision-based, gut-targeted strategies aimed at restoring microbial balance, maintaining intestinal barrier integrity, and mitigating alcohol-related harm across the lifespan.},
}
@article {pmid40645237,
year = {2025},
author = {Hofford, RS and Sens, JP and Shipman, AL and Kimble, VM and Coric, C and Meckel, KR and Kiraly, DD},
title = {Brief exposure to oral antibiotics has age-dependent effects on morphine reward and gene expression in the medial prefrontal cortex of adolescent and adult mice.},
journal = {Brain, behavior, and immunity},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.bbi.2025.07.005},
pmid = {40645237},
issn = {1090-2139},
abstract = {Adolescence is a critical period for the initiation of problematic drug use, which significantly increases the risk of developing substance use disorders later in life. This heightened vulnerability is partly attributed to the immaturity of the prefrontal cortex, a brain region both essential for decision-making and implicated in drug reward. During adolescence, peripheral systems, such as the gut microbiome, also undergo substantial changes. Emerging evidence suggests that disruptions to the gut microbiome can influence gene expression and drug reward behaviors in rodent models. In this study, we investigated the effects of oral antibiotics on morphine reward and prefrontal cortical gene expression in adolescent and adult mice. Using oral antibiotics to transiently disrupt the microbiome, we found that short-term antibiotic exposure reduced morphine place preference specifically in adolescent mice. In a separate cohort, we observed that antibiotic treatment altered the transcriptomic response to morphine in the medial prefrontal cortex across all age groups. Notably, the transcriptomic changes induced by antibiotics and morphine were age-specific, with distinct gene expression patterns observed in adolescents compared to adults. These findings establish a foundation for future research into the role of the gut microbiome in opioid reward and highlight potential gene pathways underlying age-dependent differences in opioid sensitivity.},
}
@article {pmid40645132,
year = {2025},
author = {Mckirdy, S and Koutsos, A and Nichols, B and Anderson, M and Dhami, S and Chowdhury, CR and Mascellani Bergo, A and Havlik, J and Gerasimidis, K},
title = {Micronutrient supplementation influences the composition and diet-originating function of the gut microbiome in healthy adults.},
journal = {Clinical nutrition (Edinburgh, Scotland)},
volume = {51},
number = {},
pages = {293-303},
doi = {10.1016/j.clnu.2025.06.020},
pmid = {40645132},
issn = {1532-1983},
abstract = {BACKGROUND &amp; AIMS: Studies in-vitro and in animals propose that vitamins and minerals can alter the human gut microbiome. Human trials replicating these findings are scarce or used micronutrient supplementation in supraphysiological doses. We explored the effect of multivitamin/multimineral (MVMM) supplementation on the gut microbiome, and how participant's background diet can modify this effect.<br><br>METHODS: In a randomised, controlled, cross-over study, 28 healthy adults (68 % female, mean [SD], 33 [13] years]) received either a MVMM supplement containing dosages close to the UK dietary recommendations for 23 micronutrients (intervention period) or no supplement (control period), for 10-days, separated by a 15-day washout period. Participants' diet was recorded and replicated between the two periods. Faecal microbiota composition was profiled using 16S rRNA sequencing, metabolome with [1]H NMR, short chain fatty acids (SCFAs) with gas chromatography, and sulphide concentration with colorimetry. Associations between background diet and microbiome responses during MVMM supplementation were explored using machine learning.<br><br>RESULTS: Following MVMM supplementation, the absolute abundance of Lachnoclostridium and UCG_005 taxa were lower, while the concentrations of total SCFAs, specifically propionate and butyrate, and total sulphide were higher than the control period. Compared to baseline, MVMM supplementation decreased the absolute abundance of Desulfobacterota, Actinobacteriota, Bifidobacteriaceae, Erysipelatoclostridiaceae and Veillonellaceae, and increased the concentration of propionate. Background dietary intakes of saturated fat and total carbohydrates related with the MVMM-induced effect of decreasing Desulfobacterota. Likewise, the intakes of vitamins B2, B12, and E, along with iron, related with the effect of MVMM on decreasing Erysipelatoclostridiaceae. No changes were observed within the control period.<br><br>CONCLUSION: In healthy adults, short-term MVMM supplementation influences the gut microbiota composition and diet-originating microbial metabolites and potentially host health.<br><br>REGISTRATION: This trial was registered at clinicaltrials.gov as NCT05371704.},
}
@article {pmid40645053,
year = {2025},
author = {Zhao, M and Xiong, S and Du, T and Xu, X and Li, H and Zhang, L and Xu, Y and Wei, T and Xiong, T and Xie, M},
title = {Elucidating microbial succession dynamics and flavor metabolite formation in korean style spicy cabbage fermentation: Integration of flavoromics, amplicon sequencing, and metagenomics.},
journal = {Food chemistry},
volume = {492},
number = {Pt 2},
pages = {145464},
doi = {10.1016/j.foodchem.2025.145464},
pmid = {40645053},
issn = {1873-7072},
abstract = {Korean style spicy cabbage (KSC) is a prominent fermented vegetable consumed globally. Nevertheless, microbial succession dynamics, interactions, and flavor-core microbiome correlations lack comprehensive understanding. Metabolomics revealed eight taste-active compounds and sixteen aroma-active compounds as key flavor determinants throughout fermentation. Amplicon sequencing elucidated dynamic shifts in bacterial and fungal community structures during KSC fermentation, with subsequent analyses identifying free sugars as the primary drivers of microbial succession. Spearman correlation analysis further identified Psychrobacter, Latilactobacillus, Weissella, Pseudomonas, Rothia, Candida, Vishniacozyma, Kazachstania, and Cutaneotrichosporon as core microbes driving the formation of characteristic flavor metabolites in KSC. Through metagenomic analysis, we reconstructed the metabolic network underlying the formation of characteristic flavor compounds. Our study elucidates microbial diversity dynamics and flavor metabolite formation during KSC fermentation, offering actionable insights for identifying critical fermentation phases and optimizing inoculated starter culture.},
}
@article {pmid40645046,
year = {2025},
author = {Liu, Z and Forde, CG and Stieger, M and Rubert, J},
title = {Chewing behavior and bolus particle size of rice influence carbohydrate digestion and gut microbiome metabolism in vitro.},
journal = {Food chemistry},
volume = {492},
number = {Pt 2},
pages = {145404},
doi = {10.1016/j.foodchem.2025.145404},
pmid = {40645046},
issn = {1873-7072},
abstract = {The size of ingested bolus particles and their surface area affect how accessible the substrates are to digestive enzymes and the gut microbiota. This study aimed to investigate the impact of oral breakdown of rice on the human gut microbiota in vitro. Three rice varieties with different fiber contents were chewed in vivo, then subjected to in vitro digestion and fecal batch cultures. Increasing the number of chews per bite from 5 to 40 led to higher structural breakdown and more extensive early starch hydrolysis, resulting in up to 14 % increase in the degree of starch hydrolysis during in vitro digestion, and 26-47 % smaller rice bolus particles after in vitro digestion. Higher bile salt hydrolase activity and total short-chain fatty acid levels (5-13 %) were found in less chewed rice. Untargeted lipidomics highlighted that the number of chews influenced numerous metabolites beyond SCFA.},
}
@article {pmid40645018,
year = {2025},
author = {Huang, A and Lin, B and Hu, T and Lan, J},
title = {Unraveling functional dyspepsia: Pathophysiological mechanisms, microbiota interactions, and emerging therapeutic strategies.},
journal = {Pathology, research and practice},
volume = {272},
number = {},
pages = {156118},
doi = {10.1016/j.prp.2025.156118},
pmid = {40645018},
issn = {1618-0631},
abstract = {This comprehensive review elucidates the latest advancements in understanding functional dyspepsia (FD). The article delves into the pathophysiological mechanisms of FD, including gastrointestinal motility disorders, visceral hypersensitivity, impaired gastric accommodation, compromised intestinal barrier function, and microbiota dysbiosis. It particularly emphasizes the crucial role of gut microbiota in FD pathogenesis, providing a detailed analysis of how microbiome-host interactions influence intestinal barrier function, immune regulation, and the brain-gut axis. The review also synthesizes current treatment strategies for FD, encompassing dietary modifications, pharmacological interventions, behavioral therapies, and Traditional Chinese Medicine approaches. This review uniquely integrates microbiome-barrier-immune-brain-gut axis interactions and combines Western-TCM therapeutic paradigms, providing a comprehensive framework for personalized FD management.},
}
@article {pmid40644733,
year = {2025},
author = {Zhou, Y and Wen, C and Zhang, Q and Gu, Z and Lian, L and Xue, K and Xu, T and Lin, Z and Wang, W and Zhu, H},
title = {Characteristics of oral microbiomics with soldiers in the army before and after high-intensity physical training.},
journal = {Archives of oral biology},
volume = {178},
number = {},
pages = {106347},
doi = {10.1016/j.archoralbio.2025.106347},
pmid = {40644733},
issn = {1879-1506},
abstract = {OBJECTIVES: This paper aims to investigate the changes in soldiers' oral microbiome and metabolic levels after a month of high-intensity training.<br><br>DESIGN: We collected saliva samples from 10 soldiers with good oral health and hygiene habits before and after training. Subsequently, DNA extraction, metagenomic sequencing, and phylogenetic analysis of the oral microbiome were conducted.<br><br>RESULTS: 7733 bacterial species from 113 known bacterial phyla and 2017 genera detected in 20 samples. The diversity and richness of saliva microorganisms before and after training were similar (p&#x202f;>&#x202f;0.05), while beta diversity analysis showed structural differences in microbiota at the phylum and genus levels (p&#x202f;<&#x202f;0.05). The relative abundance of 27 genera such as Proteobacteria, Neisseria, Morococcus cerebrosus and Eikenella in soldiers' saliva significantly increased after high-intensity training (p&#x202f;<&#x202f;0.05). Conversely, the relative abundance of 20 genera such as Bacteroidota, Veillonella, Parvimonas micra, Prevotella oris, Peptostreptococcus, and Treponema decreased (p&#x202f;<&#x202f;0.05). At the metabolic level, training resulted in a relative increase (p&#x202f;<&#x202f;0.05) in various pathways, including amino acid metabolism, sulfur metabolism, glutathione metabolism, and Tyrosine metabolism. By comparison, after training, carbohydrate metabolism, glycan biosynthesis, metabolism, the HIF-1 signaling pathway, and necroptosis revealed a relative decrease (p&#x202f;<&#x202f;0.05).<br><br>CONCLUSIONS: This paper reveals the changes in the saliva microbiome of soldiers after one month of high-intensity training, in which the relative abundance of biomarkers of periodontal disease, caries, and other oral diseases represented by peptostreptococcus, prevotella oris, treponema, etc., are significantly reduced, suggesting that long-term high-intensity training may have a positive effect on oral health.},
}
@article {pmid40644647,
year = {2025},
author = {Barragan-Carrillo, R and Zengin, ZB and Pal, SK},
title = {Microbiome Modulation for the Treatment of Solid Neoplasms.},
journal = {Journal of clinical oncology : official journal of the American Society of Clinical Oncology},
volume = {},
number = {},
pages = {JCO2500374},
doi = {10.1200/JCO-25-00374},
pmid = {40644647},
issn = {1527-7755},
abstract = {The interplay between the human gut microbiome and the immune system has sparked growing interest in microbiome modulation as a therapeutic strategy in oncology. Preclinical studies have identified specific bacterial species linked to improved responses to immune checkpoint inhibitors (ICIs), leading to clinical investigations in melanoma, renal cell carcinoma (RCC), and non-small cell lung cancer (NSCLC). The stool bacterial abundance of Ruminococcaceae, Akkermansia, and Bifidobacterium correlates with favorable clinical outcomes, whereas the disruption of the gut microbiome through antibiotics before or during ICI initiation is associated with higher rates of primary resistance and shorter survival. Biomarkers such as TOPOSCORE have been developed to better predict ICI benefits and estimate dysbiosis and treatment responses. Several microbiome-modulating strategies have shown potential in patients receiving treatment with ICIs-for instance, high dietary fiber intake may be linked to improved outcomes. As a separate strategy, certain probiotics appear to enhance clinical activity in early trials when incorporated into ICI-based regimens. Finally, fecal microbiota transplantation has shown safety and efficacy in ICI-refractory melanoma and yielded encouraging results in treatment-naïve patients with melanoma, NSCLC, and RCC. Although several compelling signals have been observed to date with microbiome manipulation, the field is lacking large, definitive randomized trials-these are indeed a prerequisite for any of the highlighted strategies to become a standard of care.},
}
@article {pmid40644597,
year = {2025},
author = {Hamza, YP and Kacem, MABH and Al Molawi, NH and Yassine, HM and AlKhatib, HAM and Benslimane, F and Al-Remaihi, HIKB and Awni El Kahlout, R and Ahmed El Kahlout, BI and Al Khalili, H and Al Khalili, MA and Doiphode, SH and Elmagboul, EBI and Akhter, J and Al Kuwari, EAE and Coyle, PV},
title = {Patients in hospital with confirmed bacterial airway infection are significantly more likely to have a respiratory virus co-infection.},
journal = {Journal of medical microbiology},
volume = {74},
number = {7},
pages = {},
pmid = {40644597},
issn = {1473-5644},
mesh = {Humans ; *Coinfection/microbiology/virology/epidemiology ; Male ; *Respiratory Tract Infections/microbiology/virology ; Female ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Aged ; Bacteria/genetics/isolation &amp; purification/classification ; *Virus Diseases/virology/microbiology/epidemiology/complications ; Adult ; Bronchoalveolar Lavage Fluid/microbiology/virology ; *Bacterial Infections/microbiology ; Real-Time Polymerase Chain Reaction ; Aged, 80 and over ; },
abstract = {Introduction. Respiratory viruses are seen as cofactors in bacterial airway infection, often leading to bacterial pneumonia. This study addressed their role in hospitalized patients with bacterial infection confirmed by culture, 16S real-time PCR (16S RT-PCR) and 16S rRNA sequencing (16S Sequencing). The potential for using 16S RT-PCR and 16S Sequencing as diagnostic tools was also addressed.Gap Statement. The significance of virus infections on the lung microbiome and on bacterial superinfection in hospitalized patients needs additional evidence from real-world studies.Aim. The primary objective was to assess the impact of respiratory viruses on bacterial airway infection, with the secondary objective to see if 16S Sequencing had potential as a faster diagnostic tool that could augment culture.Methodology. A total of 83 lower airway samples - 36 bronchoalveolar lavage fluids, 39 bronchial washes, 5 sputa and 3 endotracheal aspirates - were tested for respiratory virus and bacterial co-infection. Bacteria were tested by (a) culture, (b) 16S RT-PCR and (c) 16S Sequencing. The performance of culture-independent assays against culture was assessed, and the impact of confirmed viral infections on the airway bacterial load was determined.Results. Virus infections reflected those co-circulating in the community and were significantly associated with culture and 16S Sequencing-confirmed bacterial infections [1-tailed mid P exact test (χ[2]: P=0.04; P=0.05)]. There was substantive agreement of culture and 16S RT-PCR and 16S Sequencing: kappa score: 0.66 (CI: 0.50-0.82); diagnostic accuracy 83.13% (73.32-90.46%). Virus infections were highly associated with increased bacterial load by 16S RT-PCR [2-tailed χ[2] (χ[2]: 2.4 P=0.003)]. Altered microbial diversity by 16S Sequencing was seen for samples stratified by culture but not by virus detection.Conclusion. Acute respiratory viral infections were significantly associated with bacterial airway infections confirmed by culture and 16S Sequencing. Airway dysbiosis was seen with bacterial-confirmed but not viral-confirmed infections, even though the latter were highly associated with increased bacterial loads using 16S RT-PCR. This suggests that virus infections induce changes in lung bacteria missed by culture and sequencing. The study supported a potential role for 16S Sequencing and 16S RT-PCR alongside culture.},
}
@article {pmid40644523,
year = {2025},
author = {Li, T and Felton, J and Lewis, J and Cheng, Q and Meredith, R and Lu, HT and Benken, A and Dutta, PP and Liao, J and Zhao, XD and Matvekas, A and Baker, J and Hasler, WL and Babiskin, A and Walenga, R and Fang, LL and Lionberger, R and Pai, MP and Sun, D and Gianchandani, YB},
title = {An ingestible device for automated sampling and location tracing in gastrointestinal tract.},
journal = {PloS one},
volume = {20},
number = {7},
pages = {e0327667},
pmid = {40644523},
issn = {1932-6203},
mesh = {Animals ; *Gastrointestinal Tract/metabolism ; Dogs ; },
abstract = {Fluids sampled from the gastrointestinal (GI) tract are of interest for evaluating the bioequivalence of oral medications, and more generally for evaluating GI-related diseases, and for profiling the individual gut microbiome. Existing options for capturing multiple fluid samples from specific locations in the GI tract are limited and invasive, particularly for the small intestine. Here, we report the development of an ingestible capsule for the collection of multiple fluid samples along the GI tract; we additionally report the use of data from sensors within the capsule to determine the sampling regions. The capsule has an ingestible size of Φ14 × 42 mm3. Within this volume, it includes three separate cartridges that capture and retain samples within capillaries; a stepper motor for positioning the sampling cartridges at a sampling port; a 3-axis accelerometer that enables a new method of correlating sample location; a microcontroller with wireless communication and sensor data storage capabilities; and batteries to power the device. We describe in vitro characterization and in vivo tests performed with canine models that have successfully verified the capabilities of the capsule. Fluid samples from the stomach, small intestine, and colon regions of the GI tract are identified by inertial measurements taken within the capsule, and correlated to measurements of the concentration of mesalamine (a drug used for testing) and the bile salt profile in each region, respectively.},
}
@article {pmid40643767,
year = {2025},
author = {Ghasemipoor, M and Yaghoubi-Avini, M and Azimirad, M and Nabavi-Rad, A and Looha, MA and Doulberis, M and Schulz, C and Yadegar, A},
title = {Gastric microbiome-derived Lacticaseibacillus casei strain RIGLD MG-1 relieves Helicobacter pylori-induced inflammation in gastric epithelial cells in vitro.},
journal = {Molecular biology reports},
volume = {52},
number = {1},
pages = {702},
pmid = {40643767},
issn = {1573-4978},
support = {RIGLD 1281//Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran/ ; },
mesh = {Humans ; *Helicobacter pylori/pathogenicity/drug effects ; *Probiotics/pharmacology ; *Helicobacter Infections/microbiology/therapy ; Epithelial Cells/microbiology/metabolism ; *Lacticaseibacillus casei/physiology/isolation &amp; purification/metabolism ; Inflammation/microbiology ; *Gastrointestinal Microbiome ; Gastric Mucosa/microbiology/metabolism ; Male ; Female ; Cell Line ; Adult ; Middle Aged ; },
abstract = {BACKGROUND: The burden of Helicobacter pylori infection is exacerbated by rising antibiotic resistance. Probiotics, especially Lactobacillus species, have shown potential as adjunctive therapies for H. pylori infection. This study aimed to isolate a Lactobacillus strain from the gastric microbiome of healthy individuals and assess its probiotic properties against H. pylori.<br><br>METHODS AND RESULTS: Gastric biopsies were obtained from a cohort of 10 subjects, and used for bacterial isolation. The Lactobacillus strain was identified to species level using PCR and sequencing, followed by safety assessments. MTT assay was employed to measure AGS cell viability after exposure to various concentrations of H. pylori, as well as live and pasteurized Lactobacillus. Anti-inflammatory properties of the probiotic strain were assessed in AGS cells using RT-qPCR and ELISA. Additionally, the strain's potential to inhibit H. pylori adhesion and invasion was examined. Probiotic Lacticaseibacillus casei strain RIGLD MG-1 was isolated and characterized as non-pathogenic and found to be tolerant to acidic and bile-rich environments, and susceptible to several antibiotics. Live and pasteurized L. casei downregulated the expression of NF-&#x3ba;B, IL-8, TNF-&#x3b1;, and &#x3b2;-catenin, meanwhile upregulated the expression of IL-10 in H. pylori-treated cells. They also alleviated H. pylori-induced proinflammatory response by lowering IL-8 and TNF-&#x3b1;, and boosting IL-10 production. Additionally, both probiotic forms inhibited H. pylori adhesion and invasion in AGS cells.<br><br>CONCLUSION: Our results show that L. casei strain RIGLD MG-1 is safe and demonstrates significant immunomodulatory and anti-adhesion effects, making it a potential probiotic for use as adjunctive therapy to mitigate H. pylori-induced inflammation.},
}
@article {pmid40643580,
year = {2025},
author = {Alcala-Gonzalez, LG and Hinchcliff, M and McMahan, ZH},
title = {Gastrointestinal manifestations of systemic sclerosis: current approaches and emerging therapies.},
journal = {Current opinion in rheumatology},
volume = {},
number = {},
pages = {},
pmid = {40643580},
issn = {1531-6963},
abstract = {PURPOSE OF REVIEW: This review highlights recent advances in the understanding and management of gastrointestinal manifestations in systemic sclerosis (SSc). It is intended for clinicians and researchers aiming to improve diagnostic accuracy and therapeutic strategies in managing SSc-related gastrointestinal disease.<br><br>RECENT FINDINGS: Gastrointestinal involvement in SSc is highly variable in terms of clinical presentation, symptom severity, progression, timing of onset, and response to treatment. Emerging research highlights early immune-mediated damage to neural and muscular gastrointestinal tissues, microbiome alterations, and vascular dysfunction - particularly in patients with late-onset gastrointestinal disease - as key factors guiding the development of personalized, precision-based approaches for well defined patient subgroups. Recent studies underscore the value of early, objective assessment of gastrointestinal motility using tools like whole-gut transit scintigraphy and abdominal vascular ultrasound. New treatment strategies are also being explored for severe manifestations, including investigating mechanisms behind acid-suppressive therapy-resistant gastroesophageal reflux disease and implementing adjunctive therapies for gastrointestinal dysmotility.<br><br>SUMMARY: Gastrointestinal involvement in SSc poses a complex clinical challenge, particularly in patients with severe dysmotility and symptoms refractory to standard management strategies. This review offers timely, evidence-based insights to support clinicians in delivering more personalized and effective patient care and highlights critical gaps to address in future research.},
}
@article {pmid40643564,
year = {2025},
author = {Popowitch, EB and Boiditswe, SC and Patel, MZ and Aquino, JN and Hurst, JH and Steenhoff, AP and Cunningham, AL and Yoon, JW and Seed, PC and Kelly, MS},
title = {Corynebacterium rhinophilum sp. nov. isolated from the human upper respiratory tract.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {75},
number = {7},
pages = {},
doi = {10.1099/ijsem.0.006835},
pmid = {40643564},
issn = {1466-5034},
mesh = {*Corynebacterium/classification/isolation &amp; purification/genetics ; *Phylogeny ; Humans ; RNA, Ribosomal, 16S/genetics ; Fatty Acids/analysis ; Base Composition ; DNA, Bacterial/genetics ; Bacterial Typing Techniques ; Sequence Analysis, DNA ; Genome, Bacterial ; Nucleic Acid Hybridization ; United States ; Whole Genome Sequencing ; *Respiratory System/microbiology ; },
abstract = {Twelve strains of a novel Corynebacterium species were cultured from human respiratory samples collected in the USA and Botswana. Five strains underwent detailed phenotypic and chemotaxonomic characterization, while all 12 strains were included in phylogenomic analyses. Optimal growth was observed on brain heart infusion solid medium and in liquid media, including brain heart infusion and tryptic soy broth when supplemented with Tween 80, a source of the fatty acid oleic acid. Cells were Gram-positive, non-spore-forming, non-motile bacilli that exhibited catalase activity but lacked oxidase activity. Major fatty acids were 18 : 1 ω9c (oleic acid) and 16 : 0 (palmitic acid). Analysis of 16S ribosomal RNA gene sequences identified these strains as belonging to the genus Corynebacterium (family Corynebacteriaceae), with the closest relatives being Corynebacterium accolens and Corynebacterium macginleyi. Whole-genome sequencing revealed that the genomes are 2.47-2.62 Mbp in size and have a G+C content of 58.7-59.0 mol%. Average nucleotide identity and in silico DNA-DNA hybridization values for comparisons of these genomes to those of closely related phylogenetic neighbours were 93.19-93.62% and 19.9-36.3%, respectively. These results indicate that these strains represent a novel species of Corynebacterium, for which we propose the name Corynebacterium rhinophilum sp. nov., with the type strain MSK072[T] (=DSM 118652[T]=JCM 37534[T]).},
}
@article {pmid40643545,
year = {2025},
author = {Nohesara, S and Mostafavi Abdolmaleky, H and Pirani, A and Thiagalingam, S},
title = {Therapeutic Horizons: Gut Microbiome, Neuroinflammation, and Epigenetics in Neuropsychiatric Disorders.},
journal = {Cells},
volume = {14},
number = {13},
pages = {},
pmid = {40643545},
issn = {2073-4409},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Epigenesis, Genetic ; *Mental Disorders/therapy/genetics/microbiology ; Animals ; *Neuroinflammatory Diseases/therapy/genetics/microbiology ; *Inflammation ; Brain ; },
abstract = {Neuroinflammation is a hallmark of many neuropsychiatric disorders (NPD), which are among the leading causes of disability worldwide. Emerging evidence highlights the significant role of the gut microbiota (GM)-immune system-brain axis in neuroinflammation and the pathogenesis of NPD, primarily through epigenetic mechanisms. Gut microbes and their metabolites influence immune cell activity and brain function, thereby contributing to neuroinflammation and the development and progression of NPD. The enteric nervous system, the autonomic nervous system, neuroendocrine signaling, and the immune system all participate in bidirectional communication between the gut and the brain. Importantly, the interaction of each of these systems with the GM influences epigenetic pathways. Here, we first explore the intricate relationship among intestinal microbes, microbial metabolites, and immune cell activity, with a focus on epigenetic mechanisms involved in NPD pathogenesis. Next, we provide background information on the association between inflammation and epigenetic aberrations in the context of NPD. Additionally, we review emerging therapeutic strategies-such as prebiotics, probiotics, methyl-rich diets, ketogenic diet, and medications-that may modulate the GM-immune system-brain axis via epigenetic regulation for the prevention or treatment of NPD. Finally, we discuss the challenges and future directions in investigating the critical role of this axis in mental health.},
}
@article {pmid40643465,
year = {2025},
author = {Di Nicuolo, F and Teveroni, E and Devigili, A and Gasparini, C and Urbani, A and Ghi, T and Pontecorvi, A and Milardi, D and Mancini, F},
title = {Exploring OR2H1-Mediated Sperm Chemotaxis: Development and Application of a Novel Microfluidic Device.},
journal = {Cells},
volume = {14},
number = {13},
pages = {},
pmid = {40643465},
issn = {2073-4409},
mesh = {*Chemotaxis/drug effects ; Humans ; Male ; *Spermatozoa/metabolism/drug effects/cytology/physiology ; Sperm Motility/drug effects ; *Lab-On-A-Chip Devices ; *Receptors, Odorant/metabolism ; Female ; Calcium/metabolism ; },
abstract = {Microfluidic platforms have emerged as critical technologies for exploring sperm chemotaxis, providing precise gradient control, and facilitating in-depth behavioral assessment. We designed a novel, user-friendly microfluidic device that is optimized for human sperm morphology and motility. The device was validated using two well-established sperm chemoattractants, progesterone and bourgeonal, demonstrating its reliability and reproducibility. Given the key role of olfactory receptors (ORs) in mediating sperm chemotaxis, the newly developed device was employed to identify additional receptors that may contribute to sperm behavior. Using the Atlas database, we identified OR2H1 as a candidate receptor. It is enriched in testis-derived cells, particularly in early and late spermatids, and it is broadly expressed across human spermatozoa. We demonstrated that OR2H1's ligand, methional, a sulfur-containing aldehyde naturally found in vaginal fluid and biosynthesized by Lactococcus lactis, significantly enhances sperm migration and progressive motility. Methional stimulation also triggered increased intracellular calcium levels, indicating receptor activation. Computer-assisted sperm analysis revealed that methional treatment improved sperm linearity, straightness, and wobble without affecting the average velocity, suggesting enhanced directional movement. These findings provide evidence that methional promotes sperm chemotaxis via OR2H1 and highlight the potential role of the vaginal microbiome in influencing human fertility.},
}
@article {pmid40643244,
year = {2025},
author = {Seekatz, AM},
title = {Straining to define a healthy microbiome.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0079724},
doi = {10.1128/msphere.00797-24},
pmid = {40643244},
issn = {2379-5042},
abstract = {In 2020, I wrote an mSphere of Influence commentary on two studies that shaped my research perspective on the human gut microbiome (McNulty et al., Sci Transl Med 3:106ra106, 2011, https://doi.org/10.1126/scitranslmed.3002701; Hamilton et al., Gut Microbes 4:125, 2013, https://doi.org/10.4161/gmic.23571). The microbiome field has continued to progress since the publication of these studies over 10 years ago, emerging as a considerable factor in almost all areas focused on disease development. My previous commentary highlighted two areas that piqued my interest early on in my career: (i) that the extant microbial community should be considered when proposing to manipulate the microbiota, such as via probiotics or fecal microbiota transplantation, and (ii) that realized (i.e., transcribed) functional changes of the microbiota may occur independent of changes in its composition. Since writing that commentary, two microbiota-based therapeutics for the treatment of Clostridioides difficile infection have been approved, highlighting the potential success of using the microbiota to treat or prevent disease. Despite these wins and ever-growing evidence of the importance of the microbiome in managing our health, translating mechanistic studies into therapeutic value has been slower. In this minireview, I expand upon two large questions that would increase our ability to translate the microbiome into therapies, highlighting both historical and recent progress.},
}
@article {pmid40643236,
year = {2025},
author = {Negre Rodríguez, M and Pioppi, A and Kovács, &#xc1;T},
title = {The role of plant host genetics in shaping the composition and functionality of rhizosphere microbiomes.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0004124},
doi = {10.1128/msystems.00041-24},
pmid = {40643236},
issn = {2379-5077},
abstract = {The plant microbiome comprises a wide range of microorganisms associated with different plant tissues. Over the past decades, significant research efforts have focused on understanding and harnessing the plant rhizosphere microbiome for optimal plant growth and health. However, while environmental factors are often the primary focus of these studies, the influence of plant genotype remains comparatively underexplored. In fact, the plant genotype influences a multitude of factors including root morphology and exudate composition, which play an integral role in shaping the rhizosphere niche. In this review, we discuss how alterations in plant host genetics could lead to differences in the assembly and diversity of the rhizosphere microbiome. Furthermore, we summarize current approaches to decipher complex plant traits and their ecological implications in host-microbiome systems and interactions.},
}
@article {pmid40643235,
year = {2025},
author = {Wang, X and Lv, Y and Zhao, W and Xiao, X and Wang, J},
title = {D-amino acid metabolic versatility as a common adaptive strategy in the Mariana Trench microbiome.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0058125},
doi = {10.1128/msystems.00581-25},
pmid = {40643235},
issn = {2379-5077},
abstract = {UNLABELLED: Hadal trenches, the Earth's deepest marine environments, harbor thriving microbial communities that promote the turnover of recalcitrant dissolved organic matter (RDOM) under extreme conditions. However, the effects of microbes on D-amino acid (D-AA) reservoirs, which are important components of deep-sea RDOM, remain largely unknown. To address this knowledge gap, we curated a comprehensive reference database of D-AA functional genes for accurate identification of D-AA metabolic potential from metagenomic data. Using this database, we identified the presence of various D-AA anabolic and catabolic genes that were closely correlated with central carbon metabolism and ammonia oxidation genes throughout the water column and in the sediment of the Mariana Trench. Furthermore, 93.6% of the recovered bacterial and archaeal genomes contained at least one of these D-AA functional genes, substantially expanding our understanding of potential D-AA utilizers. Notably, we discovered that glutamate racemase, an enzyme previously thought to be exclusive to bacteria, is ubiquitously present in ammonia-oxidizing archaea. This finding suggests that D-glutamate could be integrated into hadal carbon and nitrogen cycling by this crucial microbial taxon. Finally, we observed an increase in both D-AA production and degradation potential with water depth, with higher levels in near-bottom seawater than in sediment. These findings suggest that diverse microbial taxa promote increased D-AA turnover in hadal zones, potentially representing a common adaptive response to extreme hadal conditions.<br><br>IMPORTANCE: Deep-sea microorganisms play a crucial role in the turnover of RDOM. In this study, we investigated the metabolic potential of D-AAs, which are important constituents of RDOM and are used for indicating the recalcitrance of organic matter. By elucidating the genetic profiles of D-AA metabolism and associated microbial taxa, we observed that D-AA metabolism is a fundamental ecological function that is prevalent in the deepest ocean. Our finding of higher D-AA turnover potentials in deeper environments challenges the conventional view of the constant recalcitrance of D-AAs, suggesting that D-AA turnover may be environmentally dependent. This insight provides a new paradigm for understanding RDOM turnover, with broad implications for marine biogeochemistry.},
}
@article {pmid40643220,
year = {2025},
author = {Zhang, Y and Noya, SB and Li, Y and Fang, J and Sehgal, A},
title = {The microbiome interacts with the circadian clock and dietary composition to regulate metabolite cycling in the Drosophila gut.},
journal = {eLife},
volume = {13},
number = {},
pages = {},
pmid = {40643220},
issn = {2050-084X},
support = {Opening Projects//Shanghai Key Laboratory of Chemical Biology/ ; 31972308//National Natural Science Foundation of China/ ; Life?//VolkswagenStiftung/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; *Circadian Clocks/physiology ; *Drosophila melanogaster/microbiology/metabolism/physiology ; *Diet ; Metabolome ; Circadian Rhythm ; },
abstract = {The gut microbiome plays a key role in the maintenance of host metabolic homeostasis and health. Most metabolic processes cycle with a 24-hour rhythm, but the extent to which the microbiome influences metabolite cycling under different conditions, such as variations in dietary composition, remains largely unknown. In this study, we utilized high temporal resolution metabolite profiling of the Drosophila gut to investigate the role of the microbiome in metabolite cycling. We find that the microbiome increases the number of oscillating metabolites despite the previous finding that it dampens transcript cycling in the gut. Time-restricted feeding also promotes metabolite cycling and does so to a larger extent in germ-free flies, thereby increasing cycling in these flies to levels comparable to those in microbiome-containing flies. Enhancement of cycling by the microbiome depends upon a circadian clock, which also maintains phase in the face of changes in the microbiome. Interestingly, a high protein diet increases microbiome-dependent metabolite cycling, while a high sugar diet suppresses it. Gene Ontology identifies amino acid metabolism as the metabolic pathway most affected by changes in the gut microbiome, the circadian clock, and timed feeding, suggesting that it is subject to regulation by multiple inputs. Collectively, our observations highlight a key role of the gut microbiome in host metabolite cycling and reveal a complex interaction with internal and external factors.},
}
@article {pmid40643116,
year = {2025},
author = {Griffin, C and Dinh, D and Singletary, D and Tellez, M and Sung, H},
title = {Characterizing the microbiome of Dujardinascaris helicina (Nematoda: Ascarididae) isolated from wild American crocodiles in Belize.},
journal = {Journal of helminthology},
volume = {99},
number = {},
pages = {e73},
doi = {10.1017/S0022149X25100369},
pmid = {40643116},
issn = {1475-2697},
mesh = {Animals ; *Alligators and Crocodiles/parasitology ; Belize ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; *Ascaridoidea/microbiology/isolation &amp; purification/classification/genetics ; *Ascaridida Infections/veterinary/parasitology ; Animals, Wild/parasitology ; Sequence Analysis, DNA ; },
abstract = {Microbiomes are communities of microorganisms that form close associations with metazoan hosts and have important roles in host biological processes. With the advent of Next Generation Sequencing, the microbiomes of myriad animals and plants have been described. However, the microbiomes of parasites have received little attention, which is surprising considering their ecological and medical importance. This study characterizes, for the first time, the microbiome of Dujardinascaris helicina, a gastrointestinal nematode parasite of the American crocodile. Dujardinascaris helicina were isolated from crocodiles residing in two geographically separated habitats across Belize. Using 16S sequencing, we compare β-diversity between sampling locations using generalized linear mixed modeling. Our results show that D. helicina microbiomes differ in composition depending on location. We also show that D. helicina microbiomes show strong shifts toward consolidation of specific taxa when proximity to human modified environments increases.},
}
@article {pmid40642988,
year = {2025},
author = {Wang, F and Wu, Y and Ni, J and Xie, Q and Shen, J and Chen, H and Ma, C and Yao, Y and Wang, J and Xu, L and Xiang, Q and Zhao, Y and Chen, Y and Li, L},
title = {Gut microbiota links to histological damage in chronic HBV infection patients and aggravates fibrosis via fecal microbiota transplantation in mice.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0076425},
doi = {10.1128/spectrum.00764-25},
pmid = {40642988},
issn = {2165-0497},
abstract = {Gut microbiota dysbiosis has been observed in HBV-related cirrhosis, but its role in early-stage disease and its correlation with liver pathology remain unclear. Moreover, whether dysbiosis is a cause or consequence of liver cirrhosis is still debated. We recruited 20 treatment-naïve patients with chronic HBV infection, assessing liver injury via biopsy. Fecal metagenomic sequencing was used to analyze the correlation between gut microbiota and liver histology. To explore the causality, fecal samples from an HBV-related cirrhosis patient were transplanted into mice with CCl4-induced liver fibrosis. Patients with significant histological damage exhibited reduced alpha diversity and greater microbial homogeneity. Species such as Eubacterium_sp_CAG_180, Gemmiger_formicilis, and Oscillibacter_sp_ER4 had decreased abundance, while Parabacteroides_distasonis, Bacteroides_dorei, and Bacteroides_finegoldii were enriched. Mice receiving fecal transplants from the cirrhotic patient showed aggravated liver fibrosis, with increased collagen deposition; elevated ALT, AST, and ALP levels; and heightened hepatic inflammatory gene expression. Additionally, abnormal bile acid profiles with elevated unconjugated bile acids (e.g., GCA and CA) were observed. Gut microbiota dysbiosis is closely associated with liver histological damage in chronic HBV infection and may drive fibrosis progression via microbial-bile acid interactions. These findings suggest potential for gut microbiota-based assessment and treatment strategies in chronic hepatitis B.IMPORTANCEThis study elucidates a significant association between gut microbiota dysbiosis and liver histological damage in patients with chronic hepatitis B (HBV), potentially exacerbating fibrosis progression through bile acid interactions. By analyzing patient gut microbiota and conducting fecal transplant experiments in mice, researchers have identified that gut microbiota dysbiosis contributes to hepatic fibrosis during chronic HBV infection. These findings underscore the importance of the gut-liver axis in HBV disease progression, indicating that monitoring or modulating gut bacteria may facilitate early diagnosis or therapeutic interventions. This research bridges the gap in understanding whether microbial alterations drive disease progression or result from it, providing a foundation for developing therapies targeting the microbiome to mitigate liver damage in chronic HBV infections.},
}
@article {pmid40642984,
year = {2025},
author = {Li, C and Hou, S and Li, J and Zhang, X and Ran, Q and Han, Y and Wang, Z and Dong, C},
title = {Drought-driven shifts in Eucommia ulmoides rhizosphere mycobiota and metabolites mediate host tolerance.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0084725},
doi = {10.1128/spectrum.00847-25},
pmid = {40642984},
issn = {2165-0497},
abstract = {Drought poses considerable challenges to the sustainable development of crops, highlighting the urgent need to improve plant resistance to drought stress. Rhizosphere mycobiota roles in Eucommia ulmoides drought adaptation remain uncharacterized. This study examines E. ulmoides' rhizosphere mycobiota diversity, its changes, and interactions with plant physiology and metabolites under drought stress using amplicon sequencing, plant physiological assessments, and non-targeted root metabolomics. Our data indicate that drought stress considerably altered the species richness and community composition of the E. ulmoides seedling rhizosphere mycobiota, affecting the co-occurrence patterns and the composition of core fungal taxa within the mycobiota. Additionally, Sordariomycetes were notably enriched in the rhizosphere of E. ulmoides under drought stress and showed a notable positive correlation with the physiological indicator soluble sugar (SS). During drought stress mid-stages, rhizosphere core fungal taxa of E. ulmoides exhibit higher diversity, increased network connectivity, and a tighter network structure. Correlation analyses show that core fungal taxa are significantly linked to malondialdehyde (MDA) content. The root metabolome's phosphatidylcholines (o-16:0/22:6(4Z,7Z,10Z,13Z,16Z,19Z)) and 8-demethyltetracenomycin C are also notably affected by the core microbial taxa. In summary, drought stress drives changes in the E. ulmoides rhizosphere mycobiota, plant physiology, and root metabolites, with MDA, SS, and 8-demethyltetracenomycin C possibly mediating the selection of specific rhizosphere fungal communities. Taken together, these data provide notable insights into plant-microbe interactions under drought stress and have important implications for improving the drought adaptability of E. ulmoides.IMPORTANCEDrought presents substantial challenges to the sustainability of crops, highlighting the need to enhance their resistance to arid conditions. Although the rhizosphere microbiome plays a crucial role in bolstering crop resilience, the dynamics and mechanisms of Eucommia ulmoides' rhizosphere mycobiota under drought conditions remain poorly understood. This study provides valuable insights into the interactions between plants and microbes under drought stress and has significant implications for improving the drought adaptability of E. ulmoides.},
}
@article {pmid40642982,
year = {2025},
author = {Qi, X and Zhang, M and Wei, T and Lin, J and Zhao, X and Yao, Y and Hu, Y and Zheng, Y},
title = {LorDist: a novel method for calculating the distance based on functional data analysis with application to longitudinal microbial data.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0154225},
doi = {10.1128/spectrum.01542-25},
pmid = {40642982},
issn = {2165-0497},
abstract = {Longitudinal human microbial data offer insights into microbiome dynamics over time. Traditional methods usually overlook temporal relationships among samples from the same subject. Here, we presented the Longitudinal Microbial Data Distance (LorDist) method, which uses functional data fitting to construct a distance matrix integrating information from the same subject at different time points. Simulation data showed that LorDist handled well up to 60% sparseness and worked robustly with various sequencing depths and time points. Empirical data analysis demonstrated that LorDist excels in capturing differences across subjects with longitudinal microbiome data. LorDist presented the potential of longitudinal microbial data in addressing temporal autocorrelation and distinguishing phenotypes.IMPORTANCELongitudinal analysis of the human microbiome is critical for understanding its dynamic role in health and disease. However, current analytical approaches struggle to address key challenges, such as data sparsity and irregular sampling, inherent to time-series microbiome studies. Here, we developed longitudinal microbial data distance (LorDist), an innovative method leveraging functional data analysis to model temporal microbial dynamics with enhanced precision. Compared to existing methods, LorDist consistently outperforms in discerning biologically meaningful group differences, even in highly sparse data sets or under fluctuating sequencing depths. Our findings demonstrate LorDist's robust performance on real-world data sets involving inflammatory bowel disease and infant gut development. By explicitly preserving the temporal structure inherent in microbiome data, LorDist enables robust detection of subtle yet critical biological shifts, paving the way for improved diagnostics and personalized therapeutic strategies in microbiome science.},
}
@article {pmid40642960,
year = {2025},
author = {Kazen, A and Grobe, JL and Kirby, JR},
title = {Gut microbial contributions to thermogenesis.},
journal = {The Journal of experimental biology},
volume = {228},
number = {14},
pages = {},
doi = {10.1242/jeb.249791},
pmid = {40642960},
issn = {1477-9145},
support = {5F31DK137415/NH/NIH HHS/United States ; DK133121/NH/NIH HHS/United States ; HL134850/NH/NIH HHS/United States ; UL1TR001436//Medical College of Wisconsin/ ; //Butenhoff Family/ ; AI108255//Advancing a Healthier Wisconsin Endowment/ ; AG075501//Advancing a Healthier Wisconsin Endowment/ ; //Susanna and Justin Mortara Innovation Fund/ ; },
mesh = {*Thermogenesis/physiology ; *Gastrointestinal Microbiome/physiology ; Animals ; Humans ; Energy Metabolism ; },
abstract = {The role of the gut microbiota in influencing physiological processes has become increasingly evident over the past several decades. One such process, thermogenesis, has become a topic of interest in recent years owing to the threat of climate change as well as the ongoing obesity epidemic. Here, we offer an overview of current knowledge regarding the contributions of the gut microbiota to thermogenesis in ecological and biomedical contexts. We first describe how the metabolic and behavioral changes associated with the gut microbiota can lead to changes in energy balance, allowing animals to adapt to environmental stressors. We then discuss how changes in the gut microbial community composition, such as through antibiotic use, can lead to dysfunctional thermoregulation and, ultimately, disease states. Finally, we consider how microbes can be exploited to improve energy balance and propose some future directions worthy of additional study.},
}
@article {pmid40642664,
year = {2025},
author = {Horwat, P and Mariowska, A and Szymanska, A and Dzieciatkowska, M and Pierudzka, W},
title = {Multimodal Interventions Targeting Gut Microbiota and Microbial Metabolites in Cognitive Impairment.},
journal = {Cureus},
volume = {17},
number = {6},
pages = {e85688},
pmid = {40642664},
issn = {2168-8184},
abstract = {Mild cognitive impairment (MCI) is a transitional stage between normal aging and Alzheimer's disease (AD). Recent studies suggest that alterations in gut microbiota and microbial metabolites are associated with cognitive decline, highlighting the gut-brain axis as a potential therapeutic target. This narrative review explores current evidence on the relationship between gut microbiota, microbial metabolites, and MCI. It summarizes intervention strategies including probiotics, prebiotics, synbiotic, fecal microbiota transplantation, dietary modifications, medicinal herbs, phytochemicals, metformin, and lifestyle factors. Probiotic strains such as Lactobacillus and Bifidobacterium have shown cognitive benefits. Adherence to the Mediterranean and MIND diets, as well as metformin use, is associated with lower MCI risk. Novel strategies, including plant-based compounds and nature exposure, show promise in modulating gut microbiota and improving cognitive outcomes. Gut microbiota modulation represents a promising avenue for early intervention in MCI. Personalized, multifactorial approaches based on individual microbiome profiles may enhance prevention and management strategies. However, more high-quality clinical trials are needed to establish evidence-based guidelines.},
}
@article {pmid40642499,
year = {2025},
author = {Gong, J and Rao, S and Liu, X and Cheng, S and Cong, X and Zhu, D},
title = {Microbiome-metabolome integration reveals fermentation-driven divergence in bioactive compound profiles of Cardamine violifolia leaf pickles.},
journal = {Current research in food science},
volume = {11},
number = {},
pages = {101121},
pmid = {40642499},
issn = {2665-9271},
abstract = {Cardamine violifolia is an emerging cruciferous vegetable rich in nutrients and bioactive components. This study investigated the microbial community and metabolite profiles in C. violifolia leaf pickles prepared using three fermentation methods: natural fermentation (NF), inoculation with Lactiplantibacillus plantarum (LP), and inoculation with Leuconostoc mesenteroides (LM). Results revealed that fermentation significantly altered the microbial composition, with Firmicutes becoming the dominant phylum. Lactococcus and Weissella were predominant in both the NF and LM groups, while Lactiplantibacillus dominated in the LP group. Metabolomic analysis identified 865 metabolites in total, with amino acids, lipids, and alkaloids representing the most abundant classes. Fermentation enhanced the production of bioactive compounds (e.g., alkaloids, phenolic acid, flavonoids), particularly in the LP group. Correlation analysis indicated a strong relationship between specific microorganisms and active metabolites. These findings suggest that fermentation not only improved the edible and nutritional value of C. violifolia leaf pickles but also enhanced their potential health benefits.},
}
@article {pmid40642474,
year = {2025},
author = {Chandrika, KSVP and Prasad, RD and Singh, A and Gopalan, B},
title = {Fe and Zn citrate nanoparticles: effect on soil enzyme activities and microbiome.},
journal = {RSC advances},
volume = {15},
number = {29},
pages = {24058-24073},
pmid = {40642474},
issn = {2046-2069},
abstract = {Iron and zinc citrate nanoparticles (NCs) were developed and evaluated as potential soil-applied plant nutrients. This study investigates the effects of seven synthesized NC formulations-comprising individual and combined Fe and Zn citrate compositions-on soil enzymatic activity and microbial diversity. The impact of NCs was assessed across three concentrations (250, 500, and 1000 mg kg[-1] of soil) and three incubation periods (30, 60, and 90 days), and was compared to commercial Fe and Zn sources, including salts, chelates, and nano-oxides. Enzyme activities measured included dehydrogenase, urease, acid phosphatase, and alkaline phosphatase. Culture-based microbiological assays were used to quantify fungi, bacteria, and actinomycetes. The results revealed that NCs generally stimulated enzyme activity and microbial populations, particularly at concentrations ≤500 mg kg[-1]. While slight inhibition was observed at 1000 mg kg[-1] in some treatments, these effects diminished over time. Strong correlations were found between microbial abundance and enzymatic responses, particularly for dehydrogenase and urease. These findings demonstrate that citrate-stabilized Fe and Zn nanoparticles exhibit low toxicity, support microbial-mediated nutrient cycling, and represent a biosafe alternative to conventional micronutrient sources for soil application.},
}
@article {pmid40642275,
year = {2025},
author = {Csitári, G and Such, N and Menyhárt, L and Schermann, K and Humpok, K and Farkas, V and Pál, L and Dublecz, K},
title = {Effects of litter exposure and flock age of broiler breeders on hatchability and the microbial composition of eggshells, egg membranes, and egg contents.},
journal = {Frontiers in veterinary science},
volume = {12},
number = {},
pages = {1589607},
pmid = {40642275},
issn = {2297-1769},
abstract = {Floor eggs represent a significant loss for broiler breeder farms and hatcheries due to the increased risk of bacterial contamination of embryos, the hatchery environment, and newly hatched chicks. In this trial, the effects of litter exposure duration (3, 6, and 16 h) and breeder flock age (22-23 weeks vs. 65-66 weeks) were evaluated in terms of hatchability and the microbial composition of different egg components (eggshell, egg membrane, and egg content). The number of total culturable aerobic microbes on the eggshell surface increased following litter exposure and decreased after 3 h. Hatchability, however, was significantly reduced only after 16 h of exposure, primarily due to increased embryonic mortality. Litter exposure and flock age led to significant differences in microbiota composition, but only on the eggshell surface. At the phylum level, 16 h of litter exposure significantly increased the abundance of Firmicutes and decreased that of Proteobacteria. At the genus level, litter exposure resulted in increased relative abundances of Lactobacillus and Ruminococcus torques group and a decreased abundance of Staphylococcus. The microbiota of the egg membrane and egg content were similar at the phylum level; however, notable differences were observed at the genus level. Pseudomonas was dominant in the egg membrane but underrepresented in the egg content, leading to a significantly higher abundance of spoilage-associated bacterial genera in the membrane than in the content. Interestingly, the genus Flexivirga (phylum Actinobacteria) was detected in high abundance in both the egg membrane and egg content, despite not having been previously reported inside eggs. According to the results, no measurable bacterial translocation from the litter into the internal egg structures was observed. However, the frequency of floor egg collection may represent a critical factor if such eggs are intended for hatching.},
}
@article {pmid40642256,
year = {2025},
author = {Barnes, LL and Parmeshwar, N and Campbell, M and Esserman, L and Piper, M},
title = {Pilot Study: Investigating the Local Breast Microbiome in Implant-based Breast Reconstruction Using 16S rRNA Sequencing.},
journal = {Plastic and reconstructive surgery. Global open},
volume = {13},
number = {7},
pages = {e6928},
pmid = {40642256},
issn = {2169-7574},
abstract = {BACKGROUND: Prior studies have used 16S rRNA sequencing to examine and define the local breast microbiome, but this has not been investigated with respect to breast reconstruction. Periexpander fluid can be readily collected in patients with a dual-port tissue expander, which could allow us to define the local breast microbiome at any given time point. This study aimed to determine the feasibility of obtaining microbiome data from periexpander fluid and explore its potential relevance for clinical implant infections.<br><br>METHODS: We designed a pilot study including patients undergoing mastectomy with 2-stage implant-based reconstruction using dual-port tissue expanders. The periexpander fluid was obtained by accessing the aspiration port during standard postoperative visits, and this fluid was stored in a 1:1 ratio with DNA/RNA shield at -20&#xb0;C. The microbiome of each sample was defined using 16S rRNA microbiome sequencing.<br><br>RESULTS: Intraoperative and postoperative samples from 10 patients were sequenced to determine the feasibility of obtaining microbiome data from the periexpander aspirates. We were successful in obtaining microbiome data from all aspirates. Our results indicate that there are a large range of genera represented, but several genera appear to be more pervasive, including Pseudomonas, Corynebacterium, Phenylobacterium, Acinetobacter, and Staphylococcus.<br><br>CONCLUSIONS: We found that it is feasible to perform microbiome sequencing of breast tissue and periexpander aspirates to define the local breast environment. Rather than focusing on eliminating bacteria, it is critical to learn more about how we can optimize the balance of microorganisms in the breast microbiome to minimize infection risk.},
}
@article {pmid40642166,
year = {2025},
author = {Benbaibeche, H and Boumehira, AZ and Khan, NA},
title = {Natural bioactive compounds and their mechanisms of action in the management of obesity: a narrative review.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1614947},
pmid = {40642166},
issn = {2296-861X},
abstract = {Obesity is a burning public health problem that affects both children and adult population all over the world. The incidence of obesity will increase in the coming years due to the urbanization of societies, which has led to unbalanced food intake and lack of physical activity among individuals. The efficacy of pharmaceutical interventions is limited, and a large number of drugs are known to trigger side effects, leading to their removal from the market. The use of natural products that exert least significant side effects can be a good alternative to prevent and manage obesity and its associated complications. These natural products include polyphenols, carotenoids and alkaloids that are recognized for their extensive range of biomedical applications and have been in practice for several decades. Administering low-to-moderate doses can yield a number of health benefits; thereby, enhancing their utility in clinical settings. Nevertheless, their direct application poses challenges due to several issues such as low bioavailability, scalability, environmental impact, clinical inconsistency, and toxicity at high doses. This review seeks to examine and identify the effects of some natural bioactive compounds (NBCs) in the management of obesity by targeting pathophysiological pathways, discuss the challenges associated with the use of NBCs including issues of bioavailability, dosage, toxicity and analysis of the efficacy of polyphenols in different models. It is necessary of address challenges associated with the use of NBCs by developing formulation strategies, establishing a safe concentration margin, employing humanized in vitro models to enhance translatability to clinical applications, optimizing dosage and harmonizing guidelines. The review also focuses on some conclusive studies demonstrating the potential anti-obesity effects of the most studied bioactive compounds in vitro, in vivo, and in clinical human trials through the regulation of appetite, adipogenesis, inflammation, thermogenesis and energy expenditure and gut microbiome.},
}
@article {pmid40642105,
year = {2025},
author = {Jasemi, SK and Faridafshar, H and Amin, MN and Babamohamadi, M and Falahati, M and Amirian, R and Izadi, Z},
title = {NO: a key player in microbiome dynamics and cancer pathogenesis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1532255},
pmid = {40642105},
issn = {2235-2988},
mesh = {Humans ; *Neoplasms/pathology/metabolism/microbiology/etiology ; *Nitric Oxide/metabolism ; *Microbiota/physiology ; Mouth/microbiology ; Nitrates/metabolism ; Animals ; Bacteria/metabolism ; },
abstract = {The human microbiome refers to the genomic content of microorganisms inhabiting the human body, including the lungs, oral cavity, intestinal tract, esophagus, and other areas. The human oral microbiota is a diverse and complex ecosystem that includes bacteria, microeukaryotes, archaea, and viruses. These communities have a highly structured biogeography resulting from the various microenvironments in the oral cavity, shaping local metabolic exchange. Dietary nitrate (NO3 [-]) is an ion naturally present in vegetables, especially leafy greens. When consumed, it leads to the production of nitric oxide (NO). This bioactive molecule benefits bodily functions like host defense and neuronal communication and improves vascular and metabolic health. Dietary NO3 [-] is reduced to NO via the nitrate-nitrite-NO pathway, facilitated by nitrate-reducing bacteria inside the oral cavity. NO has a leading role in different types of diseases, including cancer, cardiovascular disease, and diabetes. The bioavailability of NO is greatly enhanced by the activity of bacteria residing in the mouth, which reduces NO3 [-]to NO2 [-] and increases the concentration of circulating NO2 [-]. NO is the key to causing different malignancies, including gastrointestinal cancers. NO can cause cell death by inducing DNA damage and anti-apoptotic signaling pathways. Low to moderate levels of NO derived from tumors can activate angiogenesis and promote an invasive phenotype, while high levels of NO may have an anti-tumor effect in protecting against cancer. In this review, we intend to discuss the human microbiome, dietary NO3 [-]consumption, the vital role of NO in the human body, types of cancers, and treatments based on it.},
}
@article {pmid40641932,
year = {2025},
author = {Sindaco, M and Mercanti, L and Puca, V and Mazzone, M and Di Marcantonio, MC and Muraro, R and Fiordaliso, M and Mincione, G},
title = {The human microbiota: a double-edged sword against the 'Sword of Damocles' in PDAC diagnosis and therapy.},
journal = {Frontiers in oncology},
volume = {15},
number = {},
pages = {1519277},
pmid = {40641932},
issn = {2234-943X},
abstract = {Pancreatic Ductal Adenocarcinoma (PDAC) is currently a major oncological threat given the very low 5-year survival rates of 8-9%. The tumor itself is intertwined with its surrounding tissue in a peculiar tumoral microenvironment (TME) which contributes to resistance against the host immune system and traditional clinical treatments, such as chemotherapy. One of the components of TME is the microbiota, which mainly includes the bacterial species identified in the tumor tissue at various stages. Current literature highlights an active role of the microbiota in tumorigenesis, progression, metastasis, and chemotherapy response in PDAC patients. This review gathered the most recent findings about microbial composition in PDAC patients, along with the effects of intra and extra-tumoral (GI and oral) microbial species on the TME and immune system, their role in tumor progression and immuno-modulation. This paper provides an insight on the potential use of microbes as diagnostic and prognostic markers, and as an additional therapeutic strategy. The study of microbiota offer new ways to slow down carcinogenesis, modulate the immune response, and even serve as an early diagnostic tool in the absence of specific serum markers. In the current review we will offer an inquiry on these potential roles. We sorted out the most recent literature with a comprehensive and critical approach, sourcing papers from PubMed. We exclusively opted for papers that were published in the last 5 years on journals with IF≥4, with a focus on the impact of intra-tumoral microbiome on the natural history of PDAC, from pre-tumoral lesions to metastasis.},
}
@article {pmid40641871,
year = {2025},
author = {Lu, J and Zhang, W and He, Y and Jiang, M and Liu, Z and Zhang, J and Zheng, L and Zhou, B and Luo, J and He, C and Shan, Y and Zhang, R and Fan, K and Fang, B and Wan, C},
title = {Multi-omics decodes host-specific and environmental microbiome interactions in sepsis.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1618177},
pmid = {40641871},
issn = {1664-302X},
abstract = {Sepsis is a life-threatening organ dysfunction caused by a dysregulated host response to infection, and its pathogenesis involves complex interactions between the host and the microbiome. The integration of multi-omics has important value in revealing the mechanism of host-microbiome interaction. It is a key tool for promoting accurate diagnosis and guiding dynamic treatment strategies in sepsis. However, multi-omics data integration faces technical challenges, such as data heterogeneity and platform variability, as well as analytical hurdles, such as the "curse of dimensionality." Fortunately, researchers have developed two integration strategies: data-driven and knowledge-guided approaches, which employ various dimensionality reduction techniques and integration methods to handle multi-omics datasets. This review discusses the applications of multi-omics technologies in host-microbiome interactions in sepsis, highlighting their potential in identifying novel diagnostic biomarkers and developing personalized and dynamic treatment strategies. It also summarizes commonly used systems biology resources and computational tools for data integration; the review outlines the challenges in this field and proposes potential directions for future studies.},
}
@article {pmid40641869,
year = {2025},
author = {Yang, J and Han, X and Li, Q and Wang, D and Li, Y and Zhang, Z},
title = {Potassium fertilization modulates potato (Solanum tuberosum L. V7) yield and rhizosphere microbiome dynamics.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1618600},
pmid = {40641869},
issn = {1664-462X},
abstract = {INTRODUCTION: Potassium (K) is a critical macronutrient essential for enzymatic activation, photosynthesis, metabolite transport, and stress resistance in plants. While K is known to influence soil microbial communities, the mechanistic relationships between K fertilization regimes, rhizosphere microbiome assembly, and crop productivity remain to be elucidated. This study investigated the effects of varying K fertilization rates on potato yield and associated rhizosphere microbial community dynamics throughout the key developmental stages.<br><br>METHODS: A field experiment using potato (Solanum tuberosum L. V7) was conducted in Inner Mongolia, China, during the 2024 growing season. Five K fertilization treatments (0, 120, 180, 240, and 300 kg/ha K2O) were implemented using a randomized complete block design with three replicates. Rhizosphere soil samples were collected at seedling, tuber initiation, and tuber bulking stages. High-throughput sequencing of bacterial 16S rRNA and fungal ITS1 regions was performed to characterize microbial communities. Taxonomic composition, &#x3b1;-diversity, &#x3b2;-diversity, and linear discriminant analysis effect size was conducted to assess the correlation of potato yield and microbial diversity.<br><br>RESULTS: Potato yield exhibited a quadratic relationship with K application rate, reaching maximum productivity (66,786 kg/ha) at 240 kg/ha K2O. Bacterial communities, dominated by Proteobacteria, Acidobacteriota, Actinobacteria, and Gemmatimonadota, demonstrated notable resilience across treatments. Conversely, fungal communities displayed heightened sensitivity to K fertilization, with Shannon diversity indices negatively correlated with yield (r=-0.82, p<0.05). Moderate K application (180-240 kg/ha) significantly enhanced beneficial bacterial populations, particularly Pseudomonas species, while simultaneously suppressing pathogenic Fusarium and maintaining beneficial Mortierellomycota. Both bacterial and fungal communities exhibited distinct successional trajectories, with tuber expansion stage emerging as a critical transition point in community assembly.<br><br>DISCUSSION: This investigation establishes 180-240 kg/ha K2O as the optimal application rate for maximizing potato yield while maintaining balanced rhizosphere microbial communities. K influences microbial community structure through multiple mechanisms, including ion-hormone interactions, nutrient activation processes, and pathogen regulation. These findings provide a theoretical framework for developing precision K fertilization strategies that enhance agricultural productivity while promoting the stability of the rhizosphere microbiome in potato cultivation systems.},
}
@article {pmid40641046,
year = {2025},
author = {Shi, Y and Zhang, L and Do, KA and Jenq, RR and Peterson, CB},
title = {CAT: a conditional association test for microbiome data using a permutation approach.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {4},
pages = {},
doi = {10.1093/bib/bbaf326},
pmid = {40641046},
issn = {1477-4054},
support = {P30CA016672/NH/NIH HHS/United States ; P50CA140388//SPORE/ ; CCTS TR000371//SPORE/ ; R01 HL158796/HL/NHLBI NIH HHS/United States ; R01 HL124112/HL/NHLBI NIH HHS/United States ; RP160693//Cancer Prevention and Research Institute of Texas/ ; DMS 2310955//National Science Foundation/ ; //Gladys and Roland Harriman Foundation-Bridge/ ; },
mesh = {*Microbiota ; Humans ; Phylogeny ; *Computational Biology/methods ; Algorithms ; Computer Simulation ; },
abstract = {In microbiome analysis, researchers often seek to identify taxonomic features associated with an outcome of interest. However, microbiome features are intercorrelated and linked by phylogenetic relationships, making it challenging to assess the association between an individual feature and an outcome. This paper proposes a novel conditional association test, CAT, that can account for other features and phylogenetic relatedness when testing the association between a feature and an outcome. CAT adopts a permutation approach, measuring the importance of a feature in predicting the outcome by permuting operational taxonomic unit/amplicon sequence variant counts belonging to that feature from the data and quantifying how much the association with the outcome is weakened through the change in the coefficient of determination $R^{2}
$. Compared with marginal association tests, it focuses on the added value of a feature in explaining outcome variation that is not captured by other features. By leveraging global tests including PERMANOVA and MiRKAT-based methods, CAT allows association testing for continuous, binary, categorical, count, survival, and correlated outcomes. We demonstrate through simulation studies that CAT can provide a direct quantification of feature importance that is distinct from that of marginal association tests, and illustrate CAT with applications to two real-world studies on the microbiome in melanoma patients: one examining the role of the microbiome in shaping immunotherapy response, and one investigating the association between the microbiome and survival outcomes. Our results illustrate the potential of CAT to inform the design of microbiome interventions aimed at improving clinical outcomes.},
}
@article {pmid40640723,
year = {2025},
author = {Tang, JW and Tay, ACY and Wang, L},
title = {Interpretive prediction of hyperuricemia and gout patients via machine learning analysis of human gut microbiome.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {429},
pmid = {40640723},
issn = {1471-2180},
support = {KY012023293//Research Foundation for Advanced Talents of Guandong Provincial People's Hospital/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Gout/microbiology/diagnosis ; *Machine Learning ; RNA, Ribosomal, 16S/genetics ; *Hyperuricemia/diagnosis/microbiology ; Feces/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Male ; Middle Aged ; Female ; Adult ; Aged ; Uric Acid/metabolism ; Biomarkers ; DNA, Bacterial/genetics ; },
abstract = {Hyperuricemia (HUA) and gout result from imbalances in uric acid metabolism and are closely associated with the gut microbiota. Advanced analytical methods facilitate the exploration of microbiota complexity. In this study, 16S rRNA sequencing data from stool samples of 233 patients were thoroughly collected. Machine learning (ML) and Shapley Additive exPlanations (SHAP) interpretability algorithms were applied to identify core taxa and predict the metabolic functions. The results revealed that the high-contribution core taxa identified by SHAP in each group, such as Oscillospiraceae_UCG-005 and Rhodococcus provided the basis for ML prediction. Among the five classification models, Random Forest (RF) achieved the best diagnostic performance, with prediction accuracy ranging from 82 to 96%. Metabolic function predictions indicated that the purine metabolism pathway contributes the most to distinguishing gout from other groups. In sum, ML-based 16S rRNA sequencing reveals key gut microbiome biomarkers, aiding new diagnostic strategies for HUA and gout.},
}
@article {pmid40640502,
year = {2025},
author = {Liu, L and Firrman, JA and Narrowe, AB and Mahalak, KK and Lemons, JMS and Marzorati, M and Duysburgh, C and Rotsaert, C and Van de Wiele, T},
title = {Structural and functional characterization of a porcine intestinal microbial ecosystem developed in vitro.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {24821},
pmid = {40640502},
issn = {2045-2322},
support = {8072-41000-108-00-D//USDA/ ; 8072-41000-108-00-D//USDA/ ; 8072-41000-108-00-D//USDA/ ; 8072-41000-108-00-D//USDA/ ; 8072-41000-108-00-D//USDA/ ; EOS-Homistasis project//FWO-FNR/ ; GOA-Microbes4Immunity//UGent-BOF/ ; },
mesh = {Animals ; Swine ; *Gastrointestinal Microbiome ; Metagenome ; Feces/microbiology ; *Bacteria/genetics/classification ; Metagenomics/methods ; Metabolomics ; *Intestines/microbiology ; Ecosystem ; },
abstract = {The mammalian digestive tract harbors a vast microbial community that has the potential to modulate numerous health-related processes. Multicompartment dynamic gut models have been developed to study microbial communities in a controlled environment. To verify the assumption that the experimental results produced in vitro in a mechanical device would be highly similar to those obtained from an in vivo study, in this study fecal samples from four pigs were inoculated in a simulator of the porcine intestinal microbial ecosystem (SPIME) and cultured until reaching steady state. The composition and structure of the resultant microbial communities, and the metabolites produced were compared with those harvested from the intestine of the same pigs. Taxonomic abundance identification based on shallow shotgun metagenomic sequencing revealed only 12.1% of species or 15% of metagenome-assembled genomes (MAGs) being shared across the colon compartments of the source pigs and the SPIME. Despite these overwhelming compositional shifts, higher functional conservation was indicated as measured by functional richness, MAG-level traits, CAZymes, and untargeted metabolomics. Environmental selection and bacterial functional redundancy were considered the two key elements in microbial compositional shifts and functional preservation.},
}
@article {pmid40640500,
year = {2025},
author = {Chen, C and Chen, C and Zheng, X and Wang, W and Shen, J and Jin, G and Lyu, J and Lin, L},
title = {Prediction model based on gut microbiota as a non-invasive tool for gastric cancer diagnosis.},
journal = {Applied microbiology and biotechnology},
volume = {109},
number = {1},
pages = {166},
pmid = {40640500},
issn = {1432-0614},
support = {U22A20342//Joint Funds of the National Natural Science Foundation of China/ ; U22A20342//Joint Funds of the National Natural Science Foundation of China/ ; U22A20342//Joint Funds of the National Natural Science Foundation of China/ ; U22A20342//Joint Funds of the National Natural Science Foundation of China/ ; U22A20342//Joint Funds of the National Natural Science Foundation of China/ ; U22A20342//Joint Funds of the National Natural Science Foundation of China/ ; U22A20342//Joint Funds of the National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Stomach Neoplasms/diagnosis/microbiology ; Feces/microbiology ; RNA, Ribosomal, 16S/genetics ; Biomarkers, Tumor/analysis ; Female ; Middle Aged ; Male ; Aged ; Bacteria/classification/genetics/isolation &amp; purification ; ROC Curve ; Adult ; },
abstract = {Gastric cancer (GC) is a malignant cancer of the digestive tract with high morbidity and mortality. Previous studies have shown that current diagnostic methods largely rely on invasive procedures. Moreover, there are no highly sensitive and accurate biomarkers available for early GC diagnosis. Recent studies using 16S rRNA technology show that gut microbiota can differentiate between diseased and healthy individuals. However, fewer studies emphasize the gut microbiome's value in GC diagnosis. In this study, we collected 455 fecal samples, including 100 from healthy individuals (healthy controls [HCs]), 153 from GC patients, 43 from patients with non-neoplastic diseases of the stomach, and 159 from verification individuals. Our analysis revealed a significantly increased microbial richness in the GC group (Chao1 index, P < 0.05) and distinct compositional differences (principal coordinates analysis). Linear discriminant analysis effect size analysis identified 19 HC-enriched genera (e.g., Bacteroides) and 31 GC-enriched genera (e.g., Streptococcus). The random forest model selected 20 key diagnostic genera, achieving an area under the receiver operating characteristic curve (AUC) of 0.81. By integrating 10 tumor biomarkers, the combined diagnostic model improved the AUC to 0.86 (validation set: 0.84). Tumor biomarker positivity (60.78%) did not directly correlate with microbiota, but the microbiota-biomarker model improved non-invasive diagnostic accuracy, providing a new approach for early GC screening. KEY POINTS: • Changchang Chen and Chen Chen contributed equally to this work • Gut microbiota changes significantly in gastric cancer • Microbiome shows promise as non-invasive diagnostic markers • The combined microbiota-tumor marker model improves diagnosis.},
}
@article {pmid40640466,
year = {2025},
author = {Peng, K and Liu, L and Gao, S},
title = {Harnessing microbial nanobiotics: Lactobacillus extracellular vesicles as next-generation therapeutics across physiological systems.},
journal = {World journal of microbiology &amp; biotechnology},
volume = {41},
number = {7},
pages = {261},
pmid = {40640466},
issn = {1573-0972},
mesh = {*Extracellular Vesicles/metabolism/chemistry ; Humans ; *Lactobacillus/metabolism/chemistry ; Animals ; },
abstract = {Lactobacillus-derived extracellular vesicles (LEVs) are emerging as pivotal mediators of interkingdom communication, carrying strain-specific bioactive cargo that influences diverse physiological systems, including the gut, nervous, respiratory, reproductive, and integumentary systems. These nanoscale structures demonstrate significant therapeutic potential, modulating host immunity, enhancing barrier integrity, combating pathogens, and contributing to tissue repair across numerous health contexts. However, realizing their full clinical and biotechnological promise faces substantial hurdles. Key challenges include variability in isolation and purification methods, inconsistencies in LEV yield and composition due to cultivation conditions and inherent strain differences, and the observation of context-dependent or even paradoxical effects in certain diseases. Furthermore, gaps persist in understanding their precise biogenesis, cargo sorting mechanisms, and long-term biodistribution. Future progress necessitates interdisciplinary efforts to standardize production and characterization, resolve mechanistic ambiguities, and develop robust bioengineering strategies for targeted delivery and enhanced functionality. Addressing these obstacles is crucial to harness LEVs effectively as versatile tools in precision medicine, microbiome engineering, and sustainable applications in health and industry.},
}
@article {pmid40640325,
year = {2025},
author = {Sekiya, N and Mae, A and Murai, A and Peter, MA and Goto, M and Kato, H and Ichikawa, S and Watanabe, K},
title = {Soil microbes and organic fertilizer efficiency are associated with rice field topography.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {24939},
pmid = {40640325},
issn = {2045-2322},
mesh = {*Oryza/growth &amp; development/microbiology ; *Fertilizers/analysis ; *Soil Microbiology ; Nitrogen/metabolism ; Microbiota ; Soil/chemistry ; Agriculture/methods ; Biomass ; Japan ; Bacteria/genetics/metabolism/classification ; },
abstract = {Organic rice (Oryza sativa L.) cultivation represents a pathway toward sustainable agriculture. Soil microbial communities vary with topographic features, potentially affecting organic fertilizer efficiency and crop productivity, yet the relationship between topography, soil microbes, and fertilizer performance in rice farming remains largely unexplored. On-farm trials were conducted at two locations with contrasting topography (valley bottom vs. hillslope) in Yosano Town, Japan, comparing rice plant nitrogen uptake, biomass production, and grain yields under organic fertilizer management. Soil incubation experiments and microbiome analyses were performed to investigate differences in nitrogen mineralization rates and soil microbial community composition between locations. Valley bottom fields showed higher nitrogen uptake, biomass production, and grain yield with organic fertilizer application compared to hillslope fields. These differences are associated with higher nitrogen mineralization rates and lower abundance of genes involved in denitrification and bacterial ammonia assimilation in valley bottom soils, suggesting greater nitrogen retention and plant availability. These findings provide insights into site-specific management of organic fertilizers in rice production, highlighting the need for tailored strategies based on local topographic conditions and associated soil microbial communities.},
}
@article {pmid40640255,
year = {2025},
author = {Nthebere, K and Tata, RP and Bhimireddy, P and Chandran, LP and Gudapati, J and Yadav, MBN and Sinha, NK and Admala, M},
title = {Cumulative impact of herbicides and tillage in conservation agriculture on soil microbiome, fungal diversity and crop productivity.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {24992},
pmid = {40640255},
issn = {2045-2322},
mesh = {*Soil Microbiology ; *Herbicides/pharmacology ; *Microbiota/drug effects ; *Fungi/drug effects/classification ; Zea mays/growth &amp; development/microbiology ; *Agriculture/methods ; *Crops, Agricultural/growth &amp; development ; *Crop Production/methods ; Biodiversity ; Soil/chemistry ; },
abstract = {Conservation agriculture experiment was undertaken to investigate synergistic effects of tillage and weed management on soil microbiome, and fungal diversity at vegetative (30 DAS) and tasselling (60 DAS) of maize and monitor yield. Main-treatments included T1: Conventional tillage (CT) with Cotton- CT with maize- fallow, T2: CT with Cotton- Zero tillage (ZT) with Maize- ZT with Sesbania rostrata (Sr) and T3: ZT with Cotton + Sr residues- ZT with Maize + Cotton residues- ZT with Sr + Maize stubbles. Weed management (Sub-plots) were W1: Chemical weed control, W2: Herbicide rotation, W3: Integrated weed management (IWM) and W4: Single hand-weeded. Rhizo-sphere and plane samples were collected at 30 and 60 DAS for enzymatic, microbial analysis. The results demonstrated 25.90-44.72% and 20.31-50.72% decline on microbial and enzyme activities in T1 + W1, and in T2 + W2, respectively compared to T3 and W4 combinations at 30 DAS, due to herbicidal impact, which increased by 24.67-68.41% and 20.71-62.90% at tasseling. Metabolic quotient (qCO2) decreased with T3 and W4 combinations. Kernel and system yield were 39.42% and 51.60% higher under T3 + W1 and T3 + IWM combinations, respectively. Talaromyces flavus was identified under T3 + IWM. The qCO2 was exhibited with significant negative correlation with all biological attributes, while yield did not correlate. This suggest qCO2 as potential indicator to assess agro-ecosystem. The PCA selected variables (enzymes, organic carbon, and microbial parameters) are highly supported by zero-till + residues, and can indicate improved soil health and sustained productivity.},
}
@article {pmid40640200,
year = {2025},
author = {King, OG and Yip, AYG and Horrocks, V and Miguéns Blanco, J and Marchesi, JR and Mullish, BH and Clarke, TB and McDonald, JAK},
title = {Vancomycin-resistant enterococci utilise antibiotic-enriched nutrients for intestinal colonisation.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {6376},
pmid = {40640200},
issn = {2041-1723},
support = {227795/Z/23/Z//Wellcome Trust (Wellcome)/ ; Start-up funds from the Department of Life Sciences//Imperial College London/ ; },
mesh = {*Vancomycin-Resistant Enterococci/drug effects/metabolism/growth &amp; development ; *Anti-Bacterial Agents/pharmacology ; *Gastrointestinal Microbiome/drug effects ; Enterococcus faecalis/drug effects/growth &amp; development/metabolism ; Enterococcus faecium/drug effects/metabolism/growth &amp; development ; Feces/microbiology ; *Nutrients/metabolism ; *Intestines/microbiology ; Fatty Acids, Volatile/metabolism/pharmacology ; Humans ; Animals ; Nitrogen/metabolism ; Carbon/metabolism ; Gram-Positive Bacterial Infections/microbiology ; },
abstract = {Antibiotic treatment significantly disrupts the gut microbiome and promotes vancomycin-resistant enterococci (VRE) intestinal colonisation. These disruptions cause the intestine to act as a reservoir for VRE that seed difficult-to-treat infections. Here we show that antibiotics that promote VRE intestinal colonisation increase the concentration of a wide range of nutrients and decrease the concentration of a wide range of microbial metabolites. We show significant but incomplete suppression of VRE growth by individual short chain fatty acids that were decreased in antibiotic-treated faecal microbiomes. However, mixtures of short chain fatty acids provide complete or near complete suppression of VRE growth. We show that VRE use most nutrients increased in antibiotic-treated faecal microbiomes as carbon or nitrogen sources to support their growth, where Enterococcus faecium and Enterococcus faecalis have some common and some distinct preferences for the use of these specific nutrients. Finally, we show that E. faecium and E. faecalis occupy overlapping but distinct nutrient-defined intestinal niches that promote high growth when cultured with each other and when cultured with carbapenem-resistant Enterobacteriaceae. Our results demonstrate that VRE occupy distinct intestinal niches in the antibiotic-treated intestine, defined by their abilities to utilise specific enriched nutrients and their abilities to grow with reduced concentrations of inhibitory microbial metabolites.},
}
@article {pmid40640136,
year = {2025},
author = {Focardi, A and Bramucci, AR and Ajani, P and Khalil, A and Raina, JB and Seymour, JR},
title = {Defining the ecological strategies of phytoplankton associated bacteria.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {6363},
pmid = {40640136},
issn = {2041-1723},
mesh = {*Phytoplankton/microbiology ; *Bacteria/genetics/classification/isolation &amp; purification/metabolism ; *Microbiota/genetics ; Ecosystem ; },
abstract = {Ecological interactions between phytoplankton and bacteria govern the productivity and biogeochemistry of aquatic ecosystems. However, our understanding of these partnerships primarily comes from laboratory-based model systems, meaning that little is known about the establishment and dynamics of these interactions. Here, we tracked the development of the microbiome of 15 newly isolated phytoplankton species for 400 days. After only 20 days, each phytoplankton harboured a unique bacterial assemblage. Within these assemblages, we identify (i) specialist phytoplankton associates, which are bacteria that establish long-term interactions with 1-2 phytoplankton strains; (ii) generalists, which are associated with 3 or more phytoplankton strains; and (iii) transients, which do not develop sustained associations with any phytoplankton strains. Compared to transients, the generalists and specialists are enriched in genes involved in chemotaxis, vitamin synthesis, secondary metabolite production and the ability to uptake specific phytoplankton-derived compounds. Moreover, generalists display greater potential to move between hosts and release antimicrobials. Finally, examination of co-occurrence patterns in oceanographic time-series revealed that generalists and specialists mirror their phytoplankton partner's abundance in the environment. The divergent genomic characteristics of these discrete bacterial categories highlight different ecological strategies that likely shape phytoplankton microbiomes.},
}
@article {pmid40639850,
year = {2025},
author = {Feigenberg, SJ and Costabile, F and Tanes, C and Bittinger, K and O'Connor, R and Agarwal, D and Skoufos, G and Salaris, S and Hatzigeorgiou, A and Kostopoulos, N and Lloyd, S and Friedes, C and Chen, L and Yegya-Raman, N and Cengel, K and Levin, W and Valentić, B and Quarton, T and Shestov, AA and Berman, A and Bradley, J and Maity, A and Koumenis, C and Ben-Josef, E and Facciabene, A},
title = {Enhancing outcomes in medically inoperable early-stage NSCLC with gut-targeted antibiotics and stereotactic body radiotherapy: results from a randomized pilot study.},
journal = {Journal for immunotherapy of cancer},
volume = {13},
number = {7},
pages = {},
doi = {10.1136/jitc-2024-011356},
pmid = {40639850},
issn = {2051-1426},
mesh = {Humans ; Male ; *Carcinoma, Non-Small-Cell Lung/therapy/pathology/mortality ; Female ; Pilot Projects ; *Radiosurgery/methods ; Aged ; *Gastrointestinal Microbiome/drug effects ; *Anti-Bacterial Agents/therapeutic use/pharmacology ; Middle Aged ; *Lung Neoplasms/therapy/pathology/mortality ; *Vancomycin/therapeutic use/pharmacology ; Treatment Outcome ; Neoplasm Staging ; Aged, 80 and over ; },
abstract = {BACKGROUND: Gut microbiota modulation is an emerging strategy to improve cancer therapy outcomes. This study evaluated the safety and therapeutic potential of combining oral vancomycin-a non-absorbed, gut-restricted antibiotic with primary activity against gram-positive bacteria-with stereotactic body radiotherapy (SBRT) in early-stage non-small cell lung cancer (NSCLC). The underlying hypothesis was that vancomycin-induced changes in gut microbiota could enhance the antitumor effects of SBRT.<br><br>METHODS: We conducted a randomized, open-label pilot study in patients with early-stage NSCLC. Patients received oral vancomycin (125 mg, four times daily for 5 weeks, starting 1 week prior to SBRT). Safety, progression-free survival (PFS), overall survival (OS), gut microbiota composition, gut metabolome, and immune responses were evaluated.<br><br>RESULTS: The combination of vancomycin and SBRT was well tolerated, with no grade 3 or 4 adverse events reported. Vancomycin treatment selectively depleted certain bacterial strains while enriching others, leading to significant restructuring of the gut microbiota and alterations in the gut metabolome, including reductions in short-chain fatty acids and shifts in other important immunomodulatory metabolites. These changes were associated with dendritic cell and T cell activation, suggesting enhanced systemic immune engagement. Patients receiving vancomycin showed improved outcomes, with a PFS HR of 0.42 (95% CI 0.18 to 0.96; p=0.049) and OS HR of 0.38 (95% CI 0.14 to 0.99; p=0.033), compared with controls.<br><br>CONCLUSIONS: This pilot study demonstrates that gut microbiome modulation using a gram-positive-targeting, gut-restricted antibiotic in combination with SBRT is safe and may improve clinical outcomes in early-stage NSCLC. These findings support further investigation of targeted microbiome modulation strategies as adjuvants to immunogenic therapies like radiation.<br><br>TRIAL REGISTRATION NUMBER: NCT03546829.},
}
@article {pmid40639690,
year = {2025},
author = {Newmei, K and Gorai, S and Mukherjee, S and Dey, P},
title = {Nrf2-dependent cytoprotective effects and depletion of gut microbial energy harvesting by chemically defined polyphenol-rich Clerodendrum infortunatum.},
journal = {Fitoterapia},
volume = {},
number = {},
pages = {106730},
doi = {10.1016/j.fitote.2025.106730},
pmid = {40639690},
issn = {1873-6971},
abstract = {Plants belonging to the genus Clerodendrum are consumed as functional foods to treat metabolic liver disease in the north-eastern sub-Himalayan region of India. The use of Clerodendrum spp. as hepatoprotective is mentioned in Ayurveda and Chinese traditional medicinal literatures. This study identifies a particular Clerodendrum spp. with the most superior bioactivity and evaluates the cellular mechanism behind its cytoprotective activities and its favorable impact on the gut microbiota. Twelve major Clerodendrum spp. were analyzed using GCMS, phytochemical enrichment, pathway analysis, and comparative antioxidant assays were performed. The superior most Clerodendrum sp. was chemically characterized using HPLC and tested against HepG2 and SH-SY5Y cells for cytoprotection using ML385, a pharmacological inhibitor of Nrf2, and its potential to modulate the gut microbiota using 16S rRNA sequencing. Clerodendrum infortunatum was identified as the most bioactive plant sp. with physiologically-relevant free radical scavenging capacities and containing stigmasterol, gallic acid, catechin, syringic acid, vanillic acid, rutin, p-coumaric acid and quercetin. C. infortunatum attenuated intracellular cytoprotective enzymes, lipid peroxidation and protected HepG2 and SH-SY5Y in a Nrf2-dependent manner which were otherwise affected by H2O[2]-induced cellular injury. C. infortunatum also improved gut microbial diversity, enriched the populations of gut commensals, reduced obesogenic microbes, and attenuated gut microbial metabolic functions associated with increased dietary energy harvesting capacity. In accordance to the traditional medicinal use, our data show that the hepatoprotective effects of C. infortunatum is associated with the enhancement of hepatocellular cytoprotection and a favorable modulation of the gut microbiome.},
}
@article {pmid40639662,
year = {2025},
author = {Secchi, G and Bisutti, V and Toscano, A and Pegolo, S and Giannuzzi, D and Cecchinato, A and Bittante, G and Franciosi, E},
title = {Changes in the milk and fecal microbiota in Holstein cows with subclinical intramammary infection.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2025-26401},
pmid = {40639662},
issn = {1525-3198},
abstract = {Understanding the relationship between microbial community alterations and disease can provide valuable insights for improving diagnostics, prevention, and treatment strategies. This study used 16S rRNA amplicon sequencing to investigate and compare microbial diversity in the milk and feces of Holstein cows with subclinical mastitis caused by Streptococcus agalactiae and Prototheca spp. with that of healthy cows. A bacteriological screening identified 50 Holstein cows reared in a commercial dairy farm and classified into 3 experimental groups: i) animals negative at the bacteriological examination with no history of subclinical mastitis (HLTH; n = 16), ii) animals positive at the bacteriological examination for either Streptococcus agalactiae (STRP; n = 22) or Prototheca spp. (PRTH; n = 12). The milk microbiota showed significant pathogen-specific alterations, with increased Firmicutes in STRP cows (55.6%) and Cyanobacteria in PRTH cows (17.3%), compared with healthy cows (39.2% and 0.7%, respectively). Alpha diversity (Observed ASVs, Shannon, and Evenness indices) was significantly lower in infected cows (P < 0.05), confirming a microbial imbalance. Beta diversity analysis revealed significant differences in microbial composition between healthy and infected cows (P < 0.01, PERMANOVA), but no significant differences in fecal microbiota composition. Differential abundance analysis identified Streptococcus (log2FC = 7.3, P < 0.01) as the most enriched taxon in STRP cows and Cyanobacteria (log2FC = 8.9, P < 0.001) as the most enriched in PRTH cows in milk matrix, while Macrococcus caseolyticus was significantly reduced in both infected groups (log2FC = -4.5, P < 0.05). These findings suggest that subclinical mastitis leads to significant shifts in the milk microbiota but does not alter the fecal microbiome, supporting a localized rather than systemic microbial response. This study provides novel insights into the microbial dynamics of subclinical mastitis and potential biomarkers for disease monitoring.},
}
@article {pmid40639623,
year = {2025},
author = {Liao, K and Wen, J and Liu, Z and Zhang, B and Zhang, X and Fu, Y and Zhang, W and Hu, H and Ai, K and Zhu, W and Xia, M and Lai, Y and Qian, Y and Xu, Y and Sun, F and Zhang, L and Zhong, Q and Huang, B and Wang, X},
title = {The role of intratumoral microbiome in the occurrence, proliferation, metastasis of colorectal cancer and its underlying therapeutic strategies.},
journal = {Ageing research reviews},
volume = {},
number = {},
pages = {102820},
doi = {10.1016/j.arr.2025.102820},
pmid = {40639623},
issn = {1872-9649},
abstract = {Colorectal cancer (CRC), a leading cause of cancer mortality globally, is shaped by dynamic interactions between intratumoral microbiota and the tumor microenvironment (TME). Emerging evidence highlights the critical role of intratumoral bacteria, fungi, and viruses, such as Fusobacterium nucleatum and genotoxic Escherichia coli, in driving carcinogenesis through DNA damage, immune evasion, and metabolic reprogramming. While their origins remain debated, hypotheses include mucosal barrier penetration, migration from adjacent tissues, hematogenous dissemination, and co-metastasis with tumor cells. Spatial profiling reveals non-randomized microbial distribution within immunosuppressive TME niches characterized by reduced T-cell infiltration and enriched immunosuppressive molecules. Mechanistically, microbiota-derived metabolites (e.g., butyrate) and genotoxins (e.g., colibactin) modulate host pathways, promote epithelial DNA damage, polarize immune cells (e.g., M2-like macrophages, Tregs), and collectively, these contribute to fostering tumor progression. Conversely, microbial peptides or STING pathway activation by commensals like Bifidobacterium may enhance antitumor immunity. Intratumoral microbiota significantly influences therapeutic outcomes: F. nucleatum induces chemoresistance via autophagy, while Gammaproteobacteria inactivate gemcitabine. Immunotherapy responses are similarly modulated, with microbiota either amplifying antitumor T-cell activity or suppressing immunity through cytokine-mediated pathways. Innovative strategies, including engineered probiotics, bacterial vectors for drug delivery, and nanotechnology-enabled microbial modulation (e.g., functionalized nanoparticles, biomaterial carriers), aim to exploit these interactions. However, challenges such as low microbial biomass, contamination risks, and interpatient heterogeneity complicate translational efforts. Multi-omics and spatial-profiling technologies offer promise in deciphering microbial-immune-metabolic networks, guiding personalized therapies. Future research must address the biocompatibility of microbial-nanotech hybrids and validate intratumoral microbiota as biomarkers or therapeutic targets. Bridging gut and tumor microbiome studies could unlock novel CRC management strategies, emphasizing the dual role of microbiota as oncogenic drivers and therapeutic allies in precision oncology.},
}
@article {pmid40639456,
year = {2025},
author = {Andrews, RAF and Lacey, A and Roach, H and Tomlinson, R and Kidd, EJ and Bache, K},
title = {Investigating the Effects of Probiotics during the Menopause Transition: A Systematic Review &amp; Meta-Analysis.},
journal = {Clinical nutrition ESPEN},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.clnesp.2025.07.009},
pmid = {40639456},
issn = {2405-4577},
abstract = {This review investigated the impact of probiotics during the menopause transition and explored their potential to enhance the effectiveness of estrogenic substances in perimenopausal or recently postmenopausal women. A thorough literature search of EMBASE, MEDLINE, Cochrane Library, Scopus, and Web of Science was conducted, identifying 39 studies involving 3,187 women. Quality assessments were conducted using the relevant Cochrane Risk of Bias tools. The results demonstrated that probiotics had positive effects on menopausal symptoms, urogenital health, bone health, and the efficacy and safety of estriol and isoflavones. Meta analysis of 7 studies comparing probiotics versus placebo demonstrated large effects of probiotics on menopausal symptoms (total score) [standardized mean difference (SMD) = 0.82, 95% CI -0.52 to -1.09], vasomotor symptoms (SMD = -0.96, 95% CI -1.25 to -0.68), psychological symptoms (SMD = -0.51, 95% CI -0.95 to -0.08), vaginal dryness (SMD = 0.95, 95% CI -1.40 to -0.49), and vaginal microbiome health (Nugent score) (SMD = -0.91, 95% CI -1.32 to -0.49). Meta-analysis results were nonsignificant for reducing somatic and sexual symptoms. Probiotics hold promise in addressing symptoms related to low estrogen levels and may enhance the effects of estriol and isoflavones, offering potential benefits as part of the management of menopausal women. It's important to note that the included studies had a high risk of bias, emphasising the need for further rigorous research in this area. Should findings continue to show promise, clinicians should consider incorporating probiotics into their strategies for managing menopausal symptoms. Systematic Review Registration Number: CRD42019146270.},
}
@article {pmid40639442,
year = {2025},
author = {Zhan, Z and Chen, R and Deng, Z and Gao, J},
title = {Burgeoning momentum: the present and future of hyodeoxycholic acid in host microbiome dynamics.},
journal = {Biochemical pharmacology},
volume = {},
number = {},
pages = {117133},
doi = {10.1016/j.bcp.2025.117133},
pmid = {40639442},
issn = {1873-2968},
abstract = {This review critically examines the emerging role of hyodeoxycholic acid (HDCA) in metabolic and inflammatory disorders. We analyze the current understanding of HDCA biosynthesis, highlighting species-specific differences and challenges in identifying HDCA-producing bacteria. The study evaluated the signaling mechanism by which HDCA simultaneously activates intestinal G protein-coupled bile acid receptor 1 (TGR5) and farnesoid X receptor (FXR), challenging the traditional paradigm of bile acid （BA）signaling. We assess HDCA's immunomodulatory effects, particularly its Toll-like receptor 4 (TLR4) inhibition, and discuss potential therapeutic applications in metabolic diseases and sepsis. The review addresses challenges in translating rodent studies to human applications and explores future directions, including the development of HDCA derivatives and integration with microbiome modulation strategies. Ethical and regulatory considerations for microbiome-derived therapeutics are also discussed. We propose that HDCA research may catalyze paradigm shifts in understanding host-microbiome-BA interactions, calling for interdisciplinary approaches to harness its potential fully.},
}
@article {pmid40639331,
year = {2025},
author = {Xu, S and Wang, Z},
title = {Upper vs. lower airways: Microbes shape the local milieu.},
journal = {Cell host &amp; microbe},
volume = {33},
number = {7},
pages = {1043-1045},
doi = {10.1016/j.chom.2025.06.007},
pmid = {40639331},
issn = {1934-6069},
mesh = {Humans ; *Microbiota ; *Respiratory System/microbiology/metabolism ; Inosine/metabolism ; Glutamic Acid/metabolism ; Prevotella/metabolism ; },
abstract = {In this issue of Cell Host &amp; Microbe, Wong et al. investigate the contribution of the microbiome to airway metabolism, revealing differential microbial pathways and metabolites between the upper and lower airways. Oral commensals contribute to the metabolic milieu with Prevotella melaninogenica synthesizing inosine and glutamate in the lower airways.},
}
@article {pmid40639330,
year = {2025},
author = {Liu, K and Wang, Y},
title = {Metatranscriptomics catches gut microbes in the act.},
journal = {Cell host &amp; microbe},
volume = {33},
number = {7},
pages = {1040-1042},
doi = {10.1016/j.chom.2025.06.004},
pmid = {40639330},
issn = {1934-6069},
mesh = {*Gastrointestinal Microbiome/genetics ; *Metagenomics/methods ; Humans ; *Transcriptome ; *Bacteria/genetics ; *Metagenome ; Animals ; Circadian Rhythm ; *Gastrointestinal Tract/microbiology ; },
abstract = {In this issue of Cell Host &amp; Microbe, Flores Ramos et al.[1] employ metatranscriptomics to uncover diurnal microbial functional shifts in the gut microbiome driven by time-restricted feeding. Their work highlights the value of metatranscriptomics over metagenomics in capturing real-time microbial activity and guiding therapeutic bacterial engineering.},
}
@article {pmid40638549,
year = {2025},
author = {Dasgupta, S},
title = {Unraveling the Microbiome-Asthma Axis: Metagenomic Insights from Airway and Gut Microbial Communities.},
journal = {Omics : a journal of integrative biology},
volume = {},
number = {},
pages = {},
doi = {10.1177/15578100251358958},
pmid = {40638549},
issn = {1557-8100},
abstract = {Asthma is a heterogeneous respiratory disease with complex pathogenesis involving immune dysregulation, environmental triggers, and increasingly recognized to have contributions from the human microbiome. Emerging evidence from longitudinal birth cohorts and multi-omics studies reveals that early-life microbial colonization patterns in both the gastrointestinal and respiratory tracts play a crucial role in shaping immune trajectories and influencing asthma susceptibility. This expert review highlights the findings from pivotal studies that associate dysbiosis in the gut and airway microbiota with asthma development and its diverse phenotypic manifestations. Reduced abundance of immunomodulatory genera such as Bifidobacterium, Faecalibacterium, and Lachnospira in the gut has been consistently associated with increased asthma risk. In the airways, increased colonization by potentially pathogenic taxa, including Moraxella, Haemophilus, and Streptococcus, correlates with viral respiratory infections and persistent wheezing. Microbiome diversity patterns also differ between asthma phenotypes: eosinophilic asthma typically features a community profile closer to healthy individuals, while neutrophilic asthma is marked by enrichment of pro-inflammatory bacterial species. Moreover, protective genera such as Dolosigranulum and Corynebacterium in the upper airways are associated with lower risk of asthma and reduced respiratory infections. Elucidating these microbiome-mediated mechanisms holds promise for the development of targeted microbiota-based strategies for asthma prevention and phenotype-specific therapeutic interventions. The present review unpacks these localized microbial patterns and their mechanistic implications for asthma development, severity, and endotypic variation. Finally, unraveling the microbiome-asthma axis from airway and gut microbial communities also has implications for new ways of thinking personalized medicine in the future.},
}
@article {pmid40638335,
year = {2025},
author = {Franco, EM and Alves, LA and Camargo, I and Salvatierra, GC and Garcia, MT and Chen, T and Junqueira, JC and Bastos, DC and Mattos-Graner, RO},
title = {Contribution of a LysM domain-containing protein regulated by VicRK to streptococcus sanguinis virulence.},
journal = {Virulence},
volume = {},
number = {},
pages = {2532036},
doi = {10.1080/21505594.2025.2532036},
pmid = {40638335},
issn = {2150-5608},
abstract = {Streptococcus sanguinis is a commensal member of the oral microbiome involved in opportunistic cardiovascular infections. In the present study, we investigated the contribution of ssa_0094, a gene strongly regulated by the two-component system VicRK, to functions associated with biofilm formation, immune evasion and cardiovascular virulence. In silico analysis showed that ssa_0094 encodes a protein with a LysM domain, which is highly conserved among S. sanguinis. Although not an ubiquitous gene, several commensal streptococcal species of the oronasopharynx and zoonotic strains of Streptococcus suis harbour ssa_0094 homologues. A ssa_0094 isogenic mutant (SK0094) showed defects in initiating biofilms on saliva-coated surfaces, reduced hydrophobicity and lower production of amyloid-like components when compared to the parent strain (SK36) or to the complemented mutant (SK0094+), although it showed mild changes in DNA release and production of H2O2. Deletion of ssa_0094 also impaired S. sanguinis binding to multiple human glycoproteins of plasma and/or extracellular matrix (ECM) (plasminogen, fibronectin, fibrinogen, fibrin, type I collagen and elastin), and promoted clear increases in C3b deposition, and in induction of NEtosis by neutrophils of peripheral blood. Moreover, SK0094 showed impaired invasiveness into HCAEC cells and reduced ex vivo persistence in human blood, but no clear change in virulence in a Galleria mellonella infection model. These findings indicate that ssa_0094 is highly conserved within S. sanguinis strains required for biofilm initiation as well as for multiple functions of immune evasion and cardiovascular virulence in S. sanguinis in a host-specific fashion.},
}
@article {pmid40638177,
year = {2025},
author = {Yoshimoto, Y and Ichinohe, N and Liu, H and Nagata, N and Inoue, R and Yamamoto, Y and Nagaoka, K},
title = {EFFECTS OF CLOSTRIDIUM BUTYRICUM SUPPLEMENTATION ON FECAL MICROBIOTA AND METABOLITES IN CAPTIVE RED KANGAROO (MACROPUS RUFUS).},
journal = {Journal of zoo and wildlife medicine : official publication of the American Association of Zoo Veterinarians},
volume = {56},
number = {2},
pages = {360-370},
doi = {10.1638/2024-0079},
pmid = {40638177},
issn = {1042-7260},
mesh = {Animals ; *Feces/microbiology ; *Clostridium butyricum ; *Macropodidae/microbiology ; *Probiotics/pharmacology/administration &amp; dosage ; Male ; Female ; Animals, Zoo ; *Gastrointestinal Microbiome ; Dietary Supplements ; Animal Feed/analysis ; Diet/veterinary ; },
abstract = {The red kangaroo (Macropus rufus) is a prominent marsupial species native to Australia and is kept in zoos worldwide. Captive red kangaroos are often plagued with several diseases, such as lumpy jaw, incurring high treatment costs. Recent research suggests a significant link between the gut microbiota and various diseases in many species, indicating potential benefits of probiotics in maintaining health. The microbiota of the digestive tract of red kangaroos has been reported; however, the fecal microbiota and any compositional changes in this microbiota caused by probiotic intervention remain to be elucidated. Herein, the effects of the probiotic Clostridium butyricum, which produces the short-chain fatty acid butyrate, on fecal microbiota and metabolites in red kangaroos were investigated. Fecal samples were collected from six red kangaroos free from signs of diseases (three males and three females, aged 1-2 yr) during C. butyricum supplementation and suspension periods. Fecal C. butyricum levels decreased during the suspension period and increased upon resumption by quantitative PCR analysis. Despite changes in C. butyricum levels, fecal concentrations of measured short-chain fatty acids remained unchanged. Total microbiome analysis showed no significant differences by C. butyricum supplementation. Functional predictions indicated alterations in microbial community functions, such as activating penicillin and cephalosporin biosynthesis and inactivating the bacterial secretion system during C. butyricum supplementation. Metabolomic analyses identified significant changes in pathways related to amino acid degradation and metabolism, fatty acid biosynthesis, glycolysis and glycogenesis, and the citrate cycle (the tricarboxylic acid cycle), suggesting that C. butyricum supplementation affects metabolism independent of microbiota composition. These findings suggest that C. butyricum alters metabolism. However, this study's kangaroos were supplemented with C. butyricum prior to the study period, so its impact could not be verified. Further study is also required to determine how these changes might contribute to maintaining health in captive red kangaroos.},
}
@article {pmid40638068,
year = {2025},
author = {Altendorf, S and Bertolini, M and Le Riche, A and Tosti, A and Paus, R},
title = {Frontiers in the physiology of male pattern androgenetic alopecia: Beyond the androgen horizon.},
journal = {Physiological reviews},
volume = {},
number = {},
pages = {},
doi = {10.1152/physrev.00005.2024},
pmid = {40638068},
issn = {1522-1210},
abstract = {Male pattern androgenetic alopecia (mpAGA), the most common form of hair loss in men, represents a heritable, androgen-dependent complex trait distinct from female pattern hair loss. Despite the psychosocial burden of mpAGA in some affected individuals and associations with other morbidities, we portray mpAGA as an essentially physiological phenomenon in which defined hair follicle (HF) populations in developmentally preprogrammed scalp skin regions undergo a dramatic, but reversible (mini-)organ transformation in genetically predisposed individuals. Histologically, mpAGA exhibits progressive HF miniaturization (terminal-to-vellus conversion) and anagen shortening. Clinically, this results in a characteristic balding pattern of frontotemporal and vertex scalp skin, associated with telogen effluvium. It remains unclear how exactly androgens induce this phenotype, since neither androgen receptor polymorphisms nor changes in androgen serum or local androgen skin levels persuasively explain it. It also is as yet unresolved if mpAGA-associated HF transformation and hair cycle changes are primarily driven by the HF mesenchyme, e.g. by excessive emigration and/or reduced inductive potential of dermal papilla fibroblasts, or by intraepithelial events such as prostaglandin D2-dependent reduced HF epithelial stem cell progenitor generation. While critically revisiting our limited current understanding of mpAGA physiology and the role of mpAGA-associated genes we discuss potential targets for future therapeutic intervention beyond androgens and highlight selected dysregulated signaling pathways in mpAGA. We underscore mpAGA as an instructive, accessible model for interrogating under-investigated physiological roles of immune cells, oxidative stress, aging/senescence, and the microbiome in human organ remodeling and hair cycle regulation, and define major open research questions beyond androgen receptor- mediated signaling.},
}
@article {pmid40638028,
year = {2025},
author = {Ali, SH and Fatima, M and Fatima, M and Shaikh, UA},
title = {Association of the gut microbiome with diabetic nephropathy and the mediated effect of metabolites: friend or enemy?.},
journal = {International urology and nephrology},
volume = {},
number = {},
pages = {},
pmid = {40638028},
issn = {1573-2584},
}
@article {pmid40638022,
year = {2025},
author = {Deng, Y and Xu, L and Yang, K and Lin, Z and Zang, S and Jiang, K and Li, W and Ibrahim, NA and Ma, H and Cheng, C and Feng, J},
title = {The Time Reliable Effect of Probiotic Clostridium butyricum on the Growth of Spotted Sea Bass (Lateolabrax maculatus).},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {40638022},
issn = {1867-1314},
support = {2024A1515030244//the Natural Science Fund of Guangdong/ ; 2024RC01//the Central Public-interest Scientific Institution Basal Research Fund, South China Sea Fisheries Research Institute, CAFS/ ; 2025ZX04//the Central Public-Interest Scientific Institution Basal Research Fund, CAFS/ ; 2023TD21//the Central Public-Interest Scientific Institution Basal Research Fund, CAFS/ ; 2024YFD2401403//the National Key Research and Development Program of China/ ; 2024CXTD27//the Innovative Team Building Project of Guangdong Modern Agricultural Industrial Technology System/ ; },
abstract = {Probiotic Clostridium butyricum has been demonstrated to enhance the growth of spotted sea bass (Lateolabrax maculatus). However, the time reliable effect of C. butyricum application for L. maculatus growth promotion is poorly understood, limiting our ability to make informed decisions about when the C. butyricum should be added and why. To address this, we employed multidisciplinary approach to investigate the growth response (including growth performance, intestinal morphology, digestive enzyme activities, and gut microbiome) of L. maculatus to C. butyricum supplementation throughout the entire breeding cycle (from juvenile to marketable size). The C. butyricum supplementation significantly increased the weight of L. maculatus during its early life stages. Correspondingly, 16S rRNA sequence showed that C. butyricum addition increased probiotic bacteria (including Lactobacillales), decreased pathogenic bacteria (including Enterobacterales, Burkholderiales, and Fusobacteriales), and reduced bacterial virulence processes (including quorum sensing, biofilm formation, and bacterial secretion systems) of gut microbiota in L. maculatus. Concurrently, C. butyricum supplementation increased intestinal villus height (up to 32.1%), muscle thickness (up to 115.8%), and digestive enzyme activities (up to 77.8%). Nevertheless, during the later stages of incubation, treatment with C. butyricum did not result in further improvements or even showed similar outcomes to the non-supplemented treatment. These findings emphasize that C. butyricum supplementation during the early breeding stage can significantly benefit L. maculatus growth, rather than adding it during later stages. This study provides evidence on the appropriate timing for C. butyricum supplementation in L. maculatus culture, offering timely information and technical support for its culture management.},
}
@article {pmid40637840,
year = {2025},
author = {Tortelote, GG},
title = {Therapeutic strategies for hypertension: exploring the role of microbiota-derived short-chain fatty acids in kidney physiology and development.},
journal = {Pediatric nephrology (Berlin, Germany)},
volume = {},
number = {},
pages = {},
pmid = {40637840},
issn = {1432-198X},
abstract = {Gut microbiota have emerged as a key regulator of systemic health, influencing various physiological processes, including kidney development, function, and blood pressure regulation. This review highlights the role of microbiota-derived short-chain fatty acids (SCFAs), primarily acetate, propionate, and butyrate, in the gut-kidney axis, focusing on their signaling mechanisms, vascular effects, and developmental implications. Evidence suggests that SCFAs modulate kidney development and function and exert anti-inflammatory, antioxidant, and vasoregulatory effects through specific G protein-coupled receptors (GPR41, GPR43, GPR109A, OLFR78, and OLFR558). Human studies and research using genetically modified animals have demonstrated that gut dysbiosis disrupts SCFA metabolism, potentially contributing to hypertension, endothelial dysfunction, and chronic kidney disease (CKD). Germ-free microbiota-transplantation studies revealed that the presence of gut microbiota directly influences vascular tone and systemic blood pressure via SCFA-mediated mechanisms. Furthermore, acetate, a SCFA, is shown to impact fetal kidney development and nephron progenitor cell dynamics. Sex-specific effects of gut microbiota on vascular remodeling and immune responses further highlight the complexity of microbiome-host interactions. In pediatric patients, altered SCFA profiles are associated with CKD progression and relapse in nephrotic syndrome. Clinical data suggest that plasma SCFA levels may serve as biomarkers for hypertension risk and cardiovascular outcomes in children with kidney disease. Therapeutically, interventions targeting SCFA pathways, such as probiotics, prebiotics, dietary fiber diet, and receptor agonists, may help restore gut-kidney axis balance and improve kidney and cardiovascular outcomes. This review illustrates the critical role of SCFAs as mediators linking the gut microbiota to kidney and vascular health. Continued investigation into SCFA signaling may uncover novel strategies for preventing and managing hypertension, CKD, and developmental nephropathies.},
}
@article {pmid40637783,
year = {2025},
author = {Philippe, C and Denis, LA and Fonville, M and Devriendt, B and Dufrasne, FE and Obregon, D and Maître, A and Skičková, &#x160; and Cox, E and Sprong, H and Cruz, AC and Mori, M},
title = {Diversity of the Ixodes ricinus Microbiome Across Belgian Ecoregions and Its Association with Pathogen and Symbiont Presence.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {73},
pmid = {40637783},
issn = {1432-184X},
mesh = {*Ixodes/microbiology ; Animals ; *Microbiota ; Belgium ; *Symbiosis ; *Bacteria/classification/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Nymph/microbiology ; Anaplasma phagocytophilum/isolation &amp; purification/genetics ; Biodiversity ; },
abstract = {Ticks are important vectors of zoonotic pathogens, and their presence can be influenced by the composition of the tick microbiome. In turn, this microbiome is shaped by environmental and ecological factors, as demonstrated in several studies conducted under controlled conditions. However, the extent of these influences under natural ecological conditions remains underexplored. In this study, we investigated the diversity of the microbiome and the prevalence of pathogens in Ixodes ricinus nymphs across three distinct Belgian ecoregions: Sandy Loam, Condroz, and Ardennes. Using real-time quantitative PCR (qPCR) and Oxford Nanopore 16S rRNA sequencing, we assessed how geography and pathogen presence influence tick-associated microbial communities. Our results revealed significant regional differences in microbiome composition and pathogen prevalence. Borrelia burgdorferi sensu lato (s.l.) was most prevalent in the Ardennes (9% (7.4-10.9) vs 3.8% (2.8-5.2) in the Condroz and 2.1% (1.4-3.2) in Sandy Loam) while Anaplasma phagocytophilum was more common in the Sandy Loam region (21.1% (18.7-23.8) vs 4% (3-5.4) in the Condroz and 3.2% (2.2-4.4) in the Ardennes). Endosymbionts such as Midichloria mitochondrii and Spiroplasma ixodetis also exhibited distinct geographic distributions. Network analysis identified potential pathogen-microbiota interactions, with certain bacterial taxa showing positive or negative associations with specific pathogens. Moreover, microbiome composition was influenced not only by ecoregion but also by microorganisms such as Rickettsia helvetica, suggesting that its colonization may actively shape microbial community structure, potentially through competition or facilitation mechanisms. Additionally, microbiome network robustness varied across ecoregions, highlighting the role of ecological context in shaping microbial interactions within ticks. These findings underscore the complex interplay between geography, pathogen presence, and microbial diversity in ticks, highlighting the importance of integrating these interactions to inform microbiome-based strategies for vector control and disease prevention.},
}
@article {pmid40637409,
year = {2025},
author = {Imes, AM and Pavelsky, MN and Badal, K and Kamp, DL and Briseño, JL and Sakmar, T and Vogt, MA and Nyholm, SV and Heath-Heckman, EAC and Grasse, B and Septer, AN and Mandel, MJ},
title = {Euprymna berryi as a comparative model host for Vibrio fischeri light organ symbiosis.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0000125},
doi = {10.1128/aem.00001-25},
pmid = {40637409},
issn = {1098-5336},
abstract = {Functional studies of host-microbe interactions benefit from natural model systems that enable the exploration of molecular mechanisms at the host-microbe interface. Bioluminescent Vibrio fischeri colonize the light organ of the Hawaiian bobtail squid, Euprymna scolopes, and this binary model has enabled advances in understanding host-microbe communication, colonization specificity, in vivo biofilms, intraspecific competition, and quorum sensing. The hummingbird bobtail squid, Euprymna berryi, can be generationally bred and maintained in lab settings and has had multiple genes deleted by CRISPR approaches. The prospect of expanding the utility of the light organ model system by producing multigenerational host lines led us to determine the extent to which the E. berryi light organ symbiosis parallels known processes in E. scolopes. However, the nature of the E. berryi light organ, including its microbial constituency and specificity for microbial partners, has not been examined. In this report, we isolated bacteria from E. berryi animals and tank water. Assays of bacterial behaviors required in the host, as well as host responses to bacterial colonization, illustrate largely parallel phenotypes in E. berryi and E. scolopes hatchlings. This study reveals E. berryi to be a valuable comparative model to complement studies in E. scolopes.IMPORTANCEMicrobiome studies have been substantially advanced by model systems that enable functional interrogation of the roles of the partners and the molecular communication between those partners. The Euprymna scolopes-Vibrio fischeri system has contributed foundational knowledge, revealing key roles for bacterial quorum sensing broadly and in animal hosts, for bacteria in stimulating animal development, for bacterial motility in accessing host sites, and for in vivo biofilm formation in development and specificity of an animal's microbiome. Euprymna berryi is a second bobtail squid host, and one that has recently been shown to be robust to laboratory husbandry and amenable to gene knockout. This study identifies E. berryi as a strong symbiosis model host due to features that are conserved with those of E. scolopes, which will enable the extension of functional studies in bobtail squid symbioses.},
}
@article {pmid40637405,
year = {2025},
author = {Hengoju, S and Abdissa, K and Boto, ST and Samimi, A and Martin, K and Jacobsen, ID and Rosenbaum, MA},
title = {A droplet microfluidic strategy for cultivation, investigation, and high-throughput isolation of mouse gut microbiome bacteria.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0069525},
doi = {10.1128/aem.00695-25},
pmid = {40637405},
issn = {1098-5336},
abstract = {Understanding the gut microbiome's intricate dynamics and its impact on host health necessitates the cultivation and isolation of its constituent microorganisms. Traditional culturing techniques often fall short in capturing the diversity of the gut microbiota, particularly for rare and slow-growing species. In this study, we present a droplet microfluidic platform as a high-throughput and efficient method for the cultivation and isolation of mouse gut microorganisms. Droplets, each encapsulating a single cell, were incubated under both aerobic and anaerobic conditions, thereby providing individual microenvironments without nutrient competition and facilitating the growth of a wide range of microorganisms. We validated the platform by successfully cultivating and isolating a diverse array of gut microorganisms, including strains with probiotic potential. A comparative analysis with traditional agar plating techniques revealed a higher number of unique isolates from the droplet cultivation method, demonstrating its enhanced capability to capture the cultivable fraction of the gut microbiome. Beyond isolation, 16S rDNA amplicon sequencing of the diverse microbial cultures in droplets demonstrated that our system reflects changes in microbial diversity induced by dietary interventions in mice. Droplet microfluidics offers a powerful and scalable tool for the high-throughput cultivation, evaluation, and isolation of gut microorganisms, paving the way for deeper insights into the gut microbiome's role in health and disease.IMPORTANCEThe gut microbiome plays a crucial role in health and disease, yet many of its microbial members remain difficult to cultivate using traditional methods. In this study, we present a droplet microfluidic platform that advances our ability to cultivate, isolate, and analyze mouse gut microorganisms. By providing individual microenvironments for single cells, this high-throughput method overcomes limitations of traditional culturing techniques, enhancing microbial diversity recovery compared to standard techniques. Furthermore, this platform can reflect changes in microbial diversity in response to dietary changes in mice, highlighting its potential for studying gut microbial dynamics.},
}
@article {pmid40637385,
year = {2025},
author = {Yang, L and Yang, J and Zhang, T and Xie, X and Wu, Q},
title = {Gut microbiota: a novel strategy affecting atherosclerosis.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0048224},
doi = {10.1128/spectrum.00482-24},
pmid = {40637385},
issn = {2165-0497},
abstract = {Atherosclerosis is a common chronic inflammatory cardiovascular disease affecting both coronary and peripheral arteries, which is influenced by multiple factors. It is increasingly evident that gut microbes and their byproducts play a crucial role in the development of atherosclerosis. The most representative feature of microbial dysbiosis in coronary artery disease patients is the reduction of the abundance of the phylum Bacteroidetes and the increase of the abundance of the phylum Firmicutes, which may cause changes in functional genes and metabolites. The gut microbiota and its metabolites influence the early, intermediate, and late stages of atherosclerosis mainly by inhibiting or promoting inflammatory responses. In addition, the reshaping of gut microbiota through probiotics, prebiotics, and fecal microbiota transplantation (FMT) is discussed as an alternative to traditional therapeutic methods. By summarizing how gut microbiota and their metabolites affect the process of atherosclerosis, we can better understand the complex relationship between gut microbiota and atherosclerosis.IMPORTANCEAtherosclerosis is an inflammatory cardiovascular disease, making it crucial to understand its pathogenesis and develop effective treatments. This review thoroughly examines the literature, emphasizing the gut microbiome as a key factor influencing atherosclerosis. It also explores how the gut microbiota and its metabolites impact the primary, intermediate, and advanced stages of atherosclerosis and proposes that remodeling the gut microbiota is a promising strategy for improving atherosclerosis.},
}
@article {pmid40637292,
year = {2025},
author = {Ghosh, S and Goswami, A and Bandyopadhyay, A and Saha, RG and Mandal, P},
title = {Association of Vaginal Microbiota and Sociodemographic Factors With Cervical Human Papillomavirus in the Eastern Region of India.},
journal = {Journal of medical virology},
volume = {97},
number = {7},
pages = {e70472},
doi = {10.1002/jmv.70472},
pmid = {40637292},
issn = {1096-9071},
support = {//The study was funded by the Department of Biotechnology, Govt. Of India [Grant id: BT/PR18640/BIC/101/924/2016 Dated: 20.09.2017] and DST-SERB ECR, Govt. of India [Grant id: ECR/2017/000595, Dated: 16.07.2018]./ ; },
mesh = {Humans ; Female ; India/epidemiology ; *Papillomavirus Infections/epidemiology/virology/microbiology ; Adult ; *Microbiota ; *Vagina/microbiology/virology ; RNA, Ribosomal, 16S/genetics ; Middle Aged ; Young Adult ; *Bacteria/classification/genetics/isolation &amp; purification ; Sociodemographic Factors ; Risk Factors ; *Papillomaviridae/isolation &amp; purification/classification/genetics ; Socioeconomic Factors ; Cervix Uteri/virology ; Adolescent ; High-Throughput Nucleotide Sequencing ; Uterine Cervical Neoplasms/virology/epidemiology ; Human Papillomavirus Viruses ; },
abstract = {Prolonged exposure to the High-risk Human Papillomavirus (HPV) leads to the development of cervical carcinoma. Numerous factors aid in this virus's acquisition, persistence, and clearance. This study aims to determine the association of vaginal microbiota and socio-demographic factors with oncogenic HPV infections among women from Eastern region of India. Cervical scrapes and vaginal swab samples were collected from women (n = 300) having some gynecological complaints with informed consent. Cervical cytology and HPV types were screened among them. A subset of samples (n = 12) were subjected for next generation sequencing based 16S rRNA profiling to determine the vaginal bacterial diversity among the HPV-positive and HPV-negative women with normal cervical cytology. The taxonomic profiling, diversity and relative abundance of bacterial species were determined subsequently. With appropriate statistical tests, vaginal bacterial diversity along with socio-demographic risk factors was correlated with HPV infections. A PCR-based approach further detected the bacterial taxa that were exclusively present among the groups in the whole data set. HPV infection was identified among 11.60% of individuals, with the dominance of HPV18 (80%) among carcinogenic HPV. 16S rRNA profiling revealed that the HPV-positive group had lower abundance of Firmicutes phylum and higher abundance of Proteobacteria and Actinobacteria phyla than the HPV-negative group. A positive correlation between Genus Acinetobacter and HPV positivity was established, presenting higher susceptibility for oncogenic HPV16/18 (p = 0.016; relative mean abundance = 19.67). PCR-based detection of this genus in the whole data set (n = 300), a statistically significant association with oncogenic HPV16/18 infection (p ≤ 0.01, odds ratio (OR)= 22.48 [95% CI = 5.23-96.63]) was found. Among sociodemographic factors, Tobacco users (16.67%, 4/24; OR = 6.70 [95% CI: 1.86-24.18]; p = 0.001) and field-workers (15.79%, 3/19; OR = 5.67 [95% CI: 1.40-22.99]; p = 0.007) were associated with a higher risk of HPV18 infections. Assessment of geography-specific vaginal microbiota and other lifestyle induced risk factors might contribute to acquire chronic infection of oncogenic HPV and progression to cervical cancer.},
}
@article {pmid40637175,
year = {2025},
author = {Fahim, SM and Huey, SL and Palma Molina, XE and Agarwal, N and Ridwan, P and Ji, N and Kibbee, M and Kuriyan, R and Finkelstein, JL and Mehta, S},
title = {Gut microbiome-based interventions for the management of obesity in children and adolescents aged up to 19 years.},
journal = {The Cochrane database of systematic reviews},
volume = {7},
number = {7},
pages = {CD015875},
pmid = {40637175},
issn = {1469-493X},
mesh = {Adolescent ; Child ; Child, Preschool ; Humans ; Infant ; Young Adult ; Body Mass Index ; Fecal Microbiota Transplantation ; *Gastrointestinal Microbiome ; Overweight/therapy ; *Pediatric Obesity/therapy/microbiology ; Prebiotics/administration &amp; dosage ; Probiotics/therapeutic use ; Randomized Controlled Trials as Topic ; Synbiotics/administration &amp; dosage ; },
abstract = {BACKGROUND: The epidemic of overweight and obesity affects more than 390 million children and adolescents aged 5 to 19 years and 37 million children under five years of age. Overweight and obesity are associated with both short- and long-term consequences, including chronic inflammation, metabolic diseases, as well as alterations in the gut microbiome composition. Gut microbiome-based approaches may impact microbiome-related metrics such as diversity or the abundance of intestinal bacteria, which may be linked to obesity-related outcomes. However, evidence regarding the effect of gut microbiome-based interventions for the management of obesity is limited.<br><br>OBJECTIVES: To assess the effects of gut microbiome-based interventions in the management of overweight or obesity in children and adolescents in all their diversity aged 0 to 19 years.<br><br>SEARCH METHODS: We searched CENTRAL, MEDLINE, CINAHL, Web of Science Core Collection, BIOSIS Previews, Global Index Medicus (all regions), IBECS, SciELO, PAHO, PAHO IRIS, WHO IRIS, WHOLIS, Bibliomap, TRoPHI as well as ICTRP Search Portal and ClinicalTrials.gov. The date of the last search for all databases was 24 January 2025. We did not apply any language restrictions.<br><br>SELECTION CRITERIA: We included randomised controlled trials that evaluated gut microbiome-based interventions [i.e. prebiotics, probiotics, synbiotics, short-chain fatty acids (SCFAs), and faecal microbiota transplantation (FMT)] compared to standard-of-care, placebo, or control interventions in children and adolescents aged 0 to 19 years with overweight or obesity.<br><br>DATA COLLECTION AND ANALYSIS: Two review authors independently screened titles and abstracts and full texts, extracted data, and assessed the risk of bias using the Cochrane Risk of Bias 2 tool and certainty of the evidence using Grading of Recommendations Assessment, Development and Evaluation (GRADE), a framework for assessing the certainty of evidence and making recommendations in systematic reviews. Random-effects meta-analyses were performed unless only one study per outcome was available, for which fixed-effect analyses were performed.<br><br>MAIN RESULTS: We found 17 studies (838 participants) from various countries, evaluating the effects of prebiotics, probiotics, synbiotics, SCFAs, and FMT on body mass index (BMI), body weight, waist circumference, total body fat percentage (%TBF), systolic and diastolic blood pressure, and adverse events. Of the 17 studies included, five studies were in adolescents aged 10 to 19 years, and 12 studies were in children and adolescents spanning both age groups, 0 to 19 years. Upon contacting authors for data grouped by age of the participants, no studies provided separate outcomes data for children and adolescents. The included studies were funded by either academic funding sources or grants from the public and private sectors. Additionally, 15 studies were classified as currently being conducted ('ongoing'). The certainty of evidence throughout was very low. In adolescents 10 to 19 years of age, probiotics compared to placebo or no intervention may have little to no effect on BMI, body weight, waist circumference, %TBF, blood pressure, and adverse events. Similarly, FMT compared to placebo may have little to no effect on waist circumference, %TBF, blood pressure, and adverse events in this age group. According to one study with 41 participants and in children and adolescents 0 to 19 years of age, intervention with prebiotics compared to placebo may result in a small reduction in BMI (mean difference = -0.70, 95% CI = -1.25 to -0.15) and body weight (mean difference = -1.5, 95% CI = -2.61 to -0.39). Prebiotics compared to placebo may have little to no effect on waist circumference, %TBF, systolic blood pressure, and adverse events. No data were available on the effect of prebiotics on diastolic blood pressure. Probiotics compared to placebo may have little to no effect on BMI, body weight, waist circumference, %TBF, blood pressure, and adverse events in children and adolescents (0 to 19 years). Synbiotics compared to placebo may result in a reduction in systolic blood pressure (mean difference = -40.00, 95% CI = -50.63 to -29.37) in children and adolescents (0 to 19 years); according to one study with 56 participants. The evidence is very uncertain about the effects of synbiotics compared to a placebo on BMI, body weight, waist circumference, blood pressure, and adverse events. No data were available on the effect of synbiotics compared to placebo on %TBF. Synbiotics, compared to probiotics, may have little to no effect on waist circumference, %TBF, and adverse events. No data were available on the effect of synbiotics compared to probiotics on BMI, body weight, and blood pressure. According to one study with 48 participants and very low-certainty of evidence, SCFAs compared to placebo may result in a reduction in waist circumference (mean difference = -5.08, 95% CI = -7.40 to -2.76) and BMI (mean difference = -2.26, 95% CI = -3.24 to -1.28) in children and adolescents (0-19 years). SCFAs compared to placebo may have little to no effect on adverse events. No data were available on the effect of SCFAs on body weight, %TBF, and blood pressure. Adverse events, i.e. abdominal cramps, abdominal discomfort, abdominal pain, diarrhoea, vomiting, and migraine, were reported in the prebiotics group but with very low incidence. Additionally, adverse events such as nausea and headache were reported in the SCFAs group, but with low incidence.<br><br>AUTHORS' CONCLUSIONS: In adolescents aged 10 to 19 years, gut microbiome-based interventions may result in little to no difference in obesity-related outcomes. In children and adolescents aged 0 to 19 years, prebiotics may result in a small reduction in BMI and body weight; synbiotics may result in a reduction in systolic blood pressure, and SCFAs may result in a reduction in BMI and waist circumference, albeit the certainty of evidence was very low. The evidence was of very low certainty due to few studies per comparison, small sample sizes, short intervention durations, and insufficient reporting of adverse events. More rigorous research examining different types of gut microbiome-based interventions for the management of obesity is required in children and adolescents, both in clinical and community settings. Future trials should also report methods related to randomisation, blinding, and compliance, as well as include prespecified analysis plans.},
}
@article {pmid40637165,
year = {2025},
author = {Blok, NB and Bozadjieva-Kramer, N},
title = {Unlocking the Gut: Microbiome's Role in Energy Metabolism Editorial Focus on "Reutericyclin mitigates risperidone-induced suppression of anaerobic energy expenditure".},
journal = {American journal of physiology. Regulatory, integrative and comparative physiology},
volume = {},
number = {},
pages = {},
doi = {10.1152/ajpregu.00158.2025},
pmid = {40637165},
issn = {1522-1490},
}
@article {pmid40637070,
year = {2025},
author = {Chivu, RF and Melesteu, C and Bobirca, A and Dumitrescu, DA and Melesteu, I and Mustatea, P and Bobirca, F and Patrascu, T},
title = {Advances in Gastric Carcinogenesis Related to Helicobacter Pylori.},
journal = {Chirurgia (Bucharest, Romania : 1990)},
volume = {120},
number = {3},
pages = {322-344},
doi = {10.21614/chirurgia.3147},
pmid = {40637070},
issn = {1221-9118},
mesh = {Humans ; *Stomach Neoplasms/microbiology/genetics/immunology ; *Helicobacter pylori/pathogenicity/genetics ; *Helicobacter Infections/complications/microbiology/immunology ; Risk Factors ; Epigenesis, Genetic ; Cell Transformation, Neoplastic ; Carcinogenesis ; },
abstract = {Helicobacter pylori (H. pylori), a Gram-negative bacterium, has been classified as a Group I carcinogen by the World Health Organization. It represents the most significant modifiable risk factor for gastric cancer (GC), particularly the intestinal subtype. Although global infection rates are on the decline, its role in gastric oncogenesis remains prominent, especially in areas with elevated incidence rates. This review consolidates current insights into the molecular and immunological pathways through which H. pylori contributes to gastric tumorigenesis, with a focus on epigenetic modulation, host-microbe interactions, and the influence of the gastric microbiota. Chronic inflammation, instigated by H. pylori infection, advances through the Correa cascade, culminating in neoplastic transformation. Principal virulence determinants, including CagA and VacA, compromise epithelial barriers and initiate oncogenic signaling networks such as NF-úB, STAT3, Wnt/ÃÂ[2]-catenin, and Hippo/YAP. The infection is also associated with extensive epigenetic remodeling, notably promoter hypermethylation of tumor suppressor genes like CDH1, and regulation of non-coding RNAs (including miRNAs, lncRNAs, and circRNAs). Sustained colonization drives immune polarization toward Th1 and Th17 responses, promotes immune escape mechanisms such as PD-L1 overexpression, and alters the composition of the gastric microbiome. Recent findings highlight the potential role of non-H. pylori microbial species in supporting tumor progression. While eradication of H. pylori lowers the risk of gastric cancer, it does not confer complete protection, particularly in individuals with pre-existing mucosal alterations or microbial dysbiosis. The development of H. pylori-associated gastric cancer is a multifactorial process, shaped by microbial virulence, host genetics, epigenetic shifts, and immune dynamics. A deeper understanding of these interrelated mechanisms is crucial for refining preventive measures, diagnostic accuracy, and therapeutic approaches.},
}
@article {pmid38779890,
year = {2025},
author = {Whiteside, SA and Odom John, AR},
title = {Oops, the Microbes Did It Again: Gut Dysbiosis Precedes Late-Onset Meningitis.},
journal = {The Journal of infectious diseases},
volume = {231},
number = {6},
pages = {1349-1352},
doi = {10.1093/infdis/jiae266},
pmid = {38779890},
issn = {1537-6613},
}
@article {pmid40637059,
year = {2025},
author = {Bachmann, KF and Cotoia, A and Reintam Blaser, A},
title = {Gastrointestinal function and nutritional interventions in septic shock.},
journal = {Current opinion in critical care},
volume = {},
number = {},
pages = {},
doi = {10.1097/MCC.0000000000001302},
pmid = {40637059},
issn = {1531-7072},
abstract = {PURPOSE OF THE REVIEW: Gastrointestinal (GI) dysfunction significantly impacts patient outcomes in septic shock, complicating clinical management due to its central role in systemic inflammation, barrier integrity, and nutrient assimilation. This review summarizes the evolving understanding of GI dysfunction during septic shock and provides an updated framework for clinical management.<br><br>RECENT FINDINGS: New insights from recent studies focus on individualized nutritional strategies over standardized calorie-driven targets, highlighting risks associated with aggressive enteral nutrition, such as exacerbation of gut ischemia and bowel distension, and microbial dysbiosis. Maintaining splanchnic perfusion, monitoring GI dysfunction with standardized tools, and advancing nutritional support progressively based on patient-specific gastrointestinal tolerance are current strategies. Novel adjunctive therapies targeting gut permeability and microbiome restoration have been proposed, yet robust clinical data remain limited.<br><br>SUMMARY: Clinical management should prioritize hemodynamic stabilization and organ support rather than immediately targeting any nutritional goals. Monitoring GI function systematically and tailoring nutritional interventions may prevent complications and support recovery. Future research should validate monitoring tools, refine individual patient assessment, and evaluate novel therapeutic interventions to improve patient-centered outcomes in septic shock.},
}
@article {pmid40636558,
year = {2025},
author = {Dabritz, HA and Panditrao, MV and Pandey, S and Dover, N and Barash, JR and Khouri, JM and Read, JS},
title = {Infant Botulism and Carbohydrate Blood Group Antigens: Preliminary Results from a Discordant Twin Study.},
journal = {Journal of pediatrics. Clinical practice},
volume = {17},
number = {},
pages = {200152},
pmid = {40636558},
issn = {2950-5410},
abstract = {OBJECTIVE: We investigated if specific carbohydrate blood group antigens were associated with infant botulism (IB) among discordant twins and triplets.<br><br>STUDY DESIGN: Infants in the US and Canada from 2015 to 2022 who had laboratory-confirmed IB; were members of a multiple gestation birth; and had unaffected sibling(s), were eligible to participate. Blood specimens were tested for ABO, Lewis, H, and P1 carbohydrate blood antigens. FUT2 and FUT3 genes were sequenced to determine secretor and Lewis antigen status, respectively. In addition, characteristics of IB cases in the study were compared to the singleton US-Canadian IB cases from 2015 to 2022.<br><br>RESULTS: Parents of 14 of 26 IB cases who were twins or triplets with unaffected siblings consented to participate. No statistically significant associations between blood group antigens (ABO, Lewis, H, and P1) and IB were demonstrated. Twin cases in this study were significantly younger at onset of illness (median age 8.6 vs 17.3 weeks for the singleton US-Canadian IB cases, t test P < .001); and less likely to be fed exclusively breastmilk (14% for twin vs 63% for the US-Canadian IB cases) and more likely to be mixed-fed breast milk and formula (86% for twin vs 23% for the US-Canadian IB cases, Fisher exact test P < .001).<br><br>CONCLUSIONS: In this first-of-its-kind small study of IB twin or triplet cases and their unaffected siblings, no carbohydrate blood group antigens were associated with IB. Future studies could compare the microbial composition of the gut microbiome of IB cases and uninfected twin siblings or the prevalence of ABO blood groups in IB cases vs population norms.},
}
@article {pmid40636496,
year = {2025},
author = {Ding, Z and Xu, Y and Wang, Y and Liu, M and Zhu, P and Cui, K and Yang, C and Xu, C and Feng, T and Liu, Q},
title = {Host-driven remodeling of rumen microbiota supports lactation metabolism in buffalo.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1617388},
pmid = {40636496},
issn = {1664-302X},
abstract = {INTRODUCTION: Rumen microbiota and host metabolites play a key role in regulating ruminant production performance and physiological adaptation. However, the interplay between host physiological status and rumen microbial-metabolite dynamics across lactation stages in buffaloes remains unclear.<br><br>METHODS: This study employed a multi-omics approach, integrating metagenomic and serum metabolomic analyses, to investigate microbial remodeling and metabolic adaptations in buffaloes during lactation and dry periods.<br><br>RESULTS: Metagenomic analysis revealed increased abundances of Anaerovibrio, Succiniclasticum, and Methanobrevibacter_A during lactation, associated with lipid hydrolysis, propionate production, and methanogenesis, respectively. Glycoside hydrolase families GH2, GH3, GH5, and GH13 were enriched, indicating elevated carbohydrate degradation potential. In contrast, Butyrivibrio, Fibrobacter, and Eubacterium_Q were predominant during the dry period, contributing to fiber degradation and butyrate synthesis. Functional pathways related to niacin metabolism, bicarbonate reabsorption, and neuroactive ligand-receptor interaction were significantly upregulated during lactation. Metabolomic profiling identified lactation-enriched metabolites such as indole-3-methylacetate, D-maltose, and gluconic acid, correlating with immune and metabolic indicators (e.g., IgA, glucose, LDL). Conversely, dry period metabolites such as 1-methylhistidine and 5-hydroxyindoleacetic acid indicated physiological shifts toward tissue repair and stress mitigation.<br><br>DISCUSSION: The integrative analysis revealed that host physiological demands during lactation coordinate rumen microbial restructuring to enhance triglyceride degradation, fatty acid biosynthesis, and energy mobilization, thereby supporting milk production. These findings provide novel insights into the host-driven microbiome-metabolite axis underlying lactation in buffaloes.},
}
@article {pmid40636492,
year = {2025},
author = {van Essen, RRT and Kaur, J and Li, T and Mann, RC and Sawbridge, TI},
title = {The diversity, dynamics, and culturability of bacterial and fungal communities present in warm-season pasture grass seeds.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1621463},
pmid = {40636492},
issn = {1664-302X},
abstract = {A rapidly changing climate has resulted in increasing challenges for farmers. This has led to an increase in demand for beneficial microbes to help fight these challenges faced by farmers, improving crop production under harsh conditions. Increasing temperatures caused by the changing climate will also affect the dairy industry in temperate climates around the world. This has resulted in an increasing importance of warm-season pasture grasses to fill the feed gaps left by the affected temperate grasses. In this study, we assessed the microbial communities present in commercially available warm-season pasture grass seeds. We utilised amplicon metagenomics to profile and compare the bacterial and fungal communities of seeds from three different genera of warm-season pasture grasses. Microbial isolations have also been performed to assess the culturability of the seed microbiome. Significant differences in drivers of bacterial and fungal communities within warm-season pasture grass seeds were observed. In addition, most of the bacteria present in high abundance were found to be culturable, while a relatively lower percentage of abundant fungi were culturable. Analysis of the bacterial communities showed considerable variation between different distributors, possibly driven by differing seed processing methods. This variation indicates that the bacterial communities could be manipulated by providing different bacteria to the seed to promote plant growth under different conditions. In contrast, the fungal communities were more strongly driven by the genetics of the respective host genera. This suggests that differences in fungal strain levels could be exploited for modification of fungal microbiome effects.},
}
@article {pmid40636483,
year = {2025},
author = {Xing, J and Jia, M and Zhang, G and Li, L and Liu, S and Li, G and Liu, G},
title = {The composition and predictive function of the fecal microbiota in female donkeys across different reproductive cycles.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1565360},
pmid = {40636483},
issn = {1664-302X},
abstract = {The microorganisms residing in the gastrointestinal tract of monogastric herbivores play a vital role in nutrient absorption and maintaining the host's health. However, the quantitative and functional establishment of these microorganisms in female donkeys across different reproductive cycles has not yet been examined. Knowledge regarding the composition and function of gut microbiota in female donkeys during different reproductive cycles remains limited. By applying high-throughput sequencing technology and functional prediction applied to fecal samples from female donkeys across different reproductive cycles, we characterized their gut microbial composition and predicted their functional profiles. The fecal microbiota diversity in female donkeys showed no significant differences across different reproductive cycles through alpha diversity. However, the relative abundance of Firmicutes was higher during lactation, whereas Bacteroidetes were significantly higher during pregnancy. Principal coordinate analysis (PCoA) revealed the gut microbiota composition of pregnant female donkeys differed significantly from that in lactating and non-pregnant female donkeys. Bacteroidetes and Alloprevotella dominated during pregnancy in donkeys, while Firmicutes and unidentified Clostridiales were more prevalent during lactation. For functional prediction, there were significant differences in the relative abundance of pathways in the feces of female donkeys across different reproductive cycles, such as immune system processes, metabolism, glycan biosynthesis and metabolism, environmental adaptation and cell motility (p < 0.05 or p < 0.01). By correlating metabolic functions with microbial phyla, we suggest that metabolic and immune functions associated with the gut microbiota in lactating donkeys may be reduced compared to pregnant donkeys. Principal component analysis (PCA) revealed that the functional KEGG Orthologs (KOs) in the fecal microbiota of pregnant donkeys were distinctly separated from the lactation and non-pregnant female donkeys. Microbial community composition and structure exhibit distinct characteristics across different reproductive cycle, which are closely related to the functions of the microbiome. Our findings provide a foundation for understanding the compositional and functional differences in the microbial communities of mares' feces across different reproductive cycles, offering valuable insights for the precise feeding of mares throughout different reproductive cycles.},
}
@article {pmid40636353,
year = {2025},
author = {Tan, L and Jia, F and Liu, Y},
title = {Advances in research on the role of gut microbiota in the pathogenesis and precision management of gallstone disease.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1535355},
pmid = {40636353},
issn = {2296-858X},
abstract = {Gallstone disease remains a prevalent global gastrointestinal condition with a rising incidence, posing substantial challenges to healthcare systems and public health initiatives. Advances in multi-omics and sequencing technologies have illuminated the pivotal role of gut microbiota in its pathogenesis, progression, and management. This article reviews the disrupted microbiota profiles observed in patients with gallstone disease and their connection to the metabolic pathways involved in gallstone formation, particularly focusing on cholesterol metabolism, bile acid dynamics, and inflammatory pathways. It also discusses the enduring impacts of cholecystectomy on gut microbial functions and their metabolic implications. Novel strategies targeting gut microbiota, including probiotics, microbial metabolite supplementation, dietary adjustments, integrative medicine, and emerging microbial therapies, present promising avenues for precise treatment. Furthermore, this review underscores the value of future research into multi-omics integration, microbiome engineering, and global collaborations, advocating for interdisciplinary and personalized approaches to gallstone management. However, unresolved challenges, such as ensuring stable colonization of functional microbiota, refining tailored therapeutic strategies, and assessing long-term outcomes, warrant further investigation. This work aims to provide a comprehensive resource for understanding gallstone disease within a microecological framework, supporting the development of precision medicine-based prevention and treatment paradigms.},
}
@article {pmid40636324,
year = {2025},
author = {Liu, S and Zhang, Z},
title = {Distinct Lung Adenocarcinoma-Associated Microbiota Are Associated with Inflammatory Immune Landscapes and Tumor Cell Proliferation via LCIIAR-ISG15 Regulatory Networks.},
journal = {Cancer management and research},
volume = {17},
number = {},
pages = {1315-1328},
pmid = {40636324},
issn = {1179-1322},
abstract = {INTRODUCTION: Emerging research emphasizes the critical role of local microbiota in shaping the tumor microenvironment (TME) and influencing cancer progression. Lung adenocarcinoma (LUAD) is distinguished by unique bacterial communities that appear to regulate immune responses, gene expression, and patient outcomes.<br><br>METHODS: We compiled microbiome profiles from several cancer types-including LUAD, lung squamous cell carcinoma (LUSC), breast carcinoma (BRCA), and thyroid carcinoma (THCA)-using public databases. Non-negative matrix factorization (NMF) was employed to categorize LUAD cases based on TME features, while DESeq2 was used to pinpoint bacterial taxa with differing abundance. Multi-omics networks were developed to integrate microbial, transcriptomic, and clinical data. For in vitro verification, we conducted siRNA-mediated knockdown of the long non-coding RNA LCIIAR and ISG15 in Lewis lung carcinoma cells, followed by proliferation assays.<br><br>RESULTS: In contrast to LUSC, BRCA, and THCA, LUAD exhibited distinct microbial populations, with notable enrichment of Cylindrospermopsis, Cyanothece, and Sulfolobus. NMF clustering identified two LUAD subtypes with differing prognoses. One longer survival cluster, marked by reduced bacterial presence and stronger antitumor immunity-reflected in stronger immune response, increased effector T cells activity, and greater immune cell infiltration. A competing endogenous RNA (ceRNA) network analysis established a link between LCIIAR and ISG15, both overexpressed in LUAD and associated with worse survival outcomes. Knockdown LCIIAR or ISG15 through siRNA significantly inhibited lung cancer cell proliferation, pointing to their roles in tumor growth and ceRNA-mediated regulation.<br><br>CONCLUSION: LUAD features a distinctive microbiota that engages with inflammatory and ceRNA regulatory pathways. These observations underscore the value of targeting microbiome-influenced mechanisms, such as the LCIIAR-ISG15 axis, as a promising approach to enhance treatment outcomes in lung adenocarcinoma.},
}
@article {pmid40636281,
year = {2025},
author = {Magliano, G and Morello, E and Farina, M and Radici, V and Galli, M and Brambilla, G and Malagola, M and Russo, D and Avenoso, D},
title = {A case of Severe Gastrointestinal Toxicity after Allogeneic Hematopoietic Stem Cell Transplantation: Can We Improve the Evaluation of the "Gut Fitness"?.},
journal = {Mediterranean journal of hematology and infectious diseases},
volume = {17},
number = {1},
pages = {e2025054},
pmid = {40636281},
issn = {2035-3006},
}
@article {pmid40636258,
year = {2025},
author = {Lederer, AK and Chikhladze, S and Badr, MT},
title = {Editorial: The microbiome in surgery - friend or foe?.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1629822},
doi = {10.3389/fcimb.2025.1629822},
pmid = {40636258},
issn = {2235-2988},
}
@article {pmid40636116,
year = {2025},
author = {Garcia-Gonzalez, N and Wallaeys, C and Toussaint, W and Hochepied, T and Dewaele, S and De Beul, S and Van Loke, R and Vandewalle, J and Timmermans, S and Libert, C},
title = {Generation of a new Paneth cell-specific Cre-recombinase transgenic mouse line.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1576995},
pmid = {40636116},
issn = {1664-3224},
mesh = {Animals ; *Paneth Cells/metabolism/immunology ; Mice ; Mice, Transgenic ; *Integrases/genetics/metabolism ; Mice, Inbred C57BL ; *alpha-Defensins/genetics ; Intestine, Small/metabolism ; Muramidase/metabolism ; },
abstract = {Paneth cells are located in the crypts of Lieberkühn in mammalian small intestines and are producing antimicrobial peptides to keep the microbiome under control. The genetic manipulation of Paneth cells and their tracking and depletion depend on a solid Paneth cell-specific Cre-transgenic line. Here, we describe bulk RNA sequencing (RNA-seq)-based expression data from pure, sorted Paneth cells of C57BL/6J mice and identify several strongly expressed Paneth cell-specific genes, the expression of which is stable under pathophysiological conditions, as well as in the duodenum, jejunum, and ileum. We selected the Defa24 gene regulatory sequences and generated a new Defa24iCre transgenic line using BAC technology, Tg(Defa24-icre)Cli. The resulting transgenic line provides robust expression and allows for the complete depletion of Paneth cells by cell ablation, yielding mice without any detectable lysozyme biological activity in the small intestines.},
}
@article {pmid40636107,
year = {2025},
author = {Liang, B and Tan, J and Li, J and Wang, X and Li, G and Li, H and Li, T and Gao, H},
title = {Epidemiology, molecular typing, microbiome-immune interactions and treatment strategies of endometrial cancer: a review.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1595638},
pmid = {40636107},
issn = {1664-3224},
mesh = {Humans ; *Endometrial Neoplasms/epidemiology/therapy/immunology/microbiology/etiology ; Female ; *Microbiota/immunology ; Risk Factors ; },
abstract = {This review focuses on the field of endometrial cancer. Since 2020, there have been 417,367 new cases of endometrial cancer diagnosed globally and 97,370 deaths reported. Endometrial cancer ranks second in terms of incidence among female genital malignancies and third in terms of mortality among gynecological cancers. The stage, grade, and histological subtype of endometrial cancer were closely correlated with the risk of recurrence and prognosis for survival. Meanwhile, endometrial cancer exhibits significant biological heterogeneity. The complex interactions among the reproductive tract, host cells, and the microbial environment may harbor novel disease mechanisms. In this review, we provide an overview of the epidemiological characteristics, major risk factors, histological and molecular subtypes of endometrial cancer, as well as explore the associations between the female reproductive tract microbiome, immunity, and cancer progression. We also identify the specific roles of different cytokines in the pathophysiology of endometrial cancer. By integrating findings from diverse research fields, this comprehensive review offers an in-depth understanding of the multidimensional nature of endometrial cancer and highlights the significant potential and promising avenues that microbiological factors present for advancing future cancer research and guiding the development of innovative therapeutic strategies.},
}
@article {pmid40636105,
year = {2025},
author = {Rijks, V and Zuurveld, M and Garssen, J and Kostadinova, AI and Willemsen, LEM},
title = {The potential immunomodulatory role of human milk oligosaccharides in prevention of viral infections and development of asthma in early life.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1572787},
pmid = {40636105},
issn = {1664-3224},
mesh = {Humans ; *Asthma/prevention &amp; control/immunology ; *Oligosaccharides/immunology ; *Milk, Human/immunology/chemistry ; *Respiratory Syncytial Virus Infections/immunology/prevention &amp; control ; Infant ; *Virus Diseases/prevention &amp; control/immunology ; Gastrointestinal Microbiome/immunology ; Animals ; Immunomodulation ; *Picornaviridae Infections/immunology/prevention &amp; control ; },
abstract = {Around 10% of the Western population is diagnosed with asthma, and this percentage is only expected to increase in the coming years. Allergic asthma often develops during early infancy and is characterized by chronic pulmonary type 2 inflammation and airway hyperresponsiveness. Severe viral infections in early life are thought to be a risk factor for allergic asthma. The most common causes of severe viral infections in early life are respiratory syncytial virus (RSV) and rhinovirus (RV). How viral infections in early life are related to the later development of asthma is not yet known, but the pathophysiology of RSV/RV infection and asthma overlap in several areas. RSV and RV are both able to induce type 2 immunity which may contribute to the development of allergic asthma which is driven by type 2 responses against airborne allergens such as house dust mites. In early life, infants' intestines, microbiome and immune function need to mature, and breastfeeding helps to facilitate these major steps in development. Human milk oligosaccharides (HMOs) are the third largest component of human milk and have been shown to promote the development and function of the infant microbiome and may have a beneficial effect on immune maturation by promoting type 1 and regulatory immune responses. In addition, they can stimulate epithelial barrier integrity and directly interact with glycan receptors. Certain bacteria in the gut can metabolize HMOs into short-chain fatty acids (SCFA), which can exert beneficial anti-inflammatory effects locally in the gut or systemically and help maintain barrier properties and immune homeostasis. HMOs and SCFA could have protective effects on both the immune pathways in allergic asthma and viral infections. This review describes the molecular and immunomodulatory mechanisms by which different HMOs and SCFA may help defend against viral infections and also protect against allergic asthma.},
}
@article {pmid40636093,
year = {2025},
author = {Espinosa, MA and Rivera Gutierrez, RJ and Villamarin, J and Acosta, A},
title = {Precision Medicine for Obesity Treatment.},
journal = {Journal of the Endocrine Society},
volume = {9},
number = {9},
pages = {bvaf102},
pmid = {40636093},
issn = {2472-1972},
abstract = {Obesity is a chronic, heterogeneous, and complex disease associated with increased morbidity, mortality, and health-care costs. By 2030, 1 in 2 people in the United States will have obesity. Lifestyle interventions are the cornerstone of obesity management. However, they often fail to achieve clinically significant weight loss, necessitating additional treatments involving pharmacotherapy or procedures. Advancements in obesity pharmacotherapy have improved weight-loss outcomes and reduced associated comorbidities. Despite these advances, variability in response to treatment between individuals is still considerable. This variability reflects limitations in the current "one-size-fits-all" approach to obesity management. A precision medicine approach aims to address this gap by incorporating genetic, physiological, and behavioral characteristics to guide treatment selection and improve outcomes. Advances in multi-omics technologies, such as genomics, proteomics, metabolomics, and microbiome profiling, offer new opportunities to refine patient stratification and identify novel therapeutic targets. These tools may help move obesity care toward a more individualized and mechanism-based approach.},
}
@article {pmid40635890,
year = {2025},
author = {Li, X and Liu, Y and Shen, C and Shao, C and Jiang, H},
title = {Association of dietary index for gut microbiota with frailty in middle-aged and older Americans: a cross-sectional study and mediation analysis.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1615386},
pmid = {40635890},
issn = {2296-861X},
abstract = {BACKGROUND: While frailty poses significant challenges in aging populations, evidence regarding gut microbiome-targeted nutritional strategies remains limited. The novel Dietary Index for Gut Microbiota (DI-GM), quantifying microbial-pertinent dietary patterns, provides a framework for personalized frailty mitigation.<br><br>METHODS: This cross-sectional study analyzed 12,914 middle-aged and older Americans (&#x2265;45&#x202f;years) from National Health and Nutrition Examination Survey 2005-2018. Frailty status was assessed using a validated 49-item index (non-frail &#x2264;0.21; frail >0.21). The DI-GM (range 0-10) was derived from 14 microbiota-linked dietary components through two 24-h recall interviews. Multivariable logistic regression with sensitivity analyses, restricted cubic splines (RCS), stratified analyses, and mediation effect were implemented to systematically evaluate DI-GM-frailty associations.<br><br>RESULTS: Adjusted analyses revealed a dose-dependent inverse association between DI-GM and frailty (OR&#x202f;=&#x202f;0.86, 95%CI: 0.84-0.88 per unit increase). RCS identified a nonlinear inflection at DI-GM&#x202f;=&#x202f;4.082 (p for nonlinearity&#x202f;=&#x202f;0.031), beyond which each unit elevation corresponded to 12.6% reduced frailty probability (OR&#x202f;=&#x202f;0.874, 95%CI: 0.806-0.947). Stratified analyses demonstrated enhanced protective effects in women (OR&#x202f;=&#x202f;0.84 vs. male 0.90; p for interaction&#x202f;=&#x202f;0.011) and college-educated individuals (OR&#x202f;=&#x202f;0.85 vs. 0.93; p for interaction&#x202f;=&#x202f;0.031). Mediation analysis indicated BMI mediated 38.28% (95%CI: 26.62-62.6, p&#x202f;<&#x202f;0.001) of the DI-GM effect on frailty progression.<br><br>CONCLUSION: Higher DI-GM scores associate with lower frailty prevalence, particularly among women and highly-educated populations, partially mediated through BMI modulation. These findings establish DI-GM as a microbiota-targeted nutritional guideline for age-related frailty interventions, bridging dietary patterns with microbial homeostasis in geriatric care.},
}
@article {pmid40635758,
year = {2025},
author = {Pan, J and Lin, S and Qian, Q and Fu, S and Liu, X},
title = {Gut-brain axis in post-traumatic stress disorder: microbial - mediated mechanisms and new therapeutic approaches - A narrative review.},
journal = {Frontiers in pharmacology},
volume = {16},
number = {},
pages = {1621678},
pmid = {40635758},
issn = {1663-9812},
abstract = {Post-traumatic stress disorder (PTSD) is a severe mental disorder that occurs after experiencing or witnessing a traumatic event. Not only does this disorder severely impair the quality of life and emotional wellbeing of patients, but in recent years the global rate of PTSD diagnoses has increased to 1.5-2 times, and the prevalence of PTSD associated with COVID-19 events in particular has surged to 10%-25%, underscoring the urgency of developing effective treatments. The lifetime prevalence of PTSD in the general population is estimated to be approximately 3.9%, while in high-risk populations, such as war veterans, it can be as high as 30%. As a key pathway connecting the central nervous system to peripheral organs, the gut-brain axis has received increasing attention for its role in PTSD. Although the gut-brain axis has been shown to be associated with several psychiatric disorders, especially depression, its specific role in PTSD remains undercharacterized. Existing studies suggest that specific strains of Lactobacillus (e.g., Lactobacillus reuteri) may alleviate inflammatory responses and improve PTSD-like behaviors by down-regulating the expression of pro-inflammatory factors (IL-6 and TNF-α). In this study, we used a narrative review approach to sort out the research progress of gut microbiota alteration in PTSD, and compared the characteristics of changes in specific microbial taxa (e.g., Bacteroides, Lactobacillus, etc.), the index of microbiota diversity (α/β diversity), and the levels of inflammatory markers (e.g., IL-6, TNF-α) between the animal model and the human patients, respectively, in order to We further explored the potential pathogenic mechanisms mediated by microorganisms, such as influencing the vagal pathway, hypothalamic-pituitary-adrenal (HPA) axis function, immune system and other processes involved in the pathology of PTSD, and summarized the intervention strategies targeting gut microecology, such as probiotic supplementation, dietary interventions and fecal bacteria transplantation.},
}
@article {pmid40635484,
year = {2025},
author = {You, HS and Park, JY and Seo, H and Kim, BJ and Kim, JG},
title = {Distinct microbial signatures of liquid biopsy samples during gastric carcinogenesis and insights from extracellular vesicle analysis.},
journal = {The Korean journal of internal medicine},
volume = {40},
number = {4},
pages = {571-583},
doi = {10.3904/kjim.2024.339},
pmid = {40635484},
issn = {2005-6648},
support = {2022R1F1A1069321//National Research Foundation of Korea/ ; //Ministry of Science and ICT/ ; //Chung-Ang University/ ; },
mesh = {Humans ; *Stomach Neoplasms/microbiology/pathology/diagnosis ; *Extracellular Vesicles/microbiology ; Liquid Biopsy ; Male ; Female ; Middle Aged ; Aged ; Case-Control Studies ; *Gastrointestinal Microbiome ; *Bacteria/genetics/classification ; Gastric Juice/microbiology ; *Biomarkers, Tumor ; DNA, Bacterial/genetics ; Saliva/microbiology ; Adult ; },
abstract = {BACKGROUND/AIMS: The early detection of gastric cancer is crucial for improving patient outcomes. However, its pathogenesis is not fully understood. The microbiome and extracellular vesicles (EVs) might play a role in gastric carcinogenesis. We aimed to identify gastric-carcinogenesis-associated microbial signatures and evaluate whether these features vary across disease stages.<br><br>METHODS: We enrolled 141 participants (132 patients with gastric cancer or dysplasia and 9 healthy controls). Microbial-derived EVs were isolated from gastric juice, saliva, serum, and urine. Next-generation sequencing of EV-derived bacterial DNA was performed.<br><br>RESULTS: This sequencing revealed the alpha and beta diversities and microbial composition across different disease stages. The alpha diversity was significantly increased in the gastric juice and serum of disease groups. The beta diversity showed significant differences among patient groups. Distinct microbial signatures were observed across different disease stages in all four sample types. Specific bacterial species--Cutibacterium acnes, Streptococcus oralis, Pseudomonas antarctica, Ralstonia insidiosa, and Pseudomonas yamanorum--exhibited unique abundance patterns associated with disease progression, suggesting their potential as noninvasive biomarkers.<br><br>CONCLUSION: Changes in microbial diversity and distinct microbial signatures were observed during gastric carcinogenesis in both gastric juice and extragastric samples, indicating the potential of microbial-derived EVs from liquid biopsy samples as biomarkers for gastric cancer.},
}
@article {pmid40635331,
year = {2025},
author = {Colagiero, M and Pocasangre, L and Ciancio, A and Pentimone, I and Rosso, LC},
title = {Farming System and Nematodes Affect the Rhizosphere Microbiome of Tropical Banana Plants.},
journal = {Environmental microbiology reports},
volume = {17},
number = {4},
pages = {e70155},
doi = {10.1111/1758-2229.70155},
pmid = {40635331},
issn = {1758-2229},
support = {727624//European Union Programme H2020/ ; },
mesh = {*Musa/microbiology/parasitology/growth &amp; development ; *Rhizosphere ; Animals ; *Nematoda/physiology/classification ; *Microbiota ; *Soil Microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; Costa Rica ; *Agriculture/methods ; Fungi/genetics/classification/isolation &amp; purification ; Soil/chemistry/parasitology ; Biodiversity ; RNA, Ribosomal, 16S/genetics ; },
abstract = {We studied the effects of farming systems and soil nematodes on the rhizosphere microbial profiles in three banana farming systems (conventional, barbecho and organic) compared with non-cultivated controls. Bacterial 16S Amplicon Sequence Variants (ASV) and fungal ITS1-2 OTUs were obtained by NGS from experimental fields in Costa Rica, each with a given farming system. Plant-parasitic nematodes included Meloidogyne, Helicotylenchus, Radopholus, and other species. The banana cultivation and, to a minor extent, the field management type influenced the rhizosphere ASV and OTUs abundances, with a higher diversity found in organic versus conventional crops, with the organic control as the most biodiverse. Diversity indices showed differences for the total number of individuals (lowest in conventional banana) and rare species (highest in organic controls). Fungi differed for the highest species richness in the organic controls. Soil variables affecting microbial abundance included low Fe content and acidic pH. Nematodes were associated with microbial taxa that were specific to each herbivore species or feeding group, with omnivores/predators influencing microbial profiles mostly in the organic crop and controls. The organic management had the lowest impact on the diversity of belowground nematodes and rhizosphere microbiome, highlighting its beneficial potential in sustainable banana production and agroecosystem resilience.},
}
@article {pmid40635009,
year = {2025},
author = {Schulz, C and Vilchez-Vargas, R and Öcal, E and Koch, N and Puhr-Westerheide, D and Burnell, LF and Hirner-Eppeneder, H and Benckert, J and Pech, M and Reimer, P and Verslype, C and Kuhl, C and Tran, A and Ricke, J and Malfertheiner, P and Alunni-Fabbroni, M},
title = {Profiling of the tumor-associated microbiome in patients with hepatocellular carcinoma.},
journal = {Gut pathogens},
volume = {17},
number = {1},
pages = {53},
pmid = {40635009},
issn = {1757-4749},
abstract = {BACKGROUND: Tumor tissues have been shown to host a diverse array of bacteria, suggesting a link between the intratumoral microbiota and the development and progression of cancer. The aim of this explorative study was to perform microbiome analysis in liver tumor and to evaluate its relationship with cancer stage and survival outcome.<br><br>RESULTS: We conducted an exploratory study on a cohort of 20 hepatocellular cancer patients from the SORAMIC trial. Patients were divided into curative and palliative groups according to treatment type (local ablation, alone or combined with systemic therapy). The V1-V2 regions of 16&#xa0;S rRNA were sequenced starting from archival tissues. Amplicon Sequence Variants (ASVs) were taxonomically assigned to the upper (UGI) or lower (LGI) gastrointestinal tract. Bacteria were identified in both tumoral and non-tumoral tissues, showing higher diversity and correlation between diversity and shorter survival in the palliative group (S. aureus p&#x2009;<&#x2009;0.05; B. parvula p&#x2009;<&#x2009;0.01; A. chinensis p&#x2009;<&#x2009;0.01). Both therapy groups were enriched with the genus Bacilli, including Streptococcus spp., Gemella haemolysans and Helicobacter pylori, commonly found in UGI. The results suggested that among palliative patients and those with shorter survival, G. haemolysans was more prevalent, while H. pylori was more often found in curative patients with longer survival. However none of the results were significantly different (p&#x2009;>&#x2009;0.05). A higher microbiome biodiversity was associated with an increased number of lesions (Hoylesella, Agathobacter, Sphingobium, Cardiobacterium, Photobacterium and Serratia, all with p&#x2009;<&#x2009;0.01).<br><br>CONCLUSIONS: The presence of bacteria, predominantly from communities of the UGI, suggests their translocation into liver tissue due to impaired barrier function of the upper gut or the ascending pathway along the biliary duct system. The intratumoral prevalence of bacteria with proinflammatory and oncogenic potential suggests their potential role in HCC pathomechanisms.},
}
@article {pmid40634894,
year = {2025},
author = {Liu, H and Xu, X and Wang, R and Kang, J and Shen, Y and Liu, W},
title = {Gender-specific protective effects of dietary index for gut microbiota on cardiovascular disease: insights from NHANES 2007-2020.},
journal = {BMC cardiovascular disorders},
volume = {25},
number = {1},
pages = {500},
pmid = {40634894},
issn = {1471-2261},
support = {XYJG2024003//the Teaching Reform Research Project of Postgraduate Education in 2024/ ; TDSK2024001//the Project of Provincial Colleges and Universities' Basic Scientific Research Operating Expenses Project in 2024/ ; YZSY2024005//the Yanzhao Medical Research Project of Hebei University of Traditional Chinese Medicine/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; Female ; Male ; *Cardiovascular Diseases/epidemiology/prevention &amp; control/microbiology/diagnosis ; Middle Aged ; Nutrition Surveys ; Sex Factors ; United States/epidemiology ; Adult ; Protective Factors ; Risk Assessment ; Prevalence ; Cross-Sectional Studies ; *Diet, Healthy ; Aged ; },
abstract = {BACKGROUND: Cardiovascular disease (CVD) represents a significant global health burden. The gut microbiome, as a potential regulatory factor, and its synergistic interaction with dietary patterns remains underexplored. The dietary index for gut microbiota (DI-GM), which quantifies the impact of diet on gut microbiota, has limited evidence of DI-GM's association with CVD, particularly regarding gender-specific effects and dose-response patterns.<br><br>METHODS: This study utilized data from the National Health and Nutrition Examination Survey (NHANES) 2007-2020, which included 24,111 adult participants. We employed multivariable logistic regression models to assess the relationship between DI-GM and CVD. To explore possible nonlinear associations, we carried out a restricted cubic spline (RCS) analysis. Furthermore, we conducted subgroup analysis, gender stratification analysis, and sensitivity analysis.<br><br>RESULTS: A 1-unit increase in DI-GM score was associated with a 4% reduction in CVD prevalence (adjusted OR&#x2009;=&#x2009;0.96, 95% CI: 0.93-0.98, p&#x2009;=&#x2009;0.002). Compared to the lowest quartile (Q1), the highest quartile (Q4) showed a 17% lower CVD prevalence (OR&#x2009;=&#x2009;0.83, 95% CI: 0.72-0.95, p&#x2009;=&#x2009;0.008). Subgroup analysis revealed a more pronounced association in women (OR&#x2009;=&#x2009;0.95, 95% CI: 0.92-0.99, p&#x2009;=&#x2009;0.026). Gender-stratified logistic regression and RCS confirmed a significant inverse linear relationship between DI-GM and CVD in women. Sensitivity analyses further validated the robustness of these findings.<br><br>CONCLUSION: Dietary patterns with higher DI-GM scores were found to be linked to a lower prevalence of CVD, especially among women. These findings highlight DI-GM as a microbiota-targeted dietary strategy for CVD prevention. Prospective studies integrating multi-omics data are warranted to validate causality and elucidate sex-specific microbiota-mediated pathways.},
}
@article {pmid40634580,
year = {2025},
author = {},
title = {Workouts can help gut microbes to quell cancer.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {40634580},
issn = {1476-4687},
}
@article {pmid40634535,
year = {2025},
author = {Ondee, T and Pongpirul, K and Wongsaroj, L and Senaprom, S and Wattanaphansak, S and Leelahavanichkul, A},
title = {Lactiplantibacillus plantarum dfa1 reduces obesity caused by a high carbohydrate diet by modulating inflammation and gut microbiota.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {24801},
pmid = {40634535},
issn = {2045-2322},
support = {FOODF67300006//Thailand Science Research and Innovation Fund Chulalongkorn University/ ; FOODF67300006//Thailand Science Research and Innovation Fund Chulalongkorn University/ ; N/A//Second Century Fund (C2F)/ ; N/A//Second Century Fund (C2F)/ ; N/A//Second Century Fund (C2F)/ ; N/A//Second Century Fund (C2F)/ ; },
mesh = {Animals ; *Obesity/etiology/microbiology/therapy ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Probiotics/pharmacology/administration &amp; dosage ; *Inflammation ; Male ; *Dietary Carbohydrates/adverse effects ; Mice, Inbred C57BL ; *Lactobacillaceae ; },
abstract = {Given the potential of probiotics to counteract obesity induced by high glucose diets (HGD) and the beneficial effects of high-fiber diets, this study explored the impact of Lactiplantibacillus plantarum dfa1 (Lp dfa1) in mice consuming modified diets, including a unique high-carbohydrate biscuit diet (HBD) featuring Prachuap Khiri Khan's Pineapple Cheese Cake Biscuit for its rich fiber content. Notably, the fruit-derived soluble fiber HBD might have a synbiotic effect (the enhanced beneficial bacteria in the gut) different from HGD. in The standard mouse diet (RD) with a carbohydrate: protein: fat (C: P:F) ratio of 56:13:31 served as the base, which was then modified with either glucose to form the HGD (C: P:F at 60:25:15) or blended with the high-fiber dessert to create the HBD (C: P:F at 70:9:21). Over 12 weeks, mice were fed HGD or HBD with and without daily oral administration of Lp dfa1 at 1 × 10[9] CFU. This study aimed to assess the effects on obesity indicators (weight gain, lipid profiles, fat deposition), prediabetes markers (fasting glucose, insulin, oral glucose tolerance test, and Homeostatic Model Assessment for Insulin Resistance (HOMA-IR)), intestinal health (FITC-dextran assay for enterocyte injury, serum cytokines TNF-α, IL-10, and IL-6), and liver health (enzymes, weight, histology, carbohydrate and fat components, and oxidative stress). Both HGD and HBD induced similar obesity metrics, prediabetic conditions, enterocyte injury, altered serum cytokines, and liver damage. Remarkably, Lp dfa1 administration mitigated these adverse effects with an elevation in fecal short-chain fatty acids. Microbiome analysis revealed diet-induced dysbiosis, with a notable difference between HGD and HBD impacts, particularly in the Fermicutes/Bacteroides ratio and Akkermansia spp. abundance, which was significantly elevated in the HBD + Lp group. Actinomycota with a lower Proteobacteria in HBD compared with HGD group indicate the possible different impacts between the mixed sugar with fruit-derived soluble fiber versus pure glucose. Interestingly, Lp dfa1 elevated Akkermansia spp. (a well-known beneficial probiotic against obesity) only in mice with HBD but not HGD, despite an obesity attenuation by Lp dfa1 in both HGD and HBD groups, implying the different anti-obesity mechanisms. In vitro experiments revealed Lp dfa1's supernatant reduced inflammation in Caco-2 and HepG2 cell lines, evidenced by improved transepithelial electrical resistance (TEER), expression of occludin-1 (a tight junction molecule), decreased inflammatory mediators (NF-κB, TNF-α, IL-8, IL-6, and IL-10), and elevated mucin gene. Conclusively, Lp dfa1 demonstrates a dual mechanism in preventing sugar-induced intestinal injury and supporting metabolic health: direct cellular protection and microbiome modulation. These findings highlight the additive effects of Lp dfa1 and high-fiber diets, particularly emphasizing the Pineapple Cheese Cake Biscuit-based diet's role in enhancing gut microbiota and addressing diet-induced health issues.},
}
@article {pmid40634526,
year = {2025},
author = {Tarriño, M and Gutiérrez-Bautista, JF and Durán, MJO and Garcia-Diaz, A and Cabrera-Serrano, AJ and Sainz, J and Cobo, F and Rodriguez, T and Reguera, JA and Bernal, M and López-Nevot, M&#xc1; and Sampedro, A},
title = {The role of intestinal microbiota in the humoral response to SARS-CoV-2 after mRNA-1273 vaccination.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {24731},
pmid = {40634526},
issn = {2045-2322},
support = {PI21/01708//Instituto de Salud Carlos III/ ; PI21/01708//Instituto de Salud Carlos III/ ; PI21/01708//Instituto de Salud Carlos III/ ; PI21/01708//Instituto de Salud Carlos III/ ; PI21/01708//Instituto de Salud Carlos III/ ; PI21/01708//Instituto de Salud Carlos III/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; Female ; Male ; *SARS-CoV-2/immunology ; *COVID-19/prevention &amp; control/immunology/microbiology ; *Immunity, Humoral ; Adult ; 2019-nCoV Vaccine mRNA-1273/immunology ; Immunoglobulin G/immunology/blood ; Middle Aged ; Antibodies, Viral/immunology/blood ; *COVID-19 Vaccines/immunology ; Vaccination ; Feces/microbiology ; },
abstract = {The gut microbiota plays a key role in shaping immune responses, including those induced by vaccination. Its impact on the humoral response to mRNA-based SARS-CoV-2 vaccines, however, remains underexplored. We analyzed gut microbiota composition and anti-Spike (S) IgG levels in 50 healthcare workers vaccinated with the mRNA-1273 SARS-CoV-2 vaccine. Participants were stratified into low, medium, and high responders based on IgG titers 30 days post-vaccination. Stool samples were collected at baseline, and 16 S rRNA sequencing was used to assess microbiota diversity and taxonomic profiles. Alpha diversity indices showed no significant differences across response groups. However, specific microbial signatures were associated with vaccine response. Higher relative abundance of Clostridia, Clostridiales, Ruminococcaceae, and Odoribacter splanchnicus correlated with stronger IgG responses. Functional microbiome analysis revealed enrichment of acetate-producing pathways in high responders (p = 0.012), suggesting a role for short-chain fatty acids in enhancing vaccine-induced immunity. Logistic regression and Random Forest models identified these taxa as predictors of strong antibody responses. The area under the ROC curve (AUC) for individual taxa ranged from 0.70 to 0.76, indicating moderate predictive performance. Conversely, taxa such as Hallella and Sutterella wadsworthensis were linked to lower responses. These findings support a modulatory role of the gut microbiota in mRNA vaccine immunogenicity and highlight microbial metabolic functions as potential targets to boost vaccine efficacy in personalized immunization strategies.},
}
@article {pmid40634502,
year = {2025},
author = {},
title = {Tracking microbiome-derived cell-free RNA modifications detects colorectal cancer.},
journal = {Nature biotechnology},
volume = {},
number = {},
pages = {},
pmid = {40634502},
issn = {1546-1696},
}
@article {pmid40634391,
year = {2025},
author = {Cullen, JT and Lawlor, PG and Cormican, P and Crispie, F and Slattery, H and Gardiner, GE},
title = {Bacteriome and mycobiome profiling of liquid feed for finisher pigs on commercial pig farms.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {24718},
pmid = {40634391},
issn = {2045-2322},
support = {GOIPG/2021/331//Irish Research Council/ ; },
mesh = {Animals ; *Animal Feed/microbiology/analysis ; Swine/microbiology ; *Mycobiome ; Biogenic Amines/analysis/metabolism ; Farms ; *Bacteria/genetics/classification/isolation &amp; purification ; Fermentation ; *Fungi/genetics/classification/isolation &amp; purification ; },
abstract = {The aim was to assess the quality of liquid feed for grow-finisher pigs across commercial pig farms by profiling the bacteriome and mycobiome of samples and determining biogenic amine concentrations. Amplicon sequencing of liquid feed samples revealed that bacterial and fungal community structures were influenced by the farm of origin and sampling location (mixing tank/trough) on a given farm. Decreases in alpha-diversity of liquid feed between the mixing tank and the troughs corresponded with increased relative abundances of bacteria, particularly Lactobacillus, Weissella and Leuconostoc, as well as yeasts, including Kazachstania and Dipodascus, indicative of spontaneous fermentation. The concentration of biogenic amines, resulting from amino acid loss from the feed, which likely plays a role in poorer feed efficiency, also increased between the mixing tank and the troughs. The highest biogenic amine concentrations in the feed were found on the farm that had the highest lactic acid bacteria (LAB) and yeast counts. Both Lactobacillus and Kazachstania were correlated with biogenic amine concentrations in liquid feed, highlighting the unexplored role that LAB and yeast may play in amino acid decarboxylation and biogenic amine formation in liquid feed. Factors including the use of liquid co-products in diets also impacted the liquid feed microbiome.},
}
@article {pmid40634281,
year = {2025},
author = {Bagaev, A and Sur, D and Agranyoni, O and Pe'er, N and Savita, BK and Rocha, BGS and Thanos, PK and Navon-Venezia, S and Pinhasov, A},
title = {Maternal oral sodium propionate supplementation restores gut integrity and mitigates stress-induced metabolic and behavioral outcomes in offspring.},
journal = {Translational psychiatry},
volume = {15},
number = {1},
pages = {235},
pmid = {40634281},
issn = {2158-3188},
support = {2069/17//Israel Science Foundation (ISF)/ ; },
mesh = {Animals ; *Propionates/administration &amp; dosage/pharmacology ; Female ; *Gastrointestinal Microbiome/drug effects ; Male ; Mice ; *Behavior, Animal/drug effects ; *Stress, Psychological/metabolism ; Dietary Supplements ; *Maternal Behavior/drug effects ; Pregnancy ; Mice, Inbred C57BL ; Receptors, G-Protein-Coupled/metabolism ; Administration, Oral ; Feces/chemistry/microbiology ; },
abstract = {Maternal attachment is a critical determinant of offspring's postnatal development, significantly influencing their later-life metabolic and behavioral patterns. We previously showed that stress-vulnerable, socially submissive (Sub) mice exhibit significant disruptions in gut physiology including distorted microbiome composition, lower colonic propionate levels, and increased gut permeability. These alterations exacerbated chronic inflammation, caused metabolic imbalances and reduced maternal care. In this study, we revealed a significant reduction in bacterial diversity and fecal propionate levels in Sub dams. To investigate whether maternal gut integrity could mitigate adverse offspring outcomes, we provided oral sodium propionate (SP) supplementation to Sub dams via drinking water from postpartum day (PD) 0, until weaning (PD21). SP supplementation notably improved maternal care, reflected by faster pup retrieval times and better nesting. Beneficial effects were particularly pronounced in two-month-old male offspring, demonstrating decreased anxiety-like behavior, improved sociability and enhanced short-term memory accompanied by increased abundance of specific gut bacteria (Roseburia, and Shuttleworthia genus). Additionally, male offspring exhibited significant metabolic improvements, including reduced epididymal white adipose tissue (eWAT) mass, decreased adipocyte diameter accompanied by increased eWAT mRNA expression of GPR43 and PPAR-γ. Moreover, SP supplementation increased colon length linked with increased colonic mRNA expression of GPR43, PPAR-γ and Claudin-7, highlighting the importance of propionate in tight junction regulation and inflammation. Importantly, these positive outcomes exhibited notable sex-dependent differences, with male offspring responding robustly, whereas females showed minimal behavioral or metabolic improvements following maternal SP supplementation. Overall, our findings emphasize that innate stress vulnerability-related metabolic and behavioral alterations in offspring can be mitigated by restoring the dams' gut epithelial barrier integrity, highlighting the critical role of the maternal gut environment and demonstrating clear sex-specific responses to gut microbiota-targeted interventions.},
}
@article {pmid40634275,
year = {2025},
author = {Özçam, M and Lin, DL and Gupta, CL and Li, A and Gomez, JC and Wheatley, LM and Baloh, CH and Sanda, S and Jones, SM and Lynch, SV},
title = {Gut microbial bile and amino acid metabolism associate with peanut oral immunotherapy failure.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {6330},
pmid = {40634275},
issn = {2041-1723},
support = {AI128482//U.S. Department of Health &amp; Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; AI148104//U.S. Department of Health &amp; Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; UM1AI160040//U.S. Department of Health &amp; Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; AI089473//U.S. Department of Health &amp; Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics/immunology/physiology ; *Bile Acids and Salts/metabolism ; *Peanut Hypersensitivity/therapy/immunology/microbiology ; Feces/microbiology/chemistry ; *Arachis/immunology ; *Amino Acids/metabolism ; Male ; Administration, Oral ; Female ; Child ; *Desensitization, Immunologic/methods ; Double-Blind Method ; Child, Preschool ; Treatment Failure ; RNA, Ribosomal, 16S/genetics ; Metagenomics ; Antigens, Plant/immunology ; },
abstract = {Peanut Oral Immunotherapy (POIT) holds promise for remission of peanut allergy, though treatment is protracted and successful in only a subset of patients. Because the gut microbiome has been linked to food allergy, we sought to identify fecal predictors of POIT efficacy and mechanistic insights into treatment response. Here, we conducted a secondary analysis of the IMPACT randomized, double-blind, placebo-controlled POIT trial (NCT01867671), using longitudinal fecal samples from 90 children, and performed 16S rRNA sequencing, shotgun metagenomics, and untargeted metabolomics. Integrated multi-omics analyses revealed a relationship between gut microbiome metabolic capacity and treatment outcomes. Five fecal bile acids present prior to treatment initiation predicted POIT efficacy (AUC 0.71). Treatment failure was associated with a specific bile acid profile, enhanced amino acid utilization, and higher copy number of the ptpA gene encoding a bacterial hydrolase that cleaves tripeptides containing proline residues - a feature of immunogenic peanut Ara h 2 proteins. In vitro, peanut-supplemented fecal cultures of children for whom POIT failed to induce remission evidenced reduced Ara h 2 concentrations. Thus, distal gut microbiome metabolism appears to contribute to POIT failure.},
}
@article {pmid40634132,
year = {2025},
author = {Nijat, D and Zhao, Q and Abdurixit, G and He, J and Liu, H and Li, J},
title = {An Up-to-Date Review of Traditional Chinese Medicine in the Treatment of Atherosclerosis: Components, Mechanisms, and Therapeutic Potentials.},
journal = {Phytotherapy research : PTR},
volume = {},
number = {},
pages = {},
doi = {10.1002/ptr.70037},
pmid = {40634132},
issn = {1099-1573},
support = {2023B02030//Key Research and Development Program in Xinjiang Uygur Autonomous Region/ ; 2024B02005//Key Research and Development Program in Xinjiang Uygur Autonomous Region/ ; 2023TSYCLJ0043//Tianshan Talent Training Program/ ; },
abstract = {Atherosclerosis is a chronic inflammatory disease and a major global health concern. In recent years, traditional Chinese medicines (TCMs) have demonstrated multi-target therapeutic potential against atherosclerosis by modulating inflammatory responses, oxidative stress, lipid metabolism, and gut microbiota interactions. This review systematically evaluates (1) the anti-atherogenic mechanisms of key TCM herbs (e.g., Panax ginseng, Salvia miltiorrhiza) and bioactive compounds (e.g., ginsenosides, tanshinones), (2) their synergistic effects in proprietary formulations, and (3) clinical evidence for cardiovascular protection. Notably, we highlight how TCM compounds like berberine and resveratrol target the gut-vascular axis by regulating microbiota-derived metabolites (e.g., TMAO) and improving endothelial function. While preclinical studies show promising results through Nrf2/HO-1 activation, NF-κB inhibition, and plaque stabilization, translational challenges persist, including the lack of standardization and microbiome-dependent efficacy variations. We conclude that integrating TCM's multi-component advantages with cutting-edge technologies such as bioinformatics, nanotechnology, and patient-specific multiomics including microbiome profiling could revolutionize atherosclerosis management, though rigorous clinical validation and standardization remain imperative.},
}
@article {pmid40633803,
year = {2025},
author = {Xie, D and Wang, Y and Li, J and Yang, T and Zhang, Y and Zhang, W and Doherty, M and Zhu, Y and Yang, Z and Wang, Y and Wei, J and Lei, G and Zeng, C},
title = {Correlation between Gut Dysbiosis, Metabolite Alterations and Erosive Hand Osteoarthritis - an observational study within the community-based Xiangya Osteoarthritis (XO) cohort.},
journal = {Osteoarthritis and cartilage},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.joca.2025.07.004},
pmid = {40633803},
issn = {1522-9653},
abstract = {OBJECTIVES: Erosive hand osteoarthritis (EHOA) is an aggressive subtype of hand osteoarthritis (HOA) with unclear pathogenesis. Since gut dysbiosis and related metabolite alterations may exacerbate inflammation and accelerate bone destruction, we investigated whether these abnormalities were involved in EHOA.<br><br>METHODS: Participants were drawn from the Xiangya Osteoarthritis Study. We compared gut microbial &#x3b1;-diversity and &#x3b2;-diversity between EHOA and controls (neither EHOA nor non-erosive HOA), and analyzed associations between microbial species abundance, functions, and EHOA. Targeted blood metabolomics were performed to identify microbiome-associated metabolites in EHOA. The associations between EHOA-related microbial species and blood metabolites were examine through multi-omics analyses.<br><br>RESULTS: Among 1,324 participants, significant differences in &#x3b1;-diversity (EHOA: median=4.53, non-HOA control: median=4.16; median difference=0.37 [95%CI: 0.09-0.57], P=0.016) and &#x3b2;-diversity (R&#xb2;=0.002 [95%CI: 0.0018-0.006], P=0.015) were observed at the species level between EHOA and controls. Participants with EHOA had a higher relative abundance of Alistipes senegalensis (&#x3b2; coefficient:0.17 [95%CI:0.07-0.26]) and Fournierella massiliensis (&#x3b2; coefficient:0.39 [95%CI:0.28-0.49]). Tryptophan metabolism was the main altered metabolic pathway. Targeted blood metabolomics showed higher levels of L-5-hydroxytryptophan (&#x3b2; coefficient:0.38 [95%CI:0.15-0.61]), 3-indoleglyoxylic acid (&#x3b2; coefficient:0.35 [95%CI:0.01-0.69]), 5-hydroxyindoleacetic acid (&#x3b2; coefficient:0.27 [95%CI:0.09-0.45]), indoleacrylic acid (IA) (&#x3b2; coefficient:0.23 [95%CI:0.001-0.46]), and serotonin (&#x3b2; coefficient: 0.20 [95%CI: 0.004-0.40]), alongside lower levels of L-tryptophan (&#x3b2; coefficient:-0.41 [95%CI:-0.75 to -0.06]) and indole-3-acetyl-aspartate (&#x3b2; coefficient:-1.05 [95%CI:-1.79 to -0.32]) in EHOA. IA was positively correlated with EHOA-related microbial species, particularly Alistipes senegalensis (&#x3b2; coefficient:0.20 [95%CI:0.14-0.27]).<br><br>CONCLUSIONS: A higher relative abundance of Alistipes senegalensis and alterations in tryptophan metabolites, particularly higher levels of IA, are associated with EHOA.},
}
@article {pmid40633656,
year = {2025},
author = {Chakraborty, S and Banerjee, S and Kumar, S and Ghosh, S and Mukherjee, P and Das, S and Bhattacharyya, P},
title = {Biofortified vermicompost: Exploring bacterial community dynamics and enzymatic pathways through bacteriome analysis for arsenic bioremediation in mine waste.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {382},
number = {},
pages = {126795},
doi = {10.1016/j.envpol.2025.126795},
pmid = {40633656},
issn = {1873-6424},
abstract = {The extraction of mica from open-cast mines generates substantial waste, often laden with arsenic, posing severe environmental risks. Addressing this waste is essential to mitigate co-contamination. Vermitechnology offers a promising solution by converting toxic waste into nutrient-enriched, sanitized compost suitable for agriculture. This study explored bioremediation of toxic mine tailings (MT) through aerobic composting, vermicomposting and enriched vermicomposting (with Bacillus subtilis K5BGRD). Earthworm fecundity was impaired in dense MT settings but improved in MT+CD (1:1) treatments. Vermicomposting stabilized pH, enhanced nutrient mineralization and increased potassium bioavailability compared to aerobic composting. Enriched vermicompost reduced bioavailable arsenic by 58-88 % post-maturity, alongside increased microbial diversity and enzymatic activity. Earthworms bioaccumulated arsenic, contributing to a total reduction of 14.25 %. Pearson correlation and PLS-SEM analyses highlighted reduced arsenic-induced stress upon compost maturity. Metataxonomic analysis revealed microbial similarities between V1 (MT+CD [1:1]) and EV1 (MT+CD+B [1:1:1]) composts, with enrichment of stress-resistant, bioremediating and plant growth-promoting taxa. Upon crop trial it was deduced that microbe-mediated vermicomposting, particularly when combined with recommended fertilizer doses (as in T2), not only minimized arsenic accumulation in tomato plants but also significantly enhanced yield, highlighting its potential as a sustainable and effective strategy for safe crop production in contaminated soils. The study demonstrated the symbiotic relationship between earthworms and microbes in waste-treated settings, establishing a novel feedstock combination to remediate hazardous mine waste. Ultimately, this approach has the potential to replace chemical fertilizers, improve crop yields and reduce arsenic exposure - offering a cost-effective and eco-friendly solution to mining waste management.},
}
@article {pmid40633607,
year = {2025},
author = {Linh, NV and Khang, LTP and Dinh-Hung, N and Wisetkaew, S and Therdtatha, P and Sangsawad, P and Wannavijit, S and Jitjumnong, J and Permpoonpattana, P and Van Doan, H},
title = {Effects of dietary corn silk (Zea mays L.) on growth, immune and antioxidant pathways, histological morphology, gut microbiome, and sensitivity to acute ammonia exposure in the koi carp (Cyprinus carpio var. koi).},
journal = {Comparative biochemistry and physiology. Part B, Biochemistry &amp; molecular biology},
volume = {},
number = {},
pages = {111127},
doi = {10.1016/j.cbpb.2025.111127},
pmid = {40633607},
issn = {1879-1107},
abstract = {Corn silk is a promising aquafeed additive due to its antioxidant, antibacterial, and anti-inflammatory properties. This study evaluated the impact of graded dietary levels of powdered corn silk (PCS) on growth, immunity, antioxidant enzyme activities, histology, gut microbiota composition, gene expression profiles, and sensitivity to acute ammonia exposure in koi carp (Cyprinus carpio var. koi). A total of 300 fish were assigned to five dietary treatments (0, 5, 10, 20, and 30 g/kg PCS) for eight weeks. Fish fed the PCS-30 diet showed significant improvements in growth parameters, including weight gain (WG) and specific growth rate (SGR) (p < 0.05). Antioxidant capacity (2,2'-azino-bis (3-ethylbenzothiazoline-6-sulfonic acid); ABTS) and superoxide dismutase (SOD) activity, increased dose-dependently, while malondialdehyde (MDA) levels remained unchanged (p > 0.05). Expression of the immune and antioxidant genes interleukin 8 (il-8), lysozyme (lyz), catalase (cat), nuclear factor-κB (Nf-κB), and toll-like receptor 4 (tlr4) was significantly upregulated in the PCS-20 and PCS-30 groups (p < 0.05). Histological analysis revealed progressive improvements in anterior intestinal morphology, with the PCS-30 group exhibiting the greatest villus height and width. Gut microbiota analysis showed increased relative abundance of beneficial taxa (Gammaproteobacteria, Lactobacillales, Prevotella), which positively correlated with growth and antioxidant markers, and negatively with MDA levels. Survival under acute ammonia exposure was highest in the PCS-20 and PCS-30 groups. These findings demonstrate the efficacy of PCS, particularly at 30 g/kg, in enhancing growth, immunity, and stress resilience.},
}
@article {pmid40633493,
year = {2025},
author = {Sibinga, NA and Werner, E and Tegtmeier, D and De Smet, J},
title = {Animal board invited review: The need for, and the path towards, a functional understanding of the farmed insect microbiome.},
journal = {Animal : an international journal of animal bioscience},
volume = {19},
number = {8},
pages = {101575},
doi = {10.1016/j.animal.2025.101575},
pmid = {40633493},
issn = {1751-732X},
abstract = {The rapid growth of research on industrially produced insect species over the past two decades has coincided with breakthroughs in the speed and affordability of DNA sequencing. This has allowed researchers to rapidly generate data on the microbial communities associated with farmed insects, especially the gut-residing bacteria of the two cornerstone production species: black soldier fly (BSF, Hermetia illucens) and yellow mealworm (Tenebrio molitor). A picture of the most prevalent and abundant microbes associated with these species has rapidly come into focus. Specific microbial functions have been suggested under extreme or challenging rearing settings, but less is known about the contributions of the microbiome to insect rearing under realistic production conditions. There is limited understanding of how microbial communities of farmed insects arise, are maintained, and change in response to stimuli. Likewise for seemingly basic questions: what functions do insect-associated microbes perform for the host? Which (if any) taxa are essential for healthy insects? This is not intended as a criticism of existing research; indeed, these questions turn out not to be simple. Answering them requires targeted research approaches testing specific hypotheses about farmed insect microbiome function. This review aims to recalibrate the state of knowledge by critically assessing common and emerging strategies to study these microbiomes and existing knowledge gaps about the functional role of the microbiome for BSF and mealworm. Overall, it is clear that microbes are an intrinsic part of the ecology of these two farmed insects. Reciprocal interactions between microbes and insects are extensive, though microbiome community composition depends to a large extent on environmental conditions. To date, it remains unclear how taxonomical shifts correspond to functional shifts and to what extent such changes impact insect physiology. For example, when mealworms are fed plastics, their microbiomes undergo significant changes in microbial composition. These changes are presumed to increase the ability of mealworms and their microbiota to degrade plastic, but this change in function is hard to conclusively demonstrate with current tools. Furthermore, analysis of the literature shows that taxonomically disparate microbial communities may provide similar functional benefits, e.g. lignocellulose breakdown in BSF larvae. This review therefore aims to critically assess the state of the art with regard to functional analysis of the farmed insect microbiome and how available experimental methods can be best applied to identify links between microbial functions and insect physiology and improve the efficiency and sustainability of the farmed insect industry.},
}
@article {pmid40633399,
year = {2025},
author = {Criscuolo, A and Czepiel, A and Schwartze, M and Kotz, SA},
title = {A body-brain (dis)equilibrium regulating transitions from health to pathology.},
journal = {Physics of life reviews},
volume = {54},
number = {},
pages = {94-111},
doi = {10.1016/j.plrev.2025.07.003},
pmid = {40633399},
issn = {1873-1457},
abstract = {Recent empirical evidence and theoretical propositions motivate a paradigm shift in how we investigate neurocognitive functions. Rather than looking at the brain-behaviour relationship in isolation, research shows that cognition is shaped by reciprocal, dynamical interactions between the brain and the body across multiple timescales: from ultra-slow circadian rhythm to gastrointestinal and cardiorespiratory activity. This interest in body-brain-behaviour dynamics has raised new questions about if and how autonomic functioning, the coordination of intero- and exteroception, lifestyle and dietary choices, gut microbiome composition, hormonal cycles, and inflammation can impact behaviour, general health and well-being. We carefully reviewed existing theoretical accounts and empirical evidence on the body-brain-behaviour interface and delineated new emerging avenues for multimodal, functional, ecologically valid, and personalized research that also integrates smart sensing technologies. In a synopsis, we propose the concept of a body-brain (dis)equilibrium regulating transitions from health to pathology.},
}
@article {pmid40633350,
year = {2025},
author = {Huang, C and Wang, T and Chen, W and Wang, J and Cui, M and Zheng, C and Qiu, M and Shan, M and Li, B and Zhang, L and Yu, Y and Xu, L and Fang, H},
title = {Sheep and rapeseed cake manure promote antibiotic resistome in agricultural soil.},
journal = {Journal of hazardous materials},
volume = {495},
number = {},
pages = {139157},
doi = {10.1016/j.jhazmat.2025.139157},
pmid = {40633350},
issn = {1873-3336},
abstract = {The application of manure in agriculture caused the emergence and spread of antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARB) in soil environments. However, the co-occurrence pattern and host diversity of ARGs and MGEs in soils amended with animal and green manures remains unclear. In this study, metagenomic assembly and binning techniques were employed to comprehensively explore the effects of sheep manure and green manure on soil microbiome, antibiotic resistomes, and ARG hosts. Both rapeseed cake manure and sheep manure increased the abundance and diversity of ARGs, with sheep manure particularly enhancing the abundance of ARGs conferring resistant to multidrug, quinolone, rifampicin, and macrolide-lincosamide-streptogramin (MLSB). Mobile genetic elements (MGEs), such as plasmids, transposases, and integrases, preferentially enhanced the potential mobility of some ARGs subtypes (i.e. sul2, aadA, qacH, and folp), facilitating the spread of ARGs. Additionally, sheep manure reshaped the bacterial community structure and composition as well as ARG hosts, some opportunistic pathogens (i.e. Staphylococcus, Streptococcus, and Pantoea) acquired antibiotic resistance and remained recalcitrant. It is concluded that rapeseed cake manure and sheep manure increased the co-occurrence of ARGs and MGEs, enriched the potential ARG hosts, and promoted the dissemination of ARGs in agricultural soils.},
}
@article {pmid40633153,
year = {2025},
author = {Missawi, O and Vaccari, F and Zhang, L and Miras-Moreno, B and Boughattas, I and Bandini, F and Lucini, L and Puglisi, E and Banni, M},
title = {Unleashing multi-omic approaches to address environmental microplastic hazards in marine polychaetes.},
journal = {Marine pollution bulletin},
volume = {220},
number = {},
pages = {118345},
doi = {10.1016/j.marpolbul.2025.118345},
pmid = {40633153},
issn = {1879-3363},
abstract = {The impact of an environmental microplastic mixture (< 100 μm) on marine polychaete was explored to simulate the plastic exposure patterns in the natural habitat. In this study, Hediste diversicolor was used to mimic a real scenario exposure model of five common types of widely distributed microplastics sampled from the southern Mediterranean Sea. Sediment and polychaete gut were collected for microbiome and metabolomic analysis. Interestingly, high-throughput sequencing revealed a shift in bacterial diversity depending on microplastic concentration (10, 100 and 1000 μg kg[-1]). Noteworthy, sediment revealed similar diversity with respect to the polychaete gut microbiome. Specific bacterial taxa, particularly Mesoflavibacter zeaxanthinifaciens and Vibrio cortegadensis, were notably affected, indicating adaptive responses to altered environments. The identification of different clusters of markedly altered metabolites, including indoles, benzene derivatives, coumarins, pyrones, flavonoids, cinnamates, diterpenes and sesquiterpenes, offered an insight into the physiological and pathological changes observed within the polychaete following microplastics exposure. These novel findings enhance our understanding of the intestinal hazards of environmental microplastics and underscore the potency of multi-omics investigations in unraveling the intricate mechanisms underlying microplastic toxicity.},
}
@article {pmid40632920,
year = {2025},
author = {Olsson, A and Steel, K and Cooper, R and Jones, AP and Chan, KR and Ogg, G and Irvine, AD and Flohr, C and Taams, LS},
title = {Methotrexate and ciclosporin both reduce levels of circulating IL-4 and IL-13 expressing CD4+ memory T-cells in childhood atopic dermatitis.},
journal = {Clinical and experimental dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1093/ced/llaf301},
pmid = {40632920},
issn = {1365-2230},
abstract = {Atopic dermatitis (AD) is a chronic dermatosis characterised by type-2 inflammatory responses, skin barrier anomalies, and microbiome dysregulation. The variation of AD presentation necessitates a better understanding of the underlying disease mechanisms and the modulation of immune markers over a treatment course. Globally the most used systemic therapies for moderate-to-severe AD are methotrexate (MTX) and ciclosporin (CyA). The TReatment of severe Atopic Eczema in children Trial (TREAT) was a randomised controlled trial assessing the efficacy and safety of methotrexate and ciclosporin. Peripheral blood samples from n=18 TREAT participants were analysed in a longitudinal immunological study with a focus on cytokine-expressing CD4+ T-cells. The analysis showed that both MTX and CyA were associated with a decreased percentage of IL-4 and IL-13 expressing CD4+ memory T-cells, corresponding to improved disease severity. Patients receiving MTX experienced a more sustained decrease in IL-4 expressing T-cells, which corresponds to the longer-term improved disease control observed in the MTX arm.},
}
@article {pmid40632657,
year = {2025},
author = {Bajaj, JS and Reddy, KR and Tandon, P and Lai, JC and O'Leary, JG and Wong, F and Garcia-Tsao, G and Vargas, HE and Kamath, PS and Biggins, SW and Vutien, P and Shaw, J and Limon Miro, AT and Bera, C and McGinley, JP and Sikaroodi, M and Bush, BJ and Thacker, LR and Gillevet, PM},
title = {Salivary microbiome and serum metabolomics add to clinical biomarkers to predict 6-month hospitalizations in a multi-center cirrhosis outpatient cohort.},
journal = {Hepatology (Baltimore, Md.)},
volume = {},
number = {},
pages = {},
doi = {10.1097/HEP.0000000000001462},
pmid = {40632657},
issn = {1527-3350},
abstract = {BACKGROUND AIMS: Prognosticating outcomes such as hospitalizations in cirrhosis outpatients is challenging, especially with changing etiologies and demographics. Aim: Determine impact of multi-omic strategies on outcome prediction.<br><br>APPROACH RESULTS: NACSELD3 enrolls cirrhosis outpatients with controlled/eradicated etiologies from 10 centers and follows them systematically. At baseline, clinical/demographic and cirrhosis details were recorded and saliva and serum samples were collected for microbiome and metabolome analysis respectively. Multi-omic bioinformatic studies to determine interaction of microbiota and metabolites with clinical prediction of 6-month hospitalizations were performed. 565 patients (60.2 years, 68% men, 35% alcohol, 33% MASH, 21%, eradicated HCV with MELD3.0 12) were enrolled. 163 (29%) required 6-month hospitalizations; most (75%) were liver-related. Those hospitalized had worse cirrhosis severity, co-morbidity indices, but similar demographics and oral health variables. Salivary microbiome alpha-diversity was lower (1.96&#xb1;0.48 vs. 2.09&#xb1;0.45, p=0.018) with greater pathobionts (Streptococcus, Treponema, Enterococcaceae) and lower commensal genera (Veillonella, Prevotella, Haemophilus, Lachnospiraceae spp) at baseline. Serum metabolomics showed significant separation at baseline between hospitalized/not patients using supervised analyses with microbial-origin (phenyllactate, secondary bile acids, indoles), choline moieties, and polyamine/GABA (3-ureidopropionate/spermidine) metabolites being most prominent. Area-under-the curve using random forest for clinical, microbial, and metabolomic variables were higher than that of these individually. Latent factor analysis showed clinical variables (MELD3.0, hemoglobin and albumin) with the greatest impact followed by salivary microbiota and then serum microbiome for hospitalization prediction.<br><br>CONCLUSION: In a multi-center North American outpatient cirrhosis cohort with controlled etiologies, serum metabolomics and salivary microbiome add to clinical variables to prognosticate 6-month hospitalization.},
}
@article {pmid40632459,
year = {2025},
author = {Ding, Y and Hou, Y and Lao, X},
title = {The Role of Akkermansia muciniphila in Disease Regulation.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {40632459},
issn = {1867-1314},
abstract = {In recent years, Akkermansia muciniphila (A. muciniphila), as a representative of the core gut commensal bacteria, has shown outstanding therapeutic potential in the field of microecological interventions due to its unique mucin degrading ability and host-interaction mechanism. A. muciniphila is first isolated from human feces in 2004. It colonizes the intestinal mucus layer, utilizing mucin secreted by goblet cells as its primary carbon and nitrogen source. In 2013, researchers found that supplementation with A. muciniphila could improve obesity, demonstrating the potential of A. muciniphila in the treatment of disease. Recent studies show that A. muciniphila strengthens intestinal barrier integrity, improves metabolic diseases, and mitigates inflammation through multiple mechanisms, including adenosine monophosphate-activated protein kinase (AMPK) pathway activation via Toll-like receptor (TLR) 2 stimulation and NOD-like receptor family, pyrin domain containing 3 (NLRP3) activation. A. muciniphila and its derivatives also exhibit potent anti-tumor effects. They induce tumor-necrosis-factor-related apoptosis-inducing ligand (TRAIL) upregulation, triggering extrinsic (death receptor-mediated) and intrinsic (mitochondrial) apoptosis pathways in tumor cells. Additionally, A. muciniphila promotes M1-like tumor-associated macrophages (TAMs) through NLRP3 activation and remodels the tumor microenvironment via metabolic crosstalk with intratumoral microbiota. Notably, A. muciniphila combined with programmed death-1 (PD-1) antibody boost CD8[+] T cell infiltration, thereby overcoming host resistance to PD-1 blockade. Moreover, A. muciniphila contributes to the growth of butyric acid-producing bacteria and suppresses the growth of specific bacterial populations, playing an important role in the gut microbiome network. This review evaluates recent discoveries regarding A. muciniphila's multifaceted roles in maintaining intestinal barrier integrity, ameliorating metabolic and inflammatory disorders, and enhancing anti-tumor immune responses. We also discuss its ecological effect on the gut microbiota flora and point out the therapeutic limitations and prospect which provides theoretical references to promote the development of Akkermansia muciniphila in clinical diseases, especially in tumor therapy.},
}
@article {pmid40632357,
year = {2025},
author = {Arif, TB and Damianos, JA and Rahman, AU and Hasnain, N},
title = {Fecal Microbiota Transplantation for Disorders of Gut-Brain Interaction: Current Insights, Effectiveness, and Future Perspectives.},
journal = {Current gastroenterology reports},
volume = {27},
number = {1},
pages = {50},
pmid = {40632357},
issn = {1534-312X},
mesh = {Humans ; *Fecal Microbiota Transplantation/methods ; *Dysbiosis/therapy/complications/microbiology ; *Gastrointestinal Microbiome ; *Brain-Gut Axis ; *Gastrointestinal Diseases/therapy/microbiology ; },
abstract = {PURPOSE OF REVIEW: Dysbiosis can disrupt intestinal barrier integrity and impact the immune and nervous systems, playing a significant role in developing disorders of gut-brain interaction (DGBI). This review aims to provide a comprehensive understanding of dysbiosis and its role in DGBI while examining the latest advancements in fecal microbiota transplantation (FMT). It also highlights key challenges in the field and outlines critical directions for future research to optimize FMT strategies, ultimately improving patient outcomes in this evolving treatment area.<br><br>RECENT FINDINGS: In DGBI, dysbiosis triggers immune responses, increases gut permeability, and disrupts nervous system signaling, with contributing factors including diet, antibiotics, stress, and infections. Individuals with DGBI exhibit distinct microbial imbalances, such as an increased Firmicutes-to-Bacteroidetes ratio and reduced beneficial bacteria. FMT has shown mixed results, with factors like patient selection, treatment protocols, and microbiome diversity influencing outcomes. While FMT can improve symptoms in refractory irritable bowel syndrome (IBS), effects may fade over time, requiring repeat treatments. Future FMT approaches should focus on targeted microbial interventions, considering the role of archaea, fungi, and microbial metabolites, while prioritizing optimal donor selection and large-scale trials for long-term efficacy. Despite the promising findings, FMT has not yet been widely endorsed in clinical guidelines due to the variability and heterogeneity of the data available. While much of the research has focused on IBS, studies have also explored the impact of FMT on other conditions such as functional diarrhea, functional constipation, and functional dyspepsia, which all exhibit altered microbial profiles.},
}
@article {pmid40631920,
year = {2025},
author = {Wang, X and Jun, F and Lin, C and Wang, X},
title = {Psychedelics and the Gut Microbiome: Unraveling the Interplay and Therapeutic Implications.},
journal = {ACS chemical neuroscience},
volume = {},
number = {},
pages = {},
doi = {10.1021/acschemneuro.5c00418},
pmid = {40631920},
issn = {1948-7193},
abstract = {Classic psychedelics and the gut microbiome interact bidirectionally through mechanisms involving 5-HT2A receptor signaling, neuroplasticity, and microbial metabolism. This viewpoint highlights how psychedelics may reshape microbiota and how microbes influence psychedelic efficacy, proposing microbiome-informed strategies─such as probiotics or dietary interventions─to personalize and enhance psychedelic-based mental health therapies.},
}
@article {pmid40631910,
year = {2025},
author = {Deng, Y and Leib, N and Schnautz, S and Benfadal, S and Oldenburg, J and Bieber, T and Herrmann, N},
title = {Langerhans Cell Modulation in Atopic Dermatitis Is TLR2/SOCS1-Dependent and JAK Inhibitor-Sensitive.},
journal = {Allergy},
volume = {},
number = {},
pages = {},
doi = {10.1111/all.16641},
pmid = {40631910},
issn = {1398-9995},
support = {//Christine K&#xfc;hne - Center for Allergy Research and Education/ ; EXC2151-390873048//Deutsche Forschungsgemeinschaft/ ; },
abstract = {BACKGROUND: Langerhans cells (LC) are epidermal dendritic cells building the skin's outermost immunological barrier and bridging innate and adaptive immune responses. Their sensing property of the microbiome via Toll-like receptors (TLR) is impaired in atopic dermatitis (AD). We hypothesize a desensitization of LC because of persistent Staphylococcus aureus exposure in AD and underlying mechanisms being TLR2-related.<br><br>METHODS: Human LC generated from hematopoetic stem cells were desensitized via repetitive exposure to TLR2-ligands (priming) and compared to unprimed cells for their TLR-responsiveness. JAK inhibitors impact was evaluated. Maturation marker, migration marker and behavior, cytokine release, and downstream molecule regulation were addressed by flow cytometry, qPCR, and transwell and multiplex assays.<br><br>RESULTS: Primed LC mimicked the LC behavior in AD skin, exhibiting desensitization toward TLR2-mediated activation monitored by impaired CD83/CD80/CD86 and MHCII expression as well as impaired regulation of chemokines CCR6 and CCR7, migration competence, and Th17-driving cytokines. IL-18 and IL-1&#x3b2; were elevated under these conditions. Negative regulators of the TLR2 pathway, specifically SOCS1 and IRAKM, were significantly upregulated, whereas activating molecules were hardly affected. JAK inhibitors reduced SOCS1 expression in primed cells and restored activation markers CD83/80/86 and MHCII upon TLR2 engagement, but had no effect on IRAKM expression.<br><br>CONCLUSION: Primed LC mimic the impaired LC-responsiveness toward TLR2 in AD skin. Our findings unravel a new direct contribution of LC to AD-associated IL-1&#x3b2; and IL-18 under these conditions and shed light on the mechanistical role of SOCS1 and the mode of action of JAK inhibitors.},
}
@article {pmid40631899,
year = {2025},
author = {Zhao, N and Geng, P and Perez, AG and Maya, AC and Yadav, B and Du, Y and Ge, Y},
title = {Genomic and functional characterization of a Butyricicoccus porcorum strain isolated from human gut microbiota.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0079025},
doi = {10.1128/msystems.00790-25},
pmid = {40631899},
issn = {2379-5077},
abstract = {The gut is the most complex microbial ecosystem in the body that greatly influences human immune and metabolic health. However, the functional understanding of gut microbiome is hampered by our limited ability to obtain bacterial cultures for experimental validation, particularly low-abundant species that may carry specific functions but are often overlooked by population-based analyses. Here, we isolated and characterized a novel strain of Butyricicoccus porcorum (named Bp 531D) from human gut microbiota, representing the first butyrate-producing human isolate within a phylogenetic clade of Butyricicoccus complex. Comparative whole-genome analysis revealed a unique capability of Bp 531D for one-carbon metabolism and a high abundance of mobile genetic elements, including six prophages and plentiful transposons, reflecting its evolutionary flexibility. Oral administration of the bacterium profoundly altered gut microbiome composition in C57BL/6 mice, leading to controlled microbial oxidative signaling and calibrated carbohydrate metabolic function in the gut. RNA sequencing (RNA-seq) analysis demonstrated notable functional programming of colonic ECs, whereupon Bp 531D primarily restricted the biosynthesis of cholesterols and activated the pathway of antigen processing and presentation. Furthermore, the expression of MHC class II was correlatively heightened in colonic dendritic cells (DCs), and the frequencies of interleukin-10- (IL-10) and IL-22-producing T helper 17 (Th17) cells were significantly elevated in mice treated with Bp 531D compared to controls. Our findings uncover the crucial roles of B. porcorum in supporting intestinal homeostasis and provide a novel functional modulator to potentially optimize microbial strategies for improving intestinal health.IMPORTANCEReduced abundance of the Butyricicoccus genus has been associated with human intestinal disorders, including inflammatory bowel diseases. While supplementation of B. pullicaecorum mitigates intestinal inflammation, it is unclear whether other Butyricicoccus species critically contribute to intestinal microbial and immune homeostasis. We identified a novel Butyricicoccus species within human gut microbiota and characterized its detailed intestinal functions using the C57BL/6 mouse model. Our findings may further highlight the genetic and functional diversities of the gut microbiome.},
}
@article {pmid40631880,
year = {2025},
author = {Stanojević, M and Kociszewska-Najman, B and Grünebaum, A and Chervenak, F and Kurjak, A},
title = {Quo vadis neonatologia? Where is neonatology heading in the 21st century?.},
journal = {Journal of perinatal medicine},
volume = {},
number = {},
pages = {},
pmid = {40631880},
issn = {1619-3997},
abstract = {INTRODUCTION: This comprehensive narrative review examines current paradigms, emerging trends, and future directions in neonatology through systematic analysis of contemporary literature, clinical practice patterns, and expert consensus. We synthesized evidence from recent publications, international guidelines, and clinical innovations to identify key transformation areas.<br><br>CONTENT: Several critical areas are reshaping neonatology. Gestational age has emerged as a lifelong health determinant with implications extending far beyond the neonatal period, affecting cardiovascular, metabolic, and neurodevelopmental outcomes throughout life. Global disparities in neonatal care remain unconscionably large, with survival rates for 28-week infants exceeding 90&#x202f;% in high-income countries while similar infants in low-resource settings often die from preventable causes. Artificial intelligence applications are revolutionizing predictive analytics, real-time monitoring, and decision support systems, though implementation requires careful attention to bias, transparency, and human oversight. The neonatal microbiome's crucial role in immune development and long-term health has prompted interventions targeting healthy colonization. Salutogenic approaches emphasizing health promotion rather than disease treatment are gaining recognition. Most significantly, the systematic marginalization of mothers in neonatal care is being challenged, with growing recognition of the mother-infant dyad as the fundamental unit of care.<br><br>SUMMARY AND OUTLOOK: Future neonatal care must balance technological advancement with humanistic values, addressing global disparities while maintaining scientific rigor. Success requires committing to global health equity, embracing ethical complexity at viability margins, recognizing maternal centrality, thoughtfully integrating emerging technologies, implementing salutogenic principles, and adopting lifelong health perspectives. The field's future depends on interdisciplinary collaboration, ethical reflection, and unwavering commitment to ensuring every newborn receives compassionate, high-quality care.},
}
@article {pmid40631858,
year = {2025},
author = {Qu, S and Gu, Y and Hou, X and Wei, M and Wang, M and Su, Y and Miao, Y and Yang, J and Sun, Y and Zeng, Z},
title = {Dual associations of gut and oral microbial networks with kidney transplantation.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0025225},
doi = {10.1128/msystems.00252-25},
pmid = {40631858},
issn = {2379-5077},
abstract = {UNLABELLED: Gut and oral microbiomes play an essential role in the occurrence and development of kidney disease, but their changes after kidney transplantation in patients with end-stage renal disease and their relationships with host health remain unclear. Through shotgun metagenomic sequencing of fecal and saliva samples, we found that for both gut and oral microbiome, the initial loss of species diversity after kidney transplantation led to a reduction in network nodes and interactions, but strengthened the connections among the remaining species, which started to get a recovery approximately 7-14 days later. Different network modules tended to exhibit unique functions and showed different responses to transplantation. These network changes were significantly correlated with clinical indicators, especially with estimated glomerular filtration rate, suggesting that microbial networks contributed to regulating kidney function and host health from dual dimensions. Our study provides novel insights into associating microbiomes with patient recovery after kidney transplantation and offers new diagnostic strategies.<br><br>IMPORTANCE: Understanding the dynamics of gut and oral microbiomes after kidney transplantation is crucial for improving post-transplant outcomes and managing potential complications. Through shotgun metagenomic sequencing of fecal and saliva samples from patients following kidney transplantation, our study emphasizes that, in addition to focusing on the various microbial species themselves, the topological properties of gut and oral microbial networks are also critically important for kidney function. We aim to explore the relationship between host health and the oral and gut microbiomes following kidney transplantation from an ecological perspective and extend to other diseases to advance the study of the microbiome and its clinical impact.},
}
@article {pmid40631371,
year = {2025},
author = {Billet, LS and Hernández-Gómez, O and Skelly, DK},
title = {Ranavirus Epizootics and Gut Bacteriome Dysbiosis in Tadpoles: Evidence for the Anna Karenina Principle?.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {e70022},
doi = {10.1111/mec.70022},
pmid = {40631371},
issn = {1365-294X},
support = {//Yale University/ ; //Sigma Xia/ ; //American Museum of Natural History/ ; },
abstract = {The microbiome plays a critical role in animal health, yet its responses to pathogens under natural conditions remain poorly understood. We investigated gut bacterial community (bacteriome) dynamics in wood frog (Rana sylvatica [Lithobates sylvaticus]) tadpoles during natural ranavirus outbreaks to understand how pathogen-induced disturbances shape the bacteriome. Using 16S rRNA sequencing, we compared the bacteriomes of tadpoles in ponds experiencing ranavirus die-offs with those from unaffected ponds before, during and after die-offs. Ranavirus infection significantly altered gut bacteriome composition and increased variability (dispersion), consistent with the Anna Karenina principle. Tadpoles with high infection intensities exhibited reduced bacterial diversity and shifts in community structure, including enrichment of some genera that have been linked previously to antiviral immunity. The predicted functional pathway analyses revealed shifts toward carbohydrate metabolism pathways during die-offs, suggesting microbial adaptation to altered host physiology under infection stress. Some bacteriome changes were detectable even before die-offs occurred, highlighting potential early indicators of infection in the gut bacteriome. In a pond that recovered after an epizootic, we observed partial recovery of some of the bacteria that shifted in relative abundance during the die-off, a pattern that may reflect microbial resilience within hosts, selective survival of tadpoles that never developed severe infections, or a combination of both mechanisms. Our findings demonstrate that ranavirus epizootics disrupt gut bacteriomes in amphibians while simultaneously eliciting potentially adaptive microbial responses. These insights underscore the complex interplay between immunity, microbiome dynamics, and environmental conditions during disease outbreaks, highlighting opportunities for microbiome-based interventions to support amphibian conservation.},
}
@article {pmid40631329,
year = {2025},
author = {Magossi, G and Amat, S},
title = {Optimizing bacteriophage screening and isolation methods for microbial samples derived from different body sites of cattle.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.07.04.663187},
pmid = {40631329},
issn = {2692-8205},
abstract = {Bacteriophages are gaining increased research attention as alternatives to antibiotics and microbiome manipulation tools to enhance feed efficiency and animal health in cattle. However, challenges associated with phage specificity, microbial ecosystem variations, and the absence of effective screening methods have hindered harnessing the power of phage application in cattle. The objectives of this study were to (i) optimize phage screening method for microbial samples obtained from different cattle body sites, (ii) isolate lytic phages against key bovine pathogens and commensal bacteria, and (iii) characterize the isolated phages and their bacterial hosts. A total of 1,214 samples from different cattle body sites (n = 1194) and environmental sources were screened using 13 phage detection methods, including one high-throughput approach. Eighty-three phages were isolated, primarily from ruminal fluid (59), feces (15), vaginal (7) and nasopharyngeal swabs (1), and fetal ruminal fluid (1). The bacterial hosts inhibited by these phages were from 29 genera, with Bacillus (34), Escherichia/Shigella (8), Shouchella (5), Corynebacterium (4), and Lysinibacillus (4) being the most common. No phages were identified against bovine pathogens including Trueperella pyogenes, Mannheimia haemolytica, Pasteurella multocida, or Moraxella bovis. Method 12 demonstrated the highest efficiency in phage recovery, particularly from ruminal samples. The isolation of phages against commensal bacteria from the gastrointestinal, reproductive, and respiratory tracts, and fetal gut highlights their potential for microbiome modulation to improve cattle health and feed efficiency. These findings underscore the need for further research into pathogen-targeting phage isolation in cattle.},
}
@article {pmid40631287,
year = {2025},
author = {Zuffa, S and Thomas, SP and Mohanty, I and El Abiead, Y and Deleray, V and Kvitne, KE and Kousha, A and Suzuki, E and Tsai, CM and Nguyen, G and Ho, B and Liu, GY and Nizet, V and Dorrestein, PC and Askarian, F and Tsunoda, SM},
title = {Influence of perinatal ampicillin exposure on maternal fecal microbial and metabolic profiles.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.06.30.662372},
pmid = {40631287},
issn = {2692-8205},
abstract = {UNLABELLED: Indirect exposure to antibiotics during early life, via maternal intrapartum antibiotic prophylaxis (IAP) or postpartum maternal antibiotic usage, is increasingly common and has been epidemiologically linked to altered growth and immune developmental trajectories in offspring. Nevertheless, the underlying mechanisms remain poorly understood. Here, we explored the effects of antepartum and postpartum maternal ampicillin administration on the dams' fecal microbiome and metabolic profiles in vivo . Ampicillin caused a reproducible depletion of beneficial bacterial species belonging to the Muribaculaceae family, including Muribaculum intestinale and Duncaniella dubosii , and led to cohort-dependent enrichments of Enterococcus and Prevotella species. These microbial alterations were accompanied by substantial metabolic remodeling, characterized by elevated fecal acylcarnitines and dysregulation of the bile acids profile. Intriguingly, we identified two previously uncharacterized trihydroxylated bile acids conjugated to a hexose moiety, which appeared to be associated with antibiotic exposure across public metabolomics repositories. These alterations in the fecal maternal microbiome and metabolome coincided with increased weight gain in offspring, suggesting a possible role for maternal antibiotic exposure in shaping early developmental trajectories. Further studies are warranted to elucidate the long-term implications of these changes in infant health.<br><br>IMPORTANCE: Perinatal antibiotic administration is a critical intervention to reduce maternal and neonatal infections, including early-onset group B Streptococcus (GBS) disease, a major cause of neonatal mortality. Nevertheless, mounting evidence suggests that the use of broad-spectrum antibiotics during the perinatal period in mothers can affect infant gut microbiome development, with potential consequences for immune maturation and early development. Understanding how maternal antibiotic exposure affects the gut microbiome and metabolome is essential for uncovering the potential pathways by which maternal intervention may influence offspring outcomes and for guiding strategies that balance infection control with long-term infant health.},
}
@article {pmid40631266,
year = {2025},
author = {Villa Soto, VS and Degraeve, AL and Heath, CM and Orellana, DA and Reilly, ER and Mukherjee, M and Brockert, JG and Dumlao, DS and Blank, RB and Perlmutter, N and Yu, S and Ashouri, J and Scher, JU and Patterson, AD and Turnbaugh, PJ and Nayak, RR},
title = {The gut microbiome shapes pharmacology and treatment outcomes for a key anti-inflammatory therapy.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.06.26.661733},
pmid = {40631266},
issn = {2692-8205},
abstract = {UNLABELLED: The human gut microbiome encodes a formidable metabolic repertoire that harvests nutrients from the diet, but these same pathways may also metabolize medications. Indeed, large screens have revealed extensive microbial metabolism of drugs in vitro , but the pharmacologic and clinical repercussions of microbiota-mediated metabolism in vivo remain to be discerned. As a proof-of-concept, we investigate how human gut microbes contribute to in vivo pharmacology and efficacy of a key anti-inflammatory drug, methotrexate (MTX). Specifically, we demonstrate that the gut microbiome shapes drug pharmacology in vivo in mice, both by directly metabolizing the drug and by inducing host pathways that promote drug metabolism. Moreover, interindividual variation in the human gut microbiome contributes to variation in pharmacokinetic (PK) profiles. When we quantified metabolites produced by microbes, we unexpectedly identified novel MTX metabolites, one of which, p-methylaminobenzoyl-L-glutamic acid (pMABG), was a major byproduct of microbial metabolism both in vitro and in vivo . Further, we find that a large proportion of patient-associated microbes are capable of metabolizing MTX. Finally, we show that microbial metabolism of MTX is linked to PK profiles and disease outcomes in a mouse model of inflammatory arthritis. Taken together, these findings provide evidence that the human gut microbiome causally contributes to drug pharmacology in vivo for a key anti-inflammatory drug through known and novel mechanisms. Our studies provide a framework for elucidating the clinical relevance of drug microbial metabolism in the context of treatment response. These results are a first step towards understanding and manipulating the human gut microbiome in the treatment of autoimmunity and the advancement of precision medicine for millions of patients taking MTX for immune or inflammatory conditions.<br><br>HIGHLIGHTS: The gut microbiome impacts methotrexate (MTX) pharmacology in miceThe human gut microbiome contributes to interindividual variation in MTX pharmacologyHuman gut microbes produce novel MTX metabolites, pMABG and 6-MPDAMicrobial metabolism of MTX is linked to treatment outcomes.},
}
@article {pmid40631202,
year = {2025},
author = {Palmer, SN and Mishra, A and Gan, S and Liu, D and Koh, AY and Zhan, X},
title = {Identifying Optimal Machine Learning Approaches for Microbiome-Metabolomics Integration with Stable Feature Selection.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.06.21.660858},
pmid = {40631202},
issn = {2692-8205},
abstract = {Microbiome research has been limited by methodological inconsistencies. Taxonomy-based profiling presents challenges such as data sparsity, variable taxonomic resolution, and the reliance on DNA-based profiling, which provides limited functional insight. Multi-omics integration has emerged as a promising approach to link microbiome composition with function. However, the lack of standardized methodologies and inconsistencies in machine learning strategies has hindered reproducibility. Additionally, while machine learning can be used to identify key microbial and metabolic features, the stability of feature selection across models and data types remains underexplored, despite its importance for downstream experimental validation and biomarker discovery. Here, we systematically compare Elastic Net, Random Forest, and XGBoost across five multi-omics integration strategies: Concatenation, Averaged Stacking, Weighted Non-negative Least Squares (NNLS), Lasso Stacking, and Partial Least Squares (PLS), as well as individual 'omics models. We evaluate performance across 588 binary and 735 continuous models using microbiome-derived metabolomics and taxonomic data. Additionally, we assess the impact of feature reduction on model performance and feature selection stability. Among the approaches tested, Random Forest combined with NNLS yielded the highest overall performance across diverse datasets. Tree-based methods also demonstrated consistent feature selection across data types and dimensionalities. These results demonstrate how integration strategies, algorithm selection, data dimensionality, and response type impact both predictive performance and the stability of selected features in multi-omics microbiome modeling.},
}
@article {pmid40629270,
year = {2025},
author = {Sun, B and Yu, X and Qi, H and Xu, F and Jiao, W and Fang, M and Duan, L and Zeng, X and Yang, X and Wang, X and Zhu, Y and Mi, K and Shen, A and Sun, L},
title = {The gut dysbiosis and plasma lipid metabolisms signatures in children with active tuberculosis.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {425},
pmid = {40629270},
issn = {1471-2180},
support = {82100010//Youth Fund of the National Natural Science Foundation of China/ ; 202201010925//Guangzhou Municipal Science and Technology Bureau/ ; 7222055//Beijing Natural Science Foundation/ ; 82170007//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: The human gut microbiota is an important modulator of host immune responses and has a crucial role in the development of tuberculosis (TB). Evidences suggest that metabolites may function as a bridge between gut microbiome and TB progression in children. However, the underlying interactive mechanisms are not well explored. The results may provide useful insight into the role played by the gut microbiome in pulmonary TB in children.<br><br>METHODS: To explore the gut bacterial features and its interaction with plasma lipid metabolisms in children with TB. We enrolled children aged younger than 14 years old from Beijing Children&#x2019;s Hospital and West China Second Hospital between January 2020 and June 2021. We investigated the gut bacterial community using 16S rRNA sequencing of 98 children with active TB, 37 other infectious diseases, and 80 healthy children. The plasma lipids were further analyzed using ultra-high-performance liquid chromatography coupled with mass spectrometry.<br><br>RESULTS: Children with TB showed decreased diversity and species richness indices compared to healthy children. Significant increases in the abundance of Firmicutes and Actinobacteriota combined with a decrease in the abundance of Bacteroidetes and Proteobacteria were also observed in TB children when compared with healthy controls. Among children with TB, gut bacterial composition differed in subgroups with pulmonary and extrapulmonary TB, or subgroups with different Mycobacterium tuberculosis (MTB) load. Children with TB had a higher risk of fever (OR&#x2009;=&#x2009;3.02, P&#x2009;=&#x2009;0.005) and poor appetite (OR&#x2009;=&#x2009;2.96, P&#x2009;=&#x2009;0.02) than the controls. Several bacterial genera were associated with severe illness and clinical indices, such as aspartate aminotransferase levels and fever. The plasma lipids showedc difference between TB patients and the children with other infectious diseases. Eight genera with the highest relative abundance strongly correlated with the plasma lipids.<br><br>CONCLUSIONS: The gut microbiome is compromised in TB children, with a correlation with the plasma lipid metabolites and clinical presentations. Integrating analysis of microbiome and metabolism may help improve precise diagnosis, treatment, and mechanism study for TB in children.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-025-04141-x.},
}
@article {pmid40211819,
year = {2025},
author = {Abdullahi, IN and Trabelsi, I},
title = {Guts of healthy humans, livestock, and pets harbor critical-priority and high-risk Escherichia coli clones.},
journal = {Epidemiology and health},
volume = {47},
number = {},
pages = {e2025013},
doi = {10.4178/epih.e2025013},
pmid = {40211819},
issn = {2092-7193},
mesh = {Humans ; Animals ; *Livestock/microbiology ; *Escherichia coli/genetics/drug effects/isolation &amp; purification ; *Pets/microbiology ; Anti-Bacterial Agents/pharmacology ; *Escherichia coli Infections/epidemiology/microbiology ; Drug Resistance, Bacterial ; *Gastrointestinal Microbiome ; },
abstract = {OBJECTIVES: In May 2024, the World Health Organization classified carbapenem (CARB)- and third-generation cephalosporin (3GC) resistance (R) in <italic>Escherichia coli</italic> as a critical priority, whereas colistin (COL) is a "last resort" antibiotic for their treatment. This meta-analysis evaluated the pooled prevalence, high-risk lineages, genetic relatedness, and mechanisms of CARBR, COLR, and 3GCR in <italic>E. coli</italic> from healthy humans and animals.<br><br>METHODS: We conducted a systematic review and meta-analyses following the Preferred Reporting Items for Systematic Reviews and Meta-analyses (PRISMA) criteria on all eligible studies that reported the analysis of <italic>E. coli</italic>, and antimicrobial susceptibility to CARB, COL and 3GC in <italic>E. coli</italic> from gut samples of clinically healthy humans, livestock, and pets from June 2014 to June 2024. Random-effect models and conserved signature indels phylogeny 1.4 were used to determine pooled prevalence rates (PPs) and the relatedness of publicly available <italic>E. coli</italic> genomes, respectively.<br><br>RESULTS: Of the 5,034 identified articles, 64 studies were deemed eligible. The overall PPs of 3GCR, CARBR, and COLR <italic>E. coli</italic> were 22.5% (95% confidence interval [CI], 17.5 to 28.3), 2.2% (95% CI, 1.0 to 4.7), and 15.5% (95% CI, 10.8 to 21.8), respectively. The PPs of 3GCR-, COLR- and CARBR <italic>E. coli</italic> significantly varied by hosts, continent, and year of studies (p<0.05). Diverse <italic>E. coli</italic> lineages were found, including 13 high-risk <italic>E. coli</italic> sequence types (STs), within which ST10 predominated. Phylogenomic analyses produced 4 clusters of related CARBR- and COLR <italic>E. coli</italic> strains (<25 single nucleotide polymorphism): ST940-<italic>bla</italic>OXA-181 from humans in Lebanon, ST617-<italic>mcr</italic>-1 from pigs in China, ST46-<italic>mcr</italic>-1 from poultry in Tanzania, and ST1720-<italic>mcr</italic>-1 from goats in France.<br><br>CONCLUSIONS: COLR and 3GCR are more frequent than CARBR in gut <italic>E. coli</italic>. These 10-year epidemiological data highlight the persistence and transmission of critical priority and high-risk <italic>E. coli</italic> strains in healthy humans and animals, raising significant One Health concerns.},
}
@article {pmid40631189,
year = {2025},
author = {Shahmohamadloo, RS and Gabidulin, AR and Andrews, ER and Rudman, SM},
title = {Microbiome evolution plays a secondary role in host rapid adaptation.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.06.27.661976},
pmid = {40631189},
issn = {2692-8205},
abstract = {UNLABELLED: Understanding how populations adapt to environmental change is a central goal in evolutionary biology. Microbiomes have been proposed as a source of heritable variation that is central to rapid adaptation in hosts, yet empirical evidence supporting this remains limited, particularly in naturalistic settings. We combined a field evolution experiment in Drosophila melanogaster exposed to an insecticide with microbiome manipulations to disentangle the contributions of host standing genetic variation and microbiome evolution to adaptation. Within three generations, independent populations rapidly and repeatedly evolved increased survivorship, a defining feature of resistance evolution. Adaptive changes in sub-lethal traits such as reproductive output, stress tolerance, and body size occurred with a delayed response following the evolution of resistance. Core microbiome taxa declined following insecticide exposure, and resistant populations evolved to house lower microbial abundances. Axenic rearing and microbiome transplant experiments demonstrated that adaptation via host standing genetic variation was the mechanism for resistance evolution. Microbiome evolution played a secondary and cryptic role in host adaptation by masking slowed development rates that evolved in resistant populations. Together, these results reinforce the primacy of adaptation occurring through selection on host standing genetic variation while also demonstrating the contributions of microbiome evolution in host adaptation.<br><br>SIGNIFICANCE: Identifying the mechanisms that allow organisms to adapt to environmental stress is a foundational goal in biology. Using field experimental evolution and microbiome manipulations in Drosophila melanogaster , we directly tested the relative contributions of host genomic evolution and microbiome evolution to adaptation. We found that adaptation to environmental stress occurred rapidly and repeatedly, driven primarily by selection on host standing genetic variation, with microbiome evolution acting as a secondary contributor. These findings reinforce the importance of host genetic variation in rapid adaptation and demonstrate that microbiome evolution can contribute to host evolutionary trajectories in a cryptic manner.},
}
@article {pmid40630933,
year = {2025},
author = {Takács, B and Jaksa, G and Qorri, E and Gyuris, Z and Pintér, L and Haracska, L},
title = {Advancing metagenomic classification with NABAS+: a novel alignment-based approach.},
journal = {NAR genomics and bioinformatics},
volume = {7},
number = {3},
pages = {lqaf092},
pmid = {40630933},
issn = {2631-9268},
mesh = {Humans ; *Metagenomics/methods ; Algorithms ; *Software ; *Sequence Alignment/methods ; *Metagenome ; Microbiota/genetics ; },
abstract = {Microbiome research has expanded rapidly in the last decade due to advances in sequencing technology, resulting in larger and more complex data. This has also led to the development of a plethora of metagenomic classifiers applying different algorithmic principles to classify microorganisms. However, accurate metagenomic classification remains challenging due to false positives and the need for dataset-specific tuning, limiting the comparability of distinct studies and clinical use. In this study, we demonstrate the discrepancy between current, commonly used classifiers and propose a novel classifier, NABAS+ (Novel Alignment-based Biome Analyzing Software+). NABAS+ uses BWA (Burrows-Wheeler aligner) alignment with strict RefSeq curation to ensure one reliable genome per species and filters for genomes with only high-quality reads for precise species-level identification from Illumina shotgun data. The performance of our algorithm and three commonly used classifiers was evaluated on in silico datasets modelling human gastrooral communities, as well as on deeply sequenced microbial community standards. Additionally, we illustrated the usefulness of NABAS+ in detecting pathogens in real-world clinical data. Our results show that NABAS+, due to its extensive alignment process, is superior in accuracy and sensitivity compared to leading microbiome classifiers, particularly in reducing false positives in deep-sequenced microbial samples, making it suitable for clinical diagnosis.},
}
@article {pmid40630297,
year = {2025},
author = {Hellman, T and Yeo, LF and Palmu, J and Havulinna, A and Jousilahti, P and Laitinen, V and Pärnänen, K and Salomaa, V and Lahti, L and Knight, R and Niiranen, T},
title = {Gut Microbiome as a Risk Factor for Future CKD.},
journal = {Kidney international reports},
volume = {10},
number = {6},
pages = {1673-1682},
pmid = {40630297},
issn = {2468-0249},
abstract = {INTRODUCTION: Gut microbiome has been linked with chronic kidney disease (CKD) in several small cross-sectional studies. However, the relationship between baseline gut microbiome and long-term incident CKD remains unknown.<br><br>METHODS: We performed fecal sampling and measured serum creatinine (SCR) (N = 6699) and urine albumin-to-creatinine ratio (UACR) (N = 797) in a population-based cohort examined in the year 2002. We assessed the multivariable-adjusted associations of gut metagenome with baseline SCR, baseline UACR, and register-based incident CKD.<br><br>RESULTS: The mean age of the participants was 49.5 &#xb1; 12.9 years and 45.8% were men. During a median follow-up of 18.6 years, 108 participants developed incident CKD. In prospective analyses, increased baseline gut microbiome alpha diversity was associated with lower risk of incident CKD (hazard ratio per 1 SD: 0.84; 95% confidence interval [CI]: 0.71-0.99; P = 0.04). Gut microbial beta diversity and taxa were not related to incident CKD (P &#x2265; 0.09 for all). In cross-sectional analyses, alpha diversity (beta per 1 SD: 1.28; 95% CI: 0.64-1.98; P < 0.001) and beta diversity (P = 0.002; R[2] = 0.12%) were associated with SCR, whereas no associations were observed for UACR. In total, 43 significant species-level associations with SCR were observed and 16 negative associations (37.2%) for species belonging to the Lachnospiraceae family.<br><br>CONCLUSION: Our results suggest that decreased gut microbial diversity may be related to risk of future CKD and that a potential link between the Lachnospiraceae family and desirable kidney health exists. Our results extend previous cross-sectional studies and help to establish the basis for examining gut microbiome as a CKD risk factor.},
}
@article {pmid40630283,
year = {2025},
author = {Ness, C and Svistounov, D and Solbu, MD and Petrenya, N and Boardman, N and Ytrehus, K and Jenssen, TG and Holmes, A and Simpson, SJ and Zykova, SN},
title = {Gut Microbiome Diversity and Uric Acid in Serum and Urine.},
journal = {Kidney international reports},
volume = {10},
number = {6},
pages = {1683-1693},
pmid = {40630283},
issn = {2468-0249},
abstract = {INTRODUCTION: An increasing body of evidence has shown the importance of the gut microbiota in modulating serum uric acid (SUA) levels. In this study, we aimed to determine the association between gut microbiome diversity, diet, SUA, and fractional excretion of uric acid (FEUA) in the kidney.<br><br>METHODS: A cross-sectional study was conducted in 53 adults with normal or elevated SUA and estimated glomerular filtration rate (eGFR) range from 37 to 124 ml/min per 1.73 m[2]. Fecal microbiome composition was analyzed using 16S ribosomal RNA sequencing; and alpha diversity was expressed as reverse Simpson, Shannon, and Richness indices. Dietary data were collected, and dietary patterns were identified using principal component analysis. Unadjusted linear regression and models adjusted for sex, waist-hip ratio (WHR), and eGFR were used to study the association between gut microbial diversity, dietary pattern scores, and SUA/FEUA.<br><br>RESULTS: Shannon index was negatively associated with SUA after multiple adjustment (&#x3b2; -36.4, 95% CI [-66.2 to -6.7], P = 0.017; adjusted R[2] = 0.62, P < 0.001). Sex (standardized &#x3b2; = 0.52) and WHR (standardized &#x3b2; = 0.35) had the highest effect on SUA, followed by Shannon diversity index (standardized &#x3b2; = -0.22). We found that Shannon index (standardized &#x3b2; = 0.49, P < 0.001) was positively associated with FEUA after adjustment for sex and "sweet" dietary pattern. This model explained 40% of the variability in FEUA (P < 0.001). None of the dietary patterns were associated with SUA or FEUA.<br><br>CONCLUSION: A higher gut microbial diversity was associated with lower SUA and more efficient elimination of uric acid by the kidneys. There is a need for studies assessing efficacy and safety of interventions on the gut microbiome as a treatment of hyperuricemia.},
}
@article {pmid40630189,
year = {2025},
author = {Zhang, YF and Qin, YT and Liu, ZY and Zheng, HR and Hu, XD and Wang, XL},
title = {Diversity of endophytic bacteria in mulberry (Morus spp.) scions with different genetic resources.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1618773},
pmid = {40630189},
issn = {1664-302X},
abstract = {Endophytic bacteria in plants play crucial roles in promoting plant growth, facilitating nutrient acquisition, and enhancing stress tolerance. Although many studies have recently investigated endophytic bacteria in plants, the characteristics of endophytic bacterial communities in germplasm resource populations have rarely been reported. In this study, we investigated the endophytic bacterial communities of 21 mulberry scions, representing both wild and cultivated resources, all grafted onto a common rootstock and grown under identical cultivation conditions. High-throughput sequencing of 16S rRNA amplicons was performed using the Illumina MiSeq platform. The results revealed a total of 10 phyla, 31 classes, 50 orders, 50 families, and 113 genera of endophytic bacteria in the mulberry scions. The dominant phylum was Proteobacteria (89.07%), followed by Firmicutes (5.20%) and Actinobacteria (3.10%). At the genus level, Sphingomonas (32.84%), Methylobacterium-Methylorubrum (18.64%), and Aureimonas (8.76%) were the predominant genera enriched in the scion. Wild scions exhibited more complex endophytic bacterial communities compared to cultivated scions. Among the wild germplasm, XZBS and XZMK, originating from Tibet, China, displayed distinctive Actinobacteria signatures, suggesting a potential legacy of primitive geographic adaptation. Co-occurrence network analysis indicated that Sphingomonas and Methylobacterium-Methylorubrum acted as keystone taxa, forming critical bridges within the endophytic bacterial community network in the scions. Functional predictions further indicated that endophytic bacteria from wild species showed a greater metabolic capacity for aromatic compounds, amino acids, and carbohydrates compared with those from cultivated species. Moreover, analyses of the mulberry genetic population structure and endophytic bacterial community composition suggested that differentiation between wild and cultivated resources was associated with differences in endophytic bacterial communities. This study provides new insights into the diversity of endophytic bacteria among different mulberry germplasm resources and highlights geographically unique taxa, advancing our understanding of microbiome-driven adaptation in perennial grafted plants. It also offers a valuable reference for the future utilization of functional endophytic bacteria in mulberry improvement.},
}
@article {pmid40629992,
year = {2025},
author = {Saidu, MB and Moreira, IS and Amorim, CL and Wu, R and Ho, YW and Fang, JK and Castro, PML and Gonçalves, D},
title = {Exploring the biodegradation of PET in mangrove soil and its intermediates by enriched bacterial consortia.},
journal = {Environmental technology},
volume = {},
number = {},
pages = {1-23},
doi = {10.1080/09593330.2025.2521762},
pmid = {40629992},
issn = {1479-487X},
abstract = {The biodegradation of Polyethylene terephthalate (PET) is important due to the environmental impact of plastic waste. This study investigates the degradation of PET films in soil microcosms, with and without mangrove plants, and with mangrove plants bioaugmented with a bacterial consortium (Bacillus sp.- GPB12 and Enterococcus sp.- WTP31B-5) while following the evolution of soil microcosm microbiome. The ability of bacterial consortia retrieved from soil microcosms of each tested condition to degrade PET intermediates - bis(2-hydroxyethyl) terephthalate (BHET), terephthalic acid (TPA), and monoethylene glycol (MEG) was also assessed. In the microcosms' assays with mangrove plants, variations in functional groups and surface morphology detected by FTIR and SEM analysis indicated PET degradation. Soil microcosms microbiome evolved differently according to the conditions imposed, with dominance of phylum Proteobacteria in all final microcosms. After 270 days, bacterial consortia retrieved from all soil microcosms revealed to be able to completely degrade TPA within three days. MEG degradation reached ca. 84% using the consortium retrieved from the microcosm with bioaugmented mangrove plants. BHETdegradation was ca. 96% with the consortium obtained from the microcosm with non-bioaugmented mangrove plants. These intermediates are key molecules in PET degradation pathways; thus, their degradation is an indicator of biodegradation potential. To the best of authors' knowledge, this is the first report on biodegradation of PET, BHET, TPA, and MEG by microbial community from mangrove soil, providing insights into key taxa involved in PET degradation. These findings can pave a way to develop bioremediation strategies and more efficient waste management solutions.},
}
@article {pmid40629974,
year = {2025},
author = {Haenel, A and Grzybowski, T and Skonieczna, K},
title = {Oral microbiome dynamics in Postmortem Interval estimation: research standards and guidelines.},
journal = {Archiwum medycyny sadowej i kryminologii},
volume = {75},
number = {1},
pages = {48-55},
doi = {10.4467/16891716AMSIK.25.004.21539},
pmid = {40629974},
issn = {1689-1716},
mesh = {Humans ; *Postmortem Changes ; *Mouth/microbiology ; *Microbiota ; Forensic Medicine ; },
abstract = {Determination of the postmortem interval (PMI) is a crucial aspect of forensic investigations as it verifies an alibi or narrows down suspects. Nevertheless, PMI estimation remains one of the most challenging problems in forensic science. Currently used methods are influenced by various biotic and abiotic factors affecting decomposition. Thus, determining the time of death largely depends on the skills and experience of the forensic experts. Consequently, currently used procedures are prone to inaccuracies. Lately, gut microbiome analysis has proven useful in determining the time of death. Furthermore, emerging evidence indicates that profiling the oral microbiome may also provide valuable insights into PMI estimation. In this review, we examine published reports on oral microbiome and highlight the methodological limitations that diminish their scientific value. Therefore, we summarize the research standards and guidelines for oral microbiome studies to enhance the accuracy and reproducibility of PMI studies. Consequently, standardization of this type of research could lead to the development of innovative approaches that may be implemented into routine forensic genetics practice.},
}
@article {pmid40629894,
year = {2025},
author = {Dong, Y and Yan, G and Zhang, Y and Zhou, Y and Shang, J},
title = {Gut microbiota as a predictive tool for outcomes in IgA nephropathy.},
journal = {Renal failure},
volume = {47},
number = {1},
pages = {2514184},
doi = {10.1080/0886022X.2025.2514184},
pmid = {40629894},
issn = {1525-6049},
mesh = {Humans ; *Glomerulonephritis, IGA/microbiology/drug therapy/therapy/pathology ; *Gastrointestinal Microbiome/genetics ; Male ; Female ; Adult ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; Middle Aged ; *Dysbiosis/microbiology ; Treatment Outcome ; Disease Progression ; },
abstract = {Immunoglobulin A nephropathy (IgAN) is characterized by the deposition of glycosylation-deficient IgA1 in the glomeruli and has been linked to the gut-kidney axis. This study aimed to determine if baseline differences in gut microbiota could predict therapeutic responses in IgAN patients. We analyzed fecal microbiomes of 55 biopsy-confirmed IgAN patients and followed them for over 6 months. Patients were classified as responders (n = 39) or nonresponders (n = 16) based on remission status. Fecal microbiomes were profiled using 16S rRNA sequencing, revealing significant microbiota differences. Nonresponders had increased Proteobacteria and Firmicutes, with notable enrichment of opportunistic bacteria like Escherichia-Shigella and Pseudomonas. A predictive classifier based on 24 amplicon sequence variants, with Escherichia-Shigella and Pseudomonas as key contributors, showed high accuracy in identifying nonresponders (AUC 0.9103, p < 0.0001). These findings highlight the role of microbial dysbiosis in IgAN progression and treatment response, suggesting that gut microbiota analysis could guide personalized therapy for IgAN. Future studies with larger cohorts are needed to validate these results and explore microbiome-based treatments.},
}
@article {pmid40629699,
year = {2025},
author = {Yuan, Y and Qian, XC and Chen, SM and Zhang, LL and Chen, TM and Ding, C and Liu, WZ and Chen, F and Wang, AJ},
title = {Alternating Current-Driven Bioredox Cycling Achieves in Situ Deep Mineralization of Nitroaromatic Pollutants in Sediments.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c11329},
pmid = {40629699},
issn = {1520-5851},
abstract = {Nitroaromatic compound (NAC)-contaminated sediments pose threats to aquatic ecosystems. The challenges of low mass transfer in sediments and the recalcitrance of NACs to degradation limit the effectiveness of conventional bioremediation techniques. This study demonstrates the potential of alternating current (AC)-driven bioredox cycling to overcome these barriers by coupling in situ reduction-oxidation processes. We report the successful application of AC stimulation in achieving the mineralization of nitrobenzene (NB) while elucidating its role in modulating bioredox dynamics, electron transfer, and electromicrobiome function. Sine-wave AC stimulation achieved an 87.7% reduction of NB and 90.3% mineralization of its intermediates. The AC stimulation promoted robust biofilm formation, enhanced bidirectional electrocatalytic activity, and increased microbial biomass. It also enriched a diverse microbial consortium capable of reducing NB, oxidizing aromatic intermediates, and facilitating electron transfer, as indicated by the upregulation of key enzymatic genes through multiomics analyses. Carbon metabolites from catechol meta-cleavage further supported nitro-reduction and sustained microbial viability. Compared to DC processes, AC-driven bioredox cycling reduced energy consumption by 16.8% in the remediation of NB-contaminated sediments. This approach offers a sustainable, low-carbon solution for efficient in situ biomineralization of NACs in sediments.},
}
@article {pmid40629635,
year = {2025},
author = {Zeng, B and Ren, X and Cheng, Y and Wang, C and Li, J and Jiang, L and Zhang, S and Chen, S and Yu, D and Lin, J},
title = {Correlation analysis between vaginal microecology and high-risk human papillomavirus (HR-HPV)-positive cervical squamous intraepithelial lesions (SIL).},
journal = {Medicine},
volume = {104},
number = {27},
pages = {e42914},
doi = {10.1097/MD.0000000000042914},
pmid = {40629635},
issn = {1536-5964},
mesh = {Humans ; Female ; Adult ; *Papillomavirus Infections/virology/complications/epidemiology ; *Vagina/microbiology/virology ; Middle Aged ; Risk Factors ; *Squamous Intraepithelial Lesions of the Cervix/virology/microbiology/pathology ; *Squamous Intraepithelial Lesions/virology/pathology/microbiology ; *Uterine Cervical Neoplasms/virology/pathology ; Papillomaviridae/isolation &amp; purification ; *Uterine Cervical Dysplasia/virology ; Human Papillomavirus Viruses ; },
abstract = {This study is aimed to investigate the correlation between vaginal microecology and high-risk human papillomavirus (HR-HPV)-positive cervical squamous intraepithelial lesions (SIL) using the regression analysis. Patients (n = 372) with HR-HPV-positive from January 2020 to June 2022 were recruited after preliminary confirmation by colposcopy, HPV test, and typing, as well as loop electrosurgical excision procedure. Based on the pathological results, the recruited subjects were divided into 3 groups, that is, negative for intraepithelial lesion or malignancy, low-grade SIL, and high-grade SIL (HSIL). Finally, the clinical factors, virological data, and vaginal microecological changes of the 3 experimental groups were analyzed. Age was identified as a significant risk factor for HSIL, with an OR of 1.048 (95% CI: 1.006-1.094 and P = .026). Various HR-HPV types (HPV16, HPV18, and HPV52) were closely associated with HSIL, with multiple infections significantly increasing the risk (odds ratio, OR: 5.810, P = .04). The changes in the vaginal microecology were strongly associated with HSIL, including elevated pH (>4.5), reduced hydrogen peroxide levels, and increased bacterial vaginosis (BV) prevalence. BV demonstrated a sensitivity of 66.10% and a specificity of 70.31% for predicting HSIL. Furthermore, decreased Lactobacillus levels (OR: 3.20, P < .001) showed their protective role, while elevated sialidase activity (OR: 5.610, P = .002) emerged as a significant risk factor. Accordingly, the key independent predictors for low-grade SIL and HSIL included age, infection type, pH, microbiome density, BV, and sialidase activity. The mixed infection of HPV16, HPV18, HPV52, and HPV resulting in cervical SILs could be closely related to the vaginal microecology.},
}
@article {pmid40629482,
year = {2025},
author = {Tretiak, S and Mendes Maia, T and Ducatelle, R and Cherlet, M and Rijsselaere, T and Van Immerseel, F and Impens, F and Antonissen, G},
title = {Proteomic profiling of dysbiosis-challenged broilers reveals potential blood biomarkers for intestinal health.},
journal = {Veterinary research},
volume = {56},
number = {1},
pages = {143},
pmid = {40629482},
issn = {1297-9716},
support = {Baekeland Mandate HBC.2020.2274//VLAIO/ ; BOF/STA/202209/011//Ghent University Concerted Research Action grant/ ; BOF21/GOA/033//Ghent University Concerted Research Action grant/ ; },
mesh = {Animals ; *Chickens/blood ; Biomarkers/blood ; *Dysbiosis/veterinary/microbiology/blood ; Proteomics ; *Gastrointestinal Microbiome ; *Poultry Diseases/microbiology/blood ; *Intestines/microbiology ; *Proteome ; },
abstract = {The intestinal microbiome forms a dynamic ecosystem whose balanced composition and functioning are essential for maintaining overall gut health and well-being in living organisms. In broilers, dysbiosis disrupts the microbiota-host balance, often without obvious clinical symptoms but with intestinal inflammation, and leads to impaired animal performance. This study aimed to identify host blood-based protein biomarkers that indicate intestinal inflammation and intestinal barrier dysfunction. Using mass spectrometry-based proteomics, blood plasma samples from broilers derived from an in vivo dysbiosis model were analyzed and compared to healthy controls. Microscopic histologic changes in the gut (shortened villi, increased crypt depth) were observed in the duodenal and jejunal tissue of 25-days old challenged birds. Elevated levels of permeability markers faecal ovotransferrin and serum iohexol additionally indicated increased intestinal leakage in the challenged group. The blood plasma proteome analysis enabled quantification of 388 proteins, 25 of which were significantly different between the tested groups. The challenge was marked by activation of immune and signaling pathways, and response to bacteria, while proteins related to cellular physiology, cell-cell communication, and extracellular matrix (ECM) processes were suppressed. Protein-protein interaction analysis revealed two clusters of downregulated proteins involved in ECM organization and cell adhesion. Intestinal dysbiosis in broilers demonstrated that the host prioritizes immune defense over structural maintenance. The activation of immune processes and suppression of ECM pathways highlight potential biomarkers and therapeutic targets. Data are available via ProteomeXchange with identifier PXD056546.},
}
@article {pmid40629442,
year = {2025},
author = {Matson, AP and Unterhauser, K and Rezaul, K and Lesmes, S and Zhou, Y and Michelow, IC and Hussain, N and Driscoll, MD},
title = {Source-tracking Klebsiella outbreaks in premature infants using a novel amplicon fingerprinting method.},
journal = {Antimicrobial resistance and infection control},
volume = {14},
number = {1},
pages = {83},
pmid = {40629442},
issn = {2047-2994},
mesh = {Humans ; Infant, Premature ; *Klebsiella Infections/epidemiology/microbiology ; Infant, Newborn ; Intensive Care Units, Neonatal ; *Klebsiella/genetics/classification/isolation &amp; purification ; *Disease Outbreaks ; Feces/microbiology ; Female ; *Cross Infection/microbiology/epidemiology ; Male ; Milk, Human/microbiology ; Sepsis/microbiology/epidemiology ; RNA, Ribosomal, 16S/genetics ; },
abstract = {BACKGROUND: Even with state-of-the-art infection control practices, premature infants can develop life-threatening infections in the neonatal intensive care unit (NICU). The precise sources of most NICU-associated infections frequently remain unknown and, therefore, are difficult to address. In this study, we used a novel microbiome sequencing approach to source-track lethal sepsis-causing Klebsiella, opportunistic pathogens, and commensal bacterial strains colonizing the gut of hospitalized premature infants.<br><br>METHODS: An exploratory-methods, case series was at performed Connecticut Children's Medical Center NICU in 2021. Long-read 16-23&#xa0;S rRNA gene sequencing was used to analyze fecal samples, mother's milk, and clinical bacterial isolates derived from a cluster of Klebsiella-infected, and concurrently hospitalized non-infected, premature infants who were simultaneously enrolled in a neonatal microbiome study. Distinct groups of amplicons comprising a unique fingerprint pattern for a given strain were compared among the samples to ascertain relatedness.<br><br>RESULTS: We confirmed 100% amplicon identity between lethal Klebsiella quasipneumoniae from milk, gut, blood and trachea during sepsis in twins, while differentiating other infecting and colonizing Klebsiella strains in concurrently hospitalized premature infants. The method also successfully discriminated between multiple Klebsiella strains within the gut microbiota of a non-infected infant. Additionally, we showed that human milk is the source of many early intestinal colonizers, including Klebsiella, Enterococcus, Veillonella, and Bifidobacterium strains.<br><br>CONCLUSIONS: Amplicon fingerprinting can be utilized as a high-throughput high-resolution test to assist in the investigation of nosocomial outbreaks. Additional applications such as routine monitoring of various reservoirs for potential pathogens could inform infection prevention and control strategies in the NICU.},
}
@article {pmid40629427,
year = {2025},
author = {Bell, AG and Vaughan, ER and Kasprzyk-Hordern, B and Cable, J and Temperton, B and Tyler, CR},
title = {Impacts of environmentally relevant concentrations of antibiotic cocktails on the skin microbiome of Eurasian carp (Cyprinus carpio).},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {73},
pmid = {40629427},
issn = {2524-4671},
support = {NE/R011524/1//Natural Environment Research Council/ ; NE/R011524/1//Natural Environment Research Council/ ; CGR/SD6387//NERC Environmental Bioinformatics Centre/ ; },
abstract = {BACKGROUND: The skin surfaces of fish harbour diverse assemblages of microbes (microbiomes) that play critical roles in host health and disruption of these microbiomes can lead to disease conditions. Antibiotics, widely used in medicine for human and animal health treatments, are increasingly found in waterways and this is a growing concern due to their potential to alter the balance of microbial ecosystems and drive antimicrobial resistance (AMR). The effects of antibiotics on skin microbiomes in fish, however, have been little explored. This study examines how exposure to environmental levels of antibiotics affects the skin microbiomes of Eurasian carp (Cyprinus carpio).<br><br>RESULTS: A 2-week exposure of Eurasian carp to cocktails of five antibiotics (ciprofloxacin, clarithromycin, sulfamethoxazole, trimethoprim, and tetracycline) at concentrations found in the environment resulted in significant skin bacterial community compositional shifts. Applying 16S rRNA amplicon sequencing, we found enrichment of the genus Arcicella (Proteobacteria) and depletion of Sphaerotilus (Bacteroidetes) with limited recovery even after maintaining the fish for a further two weeks in clean (antibiotic-free) water. In the low-antibiotic concentration exposure group, the tank water microbiome assemblages resembled those of the fish skin suggesting similar responses to the antibiotic treatments. Metagenomic analysis observed no increase in antibiotic resistance genes or changes in metabolic pathway abundance, possibly due to the relatively short duration of antibiotic exposure.<br><br>CONCLUSION: This study highlights that even low-level exposure to chemical mixtures can alter fish skin microbiome compositions, with limited recovery observed after cessation of exposure. These findings warrant further assessments of the long-term effects and functional consequences of these altered microbiomes on fish health, particularly in environments increasingly affected by anthropogenic chemical pollution.},
}
@article {pmid40629403,
year = {2025},
author = {Somodi, C and Dora, D and Horváth, M and Szegvari, G and Lohinai, Z},
title = {Gut microbiome changes and cancer immunotherapy outcomes associated with dietary interventions: a systematic review of preclinical and clinical evidence.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {756},
pmid = {40629403},
issn = {1479-5876},
support = {#146775//Nemzeti Kutat&#xe1;si, Fejleszt&#xe9;si &#xe9;s Innovaci&#xf3;s Alap/ ; #142287//Nemzeti Kutat&#xe1;si, Fejleszt&#xe9;si &#xe9;s Innovaci&#xf3;s Alap/ ; Bolyai Research Scholarship//Magyar Tudom&#xe1;nyos Akad&#xe9;mia/ ; },
mesh = {*Gastrointestinal Microbiome ; Humans ; Animals ; *Neoplasms/therapy/microbiology/immunology ; *Immunotherapy ; Treatment Outcome ; Mice ; *Diet ; },
abstract = {INTRODUCTION: Cancer patient's survival has gradually improved due to immune checkpoint inhibitors (ICIs). Several studies showed a possible association between the intestinal microbiome and ICI efficacy. Strategies for modifying the composition of the gut microbiome encompass various dietary interventions, which may have distinct impacts on the outcomes of ICI-treated patients. In our systematic review, we explored how dietary habits correlate with therapeutic responses in cancer patients and cancer mouse models undergoing immunotherapy.<br><br>METHODS: A systematic review was conducted using search terms: "cancer", "immunotherapy", "diet", and "microbiome", from Medline, Web of Science, Scopus, and Cochrane Library databases. The outcomes in the clinical studies were overall response rate (ORR), overall survival (OS), or progression-free survival (PFS) in human studies. In mouse studies, change in tumor size was the endpoint. The comparator attributions were questionnaire-based dietary interventions.<br><br>RESULTS: Nineteen articles met the inclusion criteria and were included in the review (6 prospective cohort studies, 1 cross-sectional observational study, and 12 mouse studies). A consistent association was observed between high (vs. low) fiber consumption and improved therapeutic response with a pooled odds ratio of 5.79 when including all human prospective cohort studies. In mice, limited availability of methionine, cysteine, and low intake of leucine and glutamine was linked to reduced tumor progression. Combining ICIs with intermittent fasting or a fasting-mimicking diet significantly decreased tumor volume in mouse melanoma models. In humans, a higher relative abundance of short-chain fatty acid (SCFA) and lactic acid-producing bacteria-particularly Faecalibacterium prausnitzii and Akkermansia muciniphila-correlated with objective response rates (ORR). Similar microbiome alterations were observed in mouse models. Increased fiber intake enhanced ICI efficacy in mice by modulating the gut microbiome, primarily via elevated SCFA production-an effect also reflected in human studies.<br><br>CONCLUSION: Intermittent fasting, high fiber, and low sugar consumption are significantly associated with better ICI outcomes. The studies revealed alterations in microbiota composition linked to diet, and these findings were confirmed in animal models, regarding the production of SCFAs and lactic acid, as well as an increase in Bacteroidota/Bacillota ratio and microbial diversity.},
}
@article {pmid40629382,
year = {2025},
author = {Song, JX and Scales, BS and Nguyen, M and Westberg, E and Witalis, B and Urban-Malinga, B and Oberbeckmann, S},
title = {Close encounters on a micro scale: microplastic sorption of polycyclic aromatic hydrocarbons and their potential effects on associated biofilm communities.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {84},
pmid = {40629382},
issn = {2524-6372},
support = {BONUS (Art 185), 03F0775A//European Union and the German Federal Ministry of Education and Research/ ; BONUS (Art 185), 03F0775A//European Union and the German Federal Ministry of Education and Research/ ; BONUS (Art 185), 03F0775A//European Union and the German Federal Ministry of Education and Research/ ; Vinnova, 2017-00001//Swedish Governmental Agency for Innovation Systems/ ; Vinnova, 2017-00001//Swedish Governmental Agency for Innovation Systems/ ; BONUS-BB/MICROPOLL/06/2017//National Centre for Research and Development, Poland (NCBR)/ ; BONUS-BB/MICROPOLL/06/2017//National Centre for Research and Development, Poland (NCBR)/ ; },
abstract = {BACKGROUND: Within systems as dynamic as the aquatic environment, it is crucial to address the impacts of an ever-growing network of emerging pollutants at their intersection. With previous research having demonstrated the capacity of microplastics (MPs) to sorb persistent organic pollutants, we ask in our study how different plastic polymers that are found throughout aquatic systems interact with polycyclic aromatic hydrocarbons (PAHs) and how this intersection of pollutants might impact the bacterial communities that form on MP surfaces. We performed an in situ incubation experiment at different sites along the Baltic Sea coast and through a PAH and 16S amplicon analysis, we investigated the sorption patterns of different substrates and their potential impacts on associated biofilm communities.<br><br>RESULTS: PAH sorption patterns of polyethylene (PE), polystyrene (PS), and aquaria stone were found to be dictated predominantly by substrate type and secondly by incubation site. While PE showed a general positive trend of sorption, stone rather leached PAHs into the environment, whereas the PAH levels of PS remained relatively unchanged following incubation. These sorption patterns correlated significantly with the composition of biofilm communities observed on all three substrate types after a 6-week incubation period. Strong correlations between specific PAHs and bacterial taxa indicate a direct relationship between these factors. Elevated levels of specific 3- and 4-ring PAHs on PE and PS coincided with higher proportions of specific taxa reportedly capable of hydrocarbon utilisation as well as a reduced diversity among biofilm communities.<br><br>CONCLUSION: The findings in our study highlight the importance of investigating contaminants such as MPs holistically, including any associated substances, to fully understand how they impact surrounding ecological systems as they traverse the different compartments of the aquatic ecosystem.},
}
@article {pmid40629225,
year = {2025},
author = {Florek, K and Komorowska, K and Ptak, J and Jarocki, M and Gontarczyk, J and Mania, R and Boluk, A and Żurawska-Płaksej, E and Łaczmański, &#x141; and Sokolski, M},
title = {Gut microbiota's role in heart failure.},
journal = {Heart failure reviews},
volume = {},
number = {},
pages = {},
pmid = {40629225},
issn = {1573-7322},
abstract = {The pathogenesis of heart failure (HF) is complex, and from an immunological perspective, the "gut-heart axis" plays a pivotal role in its development. The composition of gut microbiota differs significantly between HF patients and healthy individuals, with variations observed across different nations, HF etiologies, and stages defined by the New York Heart Association (NYHA) classification. Moreover, gut-derived metabolites such as short-chain fatty acids (SCFAs), trimethylamine N-oxide (TMAO), bile acids, and lipopolysaccharides (LPS) influence HF progression through specific mechanisms and signaling pathways. Notably, medications recommended in cardiovascular diseases and advanced interventions applied in HF, such as heart transplantation requiring immunosuppressive therapy or the implantation of mechanical circulatory support devices, are associated with significant alterations in gut microbiota composition. However, these mechanisms are still not well-established. This review aims to summarize current data on the impact of the gut microbiome on HF progression and treatment, encompassing both standard medical treatment and advanced therapies of HF.},
}
@article {pmid40629040,
year = {2025},
author = {Ju, CW and Lyu, R and Li, H and Wei, J and Parra Vitela, AJ and Dougherty, U and Kwesi, A and Luna, A and Zhu, X and Shen, S and Liu, Y and Wang, L and Cui, X and Xu, Y and Jiang, B and Ji, Y and Xia, P and West-Szymanski, DC and Sun, C and Zhong, Y and Ye, C and Moran, A and Lehmann, C and Pamer, E and Zhang, W and Bissonnette, M and Zhang, LS and He, C},
title = {Modifications of microbiome-derived cell-free RNA in plasma discriminates colorectal cancer samples.},
journal = {Nature biotechnology},
volume = {},
number = {},
pages = {},
pmid = {40629040},
issn = {1546-1696},
abstract = {Circulating cell-free RNA (cfRNA) in plasma represents a promising avenue for cancer detection. We report low-input multiple methylation sequencing, a method for profiling modification patterns in cfRNA, enabling the detection of diverse transfer RNAs and small noncoding RNAs derived from both the human genome and the microbiome. RNA modification patterns in microbiome-derived cfRNA accurately reflect host microbiota activity and hold potential for the early detection of colorectal cancer.},
}
@article {pmid40629022,
year = {2025},
author = {Teo, JJY and Ho, EXP and Ng, AHQ and How, SHC and Chng, KR and Ateş, YC and Fau'di, MT and Aung, KT and Nagarajan, N},
title = {Citywide metagenomic surveillance of food centres reveals local microbial signatures and antibiotic resistance gene enrichment.},
journal = {npj antimicrobials and resistance},
volume = {3},
number = {1},
pages = {63},
pmid = {40629022},
issn = {2731-8745},
abstract = {The distribution of microorganisms in built environments with high human traffic, such as food centres, can potentially have a significant impact on public health, particularly in the context of increasing worldwide incidence of food and fomite-related outbreaks. In many major Asian cities, public food centres are central to daily food consumption, yet there is a lack of baseline knowledge about their environmental microbiomes. We performed a city-wide metagenomic survey of food-centre microbiomes in Singapore, covering 16 centres and 240 samples, to map the abundances of microbial (bacteria, archaea, fungi, viruses) and non-microbial DNA across two timepoints. Food-centre microbiomes were found to be enriched in food-related DNA signatures compared to other environments, such as hospitals and offices, with specific food-microbe associations (e.g., Enterobacteriaceae and fish) and food DNA providing a partial explanation for the microbial profiles observed (44% of variation explained). Machine learning analysis identified a small set of microbial species (n = 22) that serve as highly accurate (>80%) location-specific signatures for various food centres, some of which persist even after 3 years. Profiling of antibiotic resistance genes (ARGs) and pathogens identified a surprising enrichment of ARGs in food centres relative to other non-healthcare environments (>2.5×), and an order of magnitude enrichment of key pathogenic species (e.g., Klebsiella pneumoniae, Enterobacter spp) even compared to hospital environments. These results highlight the contribution of diverse biotic and abiotic factors in shaping the unique microbiome profiles of different food-centre environments, and the potential for using metagenomic surveillance to understand the risk for infections and antibiotic resistance gene transmission.},
}
@article {pmid40628921,
year = {2025},
author = {Maskawa, R and Takayasu, L and Takayasu, H and Watanabe, K and Takemine, S and Kakimoto, T and Takeshita, K and Narushima, S and Suda, W and Takayasu, M},
title = {High-resolution fecal pharmacokinetic modeling in mice with orally administered antibiotics.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {24441},
pmid = {40628921},
issn = {2045-2322},
support = {24KJ1073//Japan Society for the Promotion of Science/ ; JPMJCR22N3//Japan Science and Technology Agency/ ; JPMJCR22N3//Japan Science and Technology Agency/ ; JPMJCR22N3//Japan Science and Technology Agency/ ; 23ae0121046//Japan Agency for Medical Research and Development/ ; },
mesh = {Animals ; *Anti-Bacterial Agents/pharmacokinetics/administration &amp; dosage ; *Feces/chemistry ; Administration, Oral ; Mice ; *Vancomycin/pharmacokinetics/administration &amp; dosage ; Mice, Inbred C57BL ; *Models, Biological ; Male ; Gastrointestinal Motility/drug effects ; Gastrointestinal Microbiome/drug effects ; },
abstract = {High-resolution fecal pharmacokinetics are crucial for optimizing therapeutic design and evaluating gastrointestinal motility. However, empirical studies with detailed fecal concentration over time data remain limited. This study aims to characterize fecal pharmacokinetics through high-frequency sampling and parallelized fecal concentration quantification, establishing a simple pharmacokinetics model with physiologically interpretable parameters. We quantified vancomycin concentrations in fecal samples collected at a minimum interval of 4 hours from C57BL/6N mice following a single oral administration of either a low (1 mg/mL) or high (20 mg/mL) dose. Fecal concentrations gradually increased and exhibited an exponential decay, leading to the development of a compartmental model with an absorption phase. This simple model accurately fit the experimental data and provided physiological explanations for intra- and inter-individual pharmacokinetics variability. The results suggest that inter-individual differences in pharmacokinetics are attributable to fecal elimination capacity, which may be influenced by drug dosage via changes in gastrointestinal motility. Since the model predicts antibiotic concentrations within the gastrointestinal tract, it can be applied to fundamental studies investigating the effects of antibiotics on the gut microbiome and gastrointestinal motility.},
}
@article {pmid40628728,
year = {2025},
author = {Arp, G and Jiang, AK and Dufault-Thompson, K and Levy, S and Zhong, A and Wassan, JT and Grant, MR and Li, Y and Hall, B and Jiang, X},
title = {Identification of gut bacteria reductases that biotransform steroid hormones.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {6285},
pmid = {40628728},
issn = {2041-1723},
mesh = {*Gastrointestinal Microbiome/physiology/genetics ; Humans ; Phylogeny ; Male ; Female ; *Oxidoreductases/metabolism/genetics ; *Bacteria/enzymology/genetics/classification ; *Steroids/metabolism ; Biotransformation ; Pregnenolone/metabolism ; *Bacterial Proteins/metabolism/genetics ; },
abstract = {The metabolism of steroid hormones by the gut microbiome is increasingly recognized as a key factor in human health; however, the specific enzymes mediating these transformations remain largely unidentified. In this study, we identify Δ[4]-3-ketosteroid 5β-reductase, 3β-hydroxysteroid dehydrogenase/Δ[5-4] isomerase, and Δ[6]-3-ketosteroid reductase enzyme families encoded by common human gut bacteria. Through phylogenetic reconstruction and mutagenesis, we show that 5β-reductase evolved to specialize in converting both natural and synthetic 3-ketosteroid hormones into their 5β-reduced derivatives, while Δ[6]-3-ketosteroid reductase adapted to produce Δ[6]-reduced derivatives. We also find that the novel 3β-hydroxysteroid dehydrogenase/Δ[5-4] isomerase is fused with 5β-reductase in multiple species, streamlining the conversion of pregnenolone, a 3β-hydroxy-5-ene and steroid hormone precursor, into epipregnanolone. Through metagenomic analysis, we reveal that these enzymes are prevalent in healthy populations and enriched in females compared to males. These findings lay the groundwork for mechanistic investigations into how microbial steroid metabolism modulates host hormonal physiology.},
}
@article {pmid40628719,
year = {2025},
author = {Gencel, M and Cofino, GM and Hui, C and Sahaf, Z and Gauthier, L and Matta, C and Gagné-Leroux, D and Tsang, DKL and Philpott, DP and Ramathan, S and Menendez, A and Bershtein, S and Serohijos, AWR},
title = {Quantifying the intra- and inter-species community interactions in microbiomes by dynamic covariance mapping.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {6314},
pmid = {40628719},
issn = {2041-1723},
support = {PG-408523//Gouvernement du Canada | Canadian Institutes of Health Research (Instituts de Recherche en Sant&#xe9; du Canada)/ ; RGPIN-2016-06566//Gouvernement du Canada | Natural Sciences and Engineering Research Council of Canada (Conseil de Recherches en Sciences Naturelles et en G&#xe9;nie du Canada)/ ; CRC-2022-00138//Canada Research Chairs (Chaires de recherche du Canada)/ ; 89967//National Research Foundation (NRF)/ ; },
mesh = {Animals ; *Escherichia coli/genetics/physiology/drug effects ; Mice ; *Gastrointestinal Microbiome/drug effects/genetics ; *Microbial Interactions ; *Microbiota ; Anti-Bacterial Agents/pharmacology ; Mice, Inbred C57BL ; },
abstract = {A microbiome's composition, stability, and response to perturbations are governed by its community interaction matrix, typically quantified through pairwise competition. However, in natural environments, microbes encounter multispecies interactions, complex conditions, and unculturable members. Moreover, evolutionary and ecological processes occur on overlapping timescales, making intra-species clonal diversity a critical but poorly understood factor influencing community interactions. Here, we present Dynamic Covariance Mapping (DCM), a general approach to infer microbiome interaction matrices from abundance time-series data. By combining DCM with high-resolution chromosomal barcoding, we quantify inter- and intra-species interactions during E. coli colonization in the mouse gut under three contexts: germ-free, antibiotic-perturbed, and innate microbiota. We identify distinct temporal phases in susceptible communities: (1) destabilization upon E. coli invasion, (2) partial recolonization of native bacteria, and (3) a quasi-steady state where E. coli sub-lineages coexist with resident microbes. These phases are shaped by specific interactions between E. coli clones and community members, emphasizing the dynamic and lineage-specific nature of microbial networks. Our results reveal how ecological and evolutionary dynamics jointly shape microbiome structure over time. The DCM framework provides a scalable method to dissect complex community interactions and is broadly applicable to bacterial ecosystems both in vitro and in situ.},
}
@article {pmid40628650,
year = {2025},
author = {Crawford, CJ and Reintjes, G and Solanki, V and Ricardo, MG and Harder, J and Amann, R and Hehemann, JH and Seeberger, PH},
title = {Activity-Based Tracking of Glycan Turnover in Microbiomes.},
journal = {Journal of the American Chemical Society},
volume = {},
number = {},
pages = {},
doi = {10.1021/jacs.5c07546},
pmid = {40628650},
issn = {1520-5126},
abstract = {Glycans shape microbiomes in the ocean and the gut, driving key steps in the global carbon cycle and human health. Yet, our ability to track microbial glycan turnover across microbiomes is limited, as identifying active degraders without prior genomic knowledge remains a key challenge. Here, we introduce an activity-based fluorescence resonance energy transfer (FRET) probe that enables direct visualization and quantification of glycan metabolism in complex microbial communities. As a proof of concept, we investigated α-mannan degradation, a prominent polysaccharide in algal blooms. Using automated glycan assembly, we synthesized a mannan hexasaccharide bearing a fluorescein-rhodamine FRET pair. The probe was validated using a recombinantly expressed endo-α-mannanase (GH76) from Salegentibacter sp. Hel_I_6. It was shown to function in cell lysates, pure cultures, and complex microbiomes (via plate assays and microscopy). This probe enabled spatiotemporal visualization of in situ α-mannan turnover in a marine microbiome. Glycan FRET probes are versatile tools for tracking glycan degradation across biological scales from single enzymes to microbiomes.},
}
@article {pmid40628517,
year = {2025},
author = {Yang, Y and Zhang, X and Chen, T},
title = {Research progress in the role of gut microbiota in ethanol metabolism.},
journal = {Zhong nan da xue xue bao. Yi xue ban = Journal of Central South University. Medical sciences},
volume = {50},
number = {3},
pages = {501-510},
doi = {10.11817/j.issn.1672-7347.2025.240537},
pmid = {40628517},
issn = {1672-7347},
support = {202211004855//the Scientific Research Project of Health Commission of Hunan Province/ ; },
mesh = {*Gastrointestinal Microbiome/physiology ; *Ethanol/metabolism ; Humans ; Fatty Acids, Volatile/metabolism ; Liver Diseases, Alcoholic/microbiology/metabolism ; Animals ; Alcohol Drinking/metabolism ; },
abstract = {In recent years, gut microbiota has been increasingly recognized as a key player in ethanol metabolism and the development of related diseases. On one hand, ethanol intake directly affects the gut, leading to significant alterations in microbial diversity and composition. On the other hand, gut microbiota influences ethanol-induced damage to various organs, especially the liver, through multiple metabolic byproducts (such as short-chain fatty acids like butyrate, propionate, and acetate), modulation of immune responses, alteration of intestinal barrier function, and regulation of ethanol-metabolizing enzymes. Given the close association between gut microbiota and ethanol metabolism, the gut microbiome presents a promising therapeutic target for alcohol-related liver diseases. This review summarizes recent advances in understanding how gut microbiota affects ethanol metabolism, aiming to elucidate its role in the onset and progression of ethanol-related diseases and to provide a theoretical basis and novel targets for microbiota-based interventions.},
}
@article {pmid40628430,
year = {2025},
author = {Kapicıi, &#x130; and Erken Güngör, &#xd6; and Yildirim, K and Atas, C and Yilmaz Coban, A},
title = {Impact of Z-spring appliance and clear aligner therapy on oral microorganisms in children: A clinical trial.},
journal = {Saudi medical journal},
volume = {46},
number = {7},
pages = {825-830},
doi = {10.15537/smj.2025.46.7.20250264},
pmid = {40628430},
issn = {1658-3175},
mesh = {Humans ; Child ; Male ; Female ; Streptococcus mutans/isolation &amp; purification ; Candida albicans/isolation &amp; purification ; *Dental Plaque/microbiology ; Streptococcus mitis/isolation &amp; purification ; Streptococcus salivarius/isolation &amp; purification ; *Mouth/microbiology ; },
abstract = {OBJECTIVES: To evaluate the effect of Z-spring appliance and clear aligners, used in anterior crossbite treatment, on dental plaque colonization in children.<br><br>METHODS: A 2-arm randomized controlled trial included 30 patients aged 7-12 years with anterior crossbite. Participants were divided into 2 groups: clear aligner (group A, n=15) and Z-spring appliance (group B, n=15). Dental plaque samples were collected at treatment initiation and completion, inoculated onto selective media, and analyzed for colony counts (cfu/ml) of Streptococcus mutans (S. mutans), Streptococcus mitis (S. mitis), Streptococcus salivarius (S. salivarius), and Candida albicans (C. albicans).<br><br>RESULTS: In group A, S. mutans counts significantly increased (p=0.006), while C. albicans counts decreased (p=0.039). In group B, S. mutans counts significantly decreased (p=0.002). No significant changes were observed in S. salivarius or S. mitis counts in either group.<br><br>CONCLUSION: Short-term clear aligner use in children increases S. mutans colonization, suggesting a potential risk for dental caries with prolonged treatment. Early preventive measures are crucial to mitigate this risk and ensure better oral health outcomes.ClinicalTrials.gov Reg. No. ID: NCT06858033.},
}
@article {pmid40628420,
year = {2025},
author = {Pervaiz, U and Nabeel, P and Zhao, R and Zhao, Z and Zhang, Y and Wang, D},
title = {Global Research Trends on the Links Between the Oral Microbiome and Cancer From 2014 to 2024: A Visualization Analysis.},
journal = {Journal of oral pathology &amp; medicine : official publication of the International Association of Oral Pathologists and the American Academy of Oral Pathology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jop.70000},
pmid = {40628420},
issn = {1600-0714},
support = {82203630//National Natural Science Foundation of China/ ; 81902364//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: In recent years, noteworthy connections have been discovered between human wellness and microbiota. This study aims to outline the hotspots and trends in the links between the oral microbiome and cancer over the past 10 years from a bibliometric perspective.<br><br>METHODS: Reports on original research and literature reviews on the relationship between the oral microbiome and cancer from 2014 to 2024 were retrieved from the Web of Science Core Collection and PubMed databases. CiteSpace and VOSviewer were utilized to display the research patterns.<br><br>RESULTS: A bibliometric analysis was conducted on 4638 relevant publications, of which 3450 research articles and 1188 reviews were examined. China and the United States have contributed greatly to the research on the relationship between the oral microbiota and cancer, most of which were published in Frontiers in Microbiology, Frontiers in Cellular and Infection Microbiology, and International Journal of Molecular Sciences. The Chinese Academy of Sciences (107), Sichuan University (81), and Zhejiang University (79) are the most productive institutions. Zhou Xuedong, Hao Zhang, and Christian C. Abnet are the most recognized authors. Keyword co-occurrence revealed that the terms microbiome, oral microbiota, oral cancer, inflammatory diseases, probiotics, and dysbiosis are research hotspots in the past 10&#x2009;years.<br><br>CONCLUSIONS: The knowledge map provides a helpful visual representation of the main relevant topics in research conducted in the last 10&#x2009;years on the relationship between the oral microbiome and cancer. The findings imply that oral squamous cell carcinoma, F. nucleatum, biomarkers, dysbiosis, and cancer treatment therapies have become popular topics in recent years.},
}
@article {pmid40628054,
year = {2025},
author = {Yu, S and Yoshikuni, Y},
title = {Biotechnological advances in algae-based foods: applications in nutrition and microbiome health.},
journal = {Current opinion in biotechnology},
volume = {94},
number = {},
pages = {103335},
doi = {10.1016/j.copbio.2025.103335},
pmid = {40628054},
issn = {1879-0429},
abstract = {Algae are a sustainable, nutrient-rich resource with growing potential in food biotechnology. Their ability to thrive in diverse environments makes them a promising alternative to conventional crops. Rich in proteins, essential fatty acids, and bioactive compounds, algae support the development of functional foods, including plant-based meat and seafood alternatives. Advances in synthetic biology and fermentation have enhanced algal nutrient profiles and enabled novel applications. Algae-derived polysaccharides, such as alginate, fucoidan, laminarin, and porphyran, exhibit prebiotic effects by modulating the gut microbiota and promoting SCFA production. Enzymatic hydrolysis efficiently produces bioactive oligosaccharides, while engineered microbial systems support scalable production. Algae also enable synbiotic food development by serving as both prebiotic substrates and probiotic carriers.},
}
@article {pmid40627887,
year = {2025},
author = {Kong, M and Wang, M and Liang, S and Chen, H and Zhang, S and Zheng, M and Zhang, C},
title = {Relationship between antibiotic resistance genes and microbiome in the Arctic marine sediments.},
journal = {Marine environmental research},
volume = {210},
number = {},
pages = {107345},
doi = {10.1016/j.marenvres.2025.107345},
pmid = {40627887},
issn = {1879-0291},
abstract = {The global dissemination of antibiotic resistance genes (ARGs) presents a significant threat to public health and ecosystems. The Arctic has been contaminated with ARGs due to the global spread of ARGs. However, the remote nature of the Arctic need a comprehensive characterization of the diversity and distribution of ARGs. In this study, ARGs and bacterial communities in marine sediments from the Arctic were analyzed using qPCR and 16s rRNA gene sequencing. The results indicated that the abundance of ARGs was correlated with the location of the sediments. The absolute abundance of target ARGs exhibited higher values in BJ2 and BJ3. Microbial community composition showed low similarity, with significant structural differences across samples. Proteobacteria was the dominant phylum in all sediment samples, with a large number of highly abundant unclassified genera present. Additionally, the Mantel test and correlation analyses revealed a significant relationship between the abundance of ARGs and bacterial communities. Acidobacteriota was identified as a potential host for sul1 and blaTEM. In summary, this study provides insights into the relationship between antibiotic resistance genes and microbiome in Arctic marine sediments and serves as an important reference for global ARGs management strategies.},
}
@article {pmid40627637,
year = {2025},
author = {Ramírez-Larrota, JS and Juyoux, P and Guerra, P and Eckhard, U and Gomis-Rüth, FX},
title = {Biochemical and structural characterization of the human gut microbiome metallopeptidase IgAse provides insight into its unique specificity for the Fab' region of IgA1 and IgA2.},
journal = {PLoS pathogens},
volume = {21},
number = {7},
pages = {e1013292},
pmid = {40627637},
issn = {1553-7374},
mesh = {Humans ; *Immunoglobulin A/metabolism/chemistry ; *Immunoglobulin Fab Fragments/metabolism/chemistry ; *Gastrointestinal Microbiome ; *Metalloproteases/metabolism/chemistry ; Crystallography, X-Ray ; Models, Molecular ; *Bacterial Proteins/metabolism/chemistry ; },
abstract = {Human immunoglobulin A (IgA), comprising the isotypes IgA1 and IgA2, protects ~400 m2 of mucosal surfaces against microbial infections but can also lead to aberrant IgA deposits that cause disease. Certain bacteria have evolved peptidases that cleave the hinge between the Fab and Fc fragments of IgA, undermining its immune function. These peptidases specifically target IgA1, but not IgA2, which predominates in the gut and possesses a structurally distinct hinge region. The only known IgA2-specific peptidase is IgAse from the gut microbiome member Thomasclavelia ramosa, which also targets IgA1 but no other proteins. IgAse is a ~ 140-kDa, seven-domain, membrane-bound metallopeptidase (MP). Differential scanning fluorimetry, small-angle X-ray scattering, AI-based structural predictions, mass spectrometry, and high-resolution crystallography and cryo-electron microscopy of multidomain fragments of IgAse revealed a novel 313-residue catalytic domain (CD) from the igalysin family within the metzincin MP clan. The CD is flanked by an N-terminal globular C-type lectin-like domain and a wrapping domain (WD), followed by four all-β domains. Functional studies involving a comprehensive set of constructs (wild-type and mutant), authentic and recombinant IgA fragments, and inhibitors demonstrated that the minimal functional assembly requires the CD and WD, along with the Fab and hinge region (Fab'). Modelling studies suggested that the Fab heavy-chain constant domain interacts with the N-terminal subdomain of the CD, positioning the hinge peptide for cleavage-a mechanism confirmed by mutational analysis. These findings open avenues for therapeutic strategies to inhibit the only known IgA1/IgA2 peptidase and to develop it for dissolving pathologic IgA deposits.},
}
@article {pmid40627541,
year = {2025},
author = {Hisatomi, A and Yoshida, T and Hasunuma, T and Ohkuma, M and Sakamoto, M},
title = {Difficult-to-culture micro-organisms specifically isolated using the liquid-liquid co-culture method - towards the identification of bacterial species and metabolites supporting their growth.},
journal = {Microbiology (Reading, England)},
volume = {171},
number = {7},
pages = {},
doi = {10.1099/mic.0.001581},
pmid = {40627541},
issn = {1465-2080},
mesh = {Coculture Techniques/methods ; Feces/microbiology ; RNA, Ribosomal, 16S/genetics ; *Bacteria/isolation &amp; purification/genetics/classification/metabolism/growth &amp; development ; Animals ; Phylogeny ; DNA, Bacterial/genetics ; Culture Media/chemistry ; },
abstract = {In this study, the liquid-liquid co-culture method was applied using faecal samples and specific bacterial species as growth-supporting bacteria. We aimed to isolate new, difficult-to-culture bacterial species using metabolites produced by supportive bacteria to promote the growth of small bacteria selected using filter treatment. This study aimed to identify the supporting bacteria and their metabolites that promote the growth of these isolates. Analysis of the 16S rRNA gene sequences of the isolates obtained by co-culture revealed that they were Waltera spp., Roseburia spp. and Phascolarctobacterium faecium. Roseburia spp. and Waltera spp. were isolated from several faecal samples, suggesting that they were specifically isolated using this culture method. We focused on Waltera spp. isolated from several faecal samples with unique shapes, from long to short or thin cells. The growth of Waltera spp. was not promoted by co-culture on the agar medium, suggesting that growth was only promoted by liquid-liquid co-culture. The growth of the selected small-sized Waltera spp. was promoted by co-culture, whereas the growth of the unfiltered long-cell Waltera sp. strain was suppressed by co-culture. The selected small Waltera spp. did not grow when the supporting bacterial supernatant was added, suggesting that the supporting bacteria and Waltera spp. had a symbiotic relationship through the continuous exchange of metabolites. Co-cultured supporting bacteria (diluted faecal samples) with selected small-sized Waltera spp. were predominantly Bacteroides thetaiotaomicron and Escherichia coli, compared with monoculture diluted faecal samples. We further confirmed the growth of filtered Waltera spp. by co-culturing them with B. thetaiotaomicron and E. coli. Additionally, when B. thetaiotaomicron and E. coli were co-cultured with the selected small Waltera spp., some nutrients and metabolites were reduced. Decreased metabolites were added to the medium, and selected small-sized Waltera spp. were cultured, but Waltera spp. did not grow. Therefore, it was again strongly suggested that continuous co-culturing with the supporting bacteria was important for the growth of Waltera spp. The liquid-liquid co-culture method used in this study can be used to isolate new and unique bacterial species from any environment, not just the gut microbiome. Furthermore, this co-culture method helped identify supporting bacteria and understand metabolite variations.},
}
@article {pmid40627410,
year = {2025},
author = {Erskine, E and Skinner, N and Holden, N},
title = {The contribution of irrigation water and growth substrate for microbial flux in a vertical farm.},
journal = {Letters in applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/lambio/ovaf093},
pmid = {40627410},
issn = {1472-765X},
abstract = {Controlled environmental agriculture (CEA) is an emerging technology with increasing adoption for commercial applications. However, its impact on the plant microbiome is not entirely clear. The assumption is that controlled conditions reduce the risk of introduction and spread of pathogens, human or plant. Here, we assessed the microbial flux through a commercially-relevant CEA plant growth tower from culture-dependent and independent approaches. This allowed the relationship between two of the main entry points for microbes to be determined, the circulating water system and plant growth substrates, on two crop species systems, kale and lettuce. There was a clear distinction between the taxonomic compositions of bacteria in the water-associated and coir-associated compartments. Overall, water did not contribute the most abundant members of the microbiota on plants. Rainwater, used as a top-up source of water, was not the major source of sequenced microbes in either the circulating water system or in coir compartments. The main points of expansion of cultural microbes were in the irrigation tray system and the physical presence and growth of the crop plants. The effect of UV-C, typically used to treat water, and the LED lighting system were quantified for proxy pathogen strains.},
}
@article {pmid40627403,
year = {2025},
author = {Xue, Y and Huang, M and Zhang, J and Navin, S and Tao, Y and Zeng, G},
title = {Sex-Specific Postmortem Microbiome Dynamics in Mice: Implications for Death Definitions.},
journal = {FEMS microbiology letters},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsle/fnaf070},
pmid = {40627403},
issn = {1574-6968},
abstract = {Gut microbes form a complex and dynamic symbiotic relationship with their host. However, the microbial response during the early stages following host death remains largely uncharacterized. In this study, we employed a mouse model to systematically characterize the postmortem response of the intestinal microbiota, and analyzed the dynamic changes in microbial composition during the early stages after death in both male and female mice (at 0, 0.5, 2, 6, 12, and 24 hours postmortem). Our findings reveal that sex-dimorphic shifts in microbiome composition occur as early as 2 hours postmortem. Male mice exhibited increased functional redundancy and delayed community restructuring, whereas female mice displayed earlier community shifts. These sex-specific patterns were accompanied by differences in metabolic pathway activity and biomarker taxa. Notably, the observed retention of regulatory capacity by intestinal microbes after host death offers a novel perspective on the conceptualization of death itself. We propose the term "ecological death" to describe the irreversible collapse of the host-associated microbial ecosystem following death, marking a critical transition in the functional and structural integrity of the intestinal microbiota.},
}
@article {pmid40627346,
year = {2025},
author = {Geer, M and Riwes, M},
title = {Throwing the microbiome out with the bathwater.},
journal = {Blood advances},
volume = {9},
number = {13},
pages = {3368-3369},
doi = {10.1182/bloodadvances.2025016205},
pmid = {40627346},
issn = {2473-9537},
}
@article {pmid40627052,
year = {2025},
author = {Zhou, X and Shen, X},
title = {Probiotics Modulate the Ruminal Microbiome and Metabolite Availability to Enhance Rumen Barrier Function and Growth Performance in Goats Fed a High-Concentrate Diet.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {40627052},
issn = {1867-1314},
support = {42171060//National Natural Science Foundation of China/ ; CARS-38//Modern Agricultural Industry Technology System in China/ ; 2021DB014//Innovation Development Supporting Plan Project of Key Industries in Southern Xinjiang/ ; },
abstract = {The purpose of this study was to evaluate the effects of probiotics supplementation on goats fed a high-concentrate diet in terms of growth performance, rumen fermentation, microbiome and metabolite, and barrier function. Twelve 5-month-old goats (22.74 ± 0.31 kg) were randomly assigned to two groups. The control group (CON) was given a basal diet, whereas the experimental group (PRB) was provided with a diet supplemented with 2 g/kg of a probiotics for 60 days. The results indicated that the final weight (FW) and average daily gain (ADG) were significantly increased in the PRB group compared to the CON group (p < 0.05). Rumen fluid in the PRB group showed significantly elevated levels of butyrate, ammonia nitrogen, propionate, acetate, and total volatile fatty acids, with a significantly reduced acetate/propionate (p < 0.05). Additionally, the PRB group demonstrated significant increases in rumen papilla width and density of gastric papillae (p < 0.05). The mRNA relative expression of tight junction proteins Claudin-4, Claudin-1, Occludin, and ZO-1 in the rumen epithelium was significantly upregulated (p < 0.05). Furthermore, the mRNA relative expression of the anti-inflammatory factor IL-10 was significantly elevated, whereas the pro-inflammatory factors IL-1β and TNF-α were significantly reduced (p < 0.05). 16S rDNA sequencing revealed enrichment of beneficial microbes, such as Lachnospiraceae_NK4A136_group, Christensenellaceae_R-7_group, Monoglobus, Parabacteroides, Bacteroides, and Roseburia, which promoted fiber degradation and volatile fatty acid production. Elevated metabolites, including 2-lysophosphatidylcholin, PC(18:0/0:0), tryptophol, 5-hydroxy-6-methoxyindole glucuronide, and mevalonic acid, contribute to epithelial repair, barrier function, and fermentation. Additionally, 4-nitrocatechol was associated with improved rumen papillae structure and anti-inflammatory effects. In conclusion, probiotics supplementation enhanced rumen fermentation, microbial composition, and barrier function while alleviating inflammation, ultimately improving growth performance and rumen health in goats on a high-concentrate diet.},
}
@article {pmid40626932,
year = {2025},
author = {Talwar, C and Guria, A and Hoffman, K and Biest, S and Jimenez, P and Kommagani, R},
title = {A role for gut mycobiome and altered fungal-bacterial interactions in women with endometriosis.},
journal = {Biology of reproduction},
volume = {},
number = {},
pages = {},
doi = {10.1093/biolre/ioaf148},
pmid = {40626932},
issn = {1529-7268},
abstract = {Endometriosis is a gynecological pathology prevalent in reproductive age women in which the inner uterine wall (endometrium) grows outside as ectopic lesions. The inflammation resulting from these growing implants closely associates with disease severity, causing chronic pain and infertility. Emerging studies have found altered bacterial communities in endometriosis and a causal role for gut bacteria in endometriosis. However, the role of the gut mycobiome i.e., the fungal component of the microbiome in endometriosis is a current knowledge gap that needs to be addressed. In this study, utilizing the stool samples from women with endometriosis, we found that the gut fungal communities are altered in women with endometriosis. By integrating the bacterial microbiota and studying the co-occurring relationships between fungi and bacteria, we identify the altered fungal-bacterial community interactions in endometriosis. In addition, we studied the microbial interactions with the host and identified the bacterial taxa as 'microbiome-associated host genetic variants' in endometriosis. By determining their interactions with fungi, we highlight the fungal taxa as underlying regulators of the disease. Experimentally, we demonstrate that the progression of endometriosis in mice is significantly impeded by the depletion of fungi, revealing a role for the gut mycobiome in endometriosis. Our results highlight the positive- and negative- co-abundance relationships shared between bacteria-fungi, bacteria-bacteria and microbes-host in the disease pathogenesis. These findings promise to stimulate future experimental research on the bacterial-fungal interactions that must be contemplated when designing microbiome-based therapeutic strategies using antifungal agents.},
}
@article {pmid40626910,
year = {2025},
author = {Kust, A and Zorz, J and Paniker, CC and Bouma-Gregson, K and Krishnappa, N and Liu, W and Banfield, JF and Diamond, S},
title = {Model cyanobacterial consortia reveal a consistent core microbiome independent of inoculation source or cyanobacterial host species.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf142},
pmid = {40626910},
issn = {1751-7370},
abstract = {Cyanobacteria are integral to biogeochemical cycles, influence climate processes, and hold promise for commercial applications. In natural habitats, they form complex consortia with other microorganisms, where interspecies interactions shape their ecological roles. Although in vitro studies of these consortia have significantly advanced our understanding, they often lack the biological replication needed for robust statistical analysis of shared microbiome features and functions. Moreover, the microbiomes of many model cyanobacterial strains, which are central to our understanding of cyanobacterial biology, remain poorly characterized. Here, we expanded on existing in vitro approaches by co-culturing five well-characterized model cyanobacterial strains with microorganisms filtered from three distinct freshwater sources, generating 108 stable consortia. Metagenomic analyses revealed that, despite host and inoculum diversity, these consortia converged on a similar set of non-cyanobacterial taxa, forming a 25-species core microbiome. The large number of stable consortia in this study enabled statistical validation of both previously observed and newly identified core microbiome functionalities in micronutrient biosynthesis, metabolite transport, and anoxygenic photosynthesis. Furthermore, core species showed significant enrichment of plasmids, and functions encoded on plasmids suggested plasmid-mediated roles in symbiotic interactions. Overall, our findings uncover the potential microbiomes recruited by key model cyanobacteria, demonstrate that laboratory-enriched consortia retain many taxonomic and functional traits observed more broadly in phototroph-heterotroph assemblages, and show that model cyanobacteria can serve as robust hosts for uncovering functional roles underlying cyanobacterial community dynamics.},
}
@article {pmid40626776,
year = {2025},
author = {Spanoghe, L and Domain, G and Posastiuc, F and Hettiarachchi, A and Panattoni, A and Theuns, S and Van Immerseel, F and Opsomer, G and Van Soom, A and Banchi, P},
title = {Toward standardized methods in canine vaginal microbiome research: evaluation of storage, host DNA depletion, and database selection.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0058325},
doi = {10.1128/spectrum.00583-25},
pmid = {40626776},
issn = {2165-0497},
abstract = {UNLABELLED: Standardized methods for investigating the canine vaginal microbiome are not available yet. Data using next-generation sequencing (NGS) are still limited, and methodologies lack consistency. In theory, microbiome results can be significantly affected by factors like sampling technique, storage, DNA extraction methods, and reference databases, which can all introduce bias. To address these concerns, we compared two storage methods for the sample (no medium vs. medium), examined the effect of host DNA depletion, and tested two reference databases (Emu vs. SILVA) using samples from six bitches, totaling 26 samples. Host depletion showed no significant impact on bacterial composition, nor did the storage conditions. However, when comparing reference databases, we found significant differences in beta diversity, emphasizing the importance of database choice when comparing studies. The proposed protocol paves the way for future studies on the canine vaginal microbiome, setting the basis for more precise and comprehensive microbiome profiling in this field.<br><br>IMPORTANCE: Understanding the vaginal microbiome in dogs could lead to new insights into reproductive health and fertility, but progress is limited by the lack of clear guidelines on how samples should be collected, stored, and analyzed. This study helps clarify which steps in the process truly matter and which have little impact, offering practical guidance for researchers entering this field. By highlighting where inconsistencies can influence outcomes and which methodological choices affect results, we take an important step toward more reliable and comparable research. These findings support future scientific studies and hold potential to improve veterinary care over time.},
}
@article {pmid40626762,
year = {2025},
author = {Kula, A and Kolar, O and Gilewicz, K and Qureshi, Z and Singh, A and Wolfe, AJ and Putonti, C},
title = {Complete genome sequence of Staphylococcus haemolyticus UMB6531B, isolated from a perineal swab.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0037125},
doi = {10.1128/mra.00371-25},
pmid = {40626762},
issn = {2576-098X},
abstract = {Staphylococcus haemolyticus UMB6531B was isolated from a perineal swab of a female with overactive bladder symptoms and sequenced to better characterize opportunistic pathogens of the female urogenital tract. Here, we present the complete genome sequence, which includes the chromosome as well as two complete plasmid sequences.},
}
@article {pmid40626735,
year = {2025},
author = {Kellom, M and Berg, M and Chen, I-MA and Chu, K and Clum, A and Huntemann, M and Ivanova, NN and Kyrpides, NC and Mukherjee, S and Reddy, TBK and Roux, S and Seshadri, R and Szabo, G and Varghese, NJ and Woyke, T and Eloe-Fadrosh, EA},
title = {Tetranucleotide frequencies differentiate genomic boundaries and metabolic strategies across environmental microbiomes.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0174424},
doi = {10.1128/msystems.01744-24},
pmid = {40626735},
issn = {2379-5077},
abstract = {UNLABELLED: Microbiomes are constrained by physicochemical conditions, nutrient regimes, and community interactions across diverse environments, yet genomic signatures of this adaptation remain unclear. Metagenome sequencing is a powerful technique to analyze genomic content in the context of natural environments, establishing concepts of microbial ecological trends. Here, we developed a data discovery tool-a tetranucleotide-informed metagenome stability diagram-that is publicly available in the integrated microbial genomes and microbiomes (IMG/M) platform for metagenome ecosystem analyses. We analyzed the tetranucleotide frequencies from quality-filtered and unassembled sequence data of over 12,000 metagenomes to assess ecosystem-specific microbial community composition and function. We found that tetranucleotide frequencies can differentiate communities across various natural environments and that specific functional and metabolic trends can be observed in this structuring. Our tool places metagenomes sampled from diverse environments into clusters and along gradients of tetranucleotide frequency similarity, suggesting microbiome community compositions specific to gradient conditions. Within the resulting metagenome clusters, we identify protein-coding gene identifiers that are most differentiated between ecosystem classifications. We plan for annual updates to the metagenome stability diagram in IMG/M with new data, allowing for refinement of the ecosystem classifications delineated here. This framework has the potential to inform future studies on microbiome engineering, bioremediation, and the prediction of microbial community responses to environmental change.<br><br>IMPORTANCE: Microbes adapt to diverse environments influenced by factors like temperature, acidity, and nutrient availability. We developed a new tool to analyze and visualize the genetic makeup of over 12,000 microbial communities, revealing patterns linked to specific functions and metabolic processes. This tool groups similar microbial communities and identifies characteristic genes within environments. By continually updating this tool, we aim to advance our understanding of microbial ecology, enabling applications like microbial engineering, bioremediation, and predicting responses to environmental change.},
}
@article {pmid40626727,
year = {2025},
author = {Serrador, D and Campbell, JR and Getz, LJ and Cheung, D and Shefraw, G and Kaul, R and Navarre, WW},
title = {Practical media formulations for rapid growth of Lactobacillus iners and other vaginal bacteria.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0018325},
doi = {10.1128/aem.00183-25},
pmid = {40626727},
issn = {1098-5336},
abstract = {The composition of the vaginal microbiome is closely tied to host health. Bacterial vaginosis (BV), caused by the overgrowth of specific anaerobes (e.g., Gardnerella vaginalis), is associated with negative health outcomes. A vaginal microbiome dominated by Lactobacillus species is thought to protect against BV. However, the role of Lactobacillus iners is controversial, with evidence suggesting that some strains may not protect against BV while others do. To better characterize L. iners strains, their interactions with vaginal bacteria and human cells need to be investigated in vitro, but this has been impeded by the lack of liquid media that supports rapid L. iners growth. We have developed three liquid media formulations for L. iners growth: Serrador's Lactobacillus-adapted Iscove's medium (SLIM), which supports robust L. iners growth; a vaginally adapted version of SLIM (SLIM-V); and a chemically defined version (SLIM-CD). SLIM and SLIM-V improve L. iners growth compared to previously published formulations and also support the growth of other vaginal bacteria, including Lactobacillus crispatus, Lactobacillus jensenii, Lactobacillus gasseri, and Gardnerella vaginalis. SLIM-CD leads to slower growth but may be useful for characterizing L. iners nutrient requirements or metabolite production. Importantly, SLIM and SLIM-V also support the growth of human vaginal epithelial cells, providing a foundation for future co-culture studies. Here, we present the formulations of SLIM, SLIM-V, and SLIM-CD and compare the growth of bacterial strains and human cells in these media.IMPORTANCELactobacillus iners is one of the most prevalent members of the vaginal microbiome, but whether it promotes health or leads to bacterial vaginosis is not well understood. We have developed media formulations that lead to improved L. iners growth and support growth of other vaginal bacteria and human vaginal cells. This will allow for investigation of how L. iners interacts with vaginal bacteria and the host, improving our understanding of its role in the vaginal microbiome.},
}
@article {pmid40626548,
year = {2025},
author = {Kalairaj, MS and George, I and George, SM and Farfán, SE and Lee, YJ and Rivera-Tarazona, LK and Wang, S and Abdelrahman, MK and Tasmim, S and Dana, A and Zimmern, PE and Subashchandrabose, S and Ware, TH},
title = {Controlled Release of Microorganisms from Engineered Living Materials.},
journal = {ACS applied materials &amp; interfaces},
volume = {},
number = {},
pages = {},
doi = {10.1021/acsami.5c11155},
pmid = {40626548},
issn = {1944-8252},
abstract = {Probiotics offer therapeutic benefits by modulating the local microbiome, the host immune response, and the proliferation of pathogens. Probiotics have the potential to treat complex diseases, but their persistence or colonization is required at the target site for effective treatment. Although probiotic persistence can be achieved by repeated delivery, no biomaterial that releases clinically relevant doses of metabolically active probiotics in a sustained manner has been previously described. Here, we encapsulate stiff probiotic microorganisms within relatively less stiff hydrogels and show a generic mechanism where these microorganisms proliferate and induce hydrogel fracture, resulting in microbial release. Importantly, this fracture-based mechanism leads to microorganism release with zero-order release kinetics. Using this mechanism, small (∼1 μL) engineered living materials (ELMs) release >10[8] colony-forming-units (CFUs) of Escherichia coli in 2 h. This release is sustained for at least 100 days. Cell release can be varied by more than 3 orders of magnitude by varying initial cell loading and modulating the mechanical properties of the encapsulating matrix. As the governing mechanism of microbial release is entirely mechanical, we demonstrate the controlled release of model Gram-negative, Gram-positive, and fungal probiotics from multiple hydrogel matrices.},
}
@article {pmid40626408,
year = {2025},
author = {Kim, JA and Choi, JY and Lee, SH and Choi, CY},
title = {Effects of Hyposalinity on Osmoregulation, Oxidative Stress, and Microbial Disruption in Chromis notata (Temminck &amp; Schlegel, 1843).},
journal = {Journal of experimental zoology. Part A, Ecological and integrative physiology},
volume = {},
number = {},
pages = {},
doi = {10.1002/jez.70009},
pmid = {40626408},
issn = {2471-5646},
support = {//This study was supported by a grant from the National Institute of Fisheries Science (R2025036), and by a grant from the Korea Institute of Marine Science &amp; Technology Promotion (KIMST), funded by the Ministry of Oceans and Fisheries (20220559)./ ; },
abstract = {Climate change causes substantial alterations in marine environments, including salinity reduction due to glacial melting, increased rainfall, and freshwater influx, which impose stress on marine organisms. Hypoosmotic stress leads to increased production of reactive oxygen species, thereby disrupting physiological processes, such as osmoregulation, oxidative responses, and gut microbial stability, in marine fish. Here, we investigated the responses of Chromis notata, a stenohaline damselfish, exposed to hyposaline conditions (27 and 20 psu), to better understand the effects of hyposalinity on osmoregulation, oxidative stress, and gut microbiota. Plasma osmolality was measured alongside Na[+]/K[+]-ATPase (NKA) activity in gill tissue to assess osmoregulatory changes. The plasma levels of hydrogen peroxide (H2O2) and lipid peroxidation (LPO) levels were measured as oxidative stress markers. Furthermore, 16S rRNA sequencing and RNA sequencing were conducted to analyze gut microbial diversity and transcriptomic responses, respectively. Plasma osmolality and NKA activity markedly decreased, whereas H2O2 and LPO levels remarkably increased under low-salinity conditions. The gut microbiome in the low-salinity groups exhibited decreased α-diversity and increased abundance of Proteobacteria, including pathogenic genera, whereas Lactobacillus abundance was reduced. Upregulated genes were associated with immune and inflammatory responses, including complement activation, and salt transmembrane transporter activity, whereas downregulated genes were linked to the lateral plasma membrane and mitochondrial membrane. These findings suggest that hyposaline induces oxidative stress and disrupts gut microbiome stability in C. notata, thereby triggering complex physiological and molecular responses. These findings provide insights into the challenges encountered by marine fish in coastal and oceanic ecosystems due to climate change.},
}
@article {pmid40626364,
year = {2025},
author = {Sequoia, JA and Haddock, NL and Gay, PM and Barkal, LJ and Narasimhan, P and Martinez, N and Winn, VD and Bollyky, PL},
title = {Identification of bacteriophage DNA in human umbilical cord blood.},
journal = {JCI insight},
volume = {10},
number = {13},
pages = {},
doi = {10.1172/jci.insight.183123},
pmid = {40626364},
issn = {2379-3708},
mesh = {Humans ; *Fetal Blood/virology ; Female ; Pregnancy ; *DNA, Viral/blood/genetics/isolation &amp; purification ; *Bacteriophages/genetics/isolation &amp; purification ; Adult ; Infant, Newborn ; Pre-Eclampsia/virology/blood ; Cell-Free Nucleic Acids/blood ; Chorioamnionitis/virology/blood ; Premature Birth/virology/blood ; },
abstract = {Bacteriophages, viruses that parasitize bacteria, are abundant in the human microbiome and may influence human health, in part, through their interactions with bacterial hosts. Whether endogenous bacteriophages or their products are vertically transmitted from mother to fetus during human pregnancy is not known. Here, we searched for bacteriophage sequences from five bacteriophage databases (474,031 total sequences) in cell-free DNA (cfDNA) of paired maternal and umbilical cord blood samples from two independent cohorts. First, we sequenced cfDNA from 10 pairs of maternal and cord blood samples, including four pairs affected by preeclampsia. We validated our findings in a previously published dataset of 62 paired maternal and cord blood samples, including 43 pairs from preterm or chorioamnionitis-affected deliveries. We identified 94 and 596 bacteriophage sequences in maternal and cord blood cfDNA samples from the first and second cohort, respectively. We identified 58 phage sequences across maternal-infant dyads and 581 phage sequences that were unique to a single sample. We did not identify any phage sequences consistently associated with preeclampsia, preterm, or chorioamnionitis-affected samples. This study demonstrated the presence of bacteriophage DNA in human cord blood at birth, providing evidence that the human fetus is exposed to bacteriophage DNA in utero.},
}
@article {pmid40611897,
year = {2025},
author = {Fletcher, JR and Hunter, RC},
title = {Cross-feeding interactions between Fusobacterium nucleatum and the glycan forager Segatella oris.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {40611897},
issn = {2692-8205},
abstract = {Fusobacterium nucleatum is a common member of the oral microbiota frequently associated with extraoral infections and diverse polymicrobial environments, including chronic airway diseases and colorectal tumors. Yet, its interactions with co-colonizing microbiota remain poorly defined. Here, we investigate cross-feeding interspecies dynamics between F. nucleatum and Segatella oris, a glycan-foraging anaerobe enriched in airways and gastrointestinal tumors. Using broth cultures, cell-free supernatants, and co-culture on primary human airway epithelial cells, we identify bidirectional interactions that shape nutrient acquisition, biofilm formation, gene expression, and host responses. While mucin or S. oris supernatants modestly enhanced F. nucleatum growth, both conditions triggered transcriptional remodeling, including induction of the nan operon for sialic acid catabolism, suggesting reliance on glycan degradation by S. oris. Conversely, S. oris exhibited differential expression of multiple polysaccharide utilization loci (PULs) when exposed to F. nucleatum or its metabolites. Biofilm formation by F. nucleatum was strongly inhibited by S. oris, indicative of antagonistic interactions. Dual and triple RNA-seq revealed that epithelial responses were predominately shaped by F. nucleatum, with enrichment of inflammatory and cancer-associated pathways; however, co-colonization with S. oris modulated the magnitude and specificity of host gene expression. These findings demonstrate that glycan-mediated cross-feeding and microbial interactions shape the physiology and pathogenic potential of F. nucleatum in mucosal environments. This work underscores the importance of modeling polymicrobial communities under host-relevant conditions to better understand pathobiont behavior at the epithelial interface.},
}
@article {pmid40451181,
year = {2025},
author = {Okumura, T and Hiraiwa, H and Yanagisawa, S and Murohara, T},
title = {The Gut-Heart Axis in Heart Failure: Emerging Evidence and Therapeutic Implications.},
journal = {Cardiology},
volume = {},
number = {},
pages = {1-3},
doi = {10.1159/000546542},
pmid = {40451181},
issn = {1421-9751},
}
@article {pmid40626169,
year = {2025},
author = {Boidin-Wichlacz, C and Maresca, M and Correia, I and Lequin, O and Point, V and Casanova, M and Reinbold, A and Iranzo, O and Huws, SA and Brodin, P and Oyama, LB and Tasiemski, A and Canaan, S and Cavalier, JF},
title = {Potency of all-D amino acid antimicrobial peptides derived from the bovine rumen microbiome on tuberculous and non-tuberculous mycobacteria.},
journal = {Current research in microbial sciences},
volume = {8},
number = {},
pages = {100395},
pmid = {40626169},
issn = {2666-5174},
abstract = {Despite the availability of antibiotics, tuberculosis (TB), caused by Mycobacterium tuberculosis, was once again declared the world's leading cause of death from a single infectious agent in 2023. Furthermore, the rising prevalence of drug-resistant strains of M. tuberculosis, coupled with the limitations of existing therapeutics, underscores the urgent need for new antimicrobial agents that act through different mechanisms, thereby providing novel therapeutic options. From this perspective, antimicrobial peptides (AMPs) derived from the bovine rumen microbiome have shown promise against many resistant pathogens and may therefore offer a promising alternative against TB. Here, we evaluated the efficacy of AMPs from bovine rumen microbiome, namely the Lynronne 1, 2 &amp; 3 and P15s as well as their all-D amino acid enantiomers, against non-tuberculous (M. abscessus, M. marinum and M. smegmatis) and tuberculous (M. bovis BCG, M. tuberculosis) mycobacteria. In particular, their antimycobacterial activity was assessed against extracellularly and intracellularly replicating M. tuberculosis H37Rv pathogenic strain. Their innocuity was further studied by determining their respective cytotoxicity against human cell lines and hemolytic activity on human erythrocytes. Finally, their mechanism of action was investigated by a membrane permeabilization assay and a lipid insertion assay via surface pressure measurement. Although all-D enantiomers showed increased cytotoxicity to human cell lines, they still offer a good therapeutic window with improved activity compared to their L-form counterparts, especially Lynronne 2D all and P15sD all which emerged as the best growth inhibitors of all mycobacteria. Remarkably, the all-D enantiomers also demonstrated activity against intramacrophagic replicating M. tuberculosis H37Rv, with very limited toxicity towards human cells and no hemolytic activity at their respective minimum inhibitory concentration. Membrane permeabilization and monolayer lipid insertion assays suggested that these peptides mostly act by insertion into the mycobacterial membrane resulting in a rapid membranolytic effect. These findings highlight the potential of the all-D enantiomers of Lynronne peptides, as attractive candidates for the development of new anti-TB drugs. Their effective antibacterial properties combined with low toxicity underscore Lynronne 2D all and P15sD all as building blocks for the development of promising alternatives to conventional antibiotics in the treatment of mycobacterial infections, particularly against M. tuberculosis.},
}
@article {pmid40626037,
year = {2025},
author = {Fang, J and Wu, Y and Wang, H and Zhang, J and You, L},
title = {Oral Health and Diabetic Cardiomyopathy: Mechanisms, Biomarkers, and Early Screening Approaches.},
journal = {Journal of inflammation research},
volume = {18},
number = {},
pages = {8689-8704},
pmid = {40626037},
issn = {1178-7031},
abstract = {Diabetic Cardiomyopathy (DCM) is a common cardiovascular complication in patients with diabetes. In recent years, the association between oral health and diabetic heart disease has gained increasing attention. This perspective reviews the potential mechanisms of oral diseases in diabetic heart disease, oral indicators for early screening of diabetic heart disease, and proposes future research directions. The potential mechanisms of oral diseases in diabetic heart disease primarily involve abnormal activation of inflammatory responses, dysregulation of the oral microbiome, and immune system disorders. In the context of early screening for diabetic heart disease, oral health indices, salivary biomarkers, and the oral microbiome serve as critical oral indicators with significant clinical value for early diagnosis. Future research should promote interdisciplinary diagnosis and collaboration, develop non-invasive early screening technologies, integrate multimodal and multi-omics oral data, leverage large-scale multicenter clinical data to comprehensively evaluate the association between oral health indicators and diabetic cardiomyopathy, and simultaneously train and validate precise artificial intelligence models. This perspective integrates existing research findings on the role of oral health in diabetic heart disease, highlights current research limitations, and emphasizes the need for further studies to clarify causal relationships and facilitate widespread clinical application.},
}
@article {pmid40625836,
year = {2025},
author = {Kosińska-Kaczyńska, K and Krawczyk, D and Bednorz, M and Chaberek, K and Czapska, A and Zgliczyńska, M and Goryca, K and Piątkowska, M and Bałabas, A and Czarnowski, P and Żeber-Lubecka, N},
title = {Maternal and placental microbiome and immune crosstalk in pregnancies with small-for-gestational-age fetuses - a pilot case-control study.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1596588},
pmid = {40625836},
issn = {2235-2988},
mesh = {Humans ; Female ; Pregnancy ; *Placenta/microbiology/immunology ; Pilot Projects ; *Infant, Small for Gestational Age ; Case-Control Studies ; Adult ; Cytokines/blood ; Infant, Newborn ; *Gastrointestinal Microbiome ; Feces/microbiology/chemistry ; *Microbiota ; *Fetal Growth Retardation/immunology/microbiology ; Bacteria/classification/isolation &amp; purification/genetics ; },
abstract = {INTRODUCTION: Pregnancies complicated by fetal growth restriction are associated with specific bacterial abundances and elevation of proinflammatory cytokines. The aim of the study was to simultaneously analyze the relation between the gut and placenta microbiome and cytokine profile in pregnant women with fetuses appropriate (AGA) and small for gestational age (SGA).<br><br>MATERIAL AND METHODS: Women with singleton pregnancies at or beyond 32 weeks of gestation were recruited. 11 delivered SGA newborns (study group) and 11 AGA newborns (control group). Samples of maternal venous blood, stool and placenta were collected perinatally.<br><br>RESULTS: In SGA group lower Chao index in placental samples collected from maternal side, while higher Chao index in placental samples collected from fetal side were observed. Taxonomic analysis identified four significantly less abundant genera in samples collected from maternal side. No taxa remained significant after correction in samples from fetal side, but several taxa showed trends of differing abundance. Veillonella showed a trend toward higher abundance in stool samples in SGA group, while other taxa were significant only at a lower threshold. Metabolite analysis revealed that hexanoic acid was significantly elevated compound in the stool of women from the SGA group. Proteobacteria unclassified and Halomonadaceae correlated with stool metabolites, while IL-6 and TNF-&#x3b1; correlated with specific bacterial groups.<br><br>CONCLUSIONS: Specific changes in the gut microbiome and metabolome as well as placenta microbiome of women with SGA have been observed, with additional associations with inflammatory cytokine levels, suggesting a potential role of these factors in SGA development and highlighting the need for further research.},
}
@article {pmid40625835,
year = {2025},
author = {Cumbo, F and Niccolai, E},
title = {Editorial: Microbiota in tumors: is it a new hope for treatment?.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1628182},
doi = {10.3389/fcimb.2025.1628182},
pmid = {40625835},
issn = {2235-2988},
}
@article {pmid40625831,
year = {2025},
author = {Han, Y and Ding, PH},
title = {Advancing periodontitis microbiome research: integrating design, analysis, and technology.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1616250},
pmid = {40625831},
issn = {2235-2988},
mesh = {Humans ; *Periodontitis/microbiology ; *Microbiota ; Biofilms/growth &amp; development ; Gingiva/microbiology ; Bacteria/genetics/classification ; },
abstract = {Periodontitis, a chronic inflammatory disease affecting 20%-50% of adults worldwide, is driven by polymicrobial synergy and dysbiosis. Despite numerous studies on the oral microbiota in periodontitis, significant heterogeneity exists between findings, posing challenges for treatment strategies. To understand the sources of this variability and establish standardized protocols, we reviewed the literature to identify potential factors contributing to these discrepancies. We found most studies focus on microbial communities in periodontal pockets, with fewer investigating microbial composition within gingival tissue. Research indicates that bacterial communities in gingival tissue exist as biofilms, potentially serving as reservoirs for persistent infection. Therefore, further exploration of the microbiome within periodontal tissues is needed, which may offer new insights for treatment strategies. Metatranscriptomics provides valuable insights into gene expression patterns of the oral microbiota, enabling the exploration of microbial activity at a functional level. Previous studies revealed that most upregulated virulence factors in periodontitis originate from species not traditionally considered major periodontal pathogens. However, current studies have not fully identified or revealed the functional changes in key symbiotic microbes in periodontitis. We reviewed the analytical paradigms of metatranscriptomics and found that current analysis is largely limited to assessing functional changes in known periodontal pathogens, highlighting the need for a functional-driven approach. Beyond the limitations of current analytical paradigms, the metatranscriptomics also has inherent constraints. We suggested integrating emerging high-throughput microbial sequencing technologies with functional-driven analytical strategies to provide a more comprehensive and higher-resolution insight for microbiome reconstruction in periodontitis.},
}
@article {pmid40625829,
year = {2025},
author = {Paredes Salgado, EM and Guevara, FE and Muentes, C and Flores, FJ and Magdama, F},
title = {Identifying bacterial and fungal communities associated with Fusarium-wilt symptomatic and non-symptomatic 'Gros Michel' banana plants in Ecuador.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1572860},
pmid = {40625829},
issn = {2235-2988},
mesh = {*Musa/microbiology ; *Plant Diseases/microbiology ; *Fusarium ; *Bacteria/classification/genetics/isolation &amp; purification ; Ecuador ; RNA, Ribosomal, 16S/genetics ; *Fungi/classification/genetics/isolation &amp; purification ; Rhizosphere ; Soil Microbiology ; *Microbiota ; Phylogeny ; High-Throughput Nucleotide Sequencing ; *Mycobiome ; DNA, Bacterial/genetics ; Rhizome/microbiology ; Biodiversity ; },
abstract = {Fusarium wilt of banana (FWB), caused by Fusarium oxysporum f. sp. cubense (Foc), remains a critical threat to banana production worldwide. Despite the persistence of the disease in fields planted with susceptible cultivars such as 'Gros Michel', little is known about the microbial interactions influencing symptom development. In this study, we assessed the bacterial and fungal communities associated to symptomatic and non-symptomatic 'Gros Michel' bananas plants sampled in Ecuador banana fields affected by Foc race 1. We aimed to compare their diversity, composition, and to identify potential microbial taxa that could be active in disease suppression. Samples were collected from the pseudostem, rhizome, and rhizosphere, and analyzed through high-throughput sequencing of the 16S rRNA and ITS2 regions to characterize bacterial and fungal communities, respectively. Results revealed that non-symptomatic plants harbored significantly higher bacterial diversity, particularly in pseudostem and rhizome tissues, compared to symptomatic plants. Genera including, Bacillus, Enterobacter, Paenibacillus, Pectobacterium, Herbaspirillum and Pseudomonas were enriched in non-symptomatic tissues, suggesting a potential role in disease suppression. In contrast, symptomatic plants showed an increased abundance of genera such as Klebsiella and Kosakonia. Fungal community shifts were less pronounced, indicating that bacterial dynamics may play a more critical role in disease development. These findings shed light on the key microbial taxa associated with FWB-affected banana plants and the potential role of their microbiome to plant health and disease suppression.},
}
@article {pmid40625736,
year = {2025},
author = {Chen, J and Wang, J and Fang, W and Wu, Y and Li, H and Xu, H and Zhu, Y and Cheng, Y and Yu, Z and Peng, Y},
title = {BRICS sequential therapeutic regimen as first-Line treatment for PD-L1-negative metastatic non-small cell lung cancer patients harboring EGFR/ALK wild-type status: a retrospective study.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1618110},
pmid = {40625736},
issn = {1664-3224},
mesh = {Humans ; *Carcinoma, Non-Small-Cell Lung/therapy/genetics/mortality ; Male ; Middle Aged ; Female ; Retrospective Studies ; *Lung Neoplasms/therapy/genetics/mortality/pathology ; Aged ; ErbB Receptors/genetics ; B7-H1 Antigen/metabolism ; Anaplastic Lymphoma Kinase/genetics ; Immune Checkpoint Inhibitors/therapeutic use ; *Radiosurgery/adverse effects/methods ; Adult ; Treatment Outcome ; *Antineoplastic Combined Chemotherapy Protocols/therapeutic use/adverse effects ; Combined Modality Therapy ; },
abstract = {BACKGROUND: Patients with PD-L1-negative, EGFR/ALK wild-type metastatic non-small cell lung cancer (NSCLC) exhibit limited responses to immune checkpoint inhibitors (ICIs). This study evaluates the BRICS regimen-a sequential approach combining stereotactic body radiotherapy (SBRT), probiotics, PD-1 inhibitors, and low-dose chemotherapy-to overcome immunotherapy resistance.<br><br>METHODS: This retrospective study included 23 patients treated between 2018 to 2024. Eligibility criteria: confirmed PD-L1-negative NSCLC, no actionable mutations, and measurable lesions. The BRICS regimen comprised SBRT (24 Gy in 3 fractions) to a single lesion, oral probiotics (6 g/day), low-dose chemotherapy, and PD-1 inhibitors administered every 21 days for six cycles. Outcomes included objective response rate (ORR), disease control rate (DCR), progression-free survival (PFS), overall survival (OS), and safety.<br><br>RESULTS: Median age was 62 years; 82.6% were male. ORR and DCR were both 95.7%. Median PFS was 16 months (95% CI: 9.11-22.89), and median OS was 32.7 months (95% CI: 11.53-53.87). In subgroup analysis based on prior treatment status, median PFS and OS were numerically longer in treatment-na&#xef;ve patients compared to previously treated patients (mPFS: 20.0 vs. 13.6 months; mOS: 48.0 vs. 18.0 months), though without statistical significance (P > 0.05). Poor ECOG performance status predicted poorer PFS (HR=9.908, p=0.013) and OS (HR=26.406, p=0.008). Adverse events were predominantly grade 1 to 2 (fatigue:13.2%, rash:8.7%), with no grade &#x2265;3 toxicities.<br><br>CONCLUSIONS: The BRICS regimen demonstrated promising efficacy and safety in PD-L1-negative NSCLC, potentially overcoming resistance through multimodal immunomodulation. clinical benefit was observed regardless of treatment line, with a trend toward improved outcomes when administered as first-line therapy. Prospective trials are warranted to validate these findings and explore mechanisms underlying radiotherapy-microbiome-chemotherapy synergy.},
}
@article {pmid40625706,
year = {2025},
author = {Mei, W and Chen, C and Gao, X and Zhang, W and Hu, Z and Qu, M and Wan, G and Xu, L},
title = {Niacin mitigates heat stress-induced reduction in performance of Taihe black-boned silky fowl through modulation of gut microorganisms and short-chain fatty acids.},
journal = {Frontiers in veterinary science},
volume = {12},
number = {},
pages = {1592101},
pmid = {40625706},
issn = {2297-1769},
abstract = {This study aimed to evaluate the dose-dependent effects of nicotinic acid (NA) on growth performance, cecal short-chain fatty acid (SCFA) profiles, and gut microbiome composition in Taihe black-boned silky fowl (TBsf) under heat stress (HS) conditions. In the experiment, 150 healthy male TBsf were selected and randomly assigned to five treatment groups, with 30 individuals per group. The HS groups were fed a basal diet supplemented with 0, 200, 400, and 800 mg/kg of NA, respectively. HS significantly elevated body temperature and serum heat shock protein 70 (HSP70) concentration compared with the control group (thermal neutral, TN) (p < 0.05), while reducing the growth performance and apparent digestibility of crude protein in TBsf (p < 0.05). The addition of 800 mg/kg NA to the diet significantly reduced body temperature. Compared with the HS group, the incorporation of 200-800 mg/kg NA significantly decreased serum HSP70 levels, significantly increased the average daily gain (ADG) of TBsf, and significantly decreased the feed-to-gain ratio (F/G) (p < 0.05). Cecal microbial analysis showed that, compared with the TN group, the abundance of Merdimonas, Proteobacteria, and Galbibacter significantly increased (p < 0.05), while the abundance of Bacteroides, Prevotella, and Parasutterella significantly declined (p < 0.05). Furthermore, the NA-supplemented group exhibited a significant rise in the enrichment of Olivibacter and Flintibacter (p < 0.05) and a marked reduction in the enrichment of Proteobacteria (p < 0.05). Additionally, the addition of NA significantly elevated the levels of acetic acid, butyrate, and propionic acid in the cecum (p < 0.05). In conclusion, dietary NA supplementation mitigated the adverse effects of HS on TBsf, primarily by enriching beneficial microbiota such as Bacteroides and Flintibacter, and promoting the production of SCFAs like butyric acid and acetic acid.},
}
@article {pmid40625619,
year = {2025},
author = {Kim, B and Oh, S and Yang, S and Ahn, J and Jung, K and Lee, JC and Hwang, JH and Shin, CM and Lee, HJ and Lee, HS and Kim, J and Park, KU},
title = {Distinct microbiome composition and reduced interactions in patients with pancreatic cancer.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1555479},
pmid = {40625619},
issn = {1664-302X},
abstract = {INTRODUCTION: The results of microbiome composition in patients with malignancy have been inconsistent across studies and are affected by various factors. This study aimed to identify microbiome composition of saliva, feces, and blood in patients with pancreatic cancer.<br><br>RESULTS: Overall, 31 patients with pancreatic cancer and 24 healthy controls were sex- and age-matched. Microbiome analysis of saliva, fecal, and blood samples was conducted using 16S rRNA amplicon sequencing. Baseline characteristics were comparable between patients and controls. Saliva showed insignificant difference in alpha diversity (p&#x202f;=&#x202f;0.42), whereas feces and blood exhibited a significant difference in Shannon's index (feces: 6.19 vs. 6.52, p&#x202f;=&#x202f;0.013; blood: 8.00 vs. 7.49, p&#x202f;<&#x202f;0.001) between patients and controls. Beta diversity analysis revealed significant differences between saliva, fecal, and blood samples (p&#x202f;=&#x202f;0.014, 0.001, and 0.001, respectively). Distinct microbiome compositions were identified in patients, with higher abundance of Lactobacillus, Enterobacter, and Prevotella in saliva, fecal, and blood samples, respectively. Based on microbial network analysis, patients with pancreatic cancer showed lower clustering coefficient (71% vs. 99%) and higher average path length (1.67 vs. 0.68) than healthy controls, suggesting a more compact network and stronger microbial interactions in healthy controls.<br><br>CONCLUSION: This study identified a distinctive microbiome in patients with pancreatic cancer, indicating the presence of Lactobacillus, Enterobacter, and Prevotella. A less condensed and robust microbial interaction network was observed in blood samples of patients with pancreatic cancer. These findings provide a basis for research on the connection between the microbiome and pancreatic cancer.},
}
@article {pmid40625618,
year = {2025},
author = {Hu, Y and Zheng, S and Xu, J and Zhao, Y and Wang, J and Fang, Z and Zhou, L},
title = {Gestational diabetes mellitus alters neonatal gut microbiota and increases infection susceptibility.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1600325},
pmid = {40625618},
issn = {1664-302X},
abstract = {INTRODUCTION: Gestational diabetes mellitus (GDM) affects up to 27.6% of pregnancies in certain regions and is associated with a two- to threefold increased risk of neonatal infections. Although maternal gut microbiota undergoes significant remodeling during pregnancy, the specific mechanisms governing GDM-induced microbial reprogramming in offspring and its implications for susceptibility to infections remain unclear. This study aimed to investigate the impact of GDM on the composition of neonatal gut microbiota, metabolomic profiles, and susceptibility to infections using a translational approach.<br><br>METHOD: We recruited pregnant women with and without GDM at the JinHua Municipal Central Hospital in China. Meconium and blood samples were collected from newborns within 24&#x202f;h of birth. The composition of the gut microbiota was analyzed using 16S rDNA amplicon sequencing, and short-chain fatty acids (SCFAs) were quantified using gas chromatography-mass spectrometry. Serum inflammatory markers, including interleukin-6 (IL-6), C-reactive protein (CRP), lipopolysaccharides (LPS), and procalcitonin (PCT), were measured by enzyme-linked immunosorbent assay. To establish causality, fecal microbiota transplantation (FMT) was conducted in antibiotic-treated mice using pooled samples from healthy and GDM-exposed neonates, followed by assessment of inflammatory markers and intestinal barrier integrity.<br><br>RESULTS AND DISCUSSION: GDM significantly reduced the diversity of neonatal gut microbiota and altered its composition, characterized by a depletion of beneficial taxa (Bifidobacterium, Blautia, Faecalibacterium) and an enrichment of potential pathogens (Stenotrophomonas, Chryseobacterium). These alterations were accompanied by significant reductions in fecal SCFAs, particularly acetate (49.30%), butyrate (41.00%), and propionate (17.83%). GDM-exposed neonates exhibited elevated serum inflammatory markers, including IL-6, CRP, LPS, and PCT, which correlated negatively with beneficial bacteria and positively with opportunistic pathogens. FMT experiments demonstrated that mice receiving GDM-associated microbiota developed increased systemic inflammation and compromised intestinal barrier function, as evidenced by the downregulation of tight junction proteins (ZO-1, occludin, claudin-1, mucin1). These findings suggest that GDM-induced alterations in neonatal gut microbiota composition and metabolite production may compromise intestinal barrier function and increase susceptibility to infections, highlighting the potential for microbiome-targeted interventions to mitigate infection risk in GDM-exposed neonates.},
}
@article {pmid40625617,
year = {2025},
author = {Zeng, Q and Feng, X and Hu, Y and Su, S},
title = {The human gut microbiota is associated with host lifestyle: a comprehensive narrative review.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1549160},
pmid = {40625617},
issn = {1664-302X},
abstract = {BACKGROUND: The gut microbiota serves as a critical interface between lifestyle factors and host physiology. Despite extensive research on individual domains including diet, sleep, and exercise, an integrated understanding of their synergistic effects on microbial communities remains incomplete. This knowledge gap limits our ability to develop targeted microbiome-based interventions for metabolic and immune-related disorders.<br><br>METHODS: To address this gap, we conducted a comprehensive evaluation of peer-reviewed literature from 2000 to present, identified through systematic searches of PubMed, Web of Science, and Scopus using key terms related to gut microbiota and lifestyle interventions. Our analysis focused on studies incorporating microbiome profiling techniques, controlled lifestyle interventions, and multi-omics data integration. The review prioritized mechanistic insights from both clinical and preclinical investigations while critically assessing methodological approaches across the field.<br><br>RESULTS: High-fiber dietary patterns consistently promoted the abundance of beneficial, short-chain fatty acid-producing bacteria, though with notable inter-individual variation. Circadian rhythm disruption was associated with reduced microbial diversity and expansion of pro-inflammatory bacterial taxa, paralleling increases in systemic inflammation markers. Athletic populations demonstrated unique microbial signatures characterized by enhanced metabolic potential, with distinct taxonomic profiles emerging across different sport disciplines.<br><br>CONCLUSION: This work synthesizes current evidence into a novel framework for understanding lifestyle-microbiota interactions, while identifying key challenges in study design and data interpretation. We propose standardized methodological approaches for future investigations and outline translational strategies for personalized microbiota modulation. These insights advance the potential for targeted microbial interventions to optimize metabolic and immune health outcomes.},
}
@article {pmid40625616,
year = {2025},
author = {Gilliam, FS},
title = {Linkage of strata of forest vegetation with forest soil microbiomes: a review.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1575691},
pmid = {40625616},
issn = {1664-302X},
abstract = {A major dimension of pattern and process in ecological systems is the way in which species interact. In the study of forest communities, the phenomenon of linkage among forest strata (e.g., overstory and herbaceous layer) has been well investigated and arises when forest strata interact in ways that lead to causal connections between them. Whereas trees alter the light regime of forest herb communities, the herb layer can direct survivorship among seedlings of overstory species. Less studied, however, is linkage between forest strata and forest soil microbiomes. This review examines ways in which forest vegetation and soil microbiomes exert reciprocating effects on each other that can lead to linkage, beginning with a brief literature review of several phenomena relevant to how these effects occur. Because of the coincidence of the ubiquity of soil microbes with their almost infinitely small size, their interactions-both above and belowground in nature-with forest vegetation are particularly intimate. Although the most direct link, and certainly one that likely first comes to mind, is through root/microbe interactions, foliar surfaces and internal foliar tissues can support a diverse microbiome. Following the overview of potential mechanisms, examples from two separate forest studies of how linkage was demonstrated will be summarized. In each of these studies, linkage was evident through significant correlations among axis scores generated by canonical correspondence run separately for forest vegetation and soil microbial communities.},
}
@article {pmid40625325,
year = {2025},
author = {Garcias-Bonet, N and Villela, H and García, FC and Duarte, GAS and Delgadillo-Ordoñez, N and Raimundo, I and El-Khaled, YC and Santoro, EP and Bennett-Smith, M and Nieuwenhuis, BO and Curdia, J and Zgliczynski, B and Edwards, C and Sandin, S and Osman, EO and Sicat, R and Przybysz, A and Rosado, AS and Jones, BH and Benzoni, F and Berumen, ML and Salama, K and Park, S and Aranda, M and Duarte, CM and Schmidt-Roach, S and Hauser, CAE and Truscott, T and Suggett, DJ and Voolstra, CR and Carvalho, S and Peixoto, RS},
title = {The Coral Probiotics Village: An Underwater Laboratory to Tackle the Coral Reefs Crisis.},
journal = {Ecology and evolution},
volume = {15},
number = {7},
pages = {e71558},
pmid = {40625325},
issn = {2045-7758},
abstract = {Restoration efforts are urgently needed for the conservation of coral reefs. Among emerging tools, the use of probiotics has shown promise in laboratory settings for improving coral resilience, but their validation under real-world reef conditions remains limited. Here, we present the Coral Probiotics Village (CPV) as a novel and fully operational underwater research laboratory and a testing ground designed to support the in situ testing of microbial-based coral restoration interventions. This manuscript describes the design, establishment, and scientific validation of the CPV, including continuous environmental monitoring, a summary of previously developed pilot trials of probiotic applications, and an integration of sensor networks, AI-assisted reef monitoring, and autonomous technologies. We propose the CPV as a scalable model for integrated coral restoration science and suggest its replication as a tool to accelerate applied reef conservation efforts globally.},
}
@article {pmid40625320,
year = {2025},
author = {Haque, S and Gamage, HKAH and Kardum Hjort, C and Ponton, F and Encinas-Viso, F and Paulsen, IT and Dudaniec, RY},
title = {Landscape-Wide Metabarcoding Shows Interactions Among the Gut Microbiome and Pollen Diversity in the Invasive Bumblebee, Bombus terrestris.},
journal = {Ecology and evolution},
volume = {15},
number = {7},
pages = {e71717},
pmid = {40625320},
issn = {2045-7758},
abstract = {Gut microbial communities can facilitate traits that are essential for invasive species survival in novel environments. Despite the global plethora of invasive social insect species, the role of the gut microbiome in colonisation success under novel dietary and environmental conditions is little known. The introduction of the European buff-tailed bumblebee, Bombus terrestris, to the island of Tasmania (Australia) ~30 years ago is of ecological concern due to its negative impacts on native vegetation and endemic bees. Here, we investigate how the gut microbiota of B. terrestris workers is affected by corbicular pollen diversity and environmental variation across diverse landscapes in an invaded island system. B. terrestris female workers were sampled from 19 sites across Tasmania, for which environmental data for seven variables were extracted. Using 16S rRNA and ITS2 metabarcoding on gut samples and foraged pollen, respectively, we examine how the gut microbiota of B. terrestris is influenced by pollen diversity, environmental variables and their interactions. Gut bacterial community composition was significantly predicted by site annual precipitation and the percentage of pasture, which each explained 9% of the variation. Gut bacterial diversity was also explained by precipitation and pasture (40% and 30% of the variation, respectively). Furthermore, a positive interaction between annual precipitation and annual temperature significantly predicted site gut bacterial diversity. The interaction effect of pollen diversity and summer wind velocity was also positively related to gut bacterial diversity. Our findings contribute to understanding how interactions between the local environment and pollen diet affect the bee gut microbiome and thus the health and success of invasive pollinators.},
}
@article {pmid40625277,
year = {2025},
author = {Feng, K and He, Q and Peng, X and Yang, X and Du, X and Wei, Z and Wang, S and Zou, X and Zhang, Y and Deng, Y},
title = {Temperature and Biodiversity Regulate the Robustness of Plant-Microbe Networks in Natural Forests at Large Scale.},
journal = {Global change biology},
volume = {31},
number = {7},
pages = {e70335},
doi = {10.1111/gcb.70335},
pmid = {40625277},
issn = {1365-2486},
support = {42207141//National Natural Science Foundation of China/ ; U23A2043//National Natural Science Foundation of China/ ; },
mesh = {*Biodiversity ; *Forests ; *Temperature ; *Plants/microbiology ; *Microbiota ; Soil Microbiology ; },
abstract = {The latitudinal diversity gradient (LDG) is one of the general ecological patterns and has been extensively studied in plant and microbial communities. However, whether plant-microbe networks follow latitudinal trends and the underlying mechanisms driving such patterns remain largely unknown. In this study, we used an ecological survey dataset with simultaneously investigated plant species and microbial data from 26 forests at a continental scale and constructed the plant-microbe networks for each forest across the latitude gradients. We observed clear latitudinal patterns in plant-microbe networks, consistent with the LDG. Specifically, both the richness of networked species and the nestedness of the network architecture declined from tropical to temperate forests. Moreover, the plant-level network robustness decreased with increasing latitude, and positive biodiversity-robustness relationships were observed for plants and microbes. Mean annual temperature (MAT) was the most important factor for the observed latitudinal patterns, especially for plant-microbe network stability, evidenced by the robustness index. Additionally, MAT had a stronger effect on plant robustness than soil pH, primarily through its influence on plant diversity. Overall, this study demonstrated the latitudinal distribution patterns of the plant-microbe networks in natural forests and highlighted the positive relationship between biodiversity and robustness through plant-microbe interaction processes.},
}
@article {pmid40625255,
year = {2025},
author = {Choi, HS and Kim, MS and Yu, MH and You, J and Seon, D and Ko, G and Unno, T and Lee, MY and Kim, YS},
title = {Long-term Effects of Potassium-competitive Acid Blockers and Proton Pump Inhibitors on Gastrin, Gastric Emptying Rate, and Small Intestinal Microbiota in Rats.},
journal = {Journal of neurogastroenterology and motility},
volume = {31},
number = {3},
pages = {384-395},
doi = {10.5056/jnm25024},
pmid = {40625255},
issn = {2093-0879},
abstract = {BACKGROUND/AIMS: Proton pump inhibitors (PPIs) are widely used for gastric acid suppression but are associated with adverse effects such as hypergastrinemia and delayed gastric emptying (GE). Potassium-competitive acid blockers (P-CABs), a new class of acid suppressants, rapidly and sustainably inhibit gastric acid secretion. We compared the long-term effects of different P-CABs and PPIs on gastric pH, serum gastrin levels, GE, and small intestinal microbiota in a rat model.<br><br>METHODS: Seventy-two male Sprague-Dawley rats were assigned to receive control, esomeprazole, tegoprazan, or vonoprazan by oral gavage for 1, 2, or 4 weeks. After sacrifice, gastric pH, serum gastrin levels, and GE were measured, and the small intestinal microbiota were analyzed using 16S ribosomal RNA sequencing.<br><br>RESULTS: All drug-treated groups exhibited significantly higher gastric pH than the control group. Tegoprazan achieved the highest pH at week 2, surpassing those of esomeprazole and vonoprazan. Serum gastrin levels were significantly elevated in all drug-treated groups but remained stable from weeks 1 to 4, indicating a plateau effect. GE was transiently delayed at week 2 but returned to baseline by week 4 in all drug-treated groups. Long-term administration of both P-CABs and PPI led to reduced microbial diversity and distinct taxonomic shifts with changes in the abundance of Prevotella and Acetatifactor in the small intestine. However, with prolonged administration, these differences in microbiota composition gradually diminished.<br><br>CONCLUSIONS: Long-term administration of P-CABs and PPIs altered gastrin levels, GE, and gut microbiota. Therefore, the acid suppression-related adverse effects of P-CABs and PPIs are expected to be similar.},
}
@article {pmid40624668,
year = {2025},
author = {Liu, S and Xu, H and Liu, L and Ma, W and Fan, H and Liu, F and Wei, Z and Hao, J and Zheng, Z and Zhao, L and Yang, B and Wu, Z},
title = {Gut microbiome dysbiosis accelerates osteoarthritis progression by inducing IFP-SM inflammation in "double-hit" mice.},
journal = {Arthritis research &amp; therapy},
volume = {27},
number = {1},
pages = {137},
pmid = {40624668},
issn = {1478-6362},
support = {GZC20240144//Postdoctoral Fellowship Program of&#xa0;China Postdoctoral Science Foundation/ ; 82402893//National Natural Science Foundation of China/ ; 2024-I2M-C&amp;T-B-026//CAMS Special Project of Clinical and Translational Medical Research/ ; 2022YFC2703901//National Key Research and Development Program of China/ ; 2022-PUMCH-D-002//National High Level Hospital Clinical Research Funding/ ; 2021-I2M-1-052 and 2022-I2M-2-001//CAMS Innovation Fund for Medical Sciences/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; *Dysbiosis/microbiology/complications ; *Osteoarthritis/microbiology/pathology/metabolism ; Mice ; Disease Progression ; *Inflammation/pathology/microbiology/metabolism ; Male ; Mice, Inbred C57BL ; Disease Models, Animal ; },
abstract = {BACKGROUND: This study investigates the complex interplay between gut microbiome dysbiosis and systemic inflammation as a critical risk factor in the pathogenesis of osteoarthritis (OA). Furthermore, it elucidates the role of gut microbiota (GMB) dysbiosis in driving OA progression.<br><br>METHODS: A refined "double-hit" murine model was developed to explore this relationship. The first intervention involved inducing gut microbiota dysbiosis through the administration of colistin and Escherichia coli, followed by surgical destabilization of the medial meniscus (DMM) to induce joint instability. The composition of the gut microbiota was analyzed using 16&#xa0;S rRNA sequencing. Gut permeability was assessed via RT-PCR and immunofluorescence (IF), while mRNA sequencing was employed to examine alterations in gene expression.<br><br>RESULTS: Treatment with colistin and E. coli significantly altered the gut microbiota composition, characterized by a marked increase in the absolute abundance of Firmicutes and a concomitant reduction in Bacteroidota and the Bacteroidota/Firmicutes (B/F) ratio. At the genus level, the absolute abundances of Muribaculaceae, Rikenellaceae_RC9_gut_group, and Roseburia were significantly diminished. GMB dysbiosis led to the downregulation of intestinal tight junction proteins, including ZO-1 and Occludin, resulting in increased intestinal permeability. Consequently, serum levels of lipopolysaccharide (LPS) were significantly elevated, indicating LPS translocation from the gut into systemic circulation. Notably, GMB dysbiosis markedly exacerbated OA progression, as evidenced by accelerated cartilage degeneration, increased osteophyte formation, and reduced bone mineral density (BMD). The OARSI scoring system revealed that OA severity in both colistin and E. coli treatment groups was significantly higher than in the control group. Additionally, GMB dysbiosis promoted the expression of inflammation-related genes in the synovium and induced M1 polarization of macrophages, demonstrated by the upregulation of CD86 and an elevated CD86/CD206 ratio. Correlation analyses indicated that Bacteroidota and the B/F ratio were positively associated with intestinal barrier integrity and negatively correlated with OA progression. In contrast, Firmicutes exhibited a positive correlation with inflammation and OA deterioration.<br><br>CONCLUSIONS: These findings collectively underscore the critical role of GMB dysbiosis in modulating intestinal permeability, systemic inflammation, and OA pathogenesis. The protective effects of Bacteroidota and the B/F ratio, as well as the detrimental impact of Firmicutes, highlight potential therapeutic targets for mitigating OA progression through GMB modulation.},
}
@article {pmid40624665,
year = {2025},
author = {Lin, F and Ma, L and Sheng, Z},
title = {Health disorders in menopausal women: microbiome alterations, associated problems, and possible treatments.},
journal = {Biomedical engineering online},
volume = {24},
number = {1},
pages = {84},
pmid = {40624665},
issn = {1475-925X},
support = {2022KY275//Zhejiang&#xa0;Provincial&#xa0;Medical&#xa0;and&#xa0;Health&#xa0;Science&#xa0;and&#xa0;Technology&#xa0;Project:&#xa0;"Research&#xa0;on&#xa0;the&#xa0;Impact&#xa0;of&#xa0;Hormone&#xa0;Therapy&#xa0;for&#xa0;Menopause&#xa0;on&#xa0;the&#xa0;Vaginal&#xa0;Microbiota&#xa0;of&#xa0;Perimenopausal&#xa0;Women&#xa0;Based&#xa0;on&#xa0;16S&#xa0;rRNA&#xa0;High-throughput&#xa0;Gene&#xa0;Sequencing&#xa0;Technology/ ; 2022KY275//Zhejiang&#xa0;Provincial&#xa0;Medical&#xa0;and&#xa0;Health&#xa0;Science&#xa0;and&#xa0;Technology&#xa0;Project:&#xa0;"Research&#xa0;on&#xa0;the&#xa0;Impact&#xa0;of&#xa0;Hormone&#xa0;Therapy&#xa0;for&#xa0;Menopause&#xa0;on&#xa0;the&#xa0;Vaginal&#xa0;Microbiota&#xa0;of&#xa0;Perimenopausal&#xa0;Women&#xa0;Based&#xa0;on&#xa0;16S&#xa0;rRNA&#xa0;High-throughput&#xa0;Gene&#xa0;Sequencing&#xa0;Technology/ ; 2022KY275//Zhejiang&#xa0;Provincial&#xa0;Medical&#xa0;and&#xa0;Health&#xa0;Science&#xa0;and&#xa0;Technology&#xa0;Project:&#xa0;"Research&#xa0;on&#xa0;the&#xa0;Impact&#xa0;of&#xa0;Hormone&#xa0;Therapy&#xa0;for&#xa0;Menopause&#xa0;on&#xa0;the&#xa0;Vaginal&#xa0;Microbiota&#xa0;of&#xa0;Perimenopausal&#xa0;Women&#xa0;Based&#xa0;on&#xa0;16S&#xa0;rRNA&#xa0;High-throughput&#xa0;Gene&#xa0;Sequencing&#xa0;Technology/ ; },
mesh = {Humans ; *Menopause ; Female ; *Microbiota ; *Health ; },
abstract = {Perimenopause marks a critical transition in women's lives, characterized by declining estrogen levels that trigger profound physiological and psychological changes, impacting quality of life and increasing susceptibility to age-related degenerative diseases. This review systematically examines the intricate relationships among menopause, disease associations, microbiome alterations, and intervention strategies. Estrogen fluctuations disrupt the microbial balance in the vagina, intestine, urethra, and oral cavity, contributing to microecological imbalance and heightened disease risk. Menopause is closely linked to a spectrum of health issues, including reproductive system disorders (e.g., uterine fibroids, ovarian cancer microbiota changes), metabolic syndromes (obesity, type 2 diabetes), cardiovascular diseases (influenced by gut microbiota and dietary patterns), osteoporosis, and mental health disturbances. Current interventions-ranging from dietary modifications (cocoa polyphenols, dietary fiber, soy isoflavones) and menopausal hormone therapy (MHT) to probiotic supplementation, plant extracts (soybean, black cohosh, red clover), and traditional therapies-exhibit distinct advantages and limitations. Technological advancements in microbiome analysis, tissue processing, and cell isolation have revolutionized diagnostic and therapeutic approaches, while immune function, socioeconomic factors, and lifestyle choices significantly modulate health outcomes. Future research should prioritize exploring synergistic intervention strategies, developing personalized health management programs, and unraveling the mechanistic links between the microbiome and menopause-related diseases. This comprehensive synthesis aims to advance evidence-based strategies for improving the health and quality of life of menopausal women.},
}
@article {pmid40624638,
year = {2025},
author = {Yan, X and Lin, X and Wu, J and Zheng, L and Liu, Y and Wu, F and Lin, Y and Lu, Y and Huang, C and Shen, B and Liu, H and Huang, R and Hou, F and Zhou, Q and Song, M and Liu, K and Zhu, F and Li, S and Lin, Y and Wang, W and Li, P and Liao, W and Zhi, F},
title = {Mitigation of chemotherapy-induced gut dysbiosis and diarrhea by supplementation with heat-killed Bacteroides fragilis.},
journal = {BMC medicine},
volume = {23},
number = {1},
pages = {408},
pmid = {40624638},
issn = {1741-7015},
support = {Y20190159//Study on the Mechanism of FUT7 regulating CD15s+eTreg cells in the Pathogenesis of Ulcerative Colitis/ ; NO.2024B03J1282//Key Technology Project in Guangzhou/ ; NO. 201809010014//Innovation Leading Team Project in Guangzhou/ ; },
mesh = {Animals ; *Dysbiosis/chemically induced/therapy/microbiology ; Male ; *Gastrointestinal Microbiome/drug effects ; Humans ; *Diarrhea/chemically induced/microbiology/therapy ; Mice ; *Bacteroides fragilis ; Mice, Inbred C57BL ; *Probiotics/therapeutic use ; Mice, Inbred BALB C ; *Antineoplastic Agents/adverse effects ; Middle Aged ; Fluorouracil/adverse effects ; Feces/microbiology ; Female ; Aged ; },
abstract = {BACKGROUND: The role of gut microbial dysbiosis in chemotherapy-induced diarrhea (CID) pathogenesis remains unclear in humans. This study investigates gut microbiota alterations in CID patients and evaluates the therapeutic potential of probiotic supplementation.<br><br>METHODS: To establish a paired cohort for longitudinal comparison and minimize confounding factors in assessing CID-related microbiota changes, strict inclusion/exclusion criteria were applied to gastrointestinal cancer patients. Fecal samples from eligible participants underwent shotgun metagenomic sequencing to comprehensively profile the gut microbiome composition and function. To evaluate probiotic efficacy and mechanisms, we utilized 6-8-week-old male BALB/c and C57BL/6 mice in established 5-FU- or CPT-11-induced CID models. Probiotic efficacy was assessed using primary (diarrhea severity) and secondary endpoints (body weight change, intestinal permeability). Mechanistic studies were conducted in murine models, complemented by IEC-6 cells and intestinal organoid experiments to elucidate microbiota-host interactions.<br><br>RESULTS: Analysis of paired fecal samples (pre- and post-chemotherapy) from 30 gastrointestinal cancer patients (n&#x2009;=&#x2009;60) revealed chemotherapy-induced reduction of Bacteroides fragilis (B. f) via metagenomics sequencing, with baseline B. f relative abundance negatively correlating with CID severity (r&#x2009;=&#x2009;&#x2009;-&#x2009;0.93, p&#x2009;=&#x2009;3.1e&#x2009;-&#x2009;12). Building on these clinical observations, in 5-FU/CPT-11-induced CID murine models, oral gavage of heat-killed B. f (hk-B. f) outperformed live bacteria in diarrhea alleviation. Mechanistically, B. f-derived succinate exacerbated diarrhea, while its capsular polysaccharide (PSA) ameliorated mice diarrhea. This discovery explains the discrepant therapeutic effect between hk-B.&#xa0;f and live B.&#xa0;f. Fluorescence tracing confirmed hk-B. f transiently localized to the upper gastrointestinal tract without extraintestinal colonization. hk-B. f preserved epithelial integrity, mitochondrial function, and intestinal organoid development (higher budding count and larger organoid surface area). Moreover, hk-B.&#xa0;f upregulated the expression of BCL2 and downregulated the expression of BAX. Shifting the balance between BCL2 and BAX alleviates intestinal epithelial apoptosis. Caspase-3 inhibition or BCL2 silencing abrogated hk-B. f's anti-apoptotic effects in IEC-6 cells.<br><br>CONCLUSIONS: Pathological process of CID can be partially explained by compositional alterations in the gut microbiota. Supplementation with hk-B.&#xa0;f reduces 5-FU-stimulated epithelial injury through mitochondrial apoptotic pathway in CID murine models. These preclinical findings suggest hk-B.&#xa0;f merits further investigation as a potential strategy for improving CID, pending clinical validation.},
}
@article {pmid40624612,
year = {2025},
author = {De, T and Ma, T and Wang, W and An, X and Liu, D and Yin, H and Wang, Q and Zhao, T and Wang, H},
title = {Intestinal microbiota in adults with cholangiocarcinoma identifies the dysregulated Blautia species and bile acid metabolic pathways.},
journal = {BMC gastroenterology},
volume = {25},
number = {1},
pages = {506},
pmid = {40624612},
issn = {1471-230X},
support = {XZ2024033//Ningxia Medical University Institutional Scientific Research Fund/ ; XZ2024033//Ningxia Medical University Institutional Scientific Research Fund/ ; XZ2024033//Ningxia Medical University Institutional Scientific Research Fund/ ; XZ2024033//Ningxia Medical University Institutional Scientific Research Fund/ ; XZ2024033//Ningxia Medical University Institutional Scientific Research Fund/ ; XZ2024033//Ningxia Medical University Institutional Scientific Research Fund/ ; XZ2024033//Ningxia Medical University Institutional Scientific Research Fund/ ; XZ2024033//Ningxia Medical University Institutional Scientific Research Fund/ ; XZ2024033//Ningxia Medical University Institutional Scientific Research Fund/ ; 2022BSB03112//the Ningxia Gut Homeostasis and Chronic Disease Prevention and Treatment Scientific and Technological Innovation Team, China/ ; 2022BSB03112//the Ningxia Gut Homeostasis and Chronic Disease Prevention and Treatment Scientific and Technological Innovation Team, China/ ; 2022BSB03112//the Ningxia Gut Homeostasis and Chronic Disease Prevention and Treatment Scientific and Technological Innovation Team, China/ ; 2022BSB03112//the Ningxia Gut Homeostasis and Chronic Disease Prevention and Treatment Scientific and Technological Innovation Team, China/ ; 2022BSB03112//the Ningxia Gut Homeostasis and Chronic Disease Prevention and Treatment Scientific and Technological Innovation Team, China/ ; 2022BSB03112//the Ningxia Gut Homeostasis and Chronic Disease Prevention and Treatment Scientific and Technological Innovation Team, China/ ; 2022BSB03112//the Ningxia Gut Homeostasis and Chronic Disease Prevention and Treatment Scientific and Technological Innovation Team, China/ ; 2022BSB03112//the Ningxia Gut Homeostasis and Chronic Disease Prevention and Treatment Scientific and Technological Innovation Team, China/ ; 2022BSB03112//the Ningxia Gut Homeostasis and Chronic Disease Prevention and Treatment Scientific and Technological Innovation Team, China/ ; 2023GKLRLX17//Program of Ningxia Science and Technology Leading Talent, China/ ; 2023GKLRLX17//Program of Ningxia Science and Technology Leading Talent, China/ ; 2023GKLRLX17//Program of Ningxia Science and Technology Leading Talent, China/ ; 2023GKLRLX17//Program of Ningxia Science and Technology Leading Talent, China/ ; 2023GKLRLX17//Program of Ningxia Science and Technology Leading Talent, China/ ; 2023GKLRLX17//Program of Ningxia Science and Technology Leading Talent, China/ ; 2023GKLRLX17//Program of Ningxia Science and Technology Leading Talent, China/ ; 2023GKLRLX17//Program of Ningxia Science and Technology Leading Talent, China/ ; 2023GKLRLX17//Program of Ningxia Science and Technology Leading Talent, China/ ; },
mesh = {Humans ; *Cholangiocarcinoma/microbiology/metabolism ; *Gastrointestinal Microbiome ; *Bile Duct Neoplasms/microbiology/metabolism ; *Bile Acids and Salts/metabolism ; Male ; Middle Aged ; Female ; Metabolic Networks and Pathways ; *Dysbiosis/microbiology ; *Clostridiales/genetics/isolation &amp; purification ; Aged ; Case-Control Studies ; Adult ; Feces/microbiology ; },
abstract = {BACKGROUND: Cholangiocarcinoma (CCA) represents a significant global health concern. The gut and bile microbiota, which can influence the gut-liver axis and disease progression, have not been thoroughly characterized in CCA patients.<br><br>METHODS: We selected two clinical centers at our hospital and collected stool samples from CCA patients and healthy controls (HC). These samples underwent whole-genome metagenomic shotgun sequencing, followed by analysis using both marker gene-based and assembly-based methods. Additionally, KEGG pathway enrichment was performed using the cholangiocarcinoma (CHOL) RNA-seq samples.<br><br>RESULTS: Our results revealed distinct dysbiosis of the gut microbiota in our regional CCA patients. The results revealed greater heterogeneity in the gut microbiome of CCA patients compared to HC samples. We found Blautia species to be significantly less abundant in CCA samples, and can distinguish CCA patients from HC. Blautia can also play a role in influencing the modification of secondary bile acids. Additionally, down-regulation of arachidonic acid and linoleic acid metabolism was observed in the tumor tissues of CHOL patients. In summary, the results revealed significant heterogeneity difference in the gut microbiome of CCA patients compared to HC samples, and detected the specifically decreased Blautia species in CCA patients, suggesting that Blautia may influence bile acid metabolic pathways. Further investigation is warranted to explore Blautia as a potential biomarker for CCA.},
}
@article {pmid40624576,
year = {2025},
author = {Liu, H and Su, Y and Ye, C and Zuo, D and Wang, L and Mei, X and Deng, W and Liu, Y and Huang, H and Hao, J and Zhao, J and Wang, D and Zhang, X and Zhu, Y and Liu, J and Yang, M and Zhu, S},
title = {Nucleotides enriched under heat stress recruit beneficial rhizomicrobes to protect plants from heat and root-rot stresses.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {160},
pmid = {40624576},
issn = {2049-2618},
support = {6254033//Beijing Municipal Natural Science Foundation/ ; U23A20202//Natural Science Foundation of China/ ; 2021YFD1601003//National Key Research and Development Program of China/ ; 2021JH002//Major Science and Technology Project of Kunming/ ; 202102AE090042//Major Science and Technology Projects in Yunnan Province/ ; },
mesh = {*Plant Roots/microbiology ; *Heat-Shock Response ; *Plant Diseases/microbiology/prevention &amp; control ; Burkholderia ; Soil Microbiology ; Disease Resistance ; Hot Temperature ; Capsicum/microbiology ; Microbiota ; Stress, Physiological ; },
abstract = {BACKGROUND: Plants thrive under biotic and abiotic stresses with the help of rhizomicrobiota. Root exudates play a pivotal role in recruiting beneficial microbes that assist plants in surviving environmental challenges, but the mechanisms of plant-microbiome interactions to resist multiple stresses remain elusive. We investigated how heat stress alters the rhizomicrobiomes of Panax notoginseng and how these heat stress-regulated microbes confer enhanced heat tolerance and disease resistance.<br><br>RESULTS: We revealed that heat stress at 36&#xa0;&#xb0;C caused thermal damage to plants while enhancing heat tolerance and disease resistance for the survival of subsequent plants. Specifically, the beneficial microbes Burkholderia sp. and Saitozyma podzolica were recruited by the heat-stressed P. notoginseng and were confirmed to be responsible for resisting multiple stresses. Heat stress-induced plant roots secrete nucleotides such as purines and pyrimidines to promote the proliferation of these two beneficial microbes rather than root-rot pathogens. The exogenous application of these nucleotides to natural soil also resulted in the enrichment of the same beneficial microbes. Cross-species validation experiments in Capsicum annuum (pepper) and Solanum lycopersicum (tomato) further demonstrated that co-application of nucleotides with beneficial microbes synergistically enhanced heat tolerance.<br><br>CONCLUSIONS: Our findings highlight a plant strategy for thriving under multiple adversities and propose a potential pathway by leveraging nucleotide-mediated recruitment of beneficial microbes for enhancing plant resilience against multiple stresses. Video Abstract.},
}
@article {pmid40624564,
year = {2025},
author = {Zhu, J and Jiang, MZ and Chen, X and Li, M and Wang, YL and Liu, C and Liu, SJ and Chen, WH},
title = {Systematic pairwise co-cultures uncover predominant negative interactions among human gut bacteria.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {161},
pmid = {40624564},
issn = {2049-2618},
support = {2022YFA1304100//Ministry of Science and Technology of the People's Republic of China/ ; 2022YFA1304100//Ministry of Science and Technology of the People's Republic of China/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Bacteria/classification/isolation &amp; purification/genetics/growth &amp; development/metabolism ; *Microbial Interactions ; Coculture Techniques ; Metagenome ; Healthy Volunteers ; Feces/microbiology ; China ; },
abstract = {BACKGROUND: Understanding pairwise bacterial interactions in the human gut is crucial for deciphering the complex networks of bacterial interactions and their contributions to host health. However, there is a lack of large-scale experiments focusing on bacterial interactions within the human gut microbiome.<br><br>METHODS: We investigated the pairwise interactions of 113 bacterial strains isolated from healthy Chinese volunteers, selected for their high abundance and functional representation of the human gut microbiome. Using mGAM agar plates, a rich medium designed to maintain community structure, we established the "PairInteraX" dataset, which includes 3233 pair combinations of culturable human gut bacteria. This dataset was analyzed to identify interaction patterns and the key factors influencing these patterns.<br><br>RESULTS: Our analysis revealed that negative interactions were predominant among the bacteria in the PairInteraX dataset. When combined with in vivo gut metagenome datasets, we noted a diminishing mutualism and an increasing competition as microbial abundances increased; consequently, the maintenance of community diversity requires the participation of various types of interactions, especially the negative interactions. We also identified key factors influencing these interaction patterns including metabolic capacity and motility.<br><br>CONCLUSIONS: This study provides a comprehensive overview of pairwise bacterial interactions within the human gut microbiome, revealing a dominance of negative interactions. Besides, metabolic capacity and motility were identified as the key factors to influence the pairwise interaction patterns. This large-scale dataset and analysis offer valuable insights for further research on microbial community dynamics and their implications for host health. Video Abstract.},
}
@article {pmid40624562,
year = {2025},
author = {Ferreira, IM and Mantovani, HC and Viquez-Umana, F and Granja-Salcedo, YT and E Silva, LFC and Koontz, A and Holder, V and Pettigrew, JE and Rodrigues, AA and Rodrigues, AN and de Abreu, MJI and de Almeida, STR and Vidigal, PMP and Siqueira, GR and de Resende, FD},
title = {Feeding amylolytic and fibrolytic exogenous enzymes in feedlot diets: effects on ruminal parameters, nitrogen balance and microbial diversity of Nellore cattle.},
journal = {Journal of animal science and biotechnology},
volume = {16},
number = {1},
pages = {96},
pmid = {40624562},
issn = {1674-9782},
support = {2022/00989-1//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2023/10911-2//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2017/50339-5//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 001//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; },
abstract = {BACKGROUND: The environmental impact of feedlot operations is a growing concern, as cattle excrete a significant portion of feed nutrients as waste. Exogenous feed enzymes (EFE) have gained interest for their potential to enhance feed efficiency in ruminants by improving nutrient digestion. However, EFE effects on ruminal parameters have shown inconsistencies, with limited research on nitrogen metabolism and rumen microbiome impacts. Moreover, the synergistic effects of combining different EFEs remain unclear. This study aimed to evaluate the effects of individual and combined EFE products in feedlot diets on ruminal fermentation parameters, nitrogen metabolism, and ruminal microbial communities. Ten rumen-cannulated Nellore steers [543 ± 28.6 kg of body weight (BW)] were distributed in a replicated Latin-square design (5 × 5) in individual pens. Treatments included: control (CON, no EFE supplementation), amylase [AML, 0.5 g/kg of diet dry matter (DM)], xylanase (FBL, 0.9 g/kg DM), half dose combination (HD, 0.25 g of AML + 0.45 g of FBL/kg of DM), and full dose combination (FD, 0.5 g of AML + 0.90 g of FBL/kg of DM). The experimental period lasted 19 d and included total urine and feces collection (d 15 to 18) and rumen fluid sampling (d 19) at 0, 4, 8, 12, and 16 h post-feeding for ammonia, volatile fatty acids (VFA), pH and microbiome analysis.<br><br>RESULTS: EFE supplemented animals exhibited lower ruminal ammonia concentrations (P&#x2009;=&#x2009;0.040), and higher acetate proportions (P&#x2009;<&#x2009;0.001) compared to the control group. EFE supplementation resulted in reduced nitrogen (N) excretion in feces (P&#x2009;=&#x2009;0.049) and urine (P&#x2009;=&#x2009;0.036), contributing to improved N retention and efficiency (P&#x2009;=&#x2009;0.045). Additionally, EFE products induced shifts in various microbial taxa at family and genera levels (P&#x2009;&#x2264;&#x2009;0.10), which may be associated with the changes observed in ruminal fermentation.<br><br>CONCLUSIONS: Our findings demonstrate that EFE supplementation enhances nitrogen retention, reduces ruminal ammonia, and alters ruminal fermentation profiles and microbial populations in feedlot cattle. While the expected synergism between amylase and xylanase did not significantly impact rumen fermentation parameters, it did induce shifts in the rumen microbiome. These results suggest that EFE supplementation may be a promising strategy for improving nutrient utilization and potentially reducing the environmental impact of feedlot operations.},
}
@article {pmid40624448,
year = {2025},
author = {Mitropoulou, G and Karapantzou, I and Prapa, I and Papanikolaou, D and Charovas, V and Kourkoutas, Y},
title = {Physicochemical, microbial, and microbiome dynamics in winery waste composting.},
journal = {Environmental science and pollution research international},
volume = {},
number = {},
pages = {},
pmid = {40624448},
issn = {1614-7499},
support = {&#x391;&#x39c;&#x398;&#x3a1;7-0074893//The European Union and National Resources under the Operational Programme "Eastern Macedonia and Thrace" 2014-2020/ ; MIS number: 5076618//The European Union and National Resources under the Operational Programme "Eastern Macedonia and Thrace" 2014-2020/ ; },
abstract = {Compared to more extensively studied composting substrates like food waste or animal manure, winery waste presents unique challenges and opportunities. Its high content of lignin, cellulose, and polyphenolic compounds demands specific microbial consortia for efficient degradation and can potentially inhibit microbial activity if not properly balanced. In the present study, analysis of winery waste composting that combines traditional microbial enumeration with high-resolution microbiome profiling, an approach rarely applied to this type of agro-industrial residue, was implemented. Moreover, a practical proof-of-concept study, for using the composted product as a partial substrate replacement in grapevine cultivation, closing the loop in vineyard waste management, was conducted. Key parameters, such as moisture content, pH, temperature, conductivity, and C/N ratio were monitored, over a 60-day period, along with changes in enzymatic activity and shifts in microbial populations, indicating dynamic microbial activity. At the end of the process, a reduction in the carbon-to-nitrogen (C/N) ratio was observed, pH was stabilized to neutral values, and dehydrogenases activity was notably decreased. Microbiome analysis revealed eight bacterial and six fungal phyla. Acidobacteria, Armatimonadetes, Bacteroidetes, Candidatus Saccharibacteria, Chloroflexi, Cyanobacteria, Planctomycetes were identified. The Ascomycota, Basidiomycota, Chytridiomycota, Entomophthoromycota, Glomeromycota, and Mucoromycota fungal phyla were also detected. The compost exhibited no phytotoxicity and supported grapevine growth comparable to commercial substrates. Winery waste microbial composting led to stable biofertilizer production, evidenced by physicochemical stability, lack of phytotoxicity, and effectiveness in promoting grapevine growth suggesting the potential of composting as a sustainable waste management solution in the winemaking industry.},
}
@article {pmid40624404,
year = {2025},
author = {Gao, T and Yun, J and Zheng, Y and Mu, C and Zhao, B},
title = {Time-dependent microbiome dynamics in orthodontic thermoplastic materials: comparing PETG and TPU.},
journal = {Clinical oral investigations},
volume = {29},
number = {8},
pages = {374},
pmid = {40624404},
issn = {1436-3771},
support = {202240182//Shanghai Municipal Health Commission/ ; SHH-2022-YJ-A01//Shanghai Stomatological Hospital/ ; },
mesh = {Humans ; *Microbiota/drug effects ; *Polyurethanes/chemistry ; *Saliva/chemistry/microbiology ; Male ; Female ; Hydrogen-Ion Concentration ; *Polyethylene Terephthalates ; *Polyethylene Glycols/chemistry ; Adult ; Time Factors ; *Orthodontic Appliances/microbiology ; Adolescent ; Young Adult ; RNA, Ribosomal, 16S ; },
abstract = {OBJECTIVES: This study compares the effects of thermoplastic polyurethane (TPU) and polyethylene terephthalate glycol (PETG) aligners on the oral microbiome and salivary pH during orthodontic treatment.<br><br>MATERIALS AND METHODS: Ten participants wore TPU and PETG aligners for 24&#xa0;h. At five time points (1&#xa0;min, 4, 8, 12, and 24&#xa0;h), saliva was collected for pH analysis, and microbial samples were taken from both aligner and supragingival plaque surfaces for 16S rRNA sequencing. Statistical analyses included repeated Measures ANOVA for pH, Kruskal-Wallis test for alpha diversity, PERMANOVA for beta diversity, and two-way ANOVA for microbial composition.<br><br>RESULTS: In Group PETG, salivary pH significantly decreased from T0 to T4 (p&#x2009;<&#x2009;0.05). No significant changes in alpha or beta microbiota diversity were observed in either group. Microbial shifts in supragingival plaque microbiomes were detected at T8 in Group PETG, while in Group TPU, these changes became evident between T12 and T24. In aligner microbiomes, Group TPU showed significant reductions in Veillonella, Actinomyces, and Fusobacterium at T24 (p&#x2009;<&#x2009;0.05). In contrast, Group PETG exhibited significant increases in Streptococcus from T4 to T24 (p&#x2009;<&#x2009;0.05) and Fusobacterium from T0 to T4 (p&#x2009;<&#x2009;0.05), followed by a decline from T4 to T24 (p&#x2009;<&#x2009;0.01).<br><br>CONCLUSIONS: PETG aligners caused significant reductions in salivary pH at T4 and triggered pronounced fluctuations at T8 in supragingival plaque microbiomes. TPU aligners caused a delayed decline in salivary pH between T8 and T12 and drove distinct structural shifts during prolonged wear from T12 to T24.<br><br>CLINICAL RELEVANCE: Material choice based on microbial impact highlights the need for personalized aligner materials and cleaning cycles.},
}
@article {pmid40624250,
year = {2025},
author = {Fukuda, T and Takagaki, M and Kaimori, J and Motooka, D and Nakamura, S and Kawabata, S and Nakamura, H and Ozaki, T and Nakagawa, R and Matsumura, T and Teranishi, K and Yamazaki, H and Isaka, Y and Kishima, H},
title = {Differences in gut microbiome between autosomal dominant polycystic kidney disease with and without intracranial aneurysms.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {24204},
pmid = {40624250},
issn = {2045-2322},
support = {22K09282//Japan Society for the Promotion of Science/ ; 21K09072//Japan Society for the Promotion of Science/ ; },
mesh = {Humans ; *Polycystic Kidney, Autosomal Dominant/microbiology/complications ; *Gastrointestinal Microbiome ; *Intracranial Aneurysm/microbiology/complications ; Female ; Male ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Adult ; Feces/microbiology ; Aged ; Bacteria/genetics/classification/isolation &amp; purification ; },
abstract = {Autosomal dominant polycystic kidney disease (ADPKD) is a genetic disorder characterized by cyst formation in the kidneys, and is associated with an elevated risk of intracranial aneurysms (IAs). Although a family history is a recognized risk factor for IAs in patients with ADPKD, emerging research suggests that gut microbiome composition may influence IA development. We investigated the relationship between the gut microbiome and the development of IA in patients with ADPKD. We recruited patients with ADPKD with (IA group) and without (non-IA group) IA from Osaka University between October 2021 and December 2023. Fecal samples were analyzed using 16S rRNA sequencing. Data were processed using the QIIME 2 pipeline to determine microbial diversity and composition. We included 60 patients: 26 in the IA and 34 in the non-IA groups. There were significant differences in microbial beta diversity between the groups. The IA group had higher abundances of Eubacterium siraeum group, Oscillibacter, Fournierella, Negativibacillus, Colidextribacter, and Adlercreutzia. The non-IA group had higher abundances of Bifidobacterium, Megamonas, Acidaminococcus, Megasphaera, and Merdibacter. There was a significant association between the gut microbiome composition and the presence of IAs in patients with ADPKD. Specific bacterial taxa were differentially abundant between patients with ADPKD with and without IAs, suggesting a potential role of the gut microbiome in the pathogenesis of IAs in this genetically predisposed population.},
}
@article {pmid40624247,
year = {2025},
author = {Lin, YT and Sayols-Baixeras, S and Baldanzi, G and Dekkers, KF and Hammar, U and Nguyen, D and Nielsen, N and Eklund, AC and Varotsis, G and Holm, JB and Nielsen, HB and Lind, L and Bergström, G and Smith, JG and Engström, G and Ärnlöv, J and Sundström, J and Orho-Melander, M and Fall, T},
title = {The association between the gut microbiome and 24-h blood pressure measurements in the SCAPIS study.},
journal = {Communications medicine},
volume = {5},
number = {1},
pages = {276},
pmid = {40624247},
issn = {2730-664X},
support = {ERC-STG-2018-801965, ERC-CoG-2014-649021, ERC-STG-2015-679242//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 2019-01471; 2018-02784; 2018-02837; 2021-03291//Vetenskapsr&#xe5;det (Swedish Research Council)/ ; 2023-0687; 20200711 (M.O-M.); 20180343, 20210357; 20200173; 20190526//Hj&#xe4;rt-Lungfonden (Swedish Heart-Lung Foundation)/ ; NNF20OC0063886//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; LUDC-IRC 15-0067//Stiftelsen f&#xf6;r&#xa0;Strategisk Forskning (Swedish Foundation for Strategic Research)/ ; },
abstract = {BACKGROUND: There is mounting evidence supporting the role of the microbiota in hypertension from experimental studies and population-based studies. We aimed to investigate the relationship between specific characteristics of the gut microbiome and 24-h ambulatory blood pressure measurements.<br><br>METHODS: The association of gut microbial species and microbial functions, determined by shotgun metagenomic sequencing of fecal samples, with 24-h ambulatory blood pressure measurements in 3695 participants and office blood pressure was assessed in multivariable-adjusted models in 2770 participants without antihypertensive medication from the Swedish CArdioPulmonary bioImage Study.<br><br>RESULTS: Gut microbiome alpha diversity was negatively associated with diastolic blood pressure variability. Additionally, four microbial species were associated with at least one of the 24-h blood pressure traits. Streptococcus sp001556435 was associated with higher systolic blood pressure, Intestinimonas massiliensis and Dysosmobacter sp001916835 with lower systolic blood pressure, Dysosmobacter sp001916835 with lower diastolic blood pressure, and ER4 sp900317525 with lower systolic blood pressure variability. Moreover, office blood pressure data from a subsample without ambulatory blood pressure measurements replicated the association of Intestinimonas massiliensis with systolic blood pressure and Dysosmobacter sp001916835 with diastolic blood pressure. Species associated with 24-h blood pressure were linked to a similar pattern of metabolites.<br><br>CONCLUSIONS: In this large cross-sectional analysis, gut microbiome alpha diversity negatively associates with diastolic blood pressure variability, and four gut microbial species associate with 24-h blood pressure traits.},
}
@article {pmid40624229,
year = {2025},
author = {Lau, HC and Zhang, X and Yu, J},
title = {Gut microbiome in metabolic dysfunction-associated steatotic liver disease and associated hepatocellular carcinoma.},
journal = {Nature reviews. Gastroenterology &amp; hepatology},
volume = {},
number = {},
pages = {},
pmid = {40624229},
issn = {1759-5053},
abstract = {Metabolic dysfunction-associated steatotic liver disease (MASLD) is the most prevalent chronic liver disease worldwide, affecting billions of the global population. It can gradually progress to more severe diseases, including steatohepatitis, cirrhosis and hepatocellular carcinoma. Studies have highlighted the importance of the gut microbiome in the pathogenesis and progression of MASLD. On the other hand, increasing evidence has revealed the clinical potential of targeting the gut microbiome to treat MASLD. In this Review, we summarize gut microbial alterations in MASLD, metabolic dysfunction-associated steatohepatitis and hepatocellular carcinoma. The mechanisms by which a dysregulated gut-liver axis contributes to disease progression are also described, including intestinal barrier dysfunction, chronic inflammation, and altered metabolic pathways (for example, bile acids) and microbial-derived metabolites (for example, short-chain fatty acids, tryptophan derivatives and endogenous ethanol). In addition, we discuss the clinical implications of utilizing the gut microbiome as a diagnostic biomarker and the therapeutic approaches to treat MASLD and related diseases such as faecal microbiota transplantation, probiotics and engineered bacteria, prebiotics and postbiotics, microbial-derived metabolites, antimicrobials and bacteriophages. Finally, we discuss current challenges in basic and translational research on the microbiome in MASLD and propose future directions to drive progress in this field.},
}
@article {pmid40624207,
year = {2025},
author = {Liu, J and Ye, Z and Zhang, Y and You, S and Sun, S and Lu, L and Su, W and Liu, J and Pu, J and Pan, H and Zhu, H and Deng, K and Yao, Y and Hu, X and Zhang, S},
title = {Multi-omics study reveals gut microbiota dysbiosis and tryptophan metabolism alterations in GH-PitNET progression.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {24261},
pmid = {40624207},
issn = {2045-2322},
support = {pumch201911867//Youth Science Foundation of Peking Union Medical College Hospital/ ; 2022-PUMCH-B-114 and 2022-PUMCH-A-026//National High Level Hospital Clinical Research Funding/ ; 2022-PUMCH-B-114 and 2022-PUMCH-A-026//National High Level Hospital Clinical Research Funding/ ; 82270405//Chinese Natural Science Foundation/ ; 20220484031//Beijing Nova Program/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Dysbiosis/microbiology/metabolism ; *Tryptophan/metabolism ; Male ; Female ; Adult ; Metabolomics/methods ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Disease Progression ; Feces/microbiology ; *Neuroendocrine Tumors/metabolism/microbiology/pathology ; *Growth Hormone-Secreting Pituitary Adenoma/metabolism/microbiology/pathology ; Case-Control Studies ; Multiomics ; Indoleacetic Acids ; },
abstract = {Growth hormone-secreting pituitary neuroendocrine tumors (GH-PitNETs) arise from the anterior pituitary gland and constitute 20-30% of all PitNETs, representing a significant subset of functional pituitary tumors. Despite their prevalence, the precise mechanisms underlying the development of these tumors remain elusive due to the complex pathophysiology of pituitary neoplasia. To investigate the potential role of the gut microbiome in GH-PitNETs, we conducted a comprehensive study involving 16S rRNA gene sequencing and metabolomics analysis of fecal and serum samples from 20 GH-PitNET patients and 30 healthy controls at Peking Union Medical College Hospital. Our findings revealed a distinct gut microbiota profile in GH-PitNET patients compared to healthy individuals, characterized by dysbiosis with increased abundance of Bacteroides and decreased abundance of Blautia and Bifidobacterium. Notably, alterations in specific bacterial taxa, including Intestinibacter bartlettii, Fusicatenibacter faecihominis, and Massilioclostridium, were observed in GH-PitNET patients. Concomitantly, serum metabolomics analysis identified 154 differentially abundant metabolites in GH-PitNET patients, with significant enrichment in pathways related to tryptophan metabolism. Among these metabolites, 3-indoleacetic acid (IAA) exhibited a obvious change, suggesting its potential research value for disease processing of GH-PitNETs. To further elucidate the mechanistic link between the gut microbiome and GH-PitNETs, we conducted in vitro and in vivo experiments, our results demonstrated that IAA could promote the proliferation of GH3 cells and significantly enhance growth hormone secretion by activating the cAMP pathway. These findings collectively suggest that gut microbiota dysbiosis may contribute to in the development and progression of GH-PitNETs by contributing to metabolic disturbances.},
}
@article {pmid40624115,
year = {2025},
author = {Liu, L and Wei, L and Mou, FX and Zhang, W and Wang, RF and Wang, Q and Wang, F},
title = {Oral microbiome dysbiosis in women with a history of pregnancy loss: a metagenomic cross-sectional study.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {24242},
pmid = {40624115},
issn = {2045-2322},
support = {Grant No. YJS-BD-19//the Special Fund for Doctoral Student Training of The Second Hospital of Lanzhou University in 2019/ ; Grant No. 071100107//The Science Foundation of Lanzhou University/ ; },
mesh = {Humans ; Female ; *Dysbiosis/microbiology ; Pregnancy ; Adult ; Cross-Sectional Studies ; Metagenomics/methods ; *Microbiota/genetics ; *Abortion, Spontaneous/microbiology ; Mouth Mucosa/microbiology ; Metagenome ; *Mouth/microbiology ; Young Adult ; },
abstract = {Pregnancy loss is a prevalent condition among women of reproductive age, significantly affecting fertility and psychological well-being. Despite advances in understanding the etiology of pregnancy loss, the role of the oral microbiome-its composition and metabolic activity-in influencing pregnancy outcomes remains underexplored. Previous studies have suggested that imbalances in the microbiota may contribute to adverse health outcomes, but few have investigated its association with pregnancy loss specifically. A total of 182 women of childbearing age were recruited for this study and divided into two groups: those with a history of pregnancy loss (n = 70) and a control group with no history of adverse pregnancy outcomes (n = 112). Clinical data and buccal mucosa samples were collected for metagenomic analysis. The inclusion of participants was based on their reproductive history, with particular attention to selecting women with at least one confirmed pregnancy loss and those with at least one successful live birth to serve as controls. The oral microbiota of women in the pregnancy loss group exhibited significantly lower richness and diversity compared to the control group (p < 0.05). Notably, specific genera such as Faecalibacterium, Roseburia, and Bacteroides were positively correlated with pregnancy loss, whereas Pseudomonas and Leptotrichia were correlated with it. These findings suggest a potential microbial dysbiosis associated with pregnancy loss. Our study identifies significant oral microbiota dysbiosis in women with pregnancy loss, characterized by reduced diversity and altered metabolic pathways. These findings underscore the potential role of oral microbial imbalance in adverse pregnancy outcomes. While our cross-sectional design and sample heterogeneity limit causal inference, they highlight the need for longitudinal cohorts and mechanistic studies. Future research integrating multi-niche microbiome profiling (e.g., gut and vaginal microbiota) is essential to unravel systemic interactions and advance targeted interventions for reproductive health.},
}
@article {pmid40624095,
year = {2025},
author = {Pellowe, SD and Zhang, A and Bignell, DRD and Peña-Castillo, L and Walsh, CJ},
title = {Gut microbiota composition is related to anxiety and aggression scores in companion dogs.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {24336},
pmid = {40624095},
issn = {2045-2322},
support = {20220468//MITACS eAccelerate Program/ ; 20201328//Seed, Bridge &amp; Multidisciplinary Fund, Memorial University of Newfoundland, Canada/ ; },
mesh = {Animals ; Dogs ; *Gastrointestinal Microbiome ; *Aggression ; *Anxiety/microbiology ; *Pets/microbiology ; Behavior, Animal ; Male ; Feces/microbiology ; Female ; },
abstract = {There is mounting evidence for a link between behaviour and the gut microbiome in animal and human health. However, the role of the gut microbiome in the development and severity of behavioural issues in companion dogs is not yet fully understood. Here, we investigated the relationship between gut microbiota composition and aggression or anxiety in pet dogs. Dogs were assigned to higher or lower anxiety and aggression groups based on their owner's responses to the Canine Behavioral Assessment &amp; Research Questionnaire (C-BARQ). Then, the gut microbiota composition of each animal, sequenced from microbial DNA extracted from fecal samples, was assessed for association with the dog's assigned behavioural group using multiple approaches. While minimal differences in relative abundance were seen between behavioural groups, machine-learning and compositional balance models could predict behavioural group based on gut microbiota composition. The genus Blautia was identified consistently across analyses, suggesting a link between this genus and anxiety in pet dogs. This study provides insight into specific bacteria that are linked to increased anxiety and aggression in pet dogs. Further research is required to identify bacteria to the species level, and to better understand the specific role of Blautia in the canine gut-brain axis.},
}
@article {pmid40624071,
year = {2025},
author = {Lee, YQ and Choi, YM and Park, SY and Kim, SK and Lee, M and Kim, D and Koduru, L and Lakshmanan, M and Jung, S and Kim, MJ and Choe, YH and Lee, DY},
title = {Genome-scale metabolic model-guided systematic framework for designing customized live biotherapeutic products.},
journal = {NPJ systems biology and applications},
volume = {11},
number = {1},
pages = {73},
pmid = {40624071},
issn = {2056-7189},
support = {32136-05-1-HD050//Korea Institute of Planning and Evaluation for Technology in Food, Agriculture, Forestry and Fisheries/ ; 32136-05-1-HD050//Korea Institute of Planning and Evaluation for Technology in Food, Agriculture, Forestry and Fisheries/ ; 2021-DD-UP-0369//Ministry of Science and ICT, South Korea/ ; RS-2024-00351458//Ministry of Science and ICT, South Korea/ ; 2021-DD-UP-0369//Ministry of Science and ICT, South Korea/ ; },
mesh = {Humans ; *Biological Products ; Models, Biological ; Microbiota/genetics ; Precision Medicine/methods ; },
abstract = {For the successful development of live biotherapeutic products (LBPs), which are promising microbiome-based therapeutics, it is required to rigorously evaluate their quality, safety, and efficacy. To this end, we present a model-guided framework where genome-scale metabolic models (GEMs) can be exploited for characterizing LBP candidate strains and their metabolic interactions with adjacent microbiome and host cells at a systems level. In this perspective, we outline a GEM-based strategy for screening, assessment, and design of personalized multi-strain LBPs.},
}
@article {pmid40624015,
year = {2025},
author = {Wang, C and Zhang, L and Kan, C and He, J and Liang, W and Xia, R and Zhu, L and Yang, J and Jiang, X and Ma, W and Liang, Z and Xiao, Z and Zhang, J and Zhong, J and Sun, X and Chang, D and Wang, Z and Zhang, G and Li, M},
title = {Benefits and challenges of host depletion methods in profiling the upper and lower respiratory microbiome.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {130},
pmid = {40624015},
issn = {2055-5008},
support = {Z211100002121135//Beijing Nova Program/ ; 32100098//National Natural Science Foundation of China/ ; 2021097//Youth Innovation Promotion Association of the Chinese Academy of Sciences/ ; KCXFZ20211020163545004//Shenzhen Scientific and Technological Foundation/ ; SZZYSM202311009//Sanming Project of Medicine in Shenzen Municipality/ ; 2022YFA1304300//National Key Research and Development Program of China/ ; },
mesh = {Humans ; Bronchoalveolar Lavage Fluid/microbiology ; *Microbiota/genetics ; *Metagenomics/methods ; *Bacteria/genetics/classification/isolation &amp; purification ; *Respiratory Tract Infections/microbiology/diagnosis ; Oropharynx/microbiology ; *Respiratory System/microbiology ; },
abstract = {Metagenomic sequencing for respiratory pathogen detection faces two challenges: efficient host DNA depletion and the representativeness of upper respiratory samples for lower tract infections. In this study, we benchmarked seven host depletion methods, including a new method (F_ase), using bronchoalveolar lavage fluid (BALF), oropharyngeal swab (OP), and mock samples. All methods significantly increased microbial reads, species richness, genes richness, and genome coverage while reduced bacterial biomass, introduced contamination, and altered microbial abundance. Some commensals and pathogens, including Prevotella spp. and Mycoplasma pneumoniae, were significantly diminished. F_ase demonstrated the most balanced performance. High-resolution microbiomes profiling revealed distinct microbial niche preferences and microbiome disparities between the upper and lower respiratory tract. In pneumonia patients, 16.7% of high-abundance species (>1%) in BALF were underrepresented (<0.1%) in OP, highlighting OP's limitations as lower respiratory proxies. This study underscores both the potential and challenges of metagenomic sequencing in advancing microbial ecology and clinical research.},
}
@article {pmid40623969,
year = {2025},
author = {Kobel, CM and Leu, A and Vera-Ponce de León, A and Øyås, O and Lai, W and Altshuler, I and Hagen, LH and Wollenberg, RD and Søndergaard, MT and Bakshani, CR and Willats, WGT and Nicoll, L and McIlroy, SJ and Hvidsten, TR and Schmidt, O and Greening, C and Tyson, GW and Roehe, R and Aho, VTE and Pope, PB},
title = {Protozoal populations drive system-wide variation in the rumen microbiome.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {6238},
pmid = {40623969},
issn = {2041-1723},
support = {0054575-SuPAcow//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; No.101000213//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; FT230100560//Department of Education and Training | Australian Research Council (ARC)/ ; },
mesh = {Animals ; *Rumen/microbiology/parasitology ; *Gastrointestinal Microbiome ; Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Cattle ; *Microbiota ; },
abstract = {While rapid progress has been made to characterize the bacterial and archaeal populations of the rumen microbiome, insight into how they interact with keystone protozoal species remains elusive. Here, we reveal two distinct system-wide rumen community types (RCT-A and RCT-B) that are not strongly associated with host phenotype nor genotype but instead linked to protozoal community patterns. We leveraged a series of multi-omic datasets to show that the dominant Epidinium spp. in animals with RCT-B employ a plethora of fiber-degrading enzymes that present enriched Prevotella spp. a favorable carbon landscape to forage upon. Conversely, animals with RCT-A, dominated by genera Isotricha and Entodinium, harbor a more even distribution of fiber, protein, and amino acid metabolizers, reflected by higher detection of metabolites from both protozoal and bacterial activity. Our results indicate that microbiome variation across key protozoal and bacterial populations is interlinked, which should act as an important consideration for future development of microbiome-based technologies.},
}
@article {pmid40623769,
year = {2025},
author = {Basoya, R and Singh, B and Basi, A and Aggarwal, S},
title = {Role of microbiome in cancer progression.},
journal = {International review of cell and molecular biology},
volume = {394},
number = {},
pages = {79-106},
doi = {10.1016/bs.ircmb.2024.12.013},
pmid = {40623769},
issn = {1937-6448},
mesh = {Humans ; *Neoplasms/microbiology/pathology/therapy ; *Disease Progression ; *Microbiota ; Animals ; },
abstract = {The human microbiome plays a crucial role in maintaining health and preventing disease. Dysbiosis, or imbalance, in the microbiome, has been linked to various diseases, including cancer. This chapter explores the influence of microbiomes on different organs, immune system modulation, and cancer development. Specific microorganisms, such as Helicobacter pylori, Escherichia coli, and human papillomavirus (HPV), contribute to gastric, colorectal, and cervical cancer through mechanisms like immunomodulation and proliferative signaling pathways. Dysbiosis-induced cancer progression involves NF-κB, Wnt/β-catenin, and JAK/STAT signaling. Recent studies highlight the microbiome's potential in cancer diagnosis and immunotherapy. Fecal Microbiota Transplantation (FMT) and predictive biomarkers, such as Porphyromonas gingivalis and Escherichia-Shigella, show promise in treating colorectal cancer. The microbiome influences tumor biology and immune response, affecting immunotherapeutic efficacy. Understanding microbiome-cancer interactions offers new opportunities for improved diagnosis and personalized therapy. This chapter provides comprehensive insights into the role of microbiome in cancer progression, emphasizing the importance of microbiome research in developing effective cancer treatments.},
}
@article {pmid40623767,
year = {2025},
author = {Abdel-Wahab, R and Kerr, TD and McGrail, DJ and Diab, A and Bentebibel, SE},
title = {The role of microbiome in CAR-T cell therapy.},
journal = {International review of cell and molecular biology},
volume = {394},
number = {},
pages = {197-212},
doi = {10.1016/bs.ircmb.2024.12.015},
pmid = {40623767},
issn = {1937-6448},
mesh = {Humans ; *Immunotherapy, Adoptive/methods ; Animals ; *Receptors, Chimeric Antigen/metabolism/immunology ; *Microbiota/immunology ; *Gastrointestinal Microbiome/immunology ; *Neoplasms/therapy/immunology/microbiology ; },
abstract = {Chimeric Antigen Receptor (CAR) T-cell therapy represents a significant advancement in treating hematologic malignancies. However, its therapeutic efficacy against solid tumors remains hindered by several challenges, including suboptimal antitumor activity, high toxicity, and the emergence of resistance mechanisms. In recent years, the microbiome has emerged as a critical modulator of cancer immunotherapy outcomes. Yet, the precise molecular and cellular pathways through which the microbiome influences CAR-T cell efficacy remain largely unexplored. This chapter provides a comprehensive review of current knowledge regarding the interactions between CAR-T cell therapy and the microbiome, with particular emphasis on gut microbial dynamics. Additionally, it underscores the existing gaps in our understanding of these interactions and highlights key preclinical and clinical findings. We also discuss innovative strategies aimed at manipulating the microbiome to enhance CAR-T cell function, thereby presenting potential avenues for optimizing therapeutic outcomes.},
}
@article {pmid40623766,
year = {2025},
author = {Karimi, N and De Anda, AB and Yang, R and Aksan, E and Grimaldo, MT and Moghaddam, SJ},
title = {The multipotential effect of microbiome in lung cancer development and progression.},
journal = {International review of cell and molecular biology},
volume = {394},
number = {},
pages = {171-196},
doi = {10.1016/bs.ircmb.2024.12.011},
pmid = {40623766},
issn = {1937-6448},
mesh = {Humans ; *Lung Neoplasms/microbiology/pathology/therapy ; *Disease Progression ; Animals ; *Microbiota ; *Gastrointestinal Microbiome ; },
abstract = {Lung cancer is the leading cause of cancer-related deaths worldwide. Despite the introduction of numerous drugs to cure this deadly disease, treatment outcomes differ significantly among patients. This differential response has drawn attention to individual patient characteristics, particularly the microbiome. In recent years, the microbiome has garnered significant interest from scientists in various fields including autoimmune, inflammatory, and cancer research. These studies have primarily focused on the composition and diversity of the gut microbiome, pointing out its fundamental effect on the development and progression of diseases such as asthma, chronic obstructive pulmonary disease (COPD), cystic fibrosis, and lung cancer. Recent findings have also highlighted the impact of the gut microbiome on the efficacy of immunotherapy in lung cancer patients. In this chapter, we will delve into the multifaceted role of microbiome in lung cancer prevention, progression, and treatment outcome.},
}
@article {pmid40623765,
year = {2025},
author = {Vig, M and Dubey, S},
title = {Gut microbiome and tumor immunotherapy.},
journal = {International review of cell and molecular biology},
volume = {394},
number = {},
pages = {147-170},
doi = {10.1016/bs.ircmb.2024.12.014},
pmid = {40623765},
issn = {1937-6448},
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; *Neoplasms/therapy/immunology/microbiology ; *Immunotherapy/methods ; Animals ; },
abstract = {Multiple innovative molecular techniques have established compelling connections between the gut microbiome and cancers. Studies have also revealed that the microbiome and microbiome-specific metabolites can significantly influence cancer treatments like chemotherapy, radiotherapy, and immunotherapy. Advancements in cancer immunotherapy driven by a targeted immune system approach have considerably improved the treatment landscape in cancer. However, the full potential of tumor immunotherapy remains to be explored, and many challenges need to be addressed. This review provides a summary of the current evidence regarding the presence of microbiota and how it can impact the response to Food and Drug Administration (FDA) approved cancer immunotherapies, such as immune checkpoint inhibitors (ICIs) or chimeric antigen receptor T (CAR-T) cell therapy. Additionally, it addresses the challenges and limitations of gut microbiome and cancer immunotherapy.},
}
@article {pmid40623764,
year = {2025},
author = {Richards, J and Davis, EL and Shakila, L and Narayanan, J and Aggarwal, S and Mishra, A and Venkata, KKM and Walther, BK and Dominic, A},
title = {Microbiome-mediated immune modulation in tumor microenvironment.},
journal = {International review of cell and molecular biology},
volume = {394},
number = {},
pages = {107-145},
doi = {10.1016/bs.ircmb.2024.12.012},
pmid = {40623764},
issn = {1937-6448},
mesh = {Humans ; *Tumor Microenvironment/immunology ; *Neoplasms/immunology/microbiology/pathology ; *Microbiota/immunology ; Animals ; },
abstract = {This chapter explores the complex interplay between the tumor microenvironment (TME), the microbiome, and the immune system. It focuses on how microbes and their metabolites influence tumor development, progression, and the subsequent immune responses. The TME is a highly complex environment made up of cancer cells, immune cells, and the extracellular matrix, where immune cells can either inhibit or promote tumor growth depending on the context. The chapter highlights several key mechanisms of interaction, including microbial metabolites, the presentation of microbial antigens by tumor or immune cells, and the role of immune checkpoints, such as PD-L1, in modulating immune responses. Certain bacteria, viruses, and fungi can trigger immune responses that lead to the destruction of cancer cells, often through processes such as immunogenic cell death (ICD). Conversely, dysbiosis, or an imbalance in microbial communities, can create a pro-tumorigenic environment, aiding in tumor progression through chronic inflammation, immune suppression, and metabolic alterations. The chapter categorizes microbial interactions with cancer into three areas: microbes directly causing cancer (e.g., Epstein-Barr virus and HPV), cancers that induce infections (e.g., obstructing the respiratory or digestive systems), and tumors located in organs with natural microbiomes, such as the gastrointestinal tract. In addition to these mechanisms, the chapter also illuminates how microbial antigens can serve as potential identifiers and tools for cancer diagnosis and treatment, offering new avenues for personalized medicine. The insights gained from this exploration are important for advancing microbial-based therapies and improving the effectiveness of immunotherapies in cancer treatment.},
}
@article {pmid40623763,
year = {2025},
author = {Agrawal, P and Mendhey, P and Kumar, R and Patel, S and Kaushik, PK and Dadsena, A and Kumar, S},
title = {Introduction to microbiomes in health and diseases.},
journal = {International review of cell and molecular biology},
volume = {394},
number = {},
pages = {1-42},
doi = {10.1016/bs.ircmb.2024.12.010},
pmid = {40623763},
issn = {1937-6448},
mesh = {Humans ; *Microbiota ; *Health ; *Disease ; Animals ; },
abstract = {The human microbiome is a complex ecological system of commensal, symbiotic, and pathogenic microorganisms that plays a crucial role in human health and disease. The microbiome includes both the living microorganisms also called microbiota and their synthesized metabolites and structural components. It is distributed to the gastrointestinal tract, skin, respiratory system, and oral cavity, each with a distinct microbial composition. Dysbiosis, or imbalance in the microbiome is linked to numerous diseases such as eczema, gastric ulcers, cardiovascular diseases, and cancer. The axes of microbial activity and their connections to disease, including the gut-skin, gut-lung, gut-brain, and gut-kidney play a crucial role in health and disease conditions. Also, the role of the microbiome in cancer development and response to therapy is examined. This book chapter underscores the importance of maintaining a balanced microbiome for overall health and the potential for microbiome-based interventions in disease prevention and treatment.},
}
@article {pmid40623407,
year = {2025},
author = {Leti, M and Garidou, L and Cuisiat, SV and Stennevin, A and Doat, G and Mias, C},
title = {Plant Extracts in Acne Management: a narrative review.},
journal = {Dermatology (Basel, Switzerland)},
volume = {},
number = {},
pages = {1-51},
doi = {10.1159/000547149},
pmid = {40623407},
issn = {1421-9832},
abstract = {BACKGROUND: Acne is a chronic inflammatory skin disease associated with impaired pilosebaceous unit function leading to the development of noninflammatory and inflammatory lesions and, in some cases, persistent post-inflammatory erythema, hyperpigmentation and scarring. Acne pathophysiology is complex, involving altered sebum production and composition, abnormal keratinization, microbiome dysbiosis, and skin inflammation. Conventional therapies, such as topical retinoids, antibiotics and benzoyl peroxide, are the first-line treatments for mild-to-moderate acne, but antibiotic resistance and local adverse effects can have a negative impact on therapeutic outcomes, leading to a growing interest in alternative strategies for disease management. The use of dermocosmetics is increasingly being recognized as a useful strategy to improve treatment outcomes and patient adherence. In particular, there has been a recent increase in research aiming to identify natural plant-based ingredients with properties that target the multiple pathogenic mechanisms involved in acne, but which have less impact on skin barrier function.<br><br>SUMMARY: This review provides a summary of the anti-acne properties of the most well-characterized plant extracts and phytocompounds used in dermocosmetic anti-acne products, based on insights gained from in vitro, ex vivo and in vivo studies. Evidence gained from clinical trials evaluating the effectiveness and safety of topical formulations containing these herbal ingredients is also presented. Finally, several less well-characterized herbal extracts and phytocompounds with promising anti-acne properties are described.<br><br>KEY MESSAGES: Although research is ongoing for many of the anti-acne herbal ingredients identified so far, this review highlights the effectiveness of topical plant-based formulations for reducing lesion counts and disease severity in acne patients, as well as the rebalancing effects of herbal ingredients on sebum composition, microbial diversity, and pilosebaceous unit cell differentiation. Taken together with the antibiofilm, anti-inflammatory, antioxidant, and skin barrier repair properties demonstrated for many of these extracts, current evidence suggests that dermocosmetics with plant-based ingredients show great promise for acne management, either as monotherapies, maintenance treatments, or in combination with conventional drugs.},
}
@article {pmid40622960,
year = {2025},
author = {Farda, B and Pellegrini, M and Coppari, L and Cacchio, P and Lunghi, E},
title = {Isolation and Identification of Bacterial Strains from Skin of Terrestrial Amphibians.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {220},
pages = {},
doi = {10.3791/67862},
pmid = {40622960},
issn = {1940-087X},
mesh = {Animals ; *Skin/microbiology ; *Bacteria/isolation &amp; purification/classification ; *Amphibians/microbiology ; *Bacteriological Techniques/methods ; Microbiota ; },
abstract = {The microbiota is a vital element of higher organisms, with the cutaneous microbiota significantly contributing to the organism's defense against external agents. There is no standard method to sample Speleomantes (Amphibia: Plethodontidae) skin microbial communities for the microbial culturing approach. To address this, we have developed a practical protocol for isolating bacteria from the skin of individuals and a best practice for handling and storing samples. The steps are straightforward: swabs are stored in a physiological saline solution supplemented with glycerol upon sampling. Once transferred in the laboratory, swabs can be stored at +4 °C for a maximum of 10 days to ensure the integrity of the microbial community. This study offers interesting insights into the cutaneous microbiota investigation of terrestrial amphibian species, such as those belonging to the genus Speleomantes. This approach contributes to implementing, monitoring and conserving measures for endangered species and might improve the knowledge of microbiota's function in the health and ecology of amphibians. This protocol may also have broader significance for microbiome research in many wildlife conservation scenarios.},
}
@article {pmid40622660,
year = {2025},
author = {Kong, L and Zhu, B and Zhuang, Y and Lai, J and Hu, S},
title = {Viewing Psychiatric Disorders Through Viruses: Simple Architecture, Burgeoning Implications.},
journal = {Neuroscience bulletin},
volume = {},
number = {},
pages = {},
pmid = {40622660},
issn = {1995-8218},
abstract = {A growing interest in the comprehensive pathogenic mechanisms of psychiatric disorders from the perspective of the microbiome has been witnessed in recent decades; the intrinsic link between microbiota and brain function through the microbiota-gut-brain axis or other pathways has gradually been realized. However, little research has focused on viruses-entities characterized by smaller dimensions, simpler structures, greater diversity, and more intricate interactions with their surrounding milieu compared to bacteria. To date, alterations in several populations of bacteriophages and viruses have been documented in both mouse models and patients with psychiatric disorders, including schizophrenia, major depressive disorder, autism spectrum disorder, and Alzheimer's disease, accompanied by metabolic disruptions that may directly or indirectly impact brain function. In addition, eukaryotic virus infection-mediated brain dysfunction provides insights into the psychiatric pathology involving viruses. Efforts towards virus-based diagnostic and therapeutic approaches have primarily been documented. However, limitations due to the lack of large-scale cohort studies, reliability, clinical applicability, and the unclear role of viruses in microbiota interactions pose a challenge for future studies. Nevertheless, it is conceivable that investigations into viruses herald a new era in the field of precise psychiatry.},
}
@article {pmid40622649,
year = {2025},
author = {G R, SK and V, M},
title = {Scaling Up Postbiotics Production: A Prospective Review of Processes and Health Benefits.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {40622649},
issn = {1867-1314},
abstract = {Postbiotics are bioactive compounds produced by probiotic bacteria that have taken the spotlight for their significant health benefits. These postbiotics include digestive enzymes, short-chain fatty acids, cell wall components, bacteriocins, exopolysaccharides, and vitamins. Among many health benefits, postbiotics possess immunomodulatory effect; cholesterol regulation; antimicrobial, antioxidant, and anti-inflammatory properties; enhanced gut health; and reduced risk of cardiovascular diseases, although the mechanism of action of these health benefits is yet to be fully understood. Forecast indicates a rising industrial demand for postbiotic production. This review summarizes the tools and techniques employed in optimizing postbiotic production that aid in overcoming those challenges that currently interrupt industrial scale-up. Plackett-Burman design, response surface methodology (RSM), Taguchi method, and central composite design (CCD) are significant tools for optimizing postbiotic production conditions. Molecular techniques including genetic engineering, synthetic biology tools such as CRISPR-Cas9, and metabolic engineering are potential techniques to enhance postbiotic production. Despite these advancements, challenges remain in industrial scale-up (stability, quality, yield, and consistency). Understanding the correlation between high cell density and postbiotic yield is crucial for industrial scale-up and optimized production. However, further in-depth research is in demand for industrial production of postbiotics. This review would benefit researchers exploring the mechanism of action and industrial production of postbiotics.},
}
@article {pmid40622577,
year = {2025},
author = {Holle, J and Behrens, F and Koppe, L},
title = {Pediatric and adult point of view on the gut-kidney axis in CKD.},
journal = {Pediatric nephrology (Berlin, Germany)},
volume = {},
number = {},
pages = {},
pmid = {40622577},
issn = {1432-198X},
abstract = {Chronic non-communicable diseases pose a significant global health challenge, with the human gut microbiota emerging as a key player in several (patho) physiological functions, including immunity, metabolic homeostasis, and inflammation. While dysbiosis, or imbalance in taxonomy and function of gut microbiota, has been implicated in chronic kidney disease (CKD), whether it is a cause or consequence of the disease remains controversial. Understanding the gut microbiota's role in CKD pathogenesis is essential for developing novel therapeutic interventions. CKD in children presents unique opportunities for studying disease-specific mechanisms due to the absence of comorbidities typically seen in adults, such as diabetes, obesity, and hypertension, although few studies exist. On the other hand, unlike the relatively stable gut microbiota of healthy adults, the infant's microbiome undergoes significant development and maturation during the early years of life. Integrating knowledge from both pediatric and adult populations may provide a comprehensive understanding of gut microbiota dysbiosis in CKD. This review aims to provide an overview of the gut microbiota's development in healthy individuals and CKD patients and discusses how these findings can inform personalized treatment approaches to CKD.},
}
@article {pmid40622440,
year = {2025},
author = {Woltsche, J and Pacher-Deutsch, C and Fürst, S and Gulden, L and Schwarzl, J and Feldbacher, N and Nepel, M and Celcer, L and Hasl, N and Rieper, V and Stadlbauer, V and Horvath, A},
title = {Microbial Dysbiosis in the Urinary Microbiome of Patients with Cirrhosis.},
journal = {The American journal of gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.14309/ajg.0000000000003634},
pmid = {40622440},
issn = {1572-0241},
abstract = {INTRODUCTION: Cirrhosis is associated with microbiome alterations beyond the gut, including skin, saliva, and serum. This study investigated the urinary microbiome (UMB) in patients with cirrhosis, who have an increased risk of urinary tract infections (UTIs).<br><br>METHODS: Midstream urine from 137 patients was analysed via 16S rRNA sequencing; 68 patients with cirrhosis and 32 non-cirrhotic controls met inclusion criteria.<br><br>RESULTS: Patients with cirrhosis showed significantly reduced alpha-diversity. The UMB of controls was enriched in Streptococcus species.<br><br>DISCUSSION: Reduced microbial diversity and lower Streptococcus abundance in patients with cirrhosis might help to explain their heightened susceptibility to UTIs.},
}
@article {pmid39386636,
year = {2025},
author = {Boyd, AI and Kafer, LA and Escapa, IF and Kambal, A and Tariq, H and Hilsenbeck, SG and Nguyen-Phuc, H and Rajan, A and Lensmire, JM and Patras, KA and Piedra, PA and Blutt, SE and Lemon, KP},
title = {Nasal microbionts differentially colonize and elicit cytokines in human nasal epithelial organoids.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.09.25.614934},
pmid = {39386636},
issn = {2692-8205},
support = {U19 AI144297/AI/NIAID NIH HHS/United States ; U19 AI116497/AI/NIAID NIH HHS/United States ; P30 DK056338/DK/NIDDK NIH HHS/United States ; U19 AI157981/AI/NIAID NIH HHS/United States ; P30 ES030285/ES/NIEHS NIH HHS/United States ; P30 CA125123/CA/NCI NIH HHS/United States ; },
abstract = {UNLABELLED: Nasal colonization by Staphylococcus aureus or Streptococcus pneumoniae is associated with an increased risk of infection by these pathobionts, whereas nasal colonization by Dolosigranulum species is associated with health. H uman n asal epithelial o rganoids (HNOs) physiologically recapitulate human nasal respiratory epithelium with a robust mucociliary blanket. We reproducibly monocolonized HNOs with these three bacteria for up to 48 hours with varying kinetics across species. HNOs tolerated bacterial monocolonization with localization of bacteria to the mucus layer and with minimal cytotoxicity compared to uncolonized HNOs. Human nasal epithelium exhibited both species-specific and general cytokine responses, without induction of type I interferons, consistent with colonization rather than infection. Only live S. aureus colonization robustly induced IL-1 family cytokines, suggestive of inflammasome signaling. D. pigrum and live S. aureus decreased CXCL10, whereas S. pneumoniae increased CXCL11, chemokines involved in antimicrobial responses to both viruses and bacteria. Overall, HNOs are a compelling model system to reveal host-microbe dynamics at the human nasal mucosa.<br><br>IMPORTANCE: Human nasal microbiota often includes highly pathogenic members, many of which are antimicrobial resistance threats, e.g., methicillin-resistant Staphylococcus aureus and antibiotic-resistant Streptococcus pneumoniae . Preventing colonization by nasal pathobionts decreases infections and transmission. In contrast, nasal microbiome studies identify candidate beneficial bacteria that might resist pathobiont colonization, e.g., Dolosigranulum pigrum . Discovering how these microbionts colonize the human nasal passages and means to reduce pathobiont colonization is limited by previous models. This creates an urgent need for human-based models that exemplify bacterial nasal colonization. We addressed this need by developing human nasal epithelial organoids (HNOs) as a new model system of bacterial nasal colonization. HNOs accurately represent the mucosal surface of the human nasal passages enabling exploration of bacterial-epithelial interactions, which is crucial since the epithelium instigates the initial innate immune response to bacteria. Here, we identified differential epithelial cytokine responses to these three bacteria setting the stage for future research.},
}
@article {pmid40622379,
year = {2025},
author = {Mars Brisbin, M and Acord, M and Davitt, R and Bent, S and Van Mooy, BAS and Flaum, E and Norlin, A and Turner, J and Krinos, A and Alexander, H and Saito, M},
title = {Exploring the Phaeosphere: Characterizing the microbiomes of Phaeocystis antarctica colonies from the coastal Southern Ocean and laboratory culture.},
journal = {Journal of phycology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jpy.70051},
pmid = {40622379},
issn = {1529-8817},
support = {874439//Simons Foundation/ ; OPP-2224611//National Science Foundation/ ; },
abstract = {Interactions between phytoplankton and bacteria play critical roles in shaping marine ecosystems. However, the intricate relationships within these communities-particularly in rapidly changing polar environments-remain poorly understood. We use targeted methods to directly characterize the microbiomes of individual colonies of Phaeocystis antarctica, a keystone phytoplankton species in the Southern Ocean, and showed that colony microbiomes were consistent across individual colonies collected 108 nautical miles apart. These results suggest that hosting specific colony microbiomes is a shared trait across colony-forming Phaeocystis species, with different species hosting colony microbiomes suited to their respective environments. The bacterial orders Alteromonadales, Oceanospirillales, and Sphingomonadales dominated the microbiomes of all field-collected P. antarctica colonies. The relative abundances of bacterial taxa comprising the majority of field-collected colony microbiomes-for example, Paraglaciecola sp. (Alteromonadales) and Nitrincolaceae (Oceanospirillales)-correlated with Phaeocystis abundance in surface waters, highlighting their potential roles in bloom dynamics and carbon cycling. After a year of laboratory culture, we observed a reduction in colony microbiome diversity, and Caulobacterales, Cellvibrionales, and Rhodobacterales dominated the cultured colony microbiomes. Notably, abundant genera in field-collected colony microbiomes that were lost in culture were psychrophiles. The shift in microbiome structure emphasizes the importance of field-based studies to capture the complexity of microbial interactions, especially for species from polar environments that are difficult to replicate in laboratory conditions. This research provides valuable insights into the ecological significance of prokaryotic interactions with a key phytoplankton species and underscores the necessity of considering these dynamics in the context of climate-driven shifts in marine ecosystems.},
}
@article {pmid40622159,
year = {2025},
author = {Hernandez, JB and Hayer, SS and Alvarez, S and Fischer, A and Hassenstab, HR and Cooper, K and Alsafwani, ZW and Benson, AK and Suhr Van Haute, MJ and Izard, J and Song, H-S and Clayton, JB},
title = {Microbiome and metabolome association network analysis identifies Clostridium_sensu_stricto_1 as a stronger keystone genus candidate than Bifidobacterium in the gut of common marmosets.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0021425},
doi = {10.1128/msystems.00214-25},
pmid = {40622159},
issn = {2379-5077},
abstract = {The common marmoset (Callithrix jacchus), a nonhuman primate species, is a model organism of great interest due to its translational value in a variety of research settings, including the field of microbiomics. While the composition of the marmoset's gut microbiome has been somewhat described in captivity, little is known about how gut microbiota interact with each other over time and how they relate to metabolite production. To help answer this, we characterized interactions in the gut microbiome of the common marmoset by calculating the Spearman correlation coefficient between 16S rDNA-derived relative genera abundance data and targeted metabolomics data collected longitudinally from 10 captive marmosets. Association network graphs were used to visualize significant correlations and identify genera and metabolites that have high degree centrality, marking them as more influential within the microbiome. The genus Clostridium_sensu_stricto_1 engaged in the most metabolomic associations, indicating that it potentially plays a gatekeeping role over metabolites involved in microbial growth and signaling. Its associations with downregulated taurine and bile acids further suggest Clostridium_sensu_stricto_1 modifies bile acids to exert its influence. Flavonifractor and several Bacteroidales members had the most bacterial associations and were negatively associated with Bifidobacterium, indicating a potential competitive relationship. To further characterize microbiome interactions, we performed hierarchical clustering on significant within-dataset associations and developed a new "Keystone Candidate Score" metric that identified Clostridium_sensu_stricto_1 and Alloprevotella as the most influential bacteria (so-called candidate keystone genera) in the marmoset gut microbiome.IMPORTANCEPrevious studies have identified significant individuality within the gut microbiome of common marmosets. The reasons for this inter-subject variability and how it relates to health in captivity are poorly understood, owing to a lack of knowledge regarding dynamic interactions between specific microbiota. To that end, this study characterized significant temporal associations between the gut microbiome and metabolome of healthy captive marmosets. Our findings suggest that certain microbial taxa exert a stronger influence within the gut than others. Specifically, Bifidobacterium was the most abundant genus and primary driving force behind subject-specific microbiome differences, while Clostridium_sensu_stricto_1 and bacteria from the order Bacteroidales were the main sources, respectively, for significant bacteria-metabolite and bacteria-bacteria associations. Together, this suggests that Bifidobacterium may compete with the other taxa for resources and a metabolic niche in the marmoset microbiome.},
}
@article {pmid40621937,
year = {2025},
author = {Choi, A and Pia, L and Kaspar, JR},
title = {Seven genome sequences of Rothia spp. isolated from human saliva.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0046525},
doi = {10.1128/mra.00465-25},
pmid = {40621937},
issn = {2576-098X},
abstract = {Rothia are understudied commensal bacteria within the human oral cavity and respiratory tract and can cause opportunistic infections. We report the complete genome sequences of seven Rothia spp. strains isolated from pooled human saliva, including four strains of Rothia mucilaginosa (59.5% GC) and three strains of Rothia dentocariosa (53.8% GC).},
}
@article {pmid40621936,
year = {2025},
author = {Kolar, O and Appleberry, H and Wolfe, AJ and Kula, A and Putonti, C},
title = {Complete genome sequence of vaginal swab isolate Enterococcus faecalis UMB6935B, including two complete plasmids.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0036825},
doi = {10.1128/mra.00368-25},
pmid = {40621936},
issn = {2576-098X},
abstract = {Enterococcus faecalis has been identified as a member of the vaginal community of healthy females, in addition to its association with vaginitis and urinary tract infections. Here we present the hybrid assembly of an E. faecalis strain, UMB6935B, isolated from a vaginal swab from a female with overactive bladder symptoms.},
}
@article {pmid40621926,
year = {2025},
author = {Samson, R and Kumar, S and Dastager, S and Khairnar, K and Dharne, M},
title = {Deciphering the comprehensive microbiome of glacier-fed Ganges and functional aspects: implications for one health.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0172024},
doi = {10.1128/spectrum.01720-24},
pmid = {40621926},
issn = {2165-0497},
abstract = {Glacier-fed rivers are significant ecological components of the river catchments, yet their microbial diversity and the associated antimicrobial potential remain underexplored. The Ganges is a glacier-fed river of immense cultural, religious, and ecological significance that supports over 400 million people downstream, providing essential water for agriculture, industry, and daily use. Despite its importance, the microbial community composition and antimicrobial potential, across its relatively pristine origin, remain largely underexplored. One possible explanation for this could be the lower microbial load in the upstream glacier-fed region, which likely results in a reduced DNA yield, insufficient for whole-metagenome sequencing, in contrast to the more biologically diverse and nutrient-rich lower reaches. In this study, we developed an efficient DNA extraction and amplification method using low-input DNA to sequence the microbiome from sediments of the glacier-fed Ganges River in pre-monsoon and post-monsoon over 2 years. Taxonomic and functional diversity of bacterial and viral (phage) communities were analyzed, together with the seasonal variations in their composition. Significant differences in microbial communities were observed in response to seasonal shifts (P < 0.05). During the dry season, Proteobacteria and Actinobacteria were predominant, while Bacteroidetes and Firmicutes were abundant post-monsoon (P < 0.05). The microbiome harbors potential for the biosynthesis of streptomycin, phenylpropanoid, penicillin, and cephalosporins. Bacteriophages from Podoviridae, Myoviridae, and Siphoviridae showed lytic potential against putrefying and pathogenic bacteria. This first comprehensive study on the glacier-fed Ganges River highlights significant seasonal shifts in microbial diversity. The initial insights into the functional profile of the bacterial and phage diversity offer opportunities to explore various natural compounds and enzymes to tackle antimicrobial resistance under the one-health canopy.IMPORTANCEThis study addresses a knowledge gap by exploring the microbial diversity and antimicrobial potential of the glacier-fed Ganges River across different seasons. The findings reveal various taxa with biosynthetic capabilities for antimicrobial compounds. Additionally, the presence of bacteriophages with lytic potential opens up opportunities for their exploration and application spanning various domains of one health. These findings lay a foundational basis for understanding the unique properties of this riverine ecosystem and offer valuable insights into environmental conservation and the potential to tackle antimicrobial resistance.},
}
@article {pmid40621718,
year = {2025},
author = {Rai, SK and Hu, Y and Ding, M and Hu, FB and Wang, M and Chavarro, JE and McCormick, N and Choi, HK and Sun, Q},
title = {Long-term lignan intake, whole grain foods, and the risk of gout: results from two prospective cohort studies.},
journal = {Arthritis care &amp; research},
volume = {},
number = {},
pages = {},
doi = {10.1002/acr.25596},
pmid = {40621718},
issn = {2151-4658},
abstract = {OBJECTIVE: Multiple plant-based dietary patterns are inversely associated with gout, although the individual constituents driving this association remain unclear. Dietary lignans, a major group of phytoestrogens abundant in plant foods, are metabolized by the gut microflora and may modulate gout risk. We examined the associations between dietary lignan intake, certain whole grain foods rich in lignans, and incident gout.<br><br>METHODS: We analyzed data from 122,680 individuals in the Health Professionals Follow-up Study and Nurses' Health Study. We administered a food frequency questionnaire every 2-4 years. We used Cox models to evaluate associations between dietary lignans, whole grain foods, and confirmed gout.<br><br>RESULTS: Higher intakes of matairesinol (hazard ratio [HR] and 95% confidence interval [CI] comparing extreme quintiles: 0.78 [0.69, 0.90]; P trend=0.002) and secoisolariciresinol (0.78 [0.68, 0.89]; P trend=0.002) were both associated with lower gout risk, while pinoresinol and lariciresinol were not associated with gout. We found inverse associations of whole grain cold breakfast cereals (HR for those consuming &#x2265;1 serving/day 0.62 [0.53, 0.73]), cooked oatmeal/oat bran (HR for those consuming &#x2265;2 servings/week 0.78 [0.70, 0.86]), and bran added to food (HR for those consuming &#x2265;2 servings/week 0.84 [0.74, 0.95]), but not dark breads or other cooked breakfast cereals, with gout.<br><br>CONCLUSION: Higher intakes of matairesinol and secoisolariciresinol, as well as whole grain cold breakfast cereals, oatmeal, and added bran, were each significantly associated with lower gout risk. These findings support adherence to healthful plant-based diets for gout and suggest a potential role of the gut microbiome in gout pathogenesis.},
}
@article {pmid40621717,
year = {2025},
author = {Liu, S and Li, Y and Shi, Y and Rao, Z and Zhang, Y and Zhang, Y and Wang, T and Kong, H and Zhu, S and Zhu, DM and Yu, Y and Zhu, J},
title = {Multi-omics analyses of the gut microbiome, fecal metabolome, and multimodal brain MRI reveal the role of Alistipes and its related metabolites in major depressive disorder.},
journal = {Psychological medicine},
volume = {55},
number = {},
pages = {e190},
doi = {10.1017/S003329172510072X},
pmid = {40621717},
issn = {1469-8978},
support = {82471952//National Natural Science Foundation of China/ ; 82371928//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Depressive Disorder, Major/microbiology/metabolism/diagnostic imaging/physiopathology ; *Gastrointestinal Microbiome/physiology ; Male ; Magnetic Resonance Imaging ; Adult ; *Feces/microbiology/chemistry ; Female ; *Metabolome ; Middle Aged ; *Brain/diagnostic imaging ; Metabolomics ; Case-Control Studies ; *Dysbiosis/microbiology ; Multiomics ; },
abstract = {BACKGROUND: Compelling evidence claims that gut microbial dysbiosis may be causally associated with major depressive disorder (MDD), with a particular focus on Alistipes. However, little is known about the potential microbiota-gut-brain axis mechanisms by which Alistipes exerts its pathogenic effects in MDD.<br><br>METHODS: We collected data from 16S rDNA amplicon sequencing, untargeted metabolomics, and multimodal brain magnetic resonance imaging from 111 MDD patients and 102 healthy controls. We used multistage linked analyses, including group comparisons, correlation analyses, and mediation analyses, to explore the relationships between the gut microbiome (Alistipes), fecal metabolome, brain imaging, and behaviors in MDD.<br><br>RESULTS: Gut microbiome analysis demonstrated that MDD patients had a higher abundance of Alistipes relative to controls. Partial least squares regression revealed that the increased Alistipes was significantly associated with fecal metabolome in MDD, involving a range of metabolites mainly enriched for amino acid, vitamin B, and bile acid metabolism pathways. Correlation analyses showed that the Alistipes-related metabolites were associated with a wide array of brain imaging measures involving gray matter morphology, spontaneous brain function, and white matter integrity, among which the brain functional measures were, in turn, associated with affective symptoms (anxiety and anhedonia) and cognition (sustained attention) in MDD. Of more importance, further mediation analyses identified multiple significant mediation pathways where the brain functional measures in the visual cortex mediated the associations of metabolites with behavioral deficits.<br><br>CONCLUSION: Our findings provide a proof of concept that Alistipes and its related metabolites play a critical role in the pathophysiology of MDD through the microbiota-gut-brain axis.},
}
@article {pmid40621291,
year = {2025},
author = {Mima, Y and Yamamoto, M and Iozumi, K},
title = {Tacrolimus Ophthalmic Suspension Can Be an Effective Treatment Option for Biologic-Induced Refractory Conjunctivitis.},
journal = {Cureus},
volume = {17},
number = {6},
pages = {e85373},
pmid = {40621291},
issn = {2168-8184},
abstract = {Atopic dermatitis (AD) is a chronic, relapsing inflammatory skin disease characterized by intense pruritus. It is a multifactorial condition involving complex interactions among skin barrier dysfunction, immune dysregulation, genetic predisposition, and alterations in the skin microbiome. The disease is primarily driven by Th2-associated cytokines such as interleukin (IL)-4, IL-13, and IL-31, which contribute to inflammation and exacerbate pruritus, perpetuating the "itch-scratch cycle." Recently, biologics targeting Th2 cytokines - such as dupilumab, lebrikizumab, and tralokinumab - have emerged as effective treatment options for moderate-to-severe AD. Conjunctivitis is a common adverse effect associated with biologic therapies. In severe cases of conjunctivitis, continuation of biologic therapy may be difficult, highlighting the importance of appropriate ophthalmologic management. Herein, we report a case of AD successfully controlled with lebrikizumab, in which the patient developed conjunctivitis refractory to artificial tears and fluorometholone eye drops. Switching to tacrolimus ophthalmic suspension resulted in marked improvement. While tacrolimus eye drops are not approved for conjunctivitis, they are indicated for vernal keratoconjunctivitis and may be considered in severe cases of AD-related conjunctivitis in consultation with ophthalmologists.},
}
@article {pmid40620903,
year = {2025},
author = {Gao, C and Huang, Q and Yang, X and Cui, X and Wen, K and Liu, Y and Wang, C and Dai, Q and Xie, J and Zhu, L},
title = {Diet and environment drive the convergence of gut microbiome in wild-released giant pandas and forest musk deer.},
journal = {iScience},
volume = {28},
number = {7},
pages = {112837},
pmid = {40620903},
issn = {2589-0042},
abstract = {Reintroduction is important for recovering endangered species, and gut microbiome is crucial for successful wildlife reintroduction. This study utilized 16S rRNA high-throughput sequencing of 791 fecal samples to examine the gut microbial changes in giant pandas (Ailuropoda melanoleuca) and forest musk deer (Moschus berezovskii) across captivity, semi-release, and release stages. Our results revealed a similar transitional pattern in the gut microbiome of both species, with semi-release stage displaying an intermediate state between captive and wild microbiome. We also observed that both species are enriched in Pseudomonas and functional pathways related to amino acid metabolism, ATP-binding cassette transporters, and acetyl-CoA/propionyl-CoA carboxylase. Furthermore, the SourceTracker analysis indicated putative contributions of plant and soil microbiome to the gut microbiome of forest musk deer. These findings suggest that similar herbivorous diets and same environment may contribute to the convergence of gut microbiome. In conclusion, our study provides valuable insights for reintroducing endangered wildlife.},
}
@article {pmid40620665,
year = {2025},
author = {Jinyu, K and Jian, W and Yiwen, L and Ruonan, L and Shegan, G},
title = {Role of Oral and Esophageal Microbiota in Esophageal Squamous Cell Carcinoma.},
journal = {Clinical Medicine Insights. Oncology},
volume = {19},
number = {},
pages = {11795549251350185},
pmid = {40620665},
issn = {1179-5549},
abstract = {In China, esophageal cancer (EC) is one of the most prevalent malignant tumors of the digestive system. EC has a high incidence and mortality rate, of which esophageal squamous cell carcinoma (ESCC) accounts for more than 90%. Due to a lack of effective prevention and treatment methods, the 5 year survival rate is less than 30%. In recent years, microecology has become a hot spot in cancer research, and dysbiosis may play an important role in the etiology of EC. Presently, research on the relationship between the microbiome and ESCC remains in its early stages. This narrative review examines the relationship between the oral and esophageal microbiota and ESCC. A better understanding of this relationship may facilitate early detection and the optimization of treatment strategies.},
}
@article {pmid40620607,
year = {2025},
author = {Liu, J and Chen, Y and Wan, Q},
title = {Immune Cell Characteristics in a Gut-Kidney Axis-Induced Mouse Model of IgA Nephropathy: The Upregulated Dendritic Cells and Neutrophils.},
journal = {Journal of inflammation research},
volume = {18},
number = {},
pages = {8579-8592},
pmid = {40620607},
issn = {1178-7031},
abstract = {BACKGROUND: IgA nephropathy (IgAN) is the leading type of primary glomerulonephritis, significantly contributing to chronic kidney disease (CKD) and renal failure. The pathogenesis of IgAN is the multi-hit hypothesis regarding overproduction and accumulation of galactose-deficient (Gd-IgA1). Recent findings have revealed gut microbiota dysbiosis and immune responses are essential in the development of IgAN, attracting increasing attention. This study aimed to map mucosal immune cells in IgAN influenced by gut microbiota, investigating the role of innate immune cells in kidney damage.<br><br>METHODS: Fecal samples were acquired from both patients and controls for subsequent animal experiments. Mice received a broad-spectrum antibiotic cocktail to eliminate their intestinal microflora, followed by a gavage with fecal microbiota from clinical individuals. Murine intestinal and kidney tissues were collected for flow cytometry. Intestine and kidney histopathology, immunofluorescence, and inflammatory cytokine expression were assessed in the murine models. The mucosal epithelium's structure and function, along with the innate immune cell response, were analyzed.<br><br>RESULTS: Mice exhibited the IgAN phenotype following colonization with gut microbiota from IgAN patients. These mice (IgAN-FMT mice) showed renal dysfunction and increased pathology of tissue injury in both intestine and kidneys. IgAN-FMT mice showed heightened pro-inflammatory cytokine (IL-6 and TNF-&#x3b1;) activity, greater antibody (IgA and complement C3) deposition and decreased expression of mucosal barrier protein (ZO-1, Occludin) compared to the control group. Furthermore, CD11c[+]dendritic cells were more abundant in the murine intestine and kidneys compared to the control group.<br><br>CONCLUSION: The gut-kidney axis, including microbiota homeostasis and innate immune cell response, contributes to the pathogenesis of IgAN. Gut dysbiosis and hyperactivated immune cells like CD11c[+]dendritic cells can affect the mucosal barrier and exacerbate the renal damage, being novel insights into immunotherapeutic strategies for IgAN.},
}
@article {pmid40620487,
year = {2025},
author = {Luo, W and Zhang, S and Sun, J and Xu, J and Huang, W and Hao, R and Ou, Z and Wen, Z and Wang, D and Xiao, G and Dong, H},
title = {Microbial and clinical disparities in pneumonia: insights from metagenomic next-generation sequencing in patients with community-acquired and severe pneumonia.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1538109},
pmid = {40620487},
issn = {1664-302X},
abstract = {BACKGROUND: Community-acquired pneumonia (CAP) is a major global cause of death, with its varying symptoms and severity complicating diagnosis and treatment. Severe pneumonia (SP), a more critical form of CAP, has higher mortality and often requires intensive care. The identification of clinical markers to differentiate CAP from SP has the potential to improve treatment protocols and patient outcomes. Concurrently, metagenomic next-generation sequencing (mNGS) demonstrates significant promise in pathogen detection and in elucidating microbiome disparities between CAP and SP.<br><br>METHODS: This retrospective study analyzed clinical and pathogen data from 204 patients diagnosed with CAP and 25 patients diagnosed with SP in the Department of Respiratory and Critical Care Medicine at the Zengcheng Branch of Nanfang Hospital, Southern Medical University, spanning the period from September 2022 to June 2023. Clinical characteristics were compared, and bronchoalveolar lavage fluid (BALF) samples underwent mNGS for microbial detection and characterization. Statistical analyses, encompassing Chi-square, Fisher's exact test, Student's t-test, and LEfSe analysis, were employed to compare clinical and microbiological data between the CAP and SP cohorts.<br><br>RESULTS: Patients with SP were significantly older and exhibited higher incidences of sepsis, hypotension, tachycardia, multilobar infiltrates, and consciousness disorders compared to those with CAP. Elevated levels of C-reactive protein (CRP) and procalcitonin (PCT) were more frequently observed in SP patients. mNGS analysis identified diagnostic microbiology profiles between groups. Diverse microbiological profiles (> 5 species) were more common in SP patients (> 30% detection rate). Beta diversity analysis demonstrated significant differences in microbial community composition between CAP and SP groups (p = 0.001), though alpha diversity metrics showed no significant differences. Both LEfSe and ANCOM-BC2 analyses consistently identified Pseudomonas as a potential biomarker for SP and Streptococcus for CAP.<br><br>CONCLUSION: The substantial differences observed in clinical characteristics, pathogen profiles, and microbiomes between patients with CAP and those with SP highlight the imperative need for comprehensive diagnostic methodologies in the management of pneumonia. mNGS has demonstrated substantial utility in informing personalized treatment strategies, with the potential to enhance clinical outcomes. Future research should prioritize elucidating the dynamics of microbial communities and their impact on pneumonia severity, with the objective of refining and optimizing therapeutic strategies.},
}
@article {pmid40620214,
year = {2025},
author = {Lee, SM and Eom, KH and Jung, J and Kang, JC and Ryu, JS and Ahn, YM and Park, JY},
title = {Stress exacerbates DNCB-induced atopic dermatitis in BALB/c mice: association with modulation of the gut microbiome.},
journal = {Stress (Amsterdam, Netherlands)},
volume = {28},
number = {1},
pages = {2525801},
doi = {10.1080/10253890.2025.2525801},
pmid = {40620214},
issn = {1607-8888},
mesh = {Animals ; *Dermatitis, Atopic/microbiology/chemically induced ; *Gastrointestinal Microbiome/physiology ; Mice ; Dinitrochlorobenzene ; Mice, Inbred BALB C ; *Stress, Psychological/complications/microbiology ; Immunoglobulin E/blood ; Disease Models, Animal ; Corticosterone/blood ; Restraint, Physical ; Male ; Pruritus/microbiology ; },
abstract = {Atopic dermatitis (AD) is a widely recognized chronic inflammatory skin disease influenced by dietary habits, stress, genetic factors, and environmental factors. This study aimed to explore the impact of stress on AD exacerbation, as well as the associated changes in the gut microbiota. We utilized a 2,4-dinitrochlorobenzene (DNCB)-induced AD mouse model subjected to chronic restraint stress (CRS). The animals were divided into four groups: normal, sham control (sham), AD, and AD+CRS. Scratching behavior was significantly increased in the AD+CRS group compared to the AD group on day 28, indicating that stress exacerbates pruritus in AD. Relative abundance analysis of the gut microbiota at the phylum level revealed an increased relative abundance of Bacteroidota in both the AD and AD+CRS groups. Principal coordinate analysis revealed distinct patterns between the AD and AD+CRS groups. The relative abundance of Heminiphilus was negatively correlated with immunoglobulin E (IgE) levels, while the relative abundance of Ruminococcus exhibited significant and negative correlations with both corticosterone and IgE levels. Alistipes, which is known to aggravate AD, was notably elevated in the AD+CRS group. These findings confirm that stress-related changes in the gut microbiota composition may contribute to the exacerbation of AD, highlighting the connection among stress, immune response, and microbiome dynamics in AD progression.},
}
@article {pmid40620081,
year = {2025},
author = {Fraser, L and Bedendo, A and O'Neill, M and Taylor, J and Hackett, J and Horridge, K and Cade, J and Richardson, G and Phung, TH and Beresford, B and McCarter, A and Hewitt, C},
title = {The risks, benefits, and resource implications of different diets in gastrostomy-fed children: The YourTube mixed method study.},
journal = {Health technology assessment (Winchester, England)},
volume = {29},
number = {25},
pages = {1-21},
doi = {10.3310/RRREF7741},
pmid = {40620081},
issn = {2046-4924},
mesh = {Humans ; *Gastrostomy ; Female ; Male ; Infant ; Child, Preschool ; *Enteral Nutrition/methods/adverse effects ; Quality of Life ; Child ; *Diet ; Parents/psychology ; Food, Formulated ; Focus Groups ; Qualitative Research ; Cohort Studies ; },
abstract = {BACKGROUND: Many children receive some or all their nutritional intake via a gastrostomy. More parents are using home-blended meals to feed their children, reporting beneficial effects, such as improved gastro-oesophageal reflux and less distress.<br><br>AIM: To compare safety, outcomes and resource use of those on home-blended diets compared to formula diets.<br><br>METHODS: A mixed-methods study of gastrostomy-fed children.<br><br>WORKSTREAM 1: Qualitative study involving semistructured interviews with parents (n&#xa0;&#x2248;&#xa0;20) and young people (n&#xa0;&#x2248;&#xa0;2) and focus groups with health professionals (n&#xa0;&#x2248;&#xa0;41).<br><br>WORKSTREAM 2: Cohort study; data were collected on 180 children at months 0, 12 and 18 from parents and clinicians using standardised measures. Data included gastrointestinal symptoms, quality of life, sleep (child and parent), dietary intake, anthropometry, healthcare usage, safety outcomes and resource use. Outcomes were compared using propensity scored weighted multiple regression analyses.<br><br>RESULTS: WORKSTREAM 1: Participants believed the type of diet would most likely affect gastrointestinal symptoms, time spent on feeding, sleep and physical health.<br><br>WORKSTREAM 2: Baseline: Children receiving a home-blended diet and those receiving a formula diet were similar in terms of diagnoses and age, but those receiving a home-blended diet were more likely to live in areas of lower deprivation and their parents had higher levels of education. They also had a higher dietary fibre intake and demonstrated significantly better gastrointestinal symptom scores compared to those receiving a formula diet (beta 13.8, p&#x2005;<&#x2005;0.001). The number of gut infections and tube blockages were similar between the two groups, but stoma site infections were lower in those receiving a home-blended diet. Follow-up: There were 134 (74%) and 105 (58%) children who provided follow-up data at 12 and 18 months. Gastrointestinal symptoms were lower at all time points in the home-blended diet group, but there was no difference in change over time within or between the groups. The nutritional intake of those on a home-blended diet had higher calories/kg and fibre, and both home-blended and formula-fed children have values above the Dietary Reference Values for most micronutrients. Safety outcomes were similar between groups and over time. Total costs to the statutory sector were higher among children who were formula fed, but costs of purchasing special equipment for home-blended food and the total time spent on child care were higher for families with home-blended diet.<br><br>CONCLUSION: Findings show that home-blended diets for children who are gastrostomy fed should be seen as a safe alternative to formula feeding for children unless there is a clinical contraindication.<br><br>LIMITATIONS: The target sample for children in workstream 1 was not achieved. The observational study design means unmeasured confounding may still be an issue. Children in this cohort had been on their home-blended diets for different periods of time. A lack of good reference data for nutritional and anthropometric data for disabled children does hinder further interpretation of nutritional adequacy.<br><br>FUTURE WORK: Future research on: impact of a home-blended diet on the gut microbiome in children who are gastrostomy fed and equality of access. Children's experiences of living with a gastrostomy, nutritional requirements and quality of life should also be prioritised.<br><br>FUNDING: This synopsis presents independent research funded by the National Institute for Health and Care Research (NIHR) Health Technology Assessment programme as award number 17/76/06.},
}
@article {pmid40619937,
year = {2025},
author = {Deshmukh-Reeves, E and Shaw, M and Bilsby, C and Gourlay, CW},
title = {Biofilm Formation on Endotracheal and Tracheostomy Tubing: A Systematic Review and Meta-Analysis of Culture Data and Sampling Method.},
journal = {MicrobiologyOpen},
volume = {14},
number = {4},
pages = {e70032},
doi = {10.1002/mbo3.70032},
pmid = {40619937},
issn = {2045-8827},
support = {//This study was supported by an industrial CASE studentship between University of Kent and ICU Medical Inc./ ; },
mesh = {*Biofilms/growth &amp; development ; Humans ; *Tracheostomy/instrumentation/adverse effects ; *Intubation, Intratracheal/instrumentation/adverse effects ; *Bacteria/classification/isolation &amp; purification/genetics ; Trachea/microbiology ; Pneumonia, Ventilator-Associated/microbiology ; Equipment Contamination ; Microbiota ; },
abstract = {Biofilm formation on tracheal tubing is a key risk factor for ventilator-associated pneumonia. Endotracheal tube microbiology has been systematically reviewed, but tracheostomy tube profiles have not. Analysis of the tube-associated microbiome is not standardised, and sampling methods are varied. We compared the reported microbiomes of endotracheal and tracheostomy tubes and examined the impact of sampling by tracheal aspiration or direct culture. We searched PubMed, SCOPUS, and Web of Knowledge for clinical microbiology studies from 2000-2024, extracting tubing type, sampling method, and the most prevalent genera identified. Genera were compared by Spearman's rank correlation and pairwise analyses by Šidák's test. Extraction from 49 studies identified 30 genera. Pseudomonas was the most prevalent in all conditions followed by Klebsiella, Staphylococcus, and Acinetobacter. 25 studies performed tracheal aspiration, and 22, direct culture. Two studies used both methods. Correlation was observed between endotracheal and tracheostomy tubes, and aspirates and direct cultures (Spearman's rho = 0.69; 0.59). Pseudomonas were more prevalent in tracheostomy tubes (p < 0.0001). Coagulase-positive Staphylococci were more common in tracheal aspirates, and coagulase-negative Staphylococci in direct culture. The microbial profiles of endotracheal and tracheostomy tubes are comparable, with Pseudomonas being the most common coloniser. Our analyses suggest that tracheal aspiration can effectively identify the constituents of biofilms without requiring tube removal, making it a valuable tool for clinical researchers to analyse or monitor biofilms before extubation or device failure using existing microbiology procedures.},
}
@article {pmid40619849,
year = {2025},
author = {Yu, W and Liu, N and Gui, P and Huang, X and Feng, X and Liu, L and Yang, D and Guo, G and Xiong, C},
title = {Research trends and hotspots of nanomaterials in inflammatory bowel disease: a bibliometric analysis.},
journal = {Nanomedicine (London, England)},
volume = {},
number = {},
pages = {1-19},
doi = {10.1080/17435889.2025.2527594},
pmid = {40619849},
issn = {1748-6963},
abstract = {INTRODUCTION: Inflammatory bowel disease (IBD) is a chronic and nonspecific gastrointestinal disorder, imposing significant physical, emotional, and economic burdens on patients. In recent years, nanomaterials have shown great potential in the management of IBD. This study employs bibliometric analysis to map global research trends and intellectual landscapes in nanomaterials application for IBD.<br><br>METHOD: A comprehensive search was conducted on the Web of Science Core Collection database for studies pertaining to nanomaterials and IBD. Bibliometric and visual analysis of the included publications were facilitated by the utilization of Bibliometrix R, VOSviewer and CiteSpace software.<br><br>RESULT: A total of 879 studies were included. China, the United States, and Germany are the leading countries in this field. Georgia State University emerged as the most productive institution, while Didier Merlin and Zhang Mingzhen were identified as influential core authors. International Journal of Pharmaceutics was the most productive journal, and Journal of Controlled Release was the most cited journal. Keyword analysis highlighted "drug delivery," "gut microbiota," "reactive oxygen species" and "anti-inflammation" as dominant research frontiers, with burst keywords such as "polymeric nanoparticles" and "gut microbiotasignaling emerging trends.<br><br>CONCLUSION: These findings underscore nanomaterials' transformative potential in IBD management, particularly in targeted therapies and microbiome modulation, while emphasizing the need for interdisciplinary collaboration to address clinical translation challenges.},
}
@article {pmid40619813,
year = {2025},
author = {Sabih Ur Rehman, S and Nasar, MI and Mesquita, CS and Al Khodor, S and Notebaart, RA and Ott, S and Mundra, S and Arasardanam, RP and Muhammad, K and Alam, MT},
title = {Integrative systems biology approaches for analyzing microbiome dysbiosis and species interactions.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {4},
pages = {},
doi = {10.1093/bib/bbaf323},
pmid = {40619813},
issn = {1477-4054},
support = {G00005310//UAEU-ZU/ ; G00004960//UPAR/ ; G00004540//UPAR/ ; G00004152//UPAR/ ; },
mesh = {Humans ; *Dysbiosis/microbiology ; *Systems Biology/methods ; *Microbiota ; Metagenomics ; Metabolomics ; Proteomics ; },
abstract = {Microbiomes are crucial for human health and well-being, with microbial dysbiosis being linked to various complex diseases. Therefore, understanding the structural and functional changes in the microbiome, along with the underlying mechanisms in disease conditions, is essential. In this review, we outline the structure and function of different human microbiomes and examine how changes in their composition may contribute to diseases. We highlight critical information associated with microbial dysbiosis and explore various therapeutic strategies for restoring a healthy microbiome, including microbiota transplantation, phage therapy, probiotics, prebiotics, dietary interventions, and drug-based approaches. Further, to better understand microbiome dysbiosis, we discuss multi-omics approaches including metagenomics, metatranscriptomics, metaproteomics, and meta-metabolomics, alongside computational modeling approaches such as ecological and metabolic network analysis. We outline key challenges associated with multi-omics techniques and emphasize the importance of integrative systems biology approaches that combine multi-omics data with computational modeling. These approaches are crucial for effectively analyzing microbiome data, providing deeper insights into species interactions and microbiome dynamics. Finally, we offer insights into future research directions in the field of microbiome research. This review makes a unique contribution to microbiome research by presenting a holistic framework that integrates multi-omics data with multi-scale modeling to elucidate microbial interactions, microbiome dysbiosis, and their modulation in disease-associated contexts.},
}
@article {pmid40619698,
year = {2025},
author = {Demirli Atıcı, S},
title = {Microbiome, mechanics, and morphology: Rethinking the etiopathogenesis of pilonidal sinus disease.},
journal = {Turkish journal of surgery},
volume = {},
number = {},
pages = {},
doi = {10.47717/turkjsurg.2025.2025-5-2},
pmid = {40619698},
issn = {2564-6850},
}
@article {pmid40619655,
year = {2025},
author = {Jia, D and He, Y and Chen, Q and Zhang, Y},
title = {Gut Microbiota-Induced Long Non-Coding RNA Snhg9 Regulates the Development of Human Malignant Tumors.},
journal = {Current molecular medicine},
volume = {},
number = {},
pages = {},
doi = {10.2174/0115665240366916250629064055},
pmid = {40619655},
issn = {1875-5666},
abstract = {Gut microbes influence the progression of human malignancies through their recognition by the immune system and their effects on numerous metabolic pathways. Long non-coding RNA is a key target of intestinal microbiota involved in the progression of human malignant tumors. Current research shows that there is a close cross-talk between long non-coding RNA Snhg9 and intestinal microorganisms, and it is widely involved in the progression of human malignant tumors. An in-depth study of the interaction between long non-coding RNA and intestinal flora and the intrinsic regulatory mechanism of snhg9 will provide new and powerful therapeutic targets for future research on human malignant tumors.},
}
@article {pmid40619214,
year = {2025},
author = {Bai, X and Ihara, E and Tanaka, Y and Minoda, Y and Wada, M and Hata, Y and Esaki, M and Ogino, H and Chinen, T and Ogawa, Y},
title = {The interplay of gut microbiota and intestinal motility in gastrointestinal function.},
journal = {Journal of smooth muscle research = Nihon Heikatsukin Gakkai kikanshi},
volume = {61},
number = {},
pages = {51-58},
doi = {10.1540/jsmr.61.51},
pmid = {40619214},
issn = {1884-8796},
mesh = {Humans ; *Gastrointestinal Motility/physiology ; *Gastrointestinal Microbiome/physiology ; Bile Acids and Salts/metabolism ; Animals ; Irritable Bowel Syndrome/microbiology/physiopathology/therapy ; Probiotics/therapeutic use ; *Gastrointestinal Tract/microbiology/physiology ; Interstitial Cells of Cajal/physiology ; Fecal Microbiota Transplantation ; Prebiotics ; Constipation/microbiology ; Gastrointestinal Diseases/microbiology/therapy ; Fatty Acids, Volatile/metabolism ; },
abstract = {The relationship between gut microbiota and intestinal motility is crucial for maintaining gastrointestinal health. Intestinal motility refers to the coordinated movements of the digestive tract, essential for effective digestion, nutrient absorption, and timely waste elimination. Recent studies have demonstrated that microbiota play a crucial role not only in the maturation of intestinal motility but also in the ongoing maintenance of established motility patterns. Disruptions in motility can lead to various disorders, such as chronic constipation, irritable bowel syndrome, and chronic idiopathic pseudo-obstruction. Gut microbiota significantly influence intestinal motility through mechanisms like bile acid metabolism and the production of short-chain fatty acids. In patients with diarrhea-predominant irritable bowel syndrome, elevated primary-to-secondary bile acid ratios suggest a complex interaction between gut bacteria and bile acids that can enhance motility via receptors like TGR5. Additionally, the role of interstitial cells of Cajal in facilitating non-neuronal contractions has revolutionized our understanding of motility regulation, highlighting both neural and non-neural factors. Various therapeutic approaches, including prebiotics, probiotics, and fecal microbiota transplantation, have been explored to improve intestinal motility, although their effectiveness has been limited. Advancements in gene-related research and innovative diagnostic methods are vital for a deeper understanding of how the gut microbiome regulates motility. This review synthesizes current knowledge on the interplay between gut microbiota and intestinal motility, emphasizing the need for interdisciplinary research to develop effective treatments targeting gut microbiota for gastrointestinal disorders. By unraveling these complex interactions, we can pave the way for novel therapeutic strategies that enhance intestinal health and improve the quality of life for those affected by motility-related disorders.},
}
@article {pmid40619188,
year = {2025},
author = {Hackman, NM and Hoyt-Austin, AE and Fernández, CR and Kair, LR},
title = {Recent Advancements and Best Practices in Supporting Newborn Feeding: A Narrative Review.},
journal = {Pediatric clinics of North America},
volume = {72},
number = {4},
pages = {581-595},
doi = {10.1016/j.pcl.2025.04.001},
pmid = {40619188},
issn = {1557-8240},
mesh = {Humans ; Infant, Newborn ; *Breast Feeding/methods ; *Infant Nutritional Physiological Phenomena ; *Infant Care/methods ; Practice Guidelines as Topic ; },
abstract = {Care of the newborn can be complex and very rewarding. The pediatric clinician will face the important challenge of balancing and supporting a family's feeding plan with the health care needs of the newborn and lactating parent. This narrative review focuses on several important topics and provides valuable resources and guidance in the complex care of newborn feeding. The health benefits of breastfeeding, benefits of skin to skin, guidance on unique or complex newborn feeding situations, response to newborn weight loss, vitamin supplementation, as well as consideration of the social determinants of health in the context of infant feeding are reviewed.},
}
@article {pmid40619159,
year = {2025},
author = {Hou, J and Weng, A and Yang, Z and Huang, X and Chen, W and Wang, X},
title = {Unveiling the Link Between Oral Microbiome Diversity and Biological Ageing: A Cross-Sectional Study.},
journal = {Journal of clinical periodontology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jcpe.14172},
pmid = {40619159},
issn = {1600-051X},
abstract = {AIM: To investigate the relationship between oral microbiome diversity and biological ageing acceleration in a nationally representative U.S.<br><br>METHODS: Data from 7716 participants in NHANES (2009-2012) were analysed. Oral microbiome diversity was assessed, and biological ageing acceleration was calculated using a validated algorithm. Generalised linear models, restricted cubic splines and smooth curve fitting were applied to evaluate associations.<br><br>RESULTS: Higher &#x3b1;-diversity of the oral microbiome was significantly negatively correlated with biological ageing acceleration. Stratified analyses revealed that this protective effect was particularly pronounced in men and individuals with hypertension and diabetes. &#x3b2;-Diversity analysis showed significant differences in the association between microbial community composition and biological ageing acceleration, with immune functions potentially modulating these effects. Furthermore, key intervals of &#x3b1;-diversity were identified, which may serve as potential targets for future research on delaying ageing.<br><br>CONCLUSIONS: In the general U.S. population, greater oral microbiome diversity was associated with lower biological ageing acceleration, especially among men and those with hypertension and diabetes. This association was also observed in Mexican and Hispanic populations.},
}
@article {pmid40619037,
year = {2025},
author = {Karine da Rosa Dias, K and Tochetto, C and Muterle Varela, AP and Loiko, MR and Caroline Dos Santos, A and Frazzon, J and Roehe, PM and Mayer, FQ},
title = {Impact of weaning on piglet microbiota: differences in bacterial taxa and metabolic pathways associated with diarrhea.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {107878},
doi = {10.1016/j.micpath.2025.107878},
pmid = {40619037},
issn = {1096-1208},
abstract = {In modern pig farming, early weaning increases pigs' vulnerability to intestinal diseases due to the immaturity of their digestive and immune systems. Post-weaning diarrhea is a common issue in Brazil, leading to weight loss and slow growth, which significantly impacts the swine industry's performance. The intestinal microbiota plays a crucial role during this phase, as it is determinant for the animals' health and productivity. This study aimed to compare the microbiota of post-weaning piglets with and without diarrhea, identifying differences in the bacterial composition and microbial metabolic pathways. The most frequent phyla in both groups were Bacillota followed by Bacteriodota and Pseudomonadota, which together accounted for nearly 90% of microbiota. However, one phylum and eight bacterial families were enriched in the control group (minimum fold change of 4.6), whereas only the Fusobacteriaceae family was enriched in diarrhea group (fold change of 6.5). Moreover, 16 genera were enriched in the control group, while 12 were enriched in the diarrhea group. These findings indicate distinct microbiota compositions between the groups, suggesting an association with dysbiosis. Variations in metabolic pathways were also observed. In the diarrhea group, six pathways were enriched (fold changes of 8.12 to 263.23), most of which were associated with pathogenic and inflammatory processes. In addition, an increase in pathways linked to bacterial metabolism suggested heightened microbial activity, potentially exacerbating diarrhea. In contrast, seven metabolic pathways were enriched in the control group, many of which are essential for immune system development and strengthening, supporting healthy growth. These results highlight key differences in the microbiota and metabolic activity of piglets with and without diarrhea, providing insights that may aid in developing strategies to promote intestinal health and improve post-weaning performance.},
}
@article {pmid40619005,
year = {2025},
author = {Hullar, MAJ and Kahsai, O and Curtis, KR and Navarro, SL and Zhang, Y and Randolph, TW and Levy, L and Shojaie, A and Kratz, M and Neuhouser, ML and Lampe, PD and Raftery, D and Lampe, JW},
title = {Metabolic plasticity of the gut microbiome in response to diets differing in glycemic load in a randomized, crossover, controlled feeding study.},
journal = {The American journal of clinical nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ajcnut.2025.06.026},
pmid = {40619005},
issn = {1938-3207},
abstract = {BACKGROUND: Dietary patterns characterized by low-glycemic, minimally processed plant foods are associated with lower risk of several chronic diseases.<br><br>OBJECTIVE: Evaluate the effects of a low glycemic load (LGL) versus a high glycemic load (HGL) dietary pattern on stool bacterial community structure and metabolism.<br><br>METHODS: Participants in this crossover-controlled feeding study were healthy men and women (n=69). We identified genera, species, and genes and transcripts of metabolic pathways and bacterial enzymes using 16S rRNA gene, metagenomic and metatranscriptomic sequencing, and bioinformatic analysis.<br><br>RESULTS: Overall community structure measured by alpha and beta diversity were not significantly different across the diets although diet did significantly increase the abundance of 13 out of 161 genera (padj<0.05) and 5 species in the LGL and 7 species in the HGL diet. Gene expression in the hexitol fermentation pathway (&#x3b2;=-1.15, SE=0.24 with 95% CI (-1.63, -0.67); padj=0.002) was significantly higher in the HGL diet, whereas expression in the L-lysine biosynthesis pathway (&#x3b2; =0.20, SE=0.05 with 95% CI (0.09, 0.30); padj=0.03); was enriched in the LGL diet. The beta diversity of expressed carbohydrate-active enzymes (CAZymes) was significantly different between the diets (MiRKAT, p<0.001). CAZymes enriched in the HGL diet reflected dietary additives while CAZymes enriched in the LGL diet reflected diverse phytochemical intake. There was a significant interaction between HOMA IR and the Coenzyme A biosynthesis I pathway involved in bacterial fatty acid biosynthesis (padj=0.035) that was positive in the HGL diet (&#x3b2;=0.20, SE=0.09 with 95% CI (0.02, 0.39)) and negative in the LGL diet (&#x3b2; =-0.23, SE=0.09 with 95% CI (-0.40, -0.06)).<br><br>CONCLUSION: In healthy humans, diet impacts microbial metabolism and enzymatic activity but not the overall diversity of the gut microbiome. This emphasizes the relevance of dietary components in activating expression of specific bacterial genes and their impact on host metabolism. This trial was registered at clinicaltrials.gov as NCT00622661.},
}
@article {pmid40618920,
year = {2025},
author = {Kongsintaweesuk, S and Tunbenjasiri, K and Pongking, T and Roytrakul, S and Charoenlappanit, S and Anutrakulchai, S and Pairojkul, C and Intuyod, K and Tanasuka, P and Blair, D and Pinlaor, S and Pinlaor, P},
title = {Microcystin-LR exacerbates chronic kidney disease in rats: Insights into gut microbiome and host proteome dysregulation.},
journal = {Life sciences},
volume = {},
number = {},
pages = {123840},
doi = {10.1016/j.lfs.2025.123840},
pmid = {40618920},
issn = {1879-0631},
abstract = {AIMS: This study aimed to investigate the effects of microcystin-leucine arginine (MC-LR), an environmental nephrotoxin, on the gut-kidney axis in chronic kidney disease (CKD), focusing on interactions between the gut microbiome and host proteome.<br><br>MATERIALS AND METHODS: Male Sprague-Dawley rats were administered adenine (200&#x202f;mg/kg/day) for 10&#x202f;days to induce kidney injury, followed by MC-LR (10&#x202f;&#x3bc;g/mL/kg, i.p., every other day for 4&#x202f;weeks). Renal function (Blood urea nitrogen (BUN), Serum creatinine (SCr), and urine albumin to creatinine ratio (uACR)) and kidney pathology (EGTI histology scores and picrosirius-red staining) were assessed. Expression of kidney injury (KIM-1), fibrosis (CTGF), inflammation (HMGB1 and CD3), oxidative stress (H2AX) markers were evaluated by immunohistochemical staining. Gut microbiota was analyzed by 16S rRNA sequencing, and fecal proteomics by LC-MS/MS.<br><br>KEY FINDINGS: MC-LR markedly exacerbated adenine-induced kidney injury, leading to impair kidney function (elevated BUN, Cr, and uACR levels) and worsen kidney histopathology (higher EGTI histology scores and prominent fibrosis). Elevated expression levels of KIM1, HMBG1, CTGF, H2AX and CD3 were observed following MC-LR exposure. Notably, pro-inflammatory bacterial families (Enterococcaceae, Enterobacteriaceae) were elevated, while beneficial taxa (Bifidobacteriaceae, Muribaculaceae) decreased in the combination group. Proteomic analysis revealed upregulation of inflammatory markers (TXNIP, Itgb3bp), which correlated with Enterococcaceae abundance. Bifidobacteriaceae negatively correlated with kidney injury markers.<br><br>SIGNIFICANCE: Our study reveals that MC-LR exacerbates chronic kidney disease progression by disrupting the gut-kidney axis. We highlight gut barrier integrity and inflammation as crucial therapeutic targets, offering novel insights and intervention strategies for CKD management, particularly in beyond early stages.},
}
@article {pmid40618877,
year = {2025},
author = {Luo, Y and Tan, C and Yang, J and Zhang, G and Wu, J},
title = {Maternal exposure to tris (2-chloroethyl) phosphate during pregnancy and suckling period alters gut microbiota and SCFAs metabolism in offspring of rats.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {126777},
doi = {10.1016/j.envpol.2025.126777},
pmid = {40618877},
issn = {1873-6424},
abstract = {Tris(2-chloroethyl) phosphate (TCEP), one of the most widely used organophosphate flame retardants, is frequently detected in environmental and biological samples. However, its toxic effects on the offspring remain unknown. To explore the health risks posed by TCEP in susceptible populations, we investigated the intergenerational transmission of TCEP, gut microbiome, and disruptive effects of intestinal metabolites in the offspring. Different doses of TCEP were administered orally to female Sprague-Dawley (SD) rats throughout pregnancy or during both pregnancy and lactation periods. Concentrations of TCEP and its metabolite, BCEP, composition of the gut microbiota, and fecal concentrations of short-chain fatty acids were measured. The concentration of TCEP in the placenta of rats in the high-dose group was significantly higher than that in the control group, and BCEP was also present. Serum and fecal samples from immature offspring contained TCEP; however, no BCEP was detected in serum. Exposure to TCEP altered the intestinal microbiota of both the maternal rats and their offspring. The relative abundance of Coelenterata was significantly increased in the immature offspring. Exposure to TCEP altered the concentration of SCFAs in the feces of the rats and their offspring. Lower concentrations of acetic, propionic, and butyric acids were observed in the feces of immature offspring. Holdemanella had a significant mediating effect between TCEP exposure and intestinal concentrations of acetic and propionic acids. Maternal exposure to TCEP affects the gut microbiota balance and metabolism of offspring, suggesting the presence of a long-term risk associated with metabolic disease.},
}
@article {pmid40618613,
year = {2025},
author = {Nie, S and Shen, C and Qu, S and Chen, B and Liu, S and Ge, Y},
title = {Predicting the impact of climate warming on soil quality using bacteria and machine learning.},
journal = {Journal of environmental management},
volume = {391},
number = {},
pages = {126473},
doi = {10.1016/j.jenvman.2025.126473},
pmid = {40618613},
issn = {1095-8630},
abstract = {In the context of global warming, a substantial portion of global soil is in a state of degradation, which poses a significant threat to biodiversity and food production worldwide. Moreover, monitoring soil quality typically requires measuring numerous physical, chemical, and biological indicators, resulting in high costs. In this study, 286 soil samples were obtained from the climate-sensitive Tibetan Plateau and subjected to 16S rRNA amplicon sequencing to reveal the relationships between soil quality, soil bacteria, and climate warming. The results indicated that climate-sensitive bacteria could effectively predict soil quality indices through machine learning (R[2] > 0.76). This suggests that 16S rRNA sequencing can replace numerous soil indicators, providing comprehensive information on soil quality and reducing the costs associated with soil quality monitoring. Additionally, model predictions demonstrated a slight increase in soil quality when only the average annual temperature increased by 1.5 °C. However, when other climatic factors (precipitation and temperature during specific periods) also changed (future climate scenarios for 2021-2040 and 2080-2100), which is more realistic than only increasing the average annual temperature, soil quality declined and the greater the increase in temperature, the more severe the decline in soil quality. These findings provide valuable insights for soil management in the face of increasingly severe climate warming conditions. In summary, our research offers new perspectives for soil quality monitoring from a microbiome standpoint and indicates that future climate warming could pose a threat to soil quality.},
}
@article {pmid40618567,
year = {2025},
author = {Schäfer, L and Grundmann, SM and Hepp, V and Herrero-Encinas, J and Rühl, M and Most, E and Ringseis, R and Eder, K},
title = {Influence of Pleurotus sapidus fruiting bodies on the performance, cecal microbiome, and gene expression in the liver and breast muscle of broilers.},
journal = {Poultry science},
volume = {104},
number = {10},
pages = {105517},
doi = {10.1016/j.psj.2025.105517},
pmid = {40618567},
issn = {1525-3171},
abstract = {Mushrooms, the fruiting bodies of edible fungi, are widely used as food for humans. However, their potential, as well as that of fungal mycelia, as feed components for poultry is less acknowledged. Recent studies have shown that feeding the vegetative mycelium of Pleurotus sapidus does not affect growth performance or nutrient digestibility and causes only minimal changes in the cecal microbiota structure, liver transcriptome, and plasma metabolome of broilers. The present study aimed to comprehensively investigate the effects of feeding the fruiting bodies of P. sapidus on performance metrics, ileal nutrient digestibility, cecal microbiota composition, cecal integrity, liver transcriptome, and the expression of genes involved in protein turnover in breast muscle of broilers. A total of 72 male, 1-day-old Cobb 500 broilers were randomly assigned to three groups and fed three distinct diets containing either 0 g (PSA-F0), 25 g (PSA-F25), or 50 g (PSA-F50) of freeze-dried P. sapidus fruiting bodies per kg diet in a 35-day, three-phase feeding regimen. Final body weights and weight gain during the finisher and the whole period were significantly lower in groups PSA-F50 and PSA-F25 compared to group PSA-F0 (P < 0.05). Feed intake during the finisher and the whole period tended to be lower in groups PSA-F50 and PSA-F25 compared to group PSA-F0 (P < 0.1). Average daily apparently digested amounts of most indispensable amino acids were lower in group PSA-F50 than in group PSA-F0 (P < 0.05). Cecal microbial α-diversity indicators (Chao1 and Richness) were significantly higher in the PSA-F50 group compared to the PSA-F0 group (P < 0.05), whereas β-diversity indicators were similar between groups. Taxonomic analysis showed a higher abundance of the class Bacilli and the species unknown_Erysipelatoclostridium and a lower abundance of the class Clostridia in the PSA-F50 group compared to the PSA-F0 group (P < 0.05). Concentrations of total and individual short-chain fatty acids, including acetic acid and propionic acid, in the cecal digesta were lower in the PSA-F50 group compared to the PSA-F0 group (P < 0.05). A total of 66 differentially expressed transcripts were identified in the liver between PSA-F50 and PSA-F0 groups based on filter criteria (FC > 1.3 or FC < -1.3, P < 0.05). The mRNA levels of genes involved in critical pathways such as protein synthesis and degradation-including the mammalian target of rapamycin pathway, myogenesis, the ubiquitin-proteasome system, autophagy-lysosomal pathway, and GCN2/eIF2α pathway-did not vary across the groups. Plasma lipopolysaccharide concentration was similar across all groups. The mRNA levels of CLDN3, MUC2, and MUC5AC were elevated in the PSA-F50 group compared to the PSA-F0 group (P < 0.05), while mRNA levels of CLDN5, OCLN, MUC13, and several pro-inflammatory genes in cecal mucosa remained unchanged across groups. The observed impairment in growth performance suggests that P. sapidus fruiting bodies cannot be recommended as dietary components for broilers at the tested doses. Considering the higher β-glucan content of fruiting bodies compared to vegetative mycelia, the negative effects observed on broiler performance may be associated with their β-glucan content.},
}
@article {pmid40618523,
year = {2025},
author = {Yin, YL and Xu, YX and Wang, MT and Yang, DZ and Wang, XY and Zhou, XK and Huang, MM and Yang, S and Fei, H},
title = {Integrative analysis of microbiome and metabolome reveals the effect of deoxynivalenol on growth performance, liver and intestinal health of largemouth bass (Micropterus salmoides).},
journal = {Journal of hazardous materials},
volume = {495},
number = {},
pages = {139148},
doi = {10.1016/j.jhazmat.2025.139148},
pmid = {40618523},
issn = {1873-3336},
abstract = {This study explored the toxic effects of deoxynivalenol (DON) intake at low (100 µg·Kg[-1], LD group) and high doses (300 µg·Kg[-1], HD group) on largemouth bass (Micropterus salmoides). After a 56-day feeding trial, the HD group exhibited significantly reduced growth performance and weakened antioxidant capacity, along with elevated activities of enzymes related to metabolic dysregulation. Histopathological analysis showed an increase in hepatic cell vacuoles, as well as a shortened intestinal villi in both LD and HD groups. Notably, high-dose DON intake markedly down-regulated the expression of intestinal epithelial tight junction-related genes and proteins. Microbiome analysis indicated a significant increase in the Delftia and Acinetobacteria relative abundance, accompanied by diminished in Mycoplasma abundance in the HD group. Metabolomic profiling demonstrated that the dysregulated metabolites were mainly associated with the lysine biosynthesis pathway. Integrative multi-omics analysis revealed that pyridoxamine and diferuloylputrescine served as key biomarkers associated with Acinetobacteria. Collectively, we confirmed that high-dose DON intake induces hepatointestinal damage, thereby impairing the growth performance of largemouth bass. Our findings also further highlighted the link between DON-induced gut microbiota alterations and metabolic disorders, offering new intervention targets for alleviating DON toxicity.},
}
@article {pmid40618487,
year = {2025},
author = {Schober, JM and Wilson, N and Seyoum, MM and Lyte, JM and Bergman, MM and Oluwagbenga, EM and Fraley, GS},
title = {Effects of semi-open water and non-water enrichment on welfare, production, behavior, and microbial exposure of grow-out Pekin ducks.},
journal = {Poultry science},
volume = {104},
number = {9},
pages = {105477},
doi = {10.1016/j.psj.2025.105477},
pmid = {40618487},
issn = {1525-3171},
abstract = {Environmental enrichment plays an important role in the welfare, behavior, and health of commercially raised Pekin ducks. We assessed the effects of three enrichment treatments and a control: Nipple line (CON), whiffle ball (EED), preening cup (PC), and Pekino (PEK) on duck welfare, behavior and bacterial exposure. 525 grow-out Pekin ducks were housed in 4 pens/4 rooms with one of the four enrichment types (N = 4 pens/treatment). Body weights and body condition scores of 10 ducks/pen and FCR, ammonia level, and litter moisture % were recorded weekly. On 16 and 44 days of age, 3 ducks/pen were euthanized and their organs were weighed and whole brains collected. Behavior data were collected using scan sampling with video being recorded for 72 continuous hours for 3 weeks after enrichment placement. Weekly samples were also collected for viable bacterial counts, and 16S rRNA gene sequencing at baseline and 6 h after baseliner. Body morphometrics, FCR, ammonia levels, litter moisture % and viable bacteria were analyzed by 2-way ANOVA with repeated measures. Body condition scores were analyzed with PROC LOGISTIC (SAS 9.4). GLIMMIX procedure (SAS 9.4) was used to analyze behavior. Bacterial communities were characterized using 16S rRNA gene sequencing, and functional potential was predicted using PICRUSt2. PEK and PC ducks were largest in weight (p < 0.0001) and better nostril scores (p = 0.0005) but had dirtier feathers (p < 0.0001), worse litter conditions (p < 0.0001) and more viable bacteria in their water sources (p < 0.0001), while the PC and EED ducks had worse feather quality (p = 0.0021). Alpha and beta diversity metrics revealed that microbiota composition was significantly (p < 0.05) dependent on environmental enrichment type. Likewise, functional pathway analyses revealed distinct (p < 0.05) metabolic capacities, including aerobic respiration and amino acid biosynthesis, between microbiotas of each respective environmental enrichment niche. Our study suggests that semi-open water sources and EEDs may lead to an increase in feather pecking and a decrease in feather quality with a low number of ducks per enrichment as well as an increase in bacteria load and litter moisture.},
}
@article {pmid40618377,
year = {2025},
author = {Le, TT and Hoang, TN and Do, DH and Nguyen, XH and Huynh, C and Viet, HD and Dat, VQ and Zengler, K and Gilbert, JA and Avedissian, SN and Tran, TM and Le, J},
title = {Current state of microbiota clinical applications in neonatal and pediatric bacterial infections.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2529400},
doi = {10.1080/19490976.2025.2529400},
pmid = {40618377},
issn = {1949-0984},
mesh = {Humans ; Infant, Newborn ; Child ; *Bacterial Infections/microbiology/therapy ; Dysbiosis/microbiology/therapy ; *Gastrointestinal Microbiome ; Anti-Bacterial Agents/therapeutic use ; Fecal Microbiota Transplantation ; Probiotics/therapeutic use ; Infant ; Bacteria/classification/isolation &amp; purification/genetics ; Child, Preschool ; },
abstract = {The microbiota plays a crucial role in pediatric health by shaping immune development and influencing infection susceptibility. In infants and children, an immature microbiota may compromise immune defense, increasing the risk of bacterial infections. This review evaluates clinical trials on the microbiota's role in neonatal and pediatric bacterial infections, including sepsis, infections in pediatric cancer patients, and Clostridioides difficile-associated dysbiosis. We summarized original research articles published from 2000 to May 2024 on the microbiota and bacterial infections in neonates and children. A balanced microbiota is essential for infection prevention, particularly in premature infants and immunocompromised children. Studies of microbiome signatures in the gut, oral cavity, and nasopharynx have highlighted how microbiota composition influences infection risk, treatment response, and adverse effects from antibiotics and chemotherapy. Disruptions from antibiotic exposure, chemotherapy, and hematopoietic stem cell transplantation frequently lead to dysbiosis, characterized by depletion of commensal bacteria and overgrowth of pathobionts, including antibiotic-resistant strains such as C. difficile. Conversely, microbiota-restorative interventions, such as probiotics and fecal microbiota transplantation, show promise in reducing bacterial infections by enhancing microbial resilience. The microbiota plays a critical role in predicting and potentially treating bacterial infections in children. While antibiotics remain essential, their widespread use has significant consequences for microbiota health. Striking a balance between effective infection control and microbiota preservation is crucial, particularly in vulnerable pediatric populations. Implementing judicious antibiotic use and exploring microbiota-based therapies may mitigate long-term microbiota disruptions, ultimately improving infection outcomes and overall pediatric health.},
}
@article {pmid40618373,
year = {2025},
author = {Li, L and Yang, Z and Yi, Y and Song, Y and Zhang, W},
title = {Gut microbiota and radiation-induced injury: mechanistic insights and microbial therapies.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2528429},
doi = {10.1080/19490976.2025.2528429},
pmid = {40618373},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology/radiation effects ; *Radiation Injuries/therapy/microbiology ; Animals ; Fecal Microbiota Transplantation ; Probiotics ; Signal Transduction ; Oxidative Stress ; Neoplasms/radiotherapy ; Radiotherapy/adverse effects ; Prebiotics ; },
abstract = {Radiotherapy represents a crucial therapeutic modality in cancer treatment, yet its efficacy is frequently limited by radiation-induced toxicity. Growing evidence indicates that gut microbiota and their metabolites serve as key regulators of both radioprotective and radiosensitizing effects. This review systematically examines three fundamental regulatory mechanisms through which gut microbiota and its metabolites mitigate radiation-induced injury: (1) modulation of intestinal epithelial cell regeneration and tumor cell apoptosis via Wnt/β-catenin and PI3K/AKT/mTOR pathways; (2) immunomodulation via Toll-like receptor activation and NF-κB signaling; (3) oxidative stress management via Nrf2 signaling. We also evaluate various microbiota-targeted interventions, ranging from probiotics and prebiotics to fecal microbiota transplantation and emerging engineered microbial therapies, highlighting their potential in clinical radiotherapy. Finally, we emphasize current limitations and future research directions, underscoring the need to overcome existing challenges in microbiome analysis and therapeutic durability to fully realize the potential of precision radio-microbiome medicine, which may provide valuable references for developing personalized radiotherapy strategies based on gut microbiota and their metabolites.},
}
@article {pmid40618372,
year = {2025},
author = {Healy, DB and Wang, S and Patangia, D and Grimaud, G and Ross, RP and Stanton, C and Dempsey, EM},
title = {Late-onset sepsis treatment in very preterm infants alters longitudinal microbiome trajectory with lower abundance of Bifidobacterium despite probiotic supplementation.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2523808},
doi = {10.1080/19490976.2025.2523808},
pmid = {40618372},
issn = {1949-0984},
mesh = {Humans ; *Probiotics/administration &amp; dosage ; *Gastrointestinal Microbiome/drug effects ; Longitudinal Studies ; Infant, Newborn ; Male ; *Sepsis/microbiology/drug therapy/therapy ; Female ; *Bifidobacterium/isolation &amp; purification/genetics/growth &amp; development ; Feces/microbiology ; Anti-Bacterial Agents/therapeutic use ; RNA, Ribosomal, 16S/genetics ; Infant, Premature ; Bacteria/classification/genetics/isolation &amp; purification ; Dietary Supplements ; Infant ; },
abstract = {INTRODUCTION: Taxonomic instability within the dynamic gut microbiome of very preterm infants can be associated with various adverse outcomes. This longitudinal study was designed to follow the trajectory of microbiome composition and abundance in a cohort of probiotic supplemented very preterm infants with and without sepsis.<br><br>METHODS: Stool samples (n&#x2009;=&#x2009;180) from probiotic-supplemented participants with culture-positive sepsis (n&#x2009;=&#x2009;8) and matched healthy controls (n&#x2009;=&#x2009;10) were analyzed using 16S rRNA sequencing. Calculation of total copy number per gram (TCN/g) by DNA spiking provided estimates of total microbial load.<br><br>RESULTS: TCN/g was significantly different between infants with and without sepsis, the latter having more rapid increase and overall higher TCN/g. In adjusted analysis, sepsis was associated with a significant abundance of Escherichia-Shigella (p&#x2009;=&#x2009;0.02) and Veillonella (p&#x2009;=&#x2009;0.01). Microbial load and composition appeared to fluctuate following antibiotic administration. Analysis of pre-sepsis samples showed a non-significant trend toward lower Bifidobacterium abundance and higher Escherichia-Shigella abundance in infants with subsequent sepsis. Antibiotic administration was independently associated with significantly lower (on average 250-fold lower) Bifidobacterium (p&#x2009;=&#x2009;0.005) abundance, which remained significant after adjustment for confounders.<br><br>CONCLUSIONS: Estimation of absolute abundance reveals fluctuations and blooms in key genera within the gut microbiome of very preterm infants that may not be recognized using relative abundance alone. Very preterm neonates with sepsis have a significantly different longitudinal trajectory of microbiome development, which may, in part, extend to lower Bifidobacterium and higher Escherichia-Shigella abundance prior to the onset of sepsis. Bifidobacterium abundance appears to be particularly affected by antibiotic administration compared to other genera.},
}
@article {pmid40618170,
year = {2025},
author = {Shin, C and Ruhno, KE and Shin, JH and Hwang, S and Go, JR and Kang, M and Kim, HJ and Moon, JH and Kim, HJ},
title = {Spatial transcriptome analysis of myenteric plexus and intestinal epithelium of colon in patients with Parkinson's disease.},
journal = {Acta neuropathologica communications},
volume = {13},
number = {1},
pages = {146},
pmid = {40618170},
issn = {2051-5960},
support = {2022R1A2C2091254//National Research Foundation of Korea/ ; 11-2022-5010//Seoul National University Hospital/ ; },
mesh = {Humans ; *Myenteric Plexus/metabolism/pathology ; Male ; Female ; *Parkinson Disease/metabolism/genetics/pathology ; *Colon/metabolism/pathology ; Aged ; *Intestinal Mucosa/metabolism/pathology ; Middle Aged ; Gene Expression Profiling ; *Transcriptome ; alpha-Synuclein/metabolism ; },
abstract = {Alpha-synuclein (AS) accumulation is found in the nerve plexuses of the gastrointestinal tract in patients with Parknison's disease (PD). Moreover, alterations in microbiome composition and its metabolites were confirmed in the colon of patients with PD. However, there has been no study that evaluates transcriptomic alterations of the nerve plexus and intestinal epithelium simultaneously using in vivo tissue of patients with PD. Therefore, we aimed to investigate the gene expression profiles of the myenteric plexus and intestinal epithelium of the colon of patients with PD. Ten full-depth slides of paraffin-embedded surgical specimens of the colon or rectum from five patients with PD and five controls were included. AS accumulation was found in the myenteric plexus in all patients with PD. We performed spatial-specific transcriptomic profiling of the myenteric plexus and epithelium using the GeoMX Digital Spatial Profiler. Forty-one differentially expressed genes (DEGs) (36 up-regulated and 5 down-regulated) were identified in the myenteric plexus of patients with PD compared to controls. In the intestinal epithelium, 240 DEGs (81 up-regulated and 159 down-regulated) were identified. Pathway analysis showed upregulated response to type II interferon and lymphocyte activation, while downregulated cellular response to zinc and copper ions in the intestinal epithelium of patients with PD. In the myenteric plexus, neuroepithelial cell differentiation and axon development were upregulated. Network analysis showed the following key genes: and HLA-DRA, SERPINA1, and metallothioneins in the intestinal epithelium, and LAMP1, TUBB2A, and S100B in the myenteric plexus. This study suggests that inflammatory processes may occur in the intestinal epithelium, while neuronal regeneration mechanisms may be active in the myenteric plexus in patients with overtly developed PD. A spatial transcriptomic analysis of the brain and the gastrointestinal tract will enable a better understanding of the gut-brain axis in PD.},
}
@article {pmid40618036,
year = {2025},
author = {Sato, K and Nakashima, A and Fukuda, S and Inoue, J and Kim, YG},
title = {Fasting builds a favorable environment for effective gut microbiota modulation by microbiota-accessible carbohydrates.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {414},
pmid = {40618036},
issn = {1471-2180},
support = {JPMJSP2123//JST SPRING/ ; 2346//Sylff Research Grant/ ; JP23H02718//Japan Society for the Promotion of Science/ ; JP 23K18223//Japan Society for the Promotion of Science,Japan/ ; },
mesh = {*Gastrointestinal Microbiome/physiology ; *Fasting ; Feces/microbiology/chemistry ; Animals ; *Bacteria/classification/genetics/isolation &amp; purification ; Male ; Mice ; Immunoglobulin A/analysis ; Humans ; },
abstract = {Dietary nutrients are an important determinant of gut microbial composition (Asnicar et al, Nat Med 27:321-332, 2021; Arifuzzaman. et al, Nature 611:578-584, 2022; Bolte. et al, Gut 70:1287-1298, 2021). Commensal bacteria compete and cross-feed on host-derived nutrients to maintain stable gut microbial communities (Kolodziejczyk. et al, Nat Rev Microbiol. 17:742-753, 2019; Ma. et al, Gut Microbes 12:1785252, 2020). However, the changes to the gut bacteria induced by fasting are not well-defined. Here, we propose a powerful method to selectively and effectively increase specific gut bacteria by combining fasting and administration of microbiota-accessible carbohydrates (MACs). Fasting alters the gut microbial community structure, and the fasting + MAC intervention has profound effects on the gut microbiome with increased specific bacteria and fecal IgA levels than MAC administration alone. The changes in gut microbiota composition are specific to the type of MAC administered. We identified the most effective protocol to combine with fasting + MAC to increase the levels of specific bacteria such as Bifidobacterium. Overall, the integrating fasting with MACs effectively alters the gut microbiome, suggesting that fasting can prepare the environment for gut microbial modulation by MACs.},
}
@article {pmid40617918,
year = {2025},
author = {Jamaluddin, NF and Brovkina, O and Nor Rashid, N and Al-Maleki, AR and Lim, YA and Tan, MP and Lee, SC and Duvallet, C and Corzett, CH and Alm, E and Groussin, M and Poyet, M and Ibrahim, F},
title = {Gut microbiota profiles of peninsular Malaysian populations are associated with urbanization and lifestyle.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {24066},
pmid = {40617918},
issn = {2045-2322},
support = {RK019-2018//Universiti Malaya Partnership Grant/ ; RK019-2018//Universiti Malaya Partnership Grant/ ; RK019-2018//Universiti Malaya Partnership Grant/ ; RK019-2018//Universiti Malaya Partnership Grant/ ; RK019-2018//Universiti Malaya Partnership Grant/ ; RK019-2018//Universiti Malaya Partnership Grant/ ; Project-ID 261376515 - SFB 1182//German Science Foundation and Collaborative Research Center (CRC)/ ; Project-ID 261376515 - SFB 1182//German Science Foundation and Collaborative Research Center (CRC)/ ; Project-ID 261376515 - SFB 1182//German Science Foundation and Collaborative Research Center (CRC)/ ; Flex Fund grant, DFG project no. 28/1 AOBJ: 700895 Bio4ALL, NFDI4Microbiota//German National Research Data Infrastructure (NFDI)/ ; Flex Fund grant, DFG project no. 28/1 AOBJ: 700895 Bio4ALL, NFDI4Microbiota//German National Research Data Infrastructure (NFDI)/ ; Flex Fund grant, DFG project no. 28/1 AOBJ: 700895 Bio4ALL, NFDI4Microbiota//German National Research Data Infrastructure (NFDI)/ ; IF030-2018//Center for Microbiome Informatics and Therapeutics, MIT/ ; IF030-2018//Center for Microbiome Informatics and Therapeutics, MIT/ ; IF030-2018//Center for Microbiome Informatics and Therapeutics, MIT/ ; IF030-2018//Center for Microbiome Informatics and Therapeutics, MIT/ ; IF030-2018//Center for Microbiome Informatics and Therapeutics, MIT/ ; IF030-2018//Center for Microbiome Informatics and Therapeutics, MIT/ ; IF030-2018//Center for Microbiome Informatics and Therapeutics, MIT/ ; IF030-2018//Center for Microbiome Informatics and Therapeutics, MIT/ ; },
mesh = {Humans ; Malaysia ; *Gastrointestinal Microbiome ; *Life Style ; Male ; Female ; *Urbanization ; Adult ; Middle Aged ; Rural Population ; Urban Population ; Bacteria/classification/genetics ; Young Adult ; Diet ; RNA, Ribosomal, 16S/genetics ; },
abstract = {There is increasing evidence of distinct gut microbiome compositions between populations living industrialized and non-industrialized lifestyles worldwide. However, whether populations of Malaysia exhibit variations in their microbiome, and to what extent host lifestyle correlates with these variations, remains unclear. Malaysia's extensive geographical and sociocultural diversity provides a unique opportunity to explore how lifestyle and environmental exposures are associated with the human gut microbiome. Here, we characterized the gut microbiome of three populations in peninsular Malaysia, each representing different lifestyle contexts, and identified host factors associated with microbiome variation. Our findings suggest that lifestyle-related factors are strongly associated with differences in microbial community composition across populations. In particular, urban and rural individuals harbor gut microbiota with distinct community structures. We further identified specific taxa as potential microbial signatures of host lifestyle, with the genera Prevotella and Cryptobacteroides enriched in rural populations, while Phocaeicola, Vescimonas, and Megasphaera were more prevalent among urban individuals. In addition to lifestyle, demographic factors such as age, sex, and BMI were also associated with variation in the gut microbiome. This study highlights the influence of urbanization, lifestyle, and diet on the gut microbiome landscape of Malaysian populations and underscores the importance of considering sociocultural context in future microbiome research.},
}
@article {pmid40617850,
year = {2025},
author = {Liu, Q and Fang, W and Zheng, P and Xie, S and Jiang, X and Luo, W and Han, L and Zhao, L and Lu, L and Zhai, L and Yu, DJ and Yang, W and Lin, C and Fang, X and Bian, Z},
title = {Multi-kingdom microbiota analysis reveals bacteria-viral interplay in IBS with depression and anxiety.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {129},
pmid = {40617850},
issn = {2055-5008},
support = {ITC RC/IHK/4/7//Health@InnoHK Initiative Fund of the Hong Kong Special Administrative Region Government/ ; S/N Ref: 2023-0045//Jockey Club Traditional Chinese Medicine-driven Mental Wellness Project/ ; },
mesh = {Humans ; *Irritable Bowel Syndrome/microbiology/psychology/virology/complications ; *Gastrointestinal Microbiome ; *Depression/microbiology/virology ; Female ; Male ; *Bacteria/classification/virology/genetics/isolation &amp; purification ; Prospective Studies ; *Anxiety/microbiology/virology ; Adult ; *Bacteriophages/genetics/classification/isolation &amp; purification ; Hong Kong ; Middle Aged ; Virome ; Feces/microbiology/virology ; },
abstract = {Irritable Bowel Syndrome (IBS) is a common gastrointestinal disorder frequently accompanied by psychological symptoms. Bacterial microbiota plays a critical role in mediating local and systemic immunity, and alterations in these microbial communities have been linked to IBS. Emerging data indicate that other intestinal organisms, including bacteriophages, are closely interlinked with the bacterial microbiota and their host, yet their collective role remains to be elucidated. Here, we analyze the gut multi-kingdom microbiota of 360 IBS patients from a prospective cohort study in Hong Kong, with participants phenotyped through psychological assessment. Our findings reveal significantly lower intra-community correlations in IBS patients compared to healthy controls and highlight unique taxa patterns associated with IBS and mental disorders. Utilizing multi-omic data alongside machine learning techniques, we successfully predicted psychiatric comorbidities in IBS, achieving an average AUC of 0.78. Notably, gut viruses emerged as significant contributors to our predictive model, indicating a vital role for bacteriophages in the gut microbiome of IBS patients. We found that lysogenic phages in IBS displayed a broader host range, with Bilophia containing the most abundant prophages. Our analysis further indicates that IBS patients with depression exhibited a higher prevalence of viral-encoded auxiliary metabolic genes, specifically those involved in the sulfur metabolic pathway related to ubiquinone biosynthesis. The gut virome is increasingly reported to play an important role in the pathogenesis of many diseases. The study provides a systematic characterization of the drivers of the gut viral community and further expands our knowledge of the distinct interaction of gut viruses with their prokaryotic hosts, which is critical for understanding the viral-bacterial environment in IBS.},
}
@article {pmid40617811,
year = {2025},
author = {Zhu, B and Liang, L and Chen, S and Li, H and Huang, Y and Wang, W and Zhang, H and Zhou, J and Xiong, D and Li, X and Li, J and Ning, Y and Shi, X and Wu, F and Wu, K},
title = {Multi-kingdom microbial changes and their associations with the clinical characteristics in schizophrenia patients.},
journal = {Translational psychiatry},
volume = {15},
number = {1},
pages = {228},
pmid = {40617811},
issn = {2158-3188},
mesh = {Humans ; *Schizophrenia/microbiology/metabolism/physiopathology ; Male ; Female ; *Gastrointestinal Microbiome ; Adult ; Middle Aged ; Feces/microbiology ; Case-Control Studies ; Metabolic Networks and Pathways ; Fungi ; },
abstract = {Accumulating evidence has highlighted alterations in the gut microbiome in schizophrenia (SZ); however, the role of multi-kingdom microbiota in SZ remains inadequately understood. In this study, we performed metagenomic sequencing of fecal samples from 36 SZ patients and 55 healthy controls (HC) to profile bacterial, fungal, archaeal, and viral communities, along with functional pathways. We also conducted co-occurrence network analysis to explore the relationships among differential microbial species and metabolic pathways separately. Additionally, we assessed the associations of these differential species and functional pathways with clinical characteristics. Our findings revealed significant differences in species between SZ patients and HC, identifying not only 17 bacterial species, but also 8 fungal, 26 archaeal, and 19 viral species. Functional pathway analysis revealed 21 metabolic pathways significantly altered in SZ patients, including an increase in tryptophan metabolism, while biosynthesis of amino acids was decreased. Network analysis further uncovered more complex inter-kingdom interactions in SZ patients, with specific fungal species appearing exclusively in the SZ network. Importantly, significant associations were observed between microbial species and functional pathways with clinical characteristics, including symptom severity, cognitive function, and clinical biochemical marker. For instance, the abundance of Streptococcus vestibularis was positively correlated with homocysteine levels; the ubiquinone and other terpenoid-quinone biosynthesis was positively correlated with both symptom severity and C-reactive protein. Our findings reveal the intricate microbial dysbiosis present in SZ patients, suggesting multi-kingdom microbial interactions play a crucial role in SZ patients, highlighting promising avenues for potential diagnostic and therapeutic applications.},
}
@article {pmid40617665,
year = {2025},
author = {Koutoukoglou, P and Mountzios, G},
title = {Beyond Programmed Death-Ligand 1: Gut Microbiome Composition as a Biomarker For First-Line Chemoimmunotherapy in Advanced NSCLC.},
journal = {Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer},
volume = {20},
number = {7},
pages = {831-833},
doi = {10.1016/j.jtho.2025.04.011},
pmid = {40617665},
issn = {1556-1380},
}
@article {pmid40617511,
year = {2025},
author = {Arikawa, AY and Waterman, A and Mishra, SP and Labyak, C and Williams, C and Chaudhari, DS and Shukla, R and Kumar, V and Masternak, M and Holland, P and Golden, A and Dangiolo, M and Kociolek, J and Fraser, A and Agronin, M and Aymat, M and Yadav, H and Jain, S},
title = {Cognitive impairment is associated with alterations in diet quality and inflammatory biomarkers in older adults: a cross-sectional analysis of data collected from the Microbiome in Aging Gut and Brain (MiaGB) consortium cohort.},
journal = {The Journal of nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tjnut.2025.06.026},
pmid = {40617511},
issn = {1541-6100},
abstract = {BACKGROUND: Research suggests that gut inflammation and alterations in intestinal barrier function may be important mechanisms linking diet, systemic inflammation, and cognitive outcomes.<br><br>OBJECTIVE: The objective of this study was to explore the relationship between diet, cognitive health, and inflammatory markers in older adults. It was hypothesized that cognitive impairment would be associated with lower diet quality and higher levels of inflammatory markers.<br><br>METHODS: A cross-sectional analysis was conducted using data from the Microbiome in Aging Gut and Brain (MiaGB) consortium cohort. Participants aged 60 years and older were assessed for cognitive status using the Montreal Cognitive Assessment (MoCA), diet quality using the Healthy Eating Index-2020 (HEI-2020), and dietary inflammatory potential using the Dietary Inflammatory Index (DII). Inflammatory biomarkers were measured in plasma and stool samples, including interleukin (IL)-6, IL-1&#x3b2;, lipopolysaccharide binding protein (LBP), Toll-like receptor 4 (TLR4), and zonula occludens-1 (ZO-1).<br><br>RESULTS: Among 217 participants, 33.6% presented with cognitive impairment based on MoCA scores. There were no differences in DII and HEI-2020 scores between participants with and without cognitive impairment. The only significant finding related to the components of the HEI was a higher adequacy of dairy intake in those without cognitive impairment (54.8%) compared with those with cognitive impairment (44.4%, p=0.035). Key inflammatory markers, including IL-6, IL-1&#x3b2;, LBP, and TLR4, were elevated in those with cognitive impairment, while plasma ZO-1 levels were reduced. Stool calprotectin levels were notably higher in those with cognitive impairment, suggesting increased intestinal inflammation. There was a weak but significant correlation between stool calprotectin and DII score (rs=0.283, p=0.046).<br><br>CONCLUSION: The findings suggest that elevated inflammatory markers and disrupted intestinal barrier integrity may contribute to cognitive decline. These results highlight the need to develop dietary interventions to mitigate cognitive impairment through modulation of inflammation.},
}
@article {pmid40617320,
year = {2025},
author = {Lu, Y and Yi, F and Chen, W and Tan, X and Li, K and Yang, C and Lin, Y},
title = {Involvement of oxidative stress, lipid dysmetabolism and gut microbiol dysbiosis in oxaliplatin-induced fatty liver disease: evidence from a tree shrew model.},
journal = {Clinics and research in hepatology and gastroenterology},
volume = {},
number = {},
pages = {102645},
doi = {10.1016/j.clinre.2025.102645},
pmid = {40617320},
issn = {2210-741X},
abstract = {BACKGROUND: Oxaliplatin is cornerstone treatment for colorectal cancer, yet a significant proportion of patients develop drug-induced fatty liver disease (DILI). How it induces such liver injury is poorly understood and whether the gut microbiome is involved remains unknown.<br><br>METHODS: A male tree shrew model of oxaliplatin-induced DILI was established by six intraperitoneal injections (7 mg/kg every two weeks). During the early and late phases of liver injury, liver tissue was analyzed in terms of histopathology, oxidative stress and transcriptional profiling, while feces were subjected to microbial profiling based on 16S rRNA sequencing.<br><br>RESULTS: The model recapitulated key features of DILI, including severe hepatocyte steatosis and ballooning in the early phase after the final treatment, mild hepatic steatosis with sinusoidal dilatation in the late phase, and persistent hepatic oxidative stress during both phases. Transcriptional analysis of liver tissue identified 1503 differentially expressed genes (DEGs) between oxaliplatin-treated and control animals, of which 601 DEGs differed between treated animals in the early or late phases after the final treatment of DILI. Pathway enrichment revealed significant dysregulation in oxidative stress (e.g. NDUFA12, OSR1, MPO) and lipid metabolism (e.g., LDAH, ACACB, CH25H, LIPE) genes. Gut microbiota profiling showed an increase in the relative abundance of potentially harmful bacteria (e.g., Parabacteroides, Rikenella, Alistipes and Faecalitalea) and a concurrent decrease in the abundance of anti-oxidative bacteria (e.g., Lactococcus and Flavobacterium). Notably, abundance of several microbial genera in the gut correlated with liver expression of genes involved in oxidative stress and lipid metabolism as well as with levels of oxidative stress markers, and/or fat deposition in the liver.<br><br>CONCLUSION: Our results suggest that our tree shrew model can faithfully replicate key characteristics of oxaliplatin-induced fatty liver disease, and that such disease involves oxidative stress and lipid dysmetabolism in the liver as well as dysbiosis of microbiota in the gut.},
}
@article {pmid40617300,
year = {2025},
author = {Martin, EM and Xue, J and Smith, CJ},
title = {Effects of environmental toxicant exposures on oxytocin and vasopressin systems in the developing brain: Factors imparting risk and resilience.},
journal = {Behavioural brain research},
volume = {},
number = {},
pages = {115723},
doi = {10.1016/j.bbr.2025.115723},
pmid = {40617300},
issn = {1872-7549},
abstract = {Environmental toxicants are increasingly prevalent worldwide and associated with numerous neurodevelopmental and psychiatric health outcomes. Exposure to these toxicants, particularly during gestation and the early postnatal period, alters maternal and offspring stress responses, inflammation, and behavioral outcomes. Oxytocin (OT) and arginine vasopressin (AVP) are highly conserved neuropeptides with myriad roles in the regulation of social behavior, stress responses, and more. While developmental stress is well known to impact OT and AVP systems, a growing body of literature suggests that early-life exposure to toxicants also impacts OT and AVP system development. Here we review the evidence demonstrating that perinatal exposures to environmental toxicants program developmental trajectories of the OT and AVP systems. Perinatal exposure to flame retardants, pesticides, plastics, and air pollution induces a variety of changes to OT and AVP systems in the brain, affecting the neuropeptides themselves as well as their primary central receptors, the oxytocin receptor (OTR) and the vasopressin receptor 1a (V1aR), respectively. Next, we discuss two biological mechanisms of action that may underlie the effects of toxicant exposure on OT and AVP: endocrine disruption and maternal immune activation. Finally, we explore key factors that promote either risk or resilience to toxicant exposures, including psychosocial experience, sex, the gut microbiome, and dosage/timing of exposure. Cumulatively, the literature reviewed suggests that preventing psychosocial stress to mothers during the perinatal period while promoting positive psychosocial experiences may lessen the impact of toxicants on offspring outcomes. Furthermore, the gut microbiome may be an important intermediary, and therefore target for intervention, between toxicant exposures and OT and AVP systems in the brain.},
}
@article {pmid40617206,
year = {2025},
author = {Mu, Y and Liu, L and He, J and Zhang, H and Yu, S and Zhu, Z and Huang, Y and Mou, M and Zhang, C},
title = {Investigating the variations in microbiome and volatilome characteristics of sauce-flavor Muqu across different grades and production rounds.},
journal = {Food chemistry},
volume = {492},
number = {Pt 1},
pages = {145394},
doi = {10.1016/j.foodchem.2025.145394},
pmid = {40617206},
issn = {1873-7072},
abstract = {Muqu is the starter of high-temperature Daqu; however, the mechanisms underlying its quality formation remain unclear. Therefore, the effects of grade and round on Muqu quality were investigated. Biochemical activities were closely associated with grade, while moisture and fat content were linked to round. The volatilome was also significantly influenced by grade, with levels of differential compounds such as trimethylpyrazine, 2,3-butanediol, and methyl hexanoate showing a positive correlation with grade. In contrast, bacterial and fungal diversities were regulated by grade and round, respectively, resulting in distinct interaction patterns within the co-occurrence network. Acidity and amino acid nitrogen levels were key factors driving community assembly, and Virgibacillus, Kroppenstedtia, Thermoactinomyces, Aspergillus, and Byssochlamys were identified as the primary flavor producers. Functional predictions indicated the pivotal role of bacterial communities in flavor synthesis and fungal communities in carbohydrate metabolism. These findings provide new insights into improving Daqu quality via the Muqu grading strategy.},
}
@article {pmid40617156,
year = {2025},
author = {Sola-Leyva, A and Pérez-Prieto, I and Di Nisio, V and Panagiotis-Deligiannis, S and Blanco-Rodríguez, L and Acharya, G and Saare, M and Papaikonomou, K and Damdimopoulou, P and Salumets, A and Altmäe, S},
title = {Assessing the ovarian microbiome: lack of a distinguishable microbial signature beyond contamination.},
journal = {Reproductive biomedicine online},
volume = {51},
number = {3},
pages = {104988},
doi = {10.1016/j.rbmo.2025.104988},
pmid = {40617156},
issn = {1472-6491},
abstract = {RESEARCH QUESTION: Do the ovaries harbour commensal microbes?<br><br>DESIGN: Twenty-two ovarian tissue samples (cortex and medulla), six follicular fluid samples from gender-reassignment patients (GRP, n&#x202f;=&#x202f;11) and five ovarian cortex tissue samples from Caesarean sections (n&#x202f;=&#x202f;5), together with positive and negative controls, were analysed by bacterial 16S rRNA gene sequencing. Negative controls were obtained from saline storage buffer, air contaminants from the laboratory and operating room, and samples from clinicians and researchers handling the samples.<br><br>RESULTS: Of the 33 ovarian tissue and follicular fluid samples analysed, 63.6% did not result in any bacterial DNA amplification on PCR. As a result, only 1 out of 6 follicular fluid samples from GRP resulted in DNA amplification, while two ovarian cortex and four medulla samples from GRP, together with five ovarian samples from women undergoing Caesarean section, presented detectable bacterial DNA. Following sequencing, quality filtering and decontamination, negligible microbial reads were detected in these 12 samples. Despite strict protocols to avoid contamination during sample collection and processing, a high proportion of contaminant reads (30.3-100%, median 62.1%) were found in all the samples.<br><br>CONCLUSIONS: These findings do not support the existence of a specific ovarian microbiome in the ovaries of healthy participants. It can be concluded that the incidental detection of low-biomass bacterial genera is probably attributable to contamination.},
}
@article {pmid40617143,
year = {2025},
author = {Corrivetti, G and Monaco, F and Vignapiano, A and Marenna, A and Panarello, E and Di Gruttola, B and Landi, S and Malvone, R and Vecchi, C and Leo, S and Carmellini, P and Steardo, L and Solmi, M and Panella, R and Fasano, A},
title = {Precision medicine for depression: Improving treatment response and remission.},
journal = {Asian journal of psychiatry},
volume = {110},
number = {},
pages = {104585},
doi = {10.1016/j.ajp.2025.104585},
pmid = {40617143},
issn = {1876-2026},
abstract = {This review synthesises current knowledge to improve understanding of the pathophysiology of major depressive disorder (MDD) and optimise diagnostic, therapeutic and prognostic approaches. It examines the interplay between genetic, epigenetic, inflammatory, neurotransmitter and gut microbiome factors, together with environmental stressors and different clinical symptom presentations, in shaping MDD presentation and treatment response. Studies have revealed potential biomarkers predictive of treatment response, allowing differentiation of MDD subtypes and facilitating remission monitoring. While studies have identified potential biomarkers predictive of treatment response and enabling MDD subtype differentiation, significant challenges remain in achieving fully optimized therapeutic efficacy and widespread remission. A holistic, data-driven approach is key to addressing the complex aetiology of MDD, ultimately improving outcomes for patients and reducing the substantial burden of this prevalent disorder.},
}
@article {pmid40616950,
year = {2025},
author = {Jain, CK and Maurya, S and Singh, A},
title = {Bioinformatics-driven salivary microbial and functional profiling for identifying biomarkers in oral cancer and tobacco abusers in the Indian population.},
journal = {Archives of oral biology},
volume = {178},
number = {},
pages = {106346},
doi = {10.1016/j.archoralbio.2025.106346},
pmid = {40616950},
issn = {1879-1506},
abstract = {OBJECTIVE: To investigate alterations in the salivary microbiome and its functional potential in Oral Squamous Cell Carcinoma (OSCC) patients, tobacco abusers, and healthy individuals in order to identify microbial biomarkers and gain insight into OSCC pathogenesis.<br><br>DESIGN: Saliva-derived 16S rRNA gene sequences from OSCC patients, tobacco users, and healthy controls were obtained from the Indian Biological Data Centre (IBDC). Taxonomic classification was performed using QIIME2, and functional prediction was conducted with MicFunPred. Alpha and beta diversity, differential abundance, and pathway enrichment analyses were used to compare microbial communities and functions among the groups.<br><br>RESULTS: OSCC samples showed significantly reduced alpha diversity and distinct microbial community profiles relative to healthy controls. Genera including Porphyromonas, Streptococcus, Rothia, and Parvimonas were enriched in OSCC and are associated with inflammation and carcinogenesis. Tobacco users exhibited increased microbial richness, with dominance of Prevotella, Veillonella, and Peptostreptococcus, indicative of adaptation to chemical exposure. Functional predictions in OSCC samples indicated enrichment in pathways related to bacterial chemotaxis, lipopolysaccharide biosynthesis, glycolysis, and DNA repair. Tobacco-associated microbiota showed elevated oxidative stress response and detoxification pathways.<br><br>CONCLUSIONS: Microbial dysbiosis and functional alterations in the oral microbiome are strongly associated with OSCC and tobacco use. The identification of disease-specific microbial signatures and pathways highlights the potential of the oral microbiome as a non-invasive biomarker and therapeutic target for precision medicine in OSCC, particularly in the Indian population.},
}
@article {pmid40616901,
year = {2025},
author = {Flygel, TT and Bargheet, A and Abotsi, RE and Claassen-Weitz, S and Simms, V and Hjerde, E and Mwaikono, KS and Mchugh, G and Hameiri-Bowen, D and Pettersen, VK and Ferrand, RA and Nicol, M and Cavanagh, JP and Flaegstad, T and Sovershaeva, E},
title = {Effect of long-term azithromycin treatment on gut microbial diversity in children and adolescents with HIV-associated chronic lung disease.},
journal = {EBioMedicine},
volume = {118},
number = {},
pages = {105832},
doi = {10.1016/j.ebiom.2025.105832},
pmid = {40616901},
issn = {2352-3964},
abstract = {BACKGROUND: HIV-associated chronic lung disease (HCLD) is common in children and adolescents growing up with HIV. The use of azithromycin (AZM) reduces the rate of acute respiratory exacerbations in this population, however, impact of this treatment on the gut microbiota and associations with blood-derived inflammatory markers have not been studied.<br><br>METHODS: Children and adolescents with HCLD in Harare, Zimbabwe and Blantyre, Malawi were recruited in a double-blind, placebo-controlled trial of once-weekly AZM or placebo for 48 weeks (BREATHE trial, NCT02426112). Rectal swabs were collected at inclusion (N = 346), 48 weeks (treatment end, N = 313), and 72 weeks (six months after treatment cessation, N = 244). The bacterial composition of fecal swabs was determined using 16S rRNA gene sequencing. Plasma biomarkers at inclusion and 48 weeks were measured using Luminex multiplex bead assay.<br><br>FINDINGS: At 48 weeks, bacterial &#x3b1;-diversity was significantly lower in the AZM group, with 27 bacterial genera showing differential abundance between the study groups. The placebo group exhibited higher interconnectivity between bacterial genera at 48 weeks compared to the AZM group. Correlations between the top seven differentially abundant genera and biomarkers observed at inclusion were no longer significant at 48 weeks in both groups. Depletion of Campylobacter persisted for six months after cessation of AZM treatment.<br><br>INTERPRETATION: Long-term AZM treatment in HCLD patients affects their gut bacterial composition at least 6 months after its cessation. The consequences of reduced bacterial diversity, such as altered interaction with the immune system and risk of resistance, need further investigation to understand how to optimise gut health during long-term antibiotic treatments.<br><br>FUNDING: The study was funded by the Norwegian Research Council and Helse Nord (HNF 1387-17).},
}
@article {pmid40616741,
year = {2025},
author = {Renton, N and Pillinger, MH and Toprover, M},
title = {Gout, Hyperuricemia, and the Intestinal Microbiome.},
journal = {Inflammation},
volume = {},
number = {},
pages = {},
pmid = {40616741},
issn = {1573-2576},
abstract = {Gout is a disease of hyperuricemia (HU) leading to monosodium urate crystal deposition in the joint, resulting in inflammation and joint damage. Recently, efforts have been made to characterize the intestinal microbiome of patients who suffer from HU and gout, and pre-clinical studies have evaluated the utility of prebiotics and probiotics in alleviating gout. Herein we review recent notable studies addressing these topics. In brief, the "gouty" microbiome is characterized by reduced diversity, an elevated Bacteroides: Firmicutes ratio, and reduced presence of Akkermansia and Bifidobacterium. In anserine models, supplementation with Lactobacillus probiotic strains appears to reduce serum urate (SU) and HU-induced inflammation. Murine models suggest that the chicory-derived prebiotic inulin may reduce SU, and oral supplementation with the anti-inflammatory short-chain fatty acid butyrate may lower SU by enhancing urate excretion and alleviate HU-induced tissue inflammation. Many of these studies are limited by modest numbers of participants and/or incompletely documented experimental controls, and, in the case of animal models, questionable reproducibility in humans. Many studies have been geographically limited. There remains a need for more information regarding the features of the "gouty" microbiome in wider populations, as well as for additional well-controlled probiotic and prebiotic studies in more physiologically relevant animal models prior to clinical trials.},
}
@article {pmid40616291,
year = {2025},
author = {Facchin, S and Bonazzi, E and Tomasulo, A and Bertin, L and Lorenzon, G and Maniero, D and Zingone, F and Cardin, R and Barberio, B and Ghisa, M and Savarino, EV},
title = {Could modulating the esophageal microbiome be the answer for eosinophilic esophagitis treatment?.},
journal = {Expert review of gastroenterology &amp; hepatology},
volume = {},
number = {},
pages = {1-9},
doi = {10.1080/17474124.2025.2530606},
pmid = {40616291},
issn = {1747-4132},
abstract = {INTRODUCTION: The oral and esophageal microbiota are gaining recognition for their significance in managing Eosinophilic Esophagitis (EoE). They serve as diagnostic biomarkers and therapeutic targets.<br><br>AREAS COVERED: The primary goal of EoE treatment is to alleviate symptoms such as dysphagia, heartburn, nausea, and chest pain. These symptoms are often associated with dysfunction of the esophageal barrier, closely linked to the esophageal microbiota. The composition of the esophageal microbiota can be affected by pharmacological treatments, particularly proton pump inhibitors, corticosteroids, and dietary interventions suggested for EoE management. As a result, the intestinal microbiota may also be influenced by these pharmacological approaches. Emerging research points to the potential of probiotic treatments as a complementary option to pharmacological therapy in the management of EoE. Publications linking 'EoE' to 'microbiome-microbiota' from 2013 to 2025&#xa0;have been considered.<br><br>EXPERT OPINION: Further investigation into probiotics could expand the range of therapeutic options available alongside conventional treatments, potentially improving EoE remission rates, enhancing patient compliance, and reducing treatment-related side effects.},
}
@article {pmid40615889,
year = {2025},
author = {Park, K and Kim, Y and Kim, D and Oh, SM and Koo, TJ and Yoo, SM and Yoon, SH},
title = {Regulation of the tagatose catabolic gene cluster and development of a tagatose-inducible expression system in the probiotic Escherichia coli Nissle 1917.},
journal = {Microbial cell factories},
volume = {24},
number = {1},
pages = {158},
pmid = {40615889},
issn = {1475-2859},
support = {NRF-2022R1A2C2004292//National Research Foundation of Korea/ ; RS-2024-00401518//National Research Foundation of Korea/ ; },
mesh = {*Escherichia coli/genetics/metabolism ; *Probiotics/metabolism ; *Hexoses/metabolism ; *Gene Expression Regulation, Bacterial ; *Multigene Family ; Escherichia coli Proteins/genetics/metabolism ; Humans ; },
abstract = {BACKGROUND: The probiotic Escherichia coli Nissle 1917 (EcN) is a promising microbial chassis for therapeutic and industrial applications. However, its broad utility is limited by a lack of reliable inducible gene expression systems that precisely control gene expression.<br><br>RESULTS: We developed a tagatose-inducible expression system in EcN using D-tagatose, a naturally occurring sugar with established safety in humans, as a metabolizable inducer. Through differential RNA sequencing and sequence analysis, we identified the key regulatory elements governing D-tagatose catabolism in EcN and demonstrated that the DeoR family regulator (TagR) functions as a tagatose-responsive repressor. The developed system exhibited a strong dose-dependent response to D-tagatose, ensuring uniform and tunable gene activation across cell populations. Additionally, a catabolite repression-enabled auto-induction strategy facilitated robust biomass accumulation, followed by targeted protein production. This expression system was successfully applied to overexpress recombinant proteins under both aerobic and anaerobic conditions.<br><br>CONCLUSIONS: D-Tagatose is a naturally occurring low-calorie sugar that can serve as an inducer in vivo, including within the human gut microbiome. Thus, the tagatose-inducible expression system provides EcN with an additional tunable option for gene regulation, which may be valuable in applications such as synthetic biology and metabolic engineering.},
}
@article {pmid40615864,
year = {2025},
author = {Kim, H and Chae, Y and Cho, JH and Song, M and Kwak, J and Doo, H and Choi, Y and Kang, J and Yang, H and Lee, S and Keum, GB and Wattanaphansak, S and Kim, S and Kim, HB},
title = {Understanding the diversity and roles of the canine gut microbiome.},
journal = {Journal of animal science and biotechnology},
volume = {16},
number = {1},
pages = {95},
pmid = {40615864},
issn = {1674-9782},
support = {RS-2023-00230754//Rural Development Administration/ ; },
abstract = {The canine gut microbiome plays a vital role in overall health and well-being by regulating various physiological functions, including digestion, immune responses, energy metabolism, and even behavior and temperament. As such, a comprehensive understanding of the diversity and functional roles of the canine gut microbiome is crucial for maintaining optimal health and well-being. In healthy dogs, the gut microbiome typically consists of a diverse array of bacterial phyla, including Firmicutes, Bacteroidetes, Actinobacteria, Fusobacteria, and Proteobacteria. These microbial communities form a complex ecosystem that interacts with the host to support canine health and homeostasis. A well-balanced microbiome, known as eubiosis, represents an optimized microbial composition that enhances host health and metabolic functions. Eubiosis is shaped by interactions between host physiology and environmental factors. However, dysbiosis, a disruption of eubiosis, can contribute to various health issues, such as weight fluctuations, metabolic disorders, and behavioral changes. Maintaining eubiosis in the canine gut microbiome requires customized management strategies that consider both physiological traits and environmental influences. In this review, we explored the structure and function of the canine gut microbiome, with particular emphasis on its role in health and the key factors that influence and support its maintenance.},
}
@article {pmid40615853,
year = {2025},
author = {Li, S and Xu, Z and Diao, H and Zhou, A and Tu, D and Wang, S and Feng, Y and Feng, X and Lai, Y and Yang, S and Tang, B},
title = {Gut microbiome alterations and hepatic encephalopathy post-TIPS in liver cirrhosis patients.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {745},
pmid = {40615853},
issn = {1479-5876},
mesh = {Humans ; *Hepatic Encephalopathy/microbiology/etiology/blood ; *Liver Cirrhosis/microbiology/surgery/complications ; *Gastrointestinal Microbiome/genetics ; Male ; Female ; Middle Aged ; *Portasystemic Shunt, Transjugular Intrahepatic/adverse effects ; Ammonia/blood ; Aged ; },
abstract = {BACKGROUND: The transjugular intrahepatic portosystemic shunt (TIPS), a crucial tool for treating complications related to portal hypertension in patients with liver cirrhosis, is often associated with an increased risk of postoperative complications such as hepatic encephalopathy. Accurate preoperative prediction of the risk of developing hepatic encephalopathy is critical for optimizing the rational clinical application of TIPS.<br><br>METHODS: In this study, stool samples from 67 patients were collected preoperatively and 1&#xa0;month postoperatively and metagenomic sequencing was performed to assess the composition of the gut microbiota. The differential abundances of species and MetaCyc pathways were analyzed using microbiome multivariate associations with linear models. Correlations between variables, including species abundance, the MetaCyc pathway, and clinical characteristics, were assessed using the Pearson correlation test. Prognostic models were developed from metagenomic sequencing cohorts to predict hepatic encephalopathy (HE) and elevated blood ammonia levels.<br><br>RESULTS: We demonstrated that the abundance of Phocaeicola vulgatus increased after TIPS, and the urea cycle decreased. A positive correlation was observed between P.vulgatus and elevated blood ammonia levels (P&#x2009;<&#x2009;0.05). Patients exhibiting increased blood ammonia after TIPS showed significant enrichment of P.vulgatus (LDA&#x2009;>&#x2009;2.5), accompanied by a reduction in the urea cycle (P&#x2009;<&#x2009;0.05) and associated enzymes (P&#x2009;<&#x2009;0.05). Similar microbiota alterations were identified in patients who experienced postoperative hepatic encephalopathy. Furthermore, a comprehensive genetic profile of P.vulgatus was developed, highlighting its ability to increase amino acid metabolism. Many models have shown that the use of gut microbiota characteristics has greater predictive performance.<br><br>CONCLUSION: Multiple machine learning models revealed that P.vulgatus may serve as a significant predictive microbe for hepatic encephalopathy after TIPS, which may be closely related to its ability to metabolize ammonia. These findings establish a microbiome-based framework for postoperative complication risk stratification and personalized preoperative interventions and offer unexplored targets for future research.},
}
@article {pmid40615821,
year = {2025},
author = {Upadhyay, P and Kumar, S and Tyagi, A and Tyagi, AR and Barbhuyan, T and Gupta, S},
title = {Gut Microbiome rewiring via fecal transplants: Uncovering therapeutic avenues in Alzheimer's disease models.},
journal = {BMC neuroscience},
volume = {26},
number = {1},
pages = {39},
pmid = {40615821},
issn = {1471-2202},
support = {File no.R.12014/20/2018//Department of Health Research, India/ ; DBT Core grant//National Institute of Immunology New Delhi India/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; *Fecal Microbiota Transplantation/methods ; *Alzheimer Disease/therapy/microbiology/psychology ; Mice ; Disease Models, Animal ; Mice, Inbred C57BL ; Male ; Mice, Transgenic ; Oxidative Stress ; },
abstract = {BACKGROUND: Emerging evidence implicates the gut microbiome in Alzheimer's disease (AD) pathogenesis, yet the underlying mechanisms remain elusive. This study elucidates the bidirectional relationship between gut microbiota and AD using fecal microbiota transplantation (FMT) in a mouse model.<br><br>RESULT: Through meticulous experimentation, we conducted reciprocal FMT between AD (5xFAD) and healthy (C57BL/6) mice to unravel the impact of gut microbiome alterations on cognitive function and neuroinflammation. FMT from 5xFAD to C57BL/6 mice induced profound memory impairment and cognitive deficits, accompanied by elevated inflammatory cytokine levels, oxidative stress markers, and systemic inflammation, as evidenced by increased plasma cytokines. Conversely, transplanting healthy microbiota into 5xFAD mice yielded remarkable behavioral improvements, including enhanced spatial memory performance in the Morris water maze, directly correlating with cognitive recovery. Our findings underscore the pivotal role of the gut microbiome in AD pathogenesis and offer a promising therapeutic avenue.<br><br>CONCLUSION: Targeted modulation of the gut microbiome through strategies like FMT may offer potential benefits in Alzheimer's disease by influencing neuroinflammation, oxidative stress, and cognitive function. This comprehensive study provides novel insights into the gut-brain axis dynamics and paves the way for innovative microbiome-based interventions in AD management.},
}
@article {pmid40615170,
year = {2025},
author = {Chowdhury, R and Maddheshiya, A and Taneja, S and Bhandari, N and Majumder, PP and Strand, TA and Pandey, RM and Kurpad, AV and Mukherjee, S},
title = {Impact of an Integrated Intervention Package During Preconception, Pregnancy, and Early Childhood on the Gut Microbiome at Six Months of Age: Findings from the Women and Infants Integrated Growth Study (WINGS) Randomized Controlled Trial.},
journal = {The Journal of nutrition},
volume = {155},
number = {7},
pages = {2355-2366},
doi = {10.1016/j.tjnut.2025.04.016},
pmid = {40615170},
issn = {1541-6100},
mesh = {Humans ; Female ; *Gastrointestinal Microbiome ; Pregnancy ; Infant ; Adult ; Young Adult ; Adolescent ; Male ; Feces/microbiology ; *Preconception Care ; },
abstract = {BACKGROUND: The infant gut microbiome is essential for healthy growth and development. However, limited research has explored how interventions targeting maternal and infant health, nutrition, and psychosocial conditions during preconception, pregnancy, and early childhood impact microbiome development. To address this research gap and better understand the potential impact of such interventions, this study was designed to evaluate their effects on the infant gut microbiome.<br><br>OBJECTIVE: The aim was to evaluate the effects of an integrated intervention package on infant gut microbiome at 6 mo of age compared with routine care.<br><br>METHODS: The study was embedded in a randomized factorial trial involving women aged 18-30 y. Participants were randomly assigned to receive either a preconception intervention package or routine care until pregnancy. Pregnant women were then randomly assigned to receive a pregnancy and early childhood intervention package or routine care. The intervention included health care for growth-related conditions, nutrition, water, sanitation, and hygiene (WASH), and psychosocial care. Stool samples from 392 infants (185 from the preconception, pregnancy, and early childhood intervention group and 207 from the routine care group) were collected at 6 mo, followed by microbiome DNA isolation and high-throughput sequencing of the V3-V4 region of 16S rRNA gene. Generalized linear models were used to estimate the mean relative abundance of core gut microbiome phyla, genera, and species between the intervention and routine care groups.<br><br>RESULTS: Infants in the group who received preconception, pregnancy, and early childhood intervention had a significantly lower mean relative abundance of Klebsiella genus under the Pseudomonadota phylum (45% lower; 95% confidence interval [CI]: 18, 63) and Klebsiella pneumoniae species (38% lower; 95% CI: 8, 59) compared with routine care group. In contrast, the relative abundance of Megasphaera (72% higher; 95% CI: 7, 175), Prevotella (72% higher; 95% CI: 3, 187), and Bifidobacterium breve (34% higher; 95% CI: 2, 79) was significantly higher in the group received preconception, pregnancy and early childhood intervention compared with routine care.<br><br>CONCLUSIONS: The findings indicate that improving maternal and infant health, nutrition, and psychosocial conditions enhances the relative abundance of beneficial gut bacteria at 6 mo of age, supporting healthy growth and development. This trial was registered at Clinical Trials Registry-India as CTRI/2020/10/028770; https://ctri.nic.in/Clinicaltrials/advsearch2.php.},
}
@article {pmid40615087,
year = {2025},
author = {Wang, H and Liang, Y and Boor, PJ and Khanipov, K and Zhang, Y and Yu, X and Ambati, CSR and Putluri, N and Khan, MF},
title = {Protective role of dietary short chain fatty acid propionate against autoimmune responses and pathology of systemic lupus erythematosus in MRL-lpr mice.},
journal = {The Journal of nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tjnut.2025.06.031},
pmid = {40615087},
issn = {1541-6100},
abstract = {BACKGROUND: Systemic lupus erythematosus (SLE) is a chronic autoimmune disease (AD) that affects multiple organs, including skin and kidney. The etiology of SLE remains unclear but involves hormonal, environmental and genetic factors. Environmental factors, such as diet and microbiota-derived metabolites, among which short chain fatty acids (SCFAs) are major players, can influence AD pathogenesis.<br><br>OBJECTIVE: This study investigates the involvement of SCFAs in the pathogenesis of SLE and further investigated the effect of propionate (PA) supplementation on SLE disease outcome in MRL-lpr mice.<br><br>METHODS: Cecal SCFAs from mouse models with varying degrees of SLE disease activities (C57BL/6, MRL+/+ and MRL-lpr) were determined by LC-MS analysis. Five-week-old MRL-lpr mice were supplemented with PA (200 mM, via drinking water) for 6 weeks, and assessed autoimmunity and disease markers.<br><br>RESULTS: LC-MS analysis of cecal SCFAs showed a significant decrease of PA in MRL-lpr mice (p < 0.001). PA treatment ameliorated the autoimmune response, evident from reduced serum autoantibodies (p < 0.05 for both ANA and anti-dsDNA) and a significant alleviation of glomerulonephritis (p < 0.05). Furthermore, it restored the imbalances in gut microbiome composition and SCFAs, especially propionate (p < 0.01). Additionally, PA treatment resulted in decreased splenic activated CD4 T cells (p < 0.05) and alterations in renal inflammatory signaling pathways.<br><br>CONCLUSIONS: Our findings support the beneficial effects of propionate in alleviating SLE, and therapeutic potential of propionate or propionate-producing bacteria for SLE.},
}
@article {pmid40615083,
year = {2025},
author = {Duan, Y and Li, Y and Xu, C and Wang, W and Wang, X and Zheng, W and Hsing, JC and Wu, J and Myers, A and Hsing, AW and He, W and Zhu, S},
title = {Fried food consumption-related gut microbiota is associated with obesity, fat distribution and cardiometabolic diseases: results from two large longitudinal cohorts with sibling comparison analyses.},
journal = {The American journal of clinical nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ajcnut.2025.06.025},
pmid = {40615083},
issn = {1938-3207},
abstract = {BACKGROUND: In prospective cohort studies, the relationship between fried food consumption, gut microbiota, obesity, and cardiometabolic diseases remains unknown.<br><br>OBJECTIVE: We aimed to explore associations of fried food consumption with gut microbiota and associations of fried food consumption-related microbiota with obesity and related disorders.<br><br>METHODS: We analyzed 6,637 individuals from the WELL-China cohort (baseline 2016-2019) and 3,466 from the Lanxi cohort (baseline 2017-2019), with follow-up until June 24, 2024. Face-to-face interviews provided data on fried food consumption and other covariates. Analysis of 16S rRNA data from fecal samples collected at baseline identified microbial genera. Body composition was evaluated using dual-energy X-ray absorptiometry (DXA). The Microbiome Multivariable Associations with Linear Models (MaAsLin) helped identify genera associated with frequency of fried food consumption in the cross-sectional analysis. Cox regression models examined the relationship of fried food consumption-related microbiota with cardiometabolic diseases during follow-up. Sibling comparison analyses were used to control for unmeasured familial confounders using the between-within (BW) model.<br><br>RESULTS: Twenty-five microbial genera were significantly associated with fried food consumption frequency. Using these genera, we constructed a fried food consumption-related microbiota index. Meta-analysis of both cohorts found a positive relationship of this index with overall adiposity measures (BMI) (&#x3b2; coefficient, 0.26; 95% confidence interval (CI), 0.19-0.32) and central fat distribution parameters (including android-gynoid fat ratio (&#x3b2;, 1.48; 95% CI, 1.14-1.82)). Longitudinal analyses indicated that a higher fried food consumption-related microbiota index was linked to a higher risk of developing cardiometabolic diseases, with adjusted hazard ratios (95% CI) of 1.16 (1.07-1.27) for diabetes and 1.16 (1.06-1.26) for major adverse cardiovascular events. Sibling comparison analyses yielded similar results.<br><br>CONCLUSIONS: Fried food consumption-related microbiome is associated with a higher risk of obesity, central fat distribution, and cardiometabolic diseases, emphasizing the importance of dietary choices in the management and prevention of chronic diseases.},
}
@article {pmid40615058,
year = {2025},
author = {Vanhatalo, A and L'Heureux, JE and Black, MI and Blackwell, JR and Aizawa, K and Thompson, C and Williams, DW and van der Giezen, M and Winyard, PG and Jones, AM},
title = {Ageing modifies the oral microbiome, nitric oxide bioavailability and vascular responses to dietary nitrate supplementation.},
journal = {Free radical biology &amp; medicine},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.freeradbiomed.2025.07.002},
pmid = {40615058},
issn = {1873-4596},
abstract = {This study evaluated whether changes in the oral microbiome in response to dietary nitrate and antiseptic mouthwash treatments were related to changes in nitric oxide bioavailability and vascular function. Thirty-nine young (18-30 years) and thirty-six older (67-79 years) males and females completed a placebo-controlled, double-blind cross-over intervention including three 2-week conditions separated by 2-week washouts: placebo beetroot juice (PL), nitrate-rich beetroot juice (BR) and antiseptic mouthwash (MW). The oral microbiomes of young and older adults responded differently to BR (post BR non-metric multidimensional scaling P=0.01), while the oral microbiomes of both age groups were unaffected by PL and MW interventions. Older people, who had elevated baseline mean arterial pressure (MAP; 95±9 mmHg) compared to young adults (87±7 mmHg, P<0.001), showed decreased brachial MAP (-4±4 mmHg, P=0.003) after BR while this effect was absent in the young. Flow mediated dilatation (FMD) variables were not affected by the interventions in older adults, while in the young there was a difference in changes (from pre to post) in ΔFMD% between the MW and BR conditions (P=0.04). Decreased blood pressure in older adults correlated with increased plasma nitrite concentration (change in central MAP vs. [NO2[-]] r=-0.41, P=0.02), which in turn correlated with decreases within the co-occurring module of bacteria dominated by the genus Prevotella (P. intermedia r=-0.72, P=0.001; P. dentalis r=-0.88, P<0.0001; Crassaminicella sp. SY095 r=-0.81, P<0.0001). Greater blood pressure benefits from supplemental dietary nitrate in older compared to younger people are mediated primarily by the suppression of potentially harmful oral bacteria, that have been associated with ammonia production.},
}
@article {pmid40614920,
year = {2025},
author = {Yadav, S and Raj, RG},
title = {Parkinson's disease and the gut microbiota connection: unveiling dysbiosis and exploring therapeutic horizons.},
journal = {Neuroscience},
volume = {581},
number = {},
pages = {1-15},
doi = {10.1016/j.neuroscience.2025.07.003},
pmid = {40614920},
issn = {1873-7544},
abstract = {Parkinson's disease (PD) is a progressive neurodegenerative disorder marked by dopaminergic neuronal loss, α-synuclein aggregation, and sustained neuroinflammation. Emerging evidence supports the gut-brain-microbiota axis as a pivotal player in the disease's pathogenesis. Dysbiosis, disruptions in the gut microbial composition, has been consistently observed in individuals with PD, with notable reductions in beneficial, short-chain fatty acid-producing bacteria and elevations in pro-inflammatory microbial species. These alterations contribute to increased intestinal permeability, systemic inflammation, and heightened neuroinflammatory responses that may drive α-synuclein misfolding and dopaminergic degeneration. In addition, microbial metabolites, including lipopolysaccharides and amyloid proteins such as curli, may promote neurodegeneration via immune and molecular mimicry pathways. Recent advances highlight the bidirectional influence of the microbiota-gut-brain axis on PD symptoms, ranging from motor deficits to non-motor features like constipation, depression, and cognitive decline. Several microbiota-modulating interventions, including probiotics, prebiotics, dietary strategies, antibiotics, and fecal microbiota transplantation, have demonstrated neuroprotective potential in both preclinical and clinical contexts. However, inter-individual variability, methodological heterogeneity, and the absence of longitudinal, multi-omics-integrated studies limit current understanding. The gut microbiome also holds promise as a non-invasive biomarker for early PD detection and prognosis, though standardization remains a challenge. Future research must clarify causal mechanisms, optimize therapeutic delivery, and integrate genetic, metabolic, and environmental data to advance precision medicine approaches. This review consolidates current knowledge on gut microbiota's role in PD pathophysiology and therapeutic innovation, providing a roadmap for future research directions.},
}
@article {pmid40614884,
year = {2025},
author = {Dong, TS and Jann, K and Wang, DJ and Church, A},
title = {Understanding Whole Person Systems in Brain-Gut-Microbiome Research Through Ultra-High-field MRI Imaging.},
journal = {NeuroImage},
volume = {},
number = {},
pages = {121360},
doi = {10.1016/j.neuroimage.2025.121360},
pmid = {40614884},
issn = {1095-9572},
abstract = {The brain-gut-microbiome (BGM) axis regulates interoception, metabolism, and immunity, with dysfunction linked to IBS, obesity, and mood disorders. Ultra-high-field (UHF) MRI advances neural imaging, enhancing resolution of vagal and spinal circuits mediating gut-brain communication. UHF enables real-time tracking of interventions like vagus nerve stimulation and probiotics, linking microbiome shifts to neural adaptations. Despite challenges like signal distortions, innovations in coil design are improving imaging fidelity. Integrating neuroimaging with multi-omic profiling fosters a systems-level approach, advancing personalized therapies for BGM disorders. This commentary underscores UHF MRI's transformative potential in bridging neuroscience, microbiome science, and clinical applications.},
}
@article {pmid40614851,
year = {2025},
author = {Yang, X and Huang, X and Zheng, B and Gao, F and He, L and Xu, Q},
title = {Natural-setting evidence of stochastic-to-deterministic gut microbiome assembly and metabolic shifts in regenerating tropical sea cucumber Stichopus monotuberculatus.},
journal = {Environmental research},
volume = {285},
number = {Pt 1},
pages = {122260},
doi = {10.1016/j.envres.2025.122260},
pmid = {40614851},
issn = {1096-0953},
abstract = {Holothurians exhibit a distinctive ability to eviscerate and regenerate internal organs, making them an ideal model for investigating host-microbe interactions. This study examined the dynamics of the gut microbiome and the associated metabolome during intestinal regeneration in the tropical sea cucumber Stichopus monotuberculatus under natural conditions. Through a combination of 16S rDNA sequencing and GC-MS-based metabolomics, we determined stage-specific shifts in gut microbial communities and metabolite profiles. Early regeneration was characterized by a stochastic influx of environmental microbes, low microbial network connectivity, and high metabolite-microbe correlation complexity, which suggested that the host relied on metabolic signals to coordinate the initial colonization of a diverse microbial community sourced from environment. As regeneration advanced, the microbial network grew increasingly cohesive, environmental contribution diminished, and metabolite-microbe correlation decreased. The reestablished gut microbiome exhibited no significant structural differences compared to pre-evisceration communities. This process reflected a transition from stochastic recruitment to host-filtered deterministic assembly, ultimately restoring a stable microbiome. Core microbial taxa such as Roseburia, Faecalibacterium, and Ruegeria were associated with pathways related to nutrient provisioning, energy production, and immune regulation, suggesting their potential contributions to intestinal recovery. Metabolomic analysis revealed significant alterations in amino acid, lipid, and carbohydrate metabolism, highlighting the functional integration between the gut bacteria and regenerated host tissue. Our findings provide novel insight into the interactions among host, microbe, and environment during gut microbiome assembly, as well as highlight the balance between stochastic and deterministic factors in the formation of marine holobiont communities.},
}
@article {pmid40614836,
year = {2025},
author = {Yu, J and Zhu, H and Yu, X and Liu, Y and Zhang, J and Jiang, L and Zhang, X},
title = {Calcitriol/Vitamin D Receptor Ameliorates Fructose-Induced Enteritis-Hepatitis Axis Dysregulation in Mice.},
journal = {The Journal of nutritional biochemistry},
volume = {},
number = {},
pages = {110017},
doi = {10.1016/j.jnutbio.2025.110017},
pmid = {40614836},
issn = {1873-4847},
abstract = {Emerging evidence associates excessive fructose consumption with intestinal inflammation and metabolic dysfunction-associated steatotic liver disease (MASLD), though the underlying mechanisms remain elusive. This preclinical study systematically investigated the therapeutic potential of calcitriol/vitamin D receptor (VDR) signaling in counteracting fructose-induced gut-liver axis dysregulation using female C57BL/6J mice. Experimental groups included: (1) Control (C), (2) Fructose (F; 20% w/v fructose water for 8 weeks), (3) Fructose+Calcitriol (F+V; 300 ng/kg calcitriol gavage during weeks 4-8), and (4) Calcitriol alone (V). Key findings revealed that chronic fructose exposure induced gut microbiota dysbiosis (characterized by decreased Firmicutes/Bacteroidetes ratio), compromised intestinal barrier integrity through downregulation of tight junction proteins, depleted secretory cells (Goblet/Paneth cells), and triggered apoptosis with concomitant elevation of pro-inflammatory cytokines (TNF-α, IL-6). These intestinal alterations culminated in endotoxemia-mediated hepatic inflammation and fibrogenesis, accompanied by persistent NF-κB pathway activation. Notably, calcitriol intervention significantly restored VDR expression, enhanced autophagic flux, stimulated mucin/antimicrobial peptide production, and suppressed NF-κB-mediated inflammatory responses. In vitro validation using Caco2 and RAW264.7 cells demonstrated that VDR activation effectively reversed fructose-impaired autophagy and NF-κB hyperactivation. Microbiome analysis further indicated calcitriol's partial normalization of fructose-induced microbial shifts, suggesting microbiota-mediated mechanisms. Collectively, these findings establish that calcitriol/VDR signaling mitigates fructose-driven gut-liver axis dysfunction through coordinated regulation of autophagy, mucosal defense systems, and inflammatory pathways. This mechanistic framework positions the VDR pathway as a promising therapeutic target for enteritis-hepatitis axis disorders, warranting further clinical investigation.},
}
@article {pmid40614808,
year = {2025},
author = {He, S and Chen, C and Cao, L and Nauta, A and Liu, X and Chen, H and Spoelstra, J and Yang, B},
title = {Metabolic diversity and competitive interactions of infant-derived bifidobacteria in human milk oligosaccharides and galacto-oligosaccharides utilization.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2025-26559},
pmid = {40614808},
issn = {1525-3198},
abstract = {Human milk oligosaccharides (HMO) play a pivotal role in shaping the infant gut microbiome and immune system, primarily by selectively promoting Bifidobacterium species. Although the metabolic pathways of individual bifidobacterial strains for HMO are well-characterized, competitive interactions among multiple strains under single-HMO conditions remain poorly understood. Here, we evaluated metabolic capabilities of 15 infant-derived Bifidobacterium strains on 3 substrates: 2'-fucosyllactose (2'-FL), lacto-N-tetraose (LNT), and high-purity galacto-oligosaccharides (GOS-HP). Monoculture and mixed-culture analyses were conducted using growth kinetics, substrate consumption assays, and genomic profiling. Monoculture results demonstrated most strains exhibited robust growth on LNT and GOS-HP, whereas 2'-FL utilization varied. Genomic analysis indicated efficient HMO metabolism correlated with glycosyl hydrolase gene diversity and copy numbers. In mixed cultures, B. dentium initially dominated through monosaccharide consumption but was subsequently outcompeted by B. longum ssp. infantis and B. breve, highlighting oligosaccharide-driven competition. The LNT mixed culture resulted in a bifidobacterial community composition resembling that of breastfed infants. These findings guide oligosaccharide selection for infant formula design to better emulate human milk's microbiome-modulating benefits.},
}
@article {pmid40614713,
year = {2025},
author = {Cowan, CM and Pietras, EM},
title = {From symbiote to bad neighbor: The intestinal microbiome as a driver of CHIP.},
journal = {Cell stem cell},
volume = {32},
number = {7},
pages = {1036-1037},
doi = {10.1016/j.stem.2025.06.003},
pmid = {40614713},
issn = {1875-9777},
mesh = {*Gastrointestinal Microbiome ; Humans ; Animals ; *Hematopoietic Stem Cells/metabolism ; *Clonal Hematopoiesis ; Mice ; },
abstract = {Hematopoietic stem cells (HSCs) with mutations that can cause clonal hematopoiesis of indeterminate potential (CHIP) accumulate during aging. Agarwal et al.[1] demonstrate in Nature that intestinal barrier permeability increases with age and enables the microbial metabolite ADP-heptose to reach the bone marrow, thus driving the expansion of DNMT3A-mutant HSCs.},
}
@article {pmid40614655,
year = {2025},
author = {Ghosh, R and Sui, P and Fritze, D and Fernandez, S and Torres, A and Woodworth, J and Cigarroa, FG and Halff, GA and Kumar, AP},
title = {Characterization of metabolomic associated with pancreatic cancer patients with overweight and obesity.},
journal = {Clinical nutrition (Edinburgh, Scotland)},
volume = {51},
number = {},
pages = {240-251},
doi = {10.1016/j.clnu.2025.06.015},
pmid = {40614655},
issn = {1532-1983},
abstract = {BACKGROUND AND AIMS: The near equal incidence and mortality rates of pancreatic cancer, combined with projections that by 2050 pancreatic cancer will be the second-most fatal cancer, underscore the need to identify patients with early disease and thus interrupt this trajectory. Obesity, weight gain and waistline have been implicated in increasing the risk of pancreatic cancer. Factors such as inflammation, insulin resistance, and changes in intestinal microbiome have been suggested to be involved in obesity. Although metabolomic analyses of pancreatic cancer patients have established correlations between phospholipids, lysophospholipids with treatment outcomes, the association between metabolites, obesity, and pancreatic cancer remains largely understudied. We hypothesized that global metabolomic profile of obese and overweight pancreatic cancer patients will be different compared with healthy weight subjects with no cancer.<br><br>METHODS: Global metabolic profiles were determined in obese and overweight pancreatic cancer patients compared with healthy weight subjects using ultrahigh performance liquid chromatography-tandem mass spectroscopy.<br><br>RESULTS: Analysis of the data using the Benjamini &amp; Hochberg method to control the false discovery rate revealed statistically significant changes in branched chain amino acids, lipid metabolites including monoacyl glycerol, and fructose in overweight/obese pancreatic cancer patients relative to healthy weight.<br><br>CONCLUSION: Our findings suggest that metabolomic pathways as potential targets for high-risk pancreatic cancer patients.},
}
@article {pmid40614652,
year = {2025},
author = {Korotetskiy, I and Kuznetsova, T and Shilov, S and Zubenko, N and Ivanova, L and Korotetskaya, N and Izmailov, T},
title = {Metagenomic data insights into chicken microbiome diversity across various regions of Kazakhstan.},
journal = {Poultry science},
volume = {104},
number = {9},
pages = {105488},
doi = {10.1016/j.psj.2025.105488},
pmid = {40614652},
issn = {1525-3171},
abstract = {Understanding the gut microbiome of poultry is essential for ensuring the health, productivity, and safety of poultry products. This study aimed to assess the regional diversity and composition of chicken microbiota in Kazakhstan using high-throughput metagenomic sequencing. Tracheal and cloacal swabs were collected from chickens on private farms in five geographic locations. Pooled DNA and RNA samples were sequenced using the Ion Torrent PGM platform, and taxonomic classification was performed using Kaiju, with subsequent alpha and beta diversity analyses in R. The results revealed considerable differences in the microbial profiles between regions. Notably, Chlamydia was abundant in the Shymkent samples (>48 %) but was nearly absent elsewhere. In contrast, Pseudomonas was disproportionately dominant in Almaty (32.7 %), suggesting possible dysbiosis. This study provides the first metagenomic characterization of poultry microbiota in Kazakhstan. This highlights region-specific microbial risks and underscores the importance of spatial microbiome monitoring in poultry health management. These findings provide a basis for future strategies aimed at preventing disease outbreaks and controlling zoonotic pathogens in poultry.},
}
@article {pmid40614627,
year = {2025},
author = {Pecyna, P and Bykowska-Derda, A and Gabryel, M and Mankowska-Wierzbicka, D and Nowak-Malczewska, DM and Jaskiewicz-Rajewicz, K and Jaworska, MM and Grzymislawski, M and Dobrowolska, A and Czlapka-Matyasik, M and Gajecka, M},
title = {Blautia spp. in the gut microbiome: Its relation to dietary choices and to the nutritional status of patients with irritable bowel syndrome.},
journal = {Nutrition (Burbank, Los Angeles County, Calif.)},
volume = {138},
number = {},
pages = {112836},
doi = {10.1016/j.nut.2025.112836},
pmid = {40614627},
issn = {1873-1244},
abstract = {OBJECTIVES: Uncontrolled growth of certain Blautia spp. species could be associated with symptoms identified in patients with irritable bowel syndrome (IBS). As no studies have thus far focused on the relationship between nutrition habits, body composition, and the abundance of Blautia spp. in patients with IBS, this study aimed to determine the above-mentioned aspects.<br><br>METHODS: The gut microbiota of patients with IBS (n = 73) and a control group (n = 54) were subjected to 16S ribosomal RNA sequencing. Food frequency intake, physical activity, and socioeconomic status were measured by the Dietary Habits and Nutrition Beliefs Questionnaire KomPAN. Body composition was assessed by the air plethysmography method (BodPod, Life Measurement Inc., Concord, CA, USA).<br><br>RESULTS: Blautia spp. was more abundant in the gut microbiota of patients with IBS than in control participants. In patients with IBS, a relation was observed between the frequency of fruit intake and Blautia spp. abundance (odds ratio [OR] = 0.35; 95% confidence interval [95% CI]: 0.12-1.01; P = 0.04). When comparing all study participants, individuals with a high relative Blautia spp. abundance consumed white bread more frequently than the remaining participants (OR = 2.26; 95% CI: 1.03-4.96; P = 0.04). In turn, the high-frequency intake of wholegrain bread and legumes was related to decreased Blautia spp. abundance OR = 0.29; 95% CI: 0.10-0.94; P = 0.03 and OR = 0.38; 95% CI: 0.17-0.83; P = 0.01, respectively). A body fat percentage over 40% was related to high Blautia spp. abundance (OR = 2.85; 95% CI: 0.99-8.16; P = 0.04).<br><br>CONCLUSIONS: A diet high in wholegrain bread, legumes, and vegetables may influence Blautia spp. abundance in the gut microbiota. High levels of Blautia spp. in the gut are also related to body composition.},
}
@article {pmid40614495,
year = {2025},
author = {Su, X and Liu, M and Chen, Y and Feng, D and Xu, J and He, Y},
title = {Microplastics aging potentially enlarge the ecological risk to wetland sediments as revealed by their interactive effects on γ-HCH dissipation and methane production.},
journal = {Water research},
volume = {285},
number = {},
pages = {124137},
doi = {10.1016/j.watres.2025.124137},
pmid = {40614495},
issn = {1879-2448},
abstract = {Microplastics (MPs) have garnered global concern, yet the environmental implications of their aging remain poorly understood. Especially, their interactions with co-occurring pollutants and impacts on biogeochemical processes in wetland sediments require further investigation. Through microcosm experiments, this study systematically elucidated the differential effects of pristine vs. aged MPs on γ-hexachlorocyclohexane (γ-HCH) behavior and methanogenesis. Aged MPs exhibited enhanced γ-HCH adsorption (666.7 vs. 500.0 mg kg[-1] for pristine MPs), yet paradoxically inhibited γ-HCH dissipation in wetland sediments. This demonstrates that previous studies might oversimplify the interaction between MPs and pollutants. Concurrently, Dhc functional gene abundance on aged MP-surface biofilms declined sharply from 3015.4 to 811.4 copies g[-1] dw over 60 days, suggesting impaired functional microorganisms. Notably, aged MPs amplified CH4 production (1.64 ± 0.10 vs. 1.25 ± 0.15 mg kg[-1] day[-1] pristine MPs) and H2O2 generation (2.62 ± 0.12 vs. 2.06 ± 0.05 mmol L[-1] pristine MPs), with reduced microbial complexity and stability. Mechanistically, aging altered MP surface properties, selectively enriching mcrA functional genes and methanogenic archaea (Methanomassiliicoccus and Methanosarcina). These findings show aged MPs in suppressing pollutant dissipation (γ-HCH) while accelerating elemental cycling (CH4), driven by reactive oxygen species and microbiome shifts. Given the widespread occurrence of aged MPs in wetlands, this study underscores their underappreciated yet critical influence on wetland sediment biogeochemistry, urging prioritized research to mitigate their cascading potential risks.},
}
@article {pmid40613995,
year = {2025},
author = {Ghamari, M and Sabzi, S and Rajabi, E and Khodadadi, G and Navidifar, T and Sadeghi, Z and Bostanghadiri, N},
title = {Probiotics, Prebiotics, Synbiotics, Postbiotics, and Bioactive Agents in Modulating Harmful Oral Biofilms.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {40613995},
issn = {1867-1314},
abstract = {Oral biofilms are intricate microbial communities that can enhance oral health, yet their equilibrium is susceptible to disruption, leading to oral infectious diseases. The most prevalent of these are dental caries, periodontitis, and peri-implant infections. The formation of pathogenic biofilms is the primary cause of these diseases, and their resistance to antimicrobial agents and immune responses poses significant treatment challenges. Researchers have recently implemented microbiome-based strategies, including probiotics, prebiotics, synbiotics, and postbiotics, to modulate biofilm composition and restore microbial equilibrium. Probiotics exert their health effects by competitively inhibiting pathogenic bacteria, producing antimicrobial compounds, and interacting with the immune system. Moreover, prebiotics can selectively stimulate beneficial bacteria, while synbiotics and postbiotics increase these effects using synergistic mechanisms. Recent studies suggest that integrating these strategies into oral healthcare can offer effective, non-invasive approaches to manage biofilm-related oral infections. Notwithstanding the challenges, issues pertaining to strain-specific efficacy, probiotic viability, and long-term colonization remain to be addressed. This review has collated recent research in this area and highlights promising therapeutic directions for improving oral health outcomes.},
}
@article {pmid40613917,
year = {2025},
author = {Zakerska-Banaszak, O and Ladziak, K and Kruszka, D and Maciejewski, K and Wolko, L and Krela-Kazmierczak, I and Zawada, A and Vibeke Vestergaard, M and Dobrowolska, A and Skrzypczak-Zielinska, M},
title = {New potential biomarkers of ulcerative colitis and disease course - integrated metagenomic and metabolomic analysis among Polish patients.},
journal = {Journal of gastroenterology},
volume = {},
number = {},
pages = {},
pmid = {40613917},
issn = {1435-5922},
support = {2020/04/X/NZ2/02172//Narodowe Centrum Nauki/ ; 2021/02//Institute of Human Genetics, Polish Academy of Sciences, in Poznan, Poland/ ; },
abstract = {BACKGROUND &amp; AIM: The course of ulcerative colitis (UC) involves successive periods of remission and exacerbation but is difficult to predict. Gut dysbiosis in UC has already been intensively investigated. However, are periods of exacerbation and remission associated with specific disturbances in the composition of the intestinal microbiota and its metabolome? Our goal was to answer this question and to identify bacteria and metabolites necessary to maintain the remission.<br><br>METHODS: We enrolled 65 individuals, including 20 UC patients in remission, 15 in exacerbation, and 30 healthy controls. Metagenomic profiling of the gut microbial composition was performed based on 16S rRNA V1-V9 sequencing. Stool and serum metabolic profiles were studied by chromatography combined with mass spectrometry.<br><br>RESULTS: We revealed significant differences in the gut bacterial and metabolic composition between patients in active UC and those in remission, as well as in healthy controls. As associated with UC remission we have identified following bacteria: Akkermansia, Agathobacter, Anaerostipes, Enterorhabdus, Coprostanoligenes, Colinsella, Ruminococcus, Subdoligranulum, Lachnoclostridium, Coriobacteriales, Erysipelotrichaceae, and Family XII, and compounds - 1-hexadecanol, phytanic acid, squalene, adipic acid, cis-gondoic acid, nicotinic acid, tocopherol gamma, ergosterol and lithocholic acid. Whereas, in the serum lithocholic acid, indole and xanthine were found as potential candidates for biomarkers of UC remission.<br><br>CONCLUSION: We have demonstrated that specific bacteria, metabolites, and their correlations could be crucial in the remission of UC among Polish patients. Our results provide valuable insights and a significant source for developing new hypotheses on host-microbiome interactions in diagnosis and course of UC.},
}
@article {pmid40613843,
year = {2025},
author = {Huang, R and Jin, X and Liu, Q and Bai, X and Wu, Y and Wang, Y and He, X and Jiang, Z and Wang, L and Zhu, W},
title = {Genetic evidence for causal links between diet, gut microbiota, and hepatobiliary cancer: a Mendelian randomization study.},
journal = {AMB Express},
volume = {15},
number = {1},
pages = {100},
pmid = {40613843},
issn = {2191-0855},
support = {81874182//National Natural Science Foundation of China/ ; 81874056//National Natural Science Foundation of China/ ; 201940043//the Public Health Bureau Foundation of Shanghai/ ; 202240240//the Public Health Bureau Foundation of Shanghai/ ; 2022YFE0125300//National Key Research and Development Plan of the Ministry of Science and Technology/ ; 22ZR1413300//Shanghai Natural Science Foundation Project/ ; },
abstract = {Emerging evidence suggests a complex interplay among dietary habits, gut microbiota, and hepatobiliary cancers, yet the causal relationships remain unclear. Here, we conducted a comprehensive two-sample Mendelian randomization (MR) analysis using genetic instruments from large European cohorts to assess causality among 88 dietary components, 1080 microbiota traits, liver cancer (500 cases, 314,193 controls), and biliary tract cancer (1207 cases, 314,193 controls). We identified significant causal associations of 17 dietary and 101 microbial traits with hepatobiliary cancer risk, while 11 dietary and 70 microbiota traits showed evidence of reverse causality, indicating potential disease-driven alterations. Importantly, a two-step MR mediation analysis revealed that 43 microbial taxa and 6 metabolic pathways significantly mediated dietary influences on hepatobiliary cancer risk; notably, Mollicutes RF9 mediated 31% of the protective effect exerted by zinc on biliary tract cancer. These findings provide genetic evidence delineating gut microbiota as key intermediaries connecting dietary intake to hepatobiliary cancers, highlighting microbiome-targeted dietary strategies as potential preventive interventions. Further research is required to confirm these causal mechanisms and facilitate the development of targeted prevention and therapeutic approaches.},
}
@article {pmid40613581,
year = {2025},
author = {Dang, T and Lysenko, A and Boroevich, KA and Tsunoda, T},
title = {VBayesMM: variational Bayesian neural network to prioritize important relationships of high-dimensional microbiome multiomics data.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {4},
pages = {},
doi = {10.1093/bib/bbaf300},
pmid = {40613581},
issn = {1477-4054},
support = {JP20H03240//JSPS KAKENHI/ ; JP24K15175//JSPS KAKENHI/ ; JPMJCR2231//JST CREST/ ; },
mesh = {Bayes Theorem ; *Microbiota ; *Neural Networks, Computer ; *Metagenomics/methods ; Humans ; *Computational Biology/methods ; Algorithms ; Multiomics ; },
abstract = {The analysis of high-dimensional microbiome multiomics datasets is crucial for understanding the complex interactions between microbial communities and host physiological states across health and disease conditions. Despite their importance, current methods, such as the microbe-metabolite vectors approach, often face challenges in predicting metabolite abundances from microbial data and identifying keystone species. This arises from the vast dimensionality of metagenomics data, which complicates the inference of significant relationships, particularly the estimation of co-occurrence probabilities between microbes and metabolites. Here we propose the variational Bayesian microbiome multiomics (VBayesMM) approach, which aims to improve the prediction of metabolite abundances from microbial metagenomics data by incorporating a spike-and-slab prior within a Bayesian neural network. This allows VBayesMM to rapidly and precisely identify crucial microbial species, leading to more accurate estimations of co-occurrence probabilities between microbes and metabolites, while also robustly managing the uncertainty inherent in high-dimensional data. Moreover, we have implemented variational inference to address computational bottlenecks, enabling scalable analysis across extensive multiomics datasets. Our large-scale comparative evaluations demonstrate that VBayesMM not only outperforms existing methods in predicting metabolite abundances but also provides a scalable solution for analyzing massive datasets. VBayesMM enhances the interpretability of the Bayesian neural network by identifying a core set of influential microbial species, thus facilitating a deeper understanding of their probabilistic relationships with the host.},
}
@article {pmid40613138,
year = {2025},
author = {Filippova, VA and Laptev, GY and Ilina, LA and Yildirim, EA and Ponomareva, ES and Brazhnik, EA and Novikova, NI and Tiurina, DG and Dubrovin, AV and Dubrovina, AS and Sokolova, KA and Klyuchnikova, IA and Zaikin, VA and Griffin, DK and Romanov, MN},
title = {Comparative Genomics of Two Novel Bacillus Strains: Microbiomic Insights into the Sequences, Metabolomics, and Potential Safe Use in the Creation of Biopreparations.},
journal = {Frontiers in bioscience (Elite edition)},
volume = {17},
number = {2},
pages = {28227},
doi = {10.31083/FBE28227},
pmid = {40613138},
issn = {1945-0508},
support = {23-16-20007//Russian Science Foundation/ ; 23-16-20007//St. Petersburg Science Foundation/ ; },
mesh = {*Bacillus/genetics/metabolism ; Metabolomics ; *Genomics ; *Genome, Bacterial ; Probiotics ; Bacillus subtilis/genetics/metabolism ; },
abstract = {BACKGROUND: Bacillus bacteria are often used in the production of biopreparations. Moreover, these bacteria can be used in agriculture as probiotics or starters for manufacturing fodder preserved by fermentation (silage). The ability of Bacillus bacteria to produce many biologically active molecules and metabolites with antimicrobial activity means that these bacteria can stimulate plant growth and restore the balance of the microbiome in the digestive system of certain animals.<br><br>METHODS: Using molecular biological analysis, bioinformatic annotation, and metabolic profiling of whole genome sequences, we analyzed two promising candidates for creating biopreparations, i.e., two Bacillus strains, namely B. mucilaginosus 159 and B. subtilis 111. We compared the genomes of these two strains and characterized both their microbiomic and metabolomic features.<br><br>RESULTS: We demonstrated that both strains lacked elements contributing to the formation of toxic and virulent properties; however, both exhibited potential in the biosynthesis of B vitamins and siderophores. Additionally, these strains could synthesize many antimicrobial substances of different natures and spectrums of action. B. mucilaginosus 159 could synthesize macrolactin H (an antibiotic from the polyketide group), mersacidin (a class II lanthipeptide), and bacilysin. Meanwhile, B. subtilis 111 could synthesize andalusicin (a class III lanthipeptide), bacilysin, macrolactin H, difficidin, bacillaene (a polyene antibiotic), fengycin (a lipopeptide with antifungal activity), and surfactin (another lipopeptide). Further, a unique pathway of intracellular synthesis of the osmoprotectant glycine betaine was identified in B. subtilis 111, with the participation of betaine aldehyde dehydrogenase (BetB); this is not widely represented in bacteria of the genus Bacillus. These compounds can increase osmotic stability, which may be key for manufacturing biological starters for silage preparation.<br><br>CONCLUSIONS: These two Bacillus strains are safe for use as probiotic microorganisms or starters in producing preserved fodder. However, B. subtilis 111 may be preferable due to a wider spectrum of synthesized antimicrobial substances and vitamins. Our findings exemplify using genomic technologies to describe the microbiomic and metabolomic characteristics of significant bacterial groups such as Bacillus species.},
}
@article {pmid40613137,
year = {2025},
author = {Rajapandi, S and Sukumaran, ES and Prasad, KRN and Venkatesan, AV and Ravichandran, TAS and Sabarathinam, S},
title = {Viral Invasion of the Oral Cavity: A Review of Viral Impact on Oral Health and the Potential Use of Saliva as a Diagnostic Tool.},
journal = {Frontiers in bioscience (Elite edition)},
volume = {17},
number = {2},
pages = {33494},
doi = {10.31083/FBE33494},
pmid = {40613137},
issn = {1945-0508},
mesh = {Humans ; *Saliva/virology ; *Oral Health ; *Mouth/virology ; Microbiota ; *Mouth Diseases/virology/diagnosis ; *Virus Diseases/diagnosis/virology ; },
abstract = {The oral cavity is a complex ecosystem that harbors a diverse microbial community. Viral infections can significantly disrupt this delicate balance, leading to various oral health issues. This review delves into the intricate relationship between viruses and oral health, exploring the impact of both RNA and DNA viruses. We discuss the mechanisms through which these viruses influence the oral microbiome, modulate immune responses, and contribute to various oral diseases, including periodontal disease, oral candidiasis, and oral cancer. Additionally, we highlight the potential of saliva as a valuable diagnostic tool for viral infections and oral health assessment. By understanding the viral-oral health nexus, we can develop effective strategies for prevention, early diagnosis, and targeted interventions to improve oral health outcomes.},
}
@article {pmid40612718,
year = {2025},
author = {Tigran, A and Lusine, H and Ruzanna, H and Inesa, S and Nelli, N and Edita, G and Thomas, H and Inga, B},
title = {Anti-candida activity of Lacticaseibacillus rhamnosus R-2002 and its possible application in candidiasis prevention.},
journal = {Iranian journal of microbiology},
volume = {17},
number = {3},
pages = {441-450},
pmid = {40612718},
issn = {2008-3289},
abstract = {BACKGROUND AND OBJECTIVES: Probiotics are used for the treatment of yeast infections, they restore the balance in vaginal microbiome, adhere to epithelial cells, compete against pathogenic bacteria, acidify the environment, produce bacteriocins and modulate the immunity. The aim of the study was to investigate the anti-yeast activity (AYA) of the strain Lacticaseibacillus rhamnosus R-2002 against different Candida species.<br><br>MATERIALS AND METHODS: From 20 strains of lactic acid bacteria examined, only L. rhamnosus R-2002 strain demonstrated beneficial properties against yeast. The effects of temperature and pH on AYA and its relation to cell wall were revealed by bi-layer agar assay. The connection of AYA to the cell wall was determined with the sonicated cells.<br><br>RESULTS: R-2002 inhibited the growth of C. albicans ATCC 10291, C. tropicalis G 31 and C. albicans G4 (both isolated from vaginal samples). R-2002 maintained its AYA between a wide range of pH and its anti-yeast component/s are extracellular. The tested strain demonstrated stability against the high concentrations of progesterone and metronidazole, making it a suitable candidate for the mitigation of vaginitis.<br><br>CONCLUSION: The present study summarizes all the positive features of the strain R-2002 and its potential as a therapeutic agent in the treatment of candidiasis.},
}
@article {pmid40612483,
year = {2025},
author = {Yu, H and Pan, W and Tian, D and Gao, Y},
title = {Deciphering the complexity of enteric niches in Hirschsprung disease: from metaphorical insights to therapeutic transformation.},
journal = {Frontiers in pediatrics},
volume = {13},
number = {},
pages = {1579290},
pmid = {40612483},
issn = {2296-2360},
abstract = {Hirschsprung disease (HSCR) is a congenital disorder marked by the absence of ganglion cells in the distal bowel, resulting in severe constipation and bowel obstruction. Surgery is currently the primary treatment for HSCR. However, post-surgical outcomes are unsatisfactory, merely alleviating symptoms of intestinal obstruction. Up to one-third of HSCR patients continue to experience gastrointestinal issues post-surgery, which severely impacts their growth and development and may even threaten their lives. Cell transplantation represents a promising strategy for the radical treatment of HSCR but faces numerous challenges. The mismatch between transplanted cells and the enteric niches is one of the key obstacles in reconstructing the enteric nervous system through cell transplantation. There is an urgent need to "get to the root of the problem" to enhance our understanding of the enteric niches and overcome current limitations. This review synthesizes insights from two metaphorical narratives, "Blind Men and the Elephant" and "Rags To Riches," to provide a comprehensive re-understanding of the enteric niches and their potential for enteric neurogenesis. By examining these narratives, we underscore the importance of the enteric niches in the potential for transformative discoveries in HSCR research.},
}
@article {pmid40612471,
year = {2025},
author = {Arias, RS and Dobbs, JT and Orner, VA and Conforto, EC and Rago, AM and Cazon, LI and Sobolev, VS and Power, IL and Lamb, MC and Massa, AN},
title = {First metagenome- and metatranscriptome dataset of Thecaphora frezzii teliospores, assembly and annotation of a new bacterial genome.},
journal = {Data in brief},
volume = {61},
number = {},
pages = {111779},
pmid = {40612471},
issn = {2352-3409},
abstract = {These datasets correspond to sequencing of DNA and RNA extracted from surface-disinfected teliospores of the fungus Thecaphora frezzii Carranza and Lindquist, causal agent of smut disease in peanut (Arachis hypogaea L.). The DNA was sequenced using Pacific Biosciences (PacBio) Sequel II and RNA was sequenced in Illumina MiSeq 300 bp paired end (PE). Initial de novo assembly and Basic Local Alignment Search Tool (BLAST) of contigs to the 16S reference sequence database at NCBI had hits on seven bacterial species: Luteibacter pinisoli, Variovorax paradoxus, Rhizobium metallidurans, Caulobacter segnis, Roseateles violae, Novosphingobium rosa, Herbaspirillum seropedicae, and the fungus T. frezzii. High stringency mapping of the RNA sequences to the genomes of these organisms showed that 96% of the reads corresponded to bacteria and only 4% to T. frezzii. De novo assembly of PacBio reads revealed the whole genome of a Luteibacter sp. with 88.56% or lower similarity to those in NCBI database, whereas most RNA sequences (> 10 million reads) mapped to the new Luteibacter sp. genome assembled here. We annotated the new Luteibacter sp. genome, assessed its completeness by BUSCO, and aligned it to its closest relative, Luteibacter aegosomatissinici. We are not aware of any report that describes bacteria colonizing teliospores of T. frezzii. The DNA and RNA sequencing datasets provided here could be used to study the distribution of prokaryotes colonizing T. frezzii teliospores, and to explore the role of the microbiome of T. frezzii teliospores on the outcome of peanut smut disease.},
}
@article {pmid40612463,
year = {2025},
author = {Heredia, L and Mateo, D and Carrión, N and Torrente, M},
title = {Dataset on neuropsychological profile and microbiota composition in cognitively unimpaired elderly and Alzheimer's patients.},
journal = {Data in brief},
volume = {61},
number = {},
pages = {111778},
pmid = {40612463},
issn = {2352-3409},
abstract = {This article presents data collected from a total of 50 older adults (25 healthy controls and 25 diagnosed with Alzheimer's disease). Among the assessments performed in this sample was a comprehensive neurocognitive screening: including working memory, cognitive flexibility, perception, attention, motor coordination, inhibitory control, verbal fluency and visuo-spatial skills. The data presented also include analysis of the participants' gut microbiota using the shot gun approach in faecal samples. Finally, evaluations of the emotional state, level of functioning and adherence to the Mediterranean lifestyle of all participants are also available. Despite the limited sample size due to challenges in patient recruitment, present data could be useful in the identification of microbial signatures potentially predictive of cognitive decline or AD progression and also for helping to the design of clinical trials targeting the microbiome to assess effects on cognitive function. Furthermore, it is well known that the gut microbiota exhibits significant variability associated with lifestyle habits, diet, and geographic location, underscoring the critical influence of environmental and cultural factors in shaping its composition. These data are of utmost importance when considering regional and lifestyle-related diversity in microbiome research, as they can help researchers explore personalized therapeutic approaches and enhance participant stratification in future clinical trials.},
}
@article {pmid40612440,
year = {2025},
author = {Wenjiao, D and Yurou, W and Jiaqi, X and Yan, H and Hongfang, J and Min, C and Jianjin, G},
title = {Animal studies on the modulation of differential efficacy of polyethylene glycol loxenatide by intestinal flora.},
journal = {Frontiers in endocrinology},
volume = {16},
number = {},
pages = {1508473},
pmid = {40612440},
issn = {1664-2392},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Male ; Mice ; Mice, Inbred C57BL ; *Fecal Microbiota Transplantation ; *Diabetes Mellitus, Experimental/microbiology/drug therapy/therapy ; *Polyethylene Glycols/pharmacology ; *Diabetes Mellitus, Type 2/microbiology/drug therapy ; *Hypoglycemic Agents/pharmacology/therapeutic use ; Diet, High-Fat/adverse effects ; Blood Glucose ; },
abstract = {BACKGROUND: Gut microbiota has demonstrated an increasingly important role in the onset and development of type 2 diabetes mellitus (T2DM), Further investigations have revealed the interactions between drugs and the gut microbiome. However, there are still gaps in research regarding the potential interactions between the gut microbiota and GLP-1 and their therapeutic response in people with T2DM. In addition, Fecal microbiota transplantation (FMT) has become a promising strategy for patients with T2DM.<br><br>50 healthy male C57BL/6 mice were fed a high-fat diet in combination with STZ to establish a T2DM mouse model. 40 mice were divided into the T2DM group (n=10) and the PEX168 group (n=30). the PEX168 group was divided into two subgroups of the IE group (HbA1c &#x2264;6. 5%, n=12) and the SE group (HbA1c >6. 5%, n=12), 12 mice in each group. Using IE mice as fecal donors and SE mice as recipients, fecal microbiota transplantation was performed between the two groups, the FMT group (given fecal bacterial suspension, n=5) and the Sham group (given equal amounts of sterile saline, n=5). The intestinal microorganisms of mice in the IE group (donor) and SE group (recipient) were also analyzed for differences. To assess the protective effect of FMT on drug efficacy and T2DM, and to explore the underlying mechanisms.<br><br>RESULTS: After 10 weeks, compared with the control group, the HbA1c of the experimental group was significantly reduced, still, the level of HBA1c of the mice in the unsatisfactory group was significantly higher than that in the ideal group. Compared with the unsatisfactory group, fasting blood glucose, 2h postprandial blood glucose, blood glucose AUC and body weight were significantly reduced in the ideal group. 16srDNA sequencing showed that the levels of Bacteroidota, Akkermansia, Parabacteroides, Bifidobacteria and other bacteria in the ideal efficacy group were significantly higher than those in the non-ideal efficacy group (P<0.05). The levels of Firmicutes, Romboutsia, Clostridium, Turicibacter and other bacteria in the unsatisfactory group were significantly higher than those in the ideal group (P<0.05). The dominant flora of mice in the ideal drug efficacy group was negatively correlated with HbA1c and blood sugar, and the dominant flora of mice in the unsatisfactory drug efficacy group was positively correlated with pro-inflammatory factors such as blood sugar. Moreover, FMT treatment significantly improved the efficacy of PEX168 and liver steatosis in the group with unsatisfactory efficacy.<br><br>CONCLUSION: In summary, we used the combined method of 16S rDNA and metabolomics to systematically elucidate the efficacy of microflora on PEX168 and the possible mechanism of FMT in treating T2DM by PEX168. The difference in intestinal flora between individuals can affect the therapeutic effect of drugs. Moreover, FMT therapy can affect multiple metabolic pathways and colonization of beneficial bacteria to maintain the drug's therapeutic effect on T2DM mice.},
}
@article {pmid40612394,
year = {2025},
author = {Ma, X and Zhang, H},
title = {Meta-analysis of probiotics metabolites in gastrointestinal tract and metabolic health.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1619501},
pmid = {40612394},
issn = {2235-2988},
mesh = {Humans ; *Probiotics/metabolism ; *Gastrointestinal Tract/metabolism/microbiology ; *Gastrointestinal Microbiome ; Host Microbial Interactions ; Gene Expression Profiling ; },
abstract = {INTRODUCTION: The gastrointestinal (GI) tract acts as an essential interface between the host and the microbiota, with microbial metabolites exerting a significant role in regulating host physiology.<br><br>METHODS: Integrative network-based methodology that combines metabolite-protein interactions with tissue-specific transcriptomics to uncover host targets of probiotic-derived metabolites and determine their potential biological significance. Utilizing curated interaction data, it is about to construct metabolite-host protein network and prioritised genes using centrality metrics. Gene expression analysis across human tissues indicated that some high-degree genes, including SLC27A4, LCN12, and APOD, are abundant in GI areas including small intestine, colon, and duodenum, indicating a potential role in local host-microbe interactions. Further metabolite-specific expression analysis revealed separate but overlapping expression landscapes. 10-hydroxy-cis-12-octadecenoic acid has been associated to increased production of sialyltransferases and neuraminidase in metabolically and immunologically active tissues.<br><br>RESULTS AND DISCUSSION: Glycodeoxycholic acid was associated with high levels of lipocalins and fatty acid transporters in enterohepatic tissues, indicating functions in bile acid metabolism and lipid transport. Meanwhile, N-(1-carbamoyl-2-phenyl-ethyl) butyramide was linked to detoxifying enzymes that are highly expressed in the liver, kidney, and gastrointestinal tissues. Collectively, these data reveal a tissue-specific molecular architecture that governs host responses to microbial metabolites, notably in the GI tract. Our findings shed light on how microbial compounds interact with host pathways at both the local and systemic levels, paving the way for new microbiome-targeted treatments and precision feeding initiatives.},
}
@article {pmid40612314,
year = {2025},
author = {Sequeira-Bisson, IR and Fraser, K and Leiu, KH and Penhaligan, J and Joblin-Mills, A and Plank, LD and Murphy, R and Taylor, MW and Gasser, O and Conroy, DM and Jiang, Y and Lu, LWW and Poppitt, SD and Miles-Chan, JL},
title = {Design and conduct of a full diet-controlled, parallel, 2-week residential trial for diabetes prevention without weight loss in Asian Chinese and European Caucasian adults with prediabetes: the New Zealand SYNERGY study.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1590579},
pmid = {40612314},
issn = {2296-861X},
abstract = {BACKGROUND: The causal underpinning of increased metabolic risk and previously observed dichotomous plasma metabolome in Asian Chinese vs. European Caucasian remains undetermined and may be hypothesised as attributed to ethnicity (genetic background), pathology (dysglycaemia) and/or lifestyle (habitual diet). We aimed to investigate the underlying cause(s) and the effect of dietary intervention on biomarkers of type 2 diabetes (T2D) in cohorts with prediabetes. The diets are a generic current Best Practice Healthy Diet ('BPHD'), and a New Zealand-specific healthy diet ('SYNERGY') based on the Mediterranean Diet. We hypothesise, firstly, that 14-days of matched BPHD in Asian Chinese vs. European Caucasian cohorts (ethnicity; within-diet comparison) will attenuate the previously observed dichotomy in plasma metabolome. Secondly, that both diets will improve risk markers over 14 days vs. baseline, with significant improvement with SYNERGY compared to BPHD in Asian Chinese cohorts (diet; within-ethnicity comparison).<br><br>METHODS: We conducted a 2-week, fully diet-controlled, residential trial in 20 Asian Chinese (n&#x202f;=&#x202f;10 per diet group) and 10 European Caucasian (BPHD only) adults with prediabetes. Participants were phenotyped (dual-energy X-ray absorptiometry, magnetic resonance imaging/spectroscopy) prior to the intervention. On Day 1 (D1) and D15 assessments included anthropometry, collection of urine, faecal (microbiome analysis) and fasted blood samples, conduct of 2-h oral glucose tolerance test (established clinical, metabolome, immune markers) and indirect calorimetry (resting metabolic rate, postprandial glucose-induced thermogenesis). Additional fasted urine and blood samples were collected on D2, D7 (mid-way) and D14, with a focus group/interview on the evening of D7. Meals and snacks were calculated based on individual energy requirements for body weight maintenance, dietary compliance was supervised, and body weight monitored daily.<br><br>DISCUSSION: This study aims to identify ethnic-specific dietary responses in a fully-controlled residential setting; to determine cause/s of the dichotomous plasma metabolome between the two ethnic groups; also to validate these biomarkers as sensitive to dietary intervention using a 'whole of diet' approach. Specifically, to determine the efficacy of BPHD and SYNERGY for T2D risk amelioration in the absence of body weight loss. Findings will inform design of larger 'free-living' community interventions and explore the feasibility of use of these diets within the community.<br><br>The study was prospectively registered on 22 March 2021 with the Australian New Zealand Clinical Trials Registry ACTRN12621000318886.},
}
@article {pmid40612273,
year = {2025},
author = {Constantino-Jonapa, LA and Aguilar-Villegas, OR and Hernández-Ruiz, P and Escalona-Montaño, AR and Pallecchi, M and González-Pacheco, H and Bartolucci, G and Baldi, S and Amezcua-Guerra, LM and Amedei, A and Aguirre-García, MM},
title = {The link between inflammatory/ SCFA profiles and oral/gut microbiome: an observational study in patients with ST-segment elevation myocardial infarction.},
journal = {Current research in microbial sciences},
volume = {9},
number = {},
pages = {100423},
pmid = {40612273},
issn = {2666-5174},
abstract = {Acute myocardial infarction (AMI) is a leading cause of mortality in Mexico. The microbiota plays a crucial role in immune regulation, and its dysbiosis promotes low-grade inflammation, a key contributor to AMI development. This study aimed to compare the oral (OM) and gut microbiota (GM) composition in patients with ST-segment elevation myocardial infarction (STEMI) and healthy controls. Additionally, we explored the interaction between these microbiomes and their correlations with inflammatory profiles and metabolites. In this study, we included 36 STEMI patients and 12 healthy subjects. The composition of both GM and OM was analyzed through 16S sequencing of dental plaque and stool samples. Short-chain fatty acids (SCFAs) were measured via gas chromatography-mass spectrometry, while serum cytokines were assessed using flow cytometry. STEMI patients exhibited significant differences in OM alpha and beta diversity, while GM structure remained unchanged compared to healthy group. Several differentially abundant genera were identified in both OM and GM. Regarding SCFA profiles, Healthy subjects displayed a higher abundance of isovaleric acid, whereas isobutyric and 2-methylbutyric acids were significantly higher in STEMI patients. Moreover, correlations between circulating SCFAs, cytokines, and microbiota composition were observed in both niches. Furthermore, network analysis suggests that oral bacteria, particularly those linked to periodontal disease, can potentially influence GM by interacting with SCFA-producing bacteria. This is the first study in México to comprehensively explore OM and GM in STEMI patients. Our findings highlight the potential for developing preventive strategies against myocardial infarction by exploring both oral and gut microbiomes, as well inflammatory markers and SCFAs.},
}
@article {pmid40612152,
year = {2025},
author = {Bonde, CS and Drøhse, FB and Büdeyri Gökgöz, N and Krych, L and Nielsen, DS and Petersen, HH and Matthiesen, R and Pedersen, NR and Geldhof, P and Williams, AR and Thamsborg, SM and Mejer, H},
title = {Dietary supplementation with fermented rapeseed and seaweed modulates parasite infections and gut microbiota in outdoor pigs.},
journal = {Frontiers in veterinary science},
volume = {12},
number = {},
pages = {1565686},
pmid = {40612152},
issn = {2297-1769},
abstract = {Outdoor pig production systems can increase exposure to helminth infections such as Ascaris suum. Anthelmintic drug treatments are currently the primary strategy for controlling such infections; however, this approach is considered unsustainable due to the risk of parasites developing anthelmintic resistance. This study investigated the potential anthelmintic effect of a 2% w/w fermented rapeseed-seaweed (FRS) dietary supplement administered over an 11-12 week period in growing-finisher pigs. Outcomes assessed included parasitic fecal egg counts (FEC), serology, gut microbiota composition, and systemic inflammation. The FRS supplement consisted of 6% Saccharina latissima, 6% Ascophyllum nodosum, and 88% rapeseed meal (based on dry matter) and was provided in two different batches. Supplementation with FRS tended to lower FEC and reduce the incidence of A. suum infection. However, this effect varied between batches. FRS also influenced gut microbiota composition: pigs that were fed the second batch of FRS showed an increased relative abundance of several Bacteroidetes members (e.g., Prevotella), while unsupplemented pigs were enriched with various taxa from the Firmicutes phylum, such as Clostridium spp. Furthermore, pigs fed the second batch of FTR showed reduced daily weight gain compared to those fed the control diet. Overall, our results indicate that FRS modulates the gut microbiota toward a composition potentially associated with improved gut health and may have promise as a prebiotic or novel feed additive to help reduce helminth infections.},
}
@article {pmid40611979,
year = {2025},
author = {Setubal, JC and Paccanaro, A},
title = {Editorial: Expert opinions in genomic analysis.},
journal = {Frontiers in bioinformatics},
volume = {5},
number = {},
pages = {1641083},
doi = {10.3389/fbinf.2025.1641083},
pmid = {40611979},
issn = {2673-7647},
}
@article {pmid40611965,
year = {2025},
author = {Ivanova, M and Aarestrup, FM and Otani, S},
title = {Impact of sample multiplexing on detection of bacteria and antimicrobial resistance genes in pig microbiomes using long-read sequencing.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1597804},
pmid = {40611965},
issn = {1664-302X},
abstract = {The effects of sample multiplexing on the detection sensitivity of antimicrobial resistance genes (ARGs) and pathogenic bacteria in metagenomic sequencing remain underexplored in newer sequencing technologies such as Oxford Nanopore Technologies (ONT), despite its critical importance for surveillance applications. Here, we evaluate how different multiplexing levels (four and eight samples per flowcell) on two ONT platforms, GridION and PromethION, influence the detection of ARGs, bacterial taxa and pathogens. While overall resistome and bacterial community profiles remained comparable across multiplexing levels, ARG detection was more comprehensive in the four-plex setting with low-abundance genes. Similarly, pathogen detection was more sensitive in the four-plex, identifying a broader range of low abundant bacterial taxa compared to the eight-plex. However, triplicate sequencing of the same microbiomes revealed that these differences were primarily due to sequencing variability rather than multiplexing itself, as similar inconsistencies were observed across replicates. Given that eight-plex sequencing is more cost-effective while still capturing the overall resistome and bacterial community composition, it may be the preferred option for general surveillance. Lower multiplexing levels may be advantageous for applications requiring enhanced sensitivity, such as detailed pathogen research. These findings highlight the trade-off between multiplexing efficiency, sequencing depth, and cost in metagenomic studies.},
}
@article {pmid40611952,
year = {2025},
author = {Malal, H and Garcia, JA and Marrs, A and Ait Hamza, M and Emerson, C and Nocco, M and Lakhtar, H and Lazcano, C},
title = {Organic and inorganic fertilizers modulate the response of the soil microbiome to salinity stress.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1551586},
pmid = {40611952},
issn = {1664-302X},
abstract = {Salinity stress threatens soil microbiomes, a key driver of soil multifunctionality and health. This study employed high-throughput sequencing of 16S rRNA, PLFAs, multifunctionality index, and co-occurrence networks to gain a comprehensive understanding of the dynamic responses of soil microbiomes to salinity stress gradient (0, 0.4 and 1 mol NaCl). Additionally, we investigated how these responses are shaped by the addition of vermicompost and NPK fertilizer during short-term (2-h) and long-term (70-day) incubation periods. Salinity stress reduced bacterial and fungal phospholipid fatty acids (PLFA) concentrations in the short-term. Over the long-term, the microbial community evolved into a new pattern under salt stress, favoring the presence of Bacteriodota, a salt-tolerant phylum, while decreasing the relative abundance of Acidobacteriota and Planctomycetota, which are more salt-sensitive. Furthermore, salinity decreased species richness by 11.33% and soil multifunctionality by 21.48% but increased microbial network complexity while decreasing its stability. Incorporating vermicompost increased bacterial and fungal PLFAs, enhanced bacterial diversity by 2.33%, promoted salt-tolerant bacteria, and increased the complexity and stability of the bacterial network. Conversely, the application of NPK fertilizer reduced bacterial richness, alpha diversity and soil multifunctionality by 14.52, 5.83, and 12.34%, respectively, further disrupting the microbial community and making resilience to salinity stress more challenging. Furthermore, NPK fertilization increased bacterial network complexity but decreased its stability. This study underscores the significance of employing vermicompost to improve the health of saline soils. Furthermore, it emphasizes the negative impacts of NPK fertilizer on soil microbial structure and function and hinder its recovery from salinity's impacts.},
}
@article {pmid40611941,
year = {2025},
author = {Ramírez-Fernández, L and Saldarriaga-Córdoba, M and Silva, AX and Napolitano, C and Rodríguez-San Pedro, A},
title = {Eukaryotic gut community of the bat Myotis arescens in anthropized landscapes in Chile.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e19563},
pmid = {40611941},
issn = {2167-8359},
mesh = {*Chiroptera/microbiology/parasitology ; Chile ; Animals ; Ecosystem ; Feces/parasitology/microbiology ; *Gastrointestinal Microbiome ; Humans ; *Eukaryota/isolation &amp; purification/genetics ; },
abstract = {BACKGROUND: Human-driven environmental changes can disrupt wildlife habitats, forcing animals to adapt to fragmented or degraded ecosystems. In some cases, this leads to increased proximity between wildlife and human populations, heightening the risk of pathogen spillover. Bats, as key ecological players, are particularly sensitive to such disturbances. While some species decline in heavily altered environments, others adapt and thrive near human settlements, increasing the likelihood of encounters. Given that bats can host a wide range of zoonotic pathogens, this adaptive behavior raises important public health concerns. Despite their ecological significance and their role in zoonotic disease dynamics, the gut eukaryotes communities associated with bats remain less studied.<br><br>METHODS: This study focused on the Valpara&#xed;so Myotis (Myotis arescens), an insectivorous bat species endemic to central Chile that is significantly impacted by anthropogenic deforestation and habitat fragmentation. We characterized the gut eukaryotic communities of M. arescens through fecal sample analysis. Targeted microbial groups included fungi, metazoan parasites, and protists. High-throughput sequencing was employed to assess gut eukaryotes diversity, and beta diversity analysis was conducted to explore clustering patterns in relation to environmental variables, such as vegetation cover and land use types.<br><br>RESULTS: Our analyses revealed that the gut eukaryotic community of M. arescens consistently included taxa from the Apicomplexa, Ascomycota, and Basidiomycota phyla, with Apicomplexa being the most abundant. Beta diversity analysis showed distinct clustering by sampling location, with the percentage of native vegetation identified as the primary factor shaping gut eukaryotic community structure. Other influential variables included the presence of annual crops, orchards, water bodies, and urban areas. Notably, a high abundance of Apicomplexa-particularly amplicon sequence variants (ASVs) related to the genus Eimeria-was detected in bat feces across sites with varying degrees of anthropogenic disturbance.<br><br>CONCLUSIONS: This study highlights the significant role of native vegetation in shaping the eukaryotic gut community of M. arescens, suggesting that gut eukaryotic composition can serve as a bioindicator of bat health and habitat quality. Among the dominant taxa, members of the genus Eimeria were frequently detected across sites with varying degrees of anthropogenic disturbance. Although Eimeria is generally considered host-specific and not zoonotic, its high prevalence in bat gut communities points to the need for further research into its ecological role and potential implications for wildlife health. Overall, these findings underscore the importance of conserving native habitats to maintain ecosystem integrity and support healthy bat populations.},
}
@article {pmid40611932,
year = {2025},
author = {Yinadsawaphan, T and Kulthamrongsri, N and Malone, RM and Surapongpairat, S and Puchongmart, C and Thiravetyan, B and Imwattana, K and Na Witayanan, J},
title = {A rare case of native mitral valve infective endocarditis by Lactobacillus jensenii in a healthy young patient.},
journal = {IJID regions},
volume = {15},
number = {},
pages = {100648},
pmid = {40611932},
issn = {2772-7076},
abstract = {Lactobacillus jensenii, a Gram-positive facultative anaerobic bacterium, is part of the normal vaginal microbiome and is occasionally found in fermented foods and probiotics. It is a rare cause of infections, with infective endocarditis (IE) being exceedingly uncommon. We report a case of IE caused by Lactobacillus jensenii in a previously healthy 15-year-old female who presented with progressive dyspnea, fever, and severe mitral regurgitation. Echocardiography revealed a vegetative mass on the anterior mitral leaflet. Blood cultures identified L. jensenii using Matrix-Assisted Laser Desorption/Ionization Time-of-Flight mass spectrometry. Surgical repair confirmed myxomatous degeneration and chronic inflammation of the mitral valve. The patient fully recovered after surgery and a 6-week antibiotic course. A review of 12 reported cases of L. jensenii IE, including our case, shows a predominance in immunocompetent females, possibly due to its role as a vaginal commensal. Most cases involved native valves with underlying pathology facilitating bacterial colonization. An empirical regimen with ampicillin and gentamicin is effective against L. jensenii. A treatment duration of 4-6 weeks is sufficient, with favorable outcomes.},
}
@article {pmid40611420,
year = {2025},
author = {Rezaei, M and Jalali, A and Sadah Al-Azzawi, DH},
title = {Engineered Bacteriophages: Advances in Phage Genome Redesign Strategies for Therapeutic and Environmental Applications.},
journal = {Protein and peptide letters},
volume = {},
number = {},
pages = {},
doi = {10.2174/0109298665372719250616085616},
pmid = {40611420},
issn = {1875-5305},
abstract = {Bacteriophages, or phages, have emerged as powerful platforms in synthetic biology, offering innovative solutions for therapeutic and environmental challenges through advanced genome redesign strategies. This review explores a wide range of phage engineering techniques, including CRISPR (clustered regularly-interspaced short palindromic repeats)-Cas systems, phage display, random and site-directed mutagenesis, retrons, and rebooting approaches, highlighting their potential to create phages with tailored functionalities. CRISPR-Cas systems enable precise genome editing, allowing the development of phages with expanded host ranges, biofilm degradation capabilities, and targeted antimicrobial activity. Phage display facilitates the presentation of peptides on phage surfaces, enabling applications in targeted drug delivery, tumor imaging, and bioremediation. Beyond these, techniques like retron-mediated recombination and homologous recombination offer additional avenues for precise phage genome modification. In the therapeutic realm, engineered phages show promise in combating drug-resistant infections, modulating the microbiome, and delivering targeted therapies for cancer and other diseases. Environmentally, phage-based strategies, such as the use of phage-displayed metal-binding peptides, provide innovative solutions for bioremediation and reducing exposure to toxic heavy metals. This review also addresses challenges, such as phage resistance, immune responses, and the limitations of current engineering methods, while exploring future directions, including the development of improved CRISPR systems, phage-based biosensors, and high-throughput screening platforms. By integrating cutting-edge genome redesign strategies with diverse applications, this review underscores the transformative potential of engineered bacteriophages in addressing global healthcare and environmental sustainability challenges.},
}
@article {pmid40611411,
year = {2025},
author = {Islam, A},
title = {Advances in Microbiome Research: Implications for Infectious Disease Management and Treatment.},
journal = {Recent advances in anti-infective drug discovery},
volume = {},
number = {},
pages = {},
doi = {10.2174/0127724344384934250624040634},
pmid = {40611411},
issn = {2772-4352},
abstract = {INTRODUCTION: The human microbiome plays a pivotal role in health and disease, with microbial imbalances (dysbiosis) increasingly linked to heightened susceptibility to infections and exacerbated disease severity. This review explores how the microbiome confers protection through mechanisms, such as colonization resistance, immune modulation, and antimicrobial metabolite production, while also examining its potential as a predictive tool for infection risk and outcomes, as exemplified in COVID-19.<br><br>METHODS: This article synthesizes current literature on microbiome dynamics, leveraging advances in high-throughput sequencing, bioinformatics, and machine learning to analyze microbial profiles and identify biomarkers. It evaluates microbiome-based therapeutic strategies, including probiotics, prebiotics, and engineered microbes, and assesses challenges in translating these approaches into clinical practice.<br><br>RESULTS: Microbiome profiles demonstrate prognostic value in predicting infection risk and severity, supported by enhanced analytical tools that enable precise biomarker discovery for diagnostics and personalized medicine. Therapeutic interventions show promise in restoring microbial balance and combating infections, though clinical adoption is hindered by variability, regulatory hurdles, and the need for standardized methodologies.<br><br>CONCLUSION: Integrating microbiome insights into clinical practice requires rigorous clinical trials, standardized protocols, and resolution of ethical and regulatory challenges. Future research should focus on elucidating microbiome-host-pathogen interactions and developing targeted interventions, and advanced computational models are critical to unlocking the full potential of microbiome-based diagnostics and therapeutics for infectious disease management.},
}
@article {pmid40611327,
year = {2025},
author = {Bustos, IG and Serrano-Mayorga, CC and Guerrero, JL and Baker, JM and Brown, C and Falkowski, N and Ranjan, P and Acosta-Gonzalez, A and Mendez, LM and Garcia-Cordoba, A and Echeverry-Gutierrez, A and Bojaca, DA and Chisica-Mahecha, M and Guarin-Tequia, N and Romero-Romero, L and Gonzalez-Juarbe, N and Rodriguez, A and Cala, MP and Martin-Loeches, I and Chotirmall, SH and Dickson, RP and Reyes, LF},
title = {Longitudinal analysis of lung microbiome, immune response, and metabolism in ventilator-associated pneumonia: a cohort study.},
journal = {Critical care (London, England)},
volume = {29},
number = {1},
pages = {275},
pmid = {40611327},
issn = {1466-609X},
support = {MED-260-2019//Universidad de La Sabana , Colombia/ ; MED-260-2019//Universidad de La Sabana , Colombia/ ; MED-260-2019//Universidad de La Sabana , Colombia/ ; MED-260-2019//Universidad de La Sabana , Colombia/ ; },
mesh = {Humans ; *Pneumonia, Ventilator-Associated/physiopathology/microbiology/immunology/metabolism ; Male ; Female ; Middle Aged ; *Microbiota/physiology ; Cohort Studies ; Aged ; *Lung/microbiology/physiopathology/metabolism ; Longitudinal Studies ; Bronchoalveolar Lavage Fluid/microbiology ; Respiration, Artificial/adverse effects ; Cytokines/analysis ; },
abstract = {RATIONALE: Ventilator-associated pneumonia (VAP) is a common complication in patients under invasive mechanical ventilation (IMV), yet its underlying mechanisms remain poorly understood. This study investigated the lung microbiome, inflammatory response, and metabolism in patients undergoing IMV to identify factors that may predispose them to developing VAP.<br><br>OBJECTIVES: To investigate how changes in lung microbiome composition, inflammatory response, and metabolic profiles may predispose patients undergoing IMV to develop VAP.<br><br>METHODS: Patients requiring IMV for at least 48&#xa0;h due to non-infectious respiratory failure were enrolled. Bronchoalveolar lavage (BAL) samples were collected at baseline, upon VAP diagnosis, or after 72&#xa0;h for non-VAP cases. DNA sequencing, cytokine quantification, and metabolomic analyses were performed.<br><br>RESULTS: Of the 80 patients, 41 (51%) developed VAP. No significant differences in alpha or beta diversity of the lung microbiome were observed between groups. However, both groups showed changes in microbiome composition over time, suggesting an impact of IMV. Tumour necrosis factor-alpha (TNF-&#x3b1;) lung levels were significantly higher in VAP patients, while lung interleukin-1 beta (IL-1&#x3b2;) increased in all patients. Metabolomic analysis revealed shifts in pentose phosphate and citric acid cycle pathways, indicating a transition to anaerobic metabolism in the lungs of VAP patients.<br><br>CONCLUSIONS: Mechanical ventilation was associated with temporal changes in lung microbiome composition independent of VAP development. VAP cases exhibited higher TNF-&#x3b1; levels and metabolic profiles indicative of anaerobic adaptation, while IL-1&#x3b2; elevations were primarily linked to mechanical ventilation rather than infection.},
}
@article {pmid40611207,
year = {2025},
author = {Wang, Q and Zhang, M and Meng, M and Luo, Z and Pan, Z and Deng, L and Qin, J and Guo, B and Zhu, D and Zhang, Y and Guo, H and Liang, Y and Su, Z},
title = {Integration bile acid metabolomics and gut microbiome to study the anti-liver fibrosis effects of total alkaloids of Corydalis saxicola Bunting.},
journal = {Chinese medicine},
volume = {20},
number = {1},
pages = {106},
pmid = {40611207},
issn = {1749-8546},
support = {82060763//National Natural Science Foundation of China/ ; GXFCDP-PS-2022//Guangxi First-class Discipline Project for Pharmaceutical Sciences/ ; GXQH202409//Guangxi Youth Qihuang Scholars Training Project/ ; },
abstract = {BACKGROUND: Bile acids and gut microbiota participate in the pathogenesis of liver fibrosis (LF). The total alkaloids of Corydalis saxicola Bunting (TACS) is a traditional Chinese medicine extract that has been used to treat LF, but the underlying mechanisms are not clear. This study performed integrated metabolomics and gut microbiome analysis to study the anti-LF mechanism of TACS using a rat model.<br><br>METHODS: Ultra-performance liquid chromatography quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF/MS) was used to identify the chemical compounds in TACS. Biochemical and histopathological analysis were performed to determine the efficacy of TACS. Bile acid-targeted metabolomics was used to assess changes in the bile acid (BA) profiles in TACS-treated LF rats. 16S rRNA gene sequencing and metagenomics were used to assess changes in the gut microbiota of the TACS-treated LF rats. Antibiotic cocktail treatment and fecal microbiota transplantation (FMT) were used to determine the relationship between the gut microbiota and the anti-LF effects of TACS. Metagenomics was used to identify significantly enriched gut microbiota after TACS treatment and its correlation with the anti-LF effects was verified by in vivo experiments.<br><br>RESULTS: TACS treatment significantly reduced the levels of serum liver enzymes, fibrosis and pro-inflammatory cytokines in the liver. TACS significantly increased the levels of chenodeoxycholic acid (CDCA) and taurochenodeoxycholic acid&#xa0;(TCDCA) in the cecum and decreased the levels of cholic acid (CA) and deoxycholic acid (DCA) in the liver of the LF rats. TACS significantly increased the abundances of Lactobacillus and Akkermansia in the LF rats. Antibiotic cocktail treatment and FMT have&#xa0;shown that the effect of TACS cure liver fibrosis depends on the gut microbiota. The abundance of Lactobacillus reuteri was significantly increased by TACS. Administration of Lactobacillus reuteri via gavage ameliorated LF.<br><br>CONCLUSIONS: TACS exerted anti-LF effects in rats by modulating bile acid metabolism and gut microbiome.},
}
@article {pmid40610607,
year = {2025},
author = {Jurvansuu, J and Länsivaara, A and Palmroth, M and Kaarela, O and Hyöty, H and Oikarinen, S and Lehto, KM},
title = {Machine learning-based identification of wastewater treatment plant-specific microbial indicators using 16S rRNA gene sequencing.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {23771},
pmid = {40610607},
issn = {2045-2322},
support = {Tampere3 Innovation Competition (2017 - 2018)//City of Tampere, Finland/ ; Tampere3 Innovation Competition (2017 - 2018)//City of Tampere, Finland/ ; Tampere3 Innovation Competition (2017 - 2018)//City of Tampere, Finland/ ; Tampere3 Innovation Competition (2017 - 2018)//City of Tampere, Finland/ ; Tampere3 Innovation Competition (2017 - 2018)//City of Tampere, Finland/ ; Tampere3 Innovation Competition (2017 - 2018)//City of Tampere, Finland/ ; Tampere3 Innovation Competition (2017 - 2018)//City of Tampere, Finland/ ; },
mesh = {*Machine Learning ; *Wastewater/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/isolation &amp; purification ; *Microbiota/genetics ; Finland ; Water Purification ; },
abstract = {Effluent released from municipal wastewater treatment plants reflects the microbial communities responsible for degrading and removing contaminants within the plants. Monitoring this effluent offers essential insights into its environmental impacts, the efficiency of treatment processes, and the presence of emerging contaminants. To support improved monitoring and source attribution, our study employed a machine-learning framework to identify microbial indicators capable of distinguishing between municipal treatment plants based on effluent microbiota. We collected 57 effluent samples for sequencing of the V4 region of the 16S rRNA gene from six treatment plants in the Pirkanmaa region in Finland between 2016 and 2018. Characterising the microbiome revealed that although each plant had unique microbial profiles, their overall diversity and richness were similar. This provided a robust foundation for identifying plant-specific microbes. Using ANOVA-F for feature selection, we focused on the genus level due to its informative prevalence. Among various models tested, the Gaussian Naive Bayes model yielded the highest accuracy with the fewest relevant microbes. We identified nine bacterial genera and one archaeon, whose relative abundances predicted the origin of the effluent with 92% accuracy. Our study outlines a framework for the cost-effective and rapid identification of the origin of effluent or changes in the treatment process, demonstrating the power of machine learning in environmental monitoring and management.},
}
@article {pmid40610597,
year = {2025},
author = {Willyard, C},
title = {Home medical tests miss the mark.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {40610597},
issn = {1476-4687},
}
@article {pmid40610473,
year = {2025},
author = {Ivanova, EA and Suleymanov, AR and Nikitin, DA and Semenov, MV and Abakumov, EV},
title = {Machine learning-based mapping of Acidobacteriota and Planctomycetota using 16 S rRNA gene metabarcoding data across soils in Russia.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {23763},
pmid = {40610473},
issn = {2045-2322},
support = {24-44-00006//Russian Science Support Foundation/ ; 24-44-00006//Russian Science Support Foundation/ ; },
mesh = {*Machine Learning ; *Soil Microbiology ; *RNA, Ribosomal, 16S/genetics ; Russia ; *DNA Barcoding, Taxonomic/methods ; Soil/chemistry ; Microbiota/genetics ; *Acidobacteria/genetics/classification ; Ecosystem ; },
abstract = {The soil microbiome plays a crucial role in maintaining healthy ecosystems and supporting sustainable agriculture. Studying its biogeographical structure and distribution is essential for understanding the rates and mechanisms of microbially mediated soil ecosystem services. This study aimed to investigate the spatial distribution patterns of Acidobacteriota and Planctomycetota across soils in Russia, summarizing data from 16S rRNA gene metabarcoding of topsoils. A machine learning approach (Random Forest) was employed to generate digital distribution maps using climatic, topographic, vegetation, geological, and soil variables. Model interpration was performed using variable importance assessment and Shapley values. According to the error metrics, the Acidobacteriota model achieved a root mean squared error (RMSE) of 6.67% and an R[2] of 0.41, while the Planctomycetota model achieved an RMSE of 2.04% and an R[2] of 0.46. Both phyla exhibited similar spatial distribution patterns, with relative abundance decreasing from North to South. For Acidobacteriota, vegetation cover, surface temperature, and soil pH were significant predictors, whereas the relative abundance of Planctomycetota was mainly influenced by climatic variables. Specifically, Acidobacteriota were more abundant in areas with dense vegetation, stable surface temperatures, and acidic soils. In contrast, Planctomycetota showed reduced abundance in regions with higher levels of precipitable water vapor. These results highlight the potential of machine learning techniques to visualize predictive biogeographic patterns in soil microbial taxa abundance at the phylum level. Despite limitations related to the heterogeneous nature of source data, focusing on higher taxonomic ranks less sensitive to methodological variation enabled to identify preliminary large-scale distribution trends of microbial phyla in soils.},
}
@article {pmid40610420,
year = {2025},
author = {Knodel, S and Main, L and DeLeon, M and Lamont, A and Edward, J and Gupta, AK and Noel-Romas, L and Mohammed, S and Tattersall, T and Wong, J and Hull, M and Grennan, T and Burgener, AD},
title = {Impact of doxycycline pre-exposure prophylaxis (doxyPrEP) for sexually transmitted infections on the microbiome of men who have sex with men on HIV PrEP.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {6143},
pmid = {40610420},
issn = {2041-1723},
support = {365358//Gouvernement du Canada | Canadian Institutes of Health Research (Instituts de Recherche en Sant&#xe9; du Canada)/ ; HB3-164066//Gouvernement du Canada | Canadian Institutes of Health Research (Instituts de Recherche en Sant&#xe9; du Canada)/ ; 2P30 AI036219-26A, 5P30DA054557//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; IN-CA-276-4012//Gilead Sciences (Gilead)/ ; },
mesh = {Humans ; Male ; *Doxycycline/therapeutic use/administration &amp; dosage/pharmacology ; *Pre-Exposure Prophylaxis/methods ; Adult ; Homosexuality, Male ; *HIV Infections/prevention &amp; control ; Pilot Projects ; *Microbiota/drug effects ; *Anti-Bacterial Agents/therapeutic use/administration &amp; dosage ; Middle Aged ; *Sexually Transmitted Diseases/prevention &amp; control/microbiology/drug therapy ; RNA, Ribosomal, 16S/genetics ; Rectum/microbiology ; Emtricitabine/therapeutic use ; Sexual and Gender Minorities ; },
abstract = {Doxycycline pre-exposure prophylaxis (doxyPrEP) has shown potential in preventing bacterial sexually transmitted infections, but the impact on the microbiome is unknown. This study assessed rectal microbiome changes over 48 weeks in 41 participants on HIV PrEP (tenofovir disoproxil fumarate/emtricitabine) enrolled in an open-label, randomized pilot trial comparing immediate (100 mg PO daily started immediately and continued to week 48) versus deferred doxyPrEP (100 mg PO daily starting at week 24, continued to week 48) in HIV-negative gay and bisexual men (Clinical Trial #: NCT02844634). Primary study outcomes included feasibility, adherence, and tolerability of the dual PrEP regimen, while exploratory outcomes included rectal microbiome changes. We performed 16S rRNA sequencing from participants that collected baseline, week 24, and week 48 samples. Microbial composition did not significantly change over time in either study arm as measured by individual taxa levels, or alpha and beta diversity at the genus level. A slight decrease (< 10%) in alpha diversity was observed at the phylum level in the immediate arm, but not the deferred arm. This study shows doxyPrEP use results in minimal compositional changes in the microbiome over 12 months. Further research is needed to explore the impact of doxycycline for STI prevention on microbiome function and antimicrobial resistance.},
}
@article {pmid40609987,
year = {2025},
author = {Chen, CC and Lin, TY and Wu, WK and Panyod, S and Lin, YK and Lin, YH and Chan, ST and Wu, MS and Lee, CN and Chiang, CF},
title = {Gut-breast axis modulation through Streptococcus thermophilus TCI633 supplementation: a study on mother-infant microbiome dynamics.},
journal = {Beneficial microbes},
volume = {},
number = {},
pages = {1-8},
doi = {10.1163/18762891-bja00082},
pmid = {40609987},
issn = {1876-2891},
abstract = {Breast milk provides essential nutrition and bioactive components, including probiotics, which contribute to the development of a balanced infant microbiota and a strengthened immune system. The gut-breast axis theory suggests that the maternal gut microbiota may influence the microbiota and composition of breast milk through immune-mediated signaling. This study aimed to investigate the colonization potential of S. thermophilus TCI633 in the infant gut and to explore its possible transfer via the gut-breast axis. A total of 30 exclusively breastfeeding mother-infant pairs were recruited. Mothers took TCI633 daily for one month following hospital discharge. Breast milk, maternal feces, and infant fecal samples were collected and analyzed for microbiota composition, S. thermophilus abundance, and detection of TCI633-specific gene fragments. Results showed minor changes in the microbiota composition of breast milk and fecal samples in the TCI633 group, with a slight increase in S. thermophilus abundance. Furthermore, TCI633-specific gene fragments were detected in 66.7% of infant fecal samples, suggesting potential microbial transfer and colonisation. These findings provide preliminary evidence supporting the feasibility of TCI633 transmission via the gut-breast axis, although further research is needed to determine its functional significance.},
}
@article {pmid40609897,
year = {2025},
author = {Elhag, MRA and Abu-Median, AB and Da Boit, M and Haris, PI and Madkour, MI and Alkawamleh, DH and Faris, M},
title = {Transforming Gut Health through Ramadan Intermittent Fasting: A Review on Metabolic and Microbiomic Insights.},
journal = {Clinical nutrition ESPEN},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.clnesp.2025.06.051},
pmid = {40609897},
issn = {2405-4577},
abstract = {The gut microbiome's crucial role in health and disease has spurred interest in dietary interventions to modulate its composition and enhance microbial diversity. While approaches to optimize the microbiome exist, universal guidelines remain elusive due to the complexity of the ecosystem and interindividual variability. This review examines the biochemical changes associated with intermittent fasting (IF), specifically Ramadan intermittent fasting (RIF), which involves complete abstinence from food and fluids during daylight hours. Unlike other IF protocols, RIF's complete fasting presents a unique opportunity to investigate its specific effects on the gut microbiome and metabolic pathways. Preliminary studies suggest that RIF favorably modulates microbial profiles, potentially increasing beneficial taxa such as Akkermansia muciniphila and Bacteroides fragilis. However, limitations such as small sample sizes and heterogeneous study designs necessitate further research to fully elucidate the microbiome-driven mechanisms underlying IF's potential health benefits, particularly in relation to cancer, diabetes, and neurodegenerative diseases. Variations in key taxa, such as Dorea, Klebsiella, and Faecalibacterium, influenced by demographics, further emphasize this need. The RIF model possesses unique mechanisms among IF and holds promise for future applications.},
}
@article {pmid40609837,
year = {2025},
author = {Dubé-Zinatelli, E and Anderson, F and Ismail, N},
title = {The overlooked mental health burden of polycystic ovary syndrome: neurobiological insights into PCOS-related depression.},
journal = {Frontiers in neuroendocrinology},
volume = {},
number = {},
pages = {101203},
doi = {10.1016/j.yfrne.2025.101203},
pmid = {40609837},
issn = {1095-6808},
abstract = {Polycystic ovary syndrome (PCOS) is a prevalent endocrine disorder affecting 6-13% of reproductive-aged women worldwide. It is primarily characterized by ovarian dysfunction, hyperandrogenism, and metabolic disturbances. However, women with PCOS also face a heightened risk of depression, possibly due to dysregulation in endocrine and immune systems and gut microbiome disturbances. Symptoms of PCOS such as infertility, obesity, and hirsutism can also cause psychological distress and further exacerbate depression symptoms. Despite this comorbidity, mental health aspects of PCOS are often overlooked in the medical field, leading to insufficient support and negative impacts on the quality of life of PCOS patients. This review explores how distinct PCOS phenotypes influence physiological and psychological outcomes and the possible biological mechanisms involved. We also examine the effects of existing treatments on PCOS symptoms and depression. Addressing both physiological and psychological challenges is crucial for developing targeted, personalized interventions that improve outcomes for individuals diagnosed with PCOS.},
}
@article {pmid40609823,
year = {2025},
author = {Spalanzani, RN and Vasconcelos, TM and Bavia, L and Rodrigues, LS and Mesa, D and Fonseca, AS and Cavalli, LR and Dalla-Costa, LM},
title = {Comprehensive overview of the complex gut microbiota-miRNA crosstalk in immunocompromised pediatric patients.},
journal = {Life sciences},
volume = {},
number = {},
pages = {123833},
doi = {10.1016/j.lfs.2025.123833},
pmid = {40609823},
issn = {1879-0631},
abstract = {Immunocompromised pediatric patients, particularly those diagnosed with leukemia, often experience immune suppression due to prolonged use of immunosuppressive medication and chemotherapy. Consequently, these patients are highly vulnerable to infections caused by both pathogenic and non-pathogenic microorganisms. To prevent such infections, antibiotics and antifungals are routinely administered as prophylactic treatments. However, the use of antimicrobials significantly impacts the patient's microbiota, particularly the gut microbiota, which plays a crucial role in immunomodulating the mucosa and maintaining the integrity of the intestinal epithelium. Disruption of these functions may transform the intestinal epithelium into a potential entry point for harmful microorganisms. The regulation of gut homeostasis and the composition of the intestinal microbiota have been linked to different host-derived microRNAs (miRNAs) that regulate gene expression. Intestinal epithelial cells release miRNAs into the lumen, where they modulate the growth of gut microbes and the microbiota's composition. This review summarizes current insights into the relationship between the gut microbiota and intestinal miRNAs, emphasizing their potential as diagnostic and prognostic biomarkers for immunocompromised pediatric patients.},
}
@article {pmid40609813,
year = {2025},
author = {Wang, Y and Wang, X and Xu, X and Liu, M and Wang, J and Ye, H and Zhao, C and Xu, J and Wang, S and Chen, T and Wang, N and Lin, Y and Zheng, W and Bai, Y and Liu, Q},
title = {Sang Zhu Yang Zheng herbal tea: A multi-faceted approach to immunomodulation in the prevention and treatment of respiratory tract infectious diseases.},
journal = {Journal of ethnopharmacology},
volume = {352},
number = {},
pages = {120229},
doi = {10.1016/j.jep.2025.120229},
pmid = {40609813},
issn = {1872-7573},
abstract = {Dysregulation of the upper respiratory tract microbiota, host metabolite profiles, and immune lymphocyte subpopulations is critical in the pathogenesis of respiratory tract infectious diseases (RTIs). Sang Zhu Yang Zheng herbal tea (SZYZ) has emerged as a promising intervention for RTIs, yet its underlying mechanism remains unclear.<br><br>AIM OF THE STUDY: This study aims to investigate the immunomodulatory mechanisms of SZYZ underlying its role in the prevention and treatment of RTIs.<br><br>MATERIALS AND METHODS: Human studies were conducted to investigate SZYZ's immunomodulatory effects in preventing RTIs in healthy individuals. In healthy human subjects, SZYZ administration was evaluated for its impact on immune cell counts, airway microbiota composition, and metabolic profiles using advanced sequencing and metabonomic techniques. Murine models were utilized to explore SZYZ's preventive and therapeutic effects, as well as its underlying mechanisms against RTIs, with a focus on influenza A virus (IAV) infection. Murine models were employed with H1N1 PR8 virus infection, and study the therapeutic efficacy and mechanisms of SZYZ alone or in combination with oseltamivir.<br><br>RESULTS: In healthy humans, SZYZ profoundly increased the total T cells, B cells, CD4[+] T cells, and CD8[+] T cells. 16S rRNA sequencing showed decreased airway microbes' diversity, enrichment of the genera Bacteroides and Bifidobacterium, and lowered phyla Actinobacteria, Synergistetes, and several opportunistic pathogens, including Actinomyces, Fretibacterium, Mobiluncus, and Cloacibacillus, and inhibited microbe functions of human disease and bacterial infectious pathways, after administration. Serum and fecal metabonomic identified changes in 138 and 197 metabolites, respectively. Airway Actinobacteria were negatively corelated to total T cells and CD8[+]T cells count. Serum methyl hexadecanoic acid levels were negatively correlated with T cell counts and positively with Actinobacteria abundance. In IAV-infected mice, SZYZ, administered either as a prophylactic intervention or in combination with oseltamivir, significantly reduced mortality and pathological damage, which were related to immunomodulatory mechanisms of oxidative stress, inflammatory cytokines, and lymphocyte ratio.<br><br>CONCLUSION: We comprehensively elucidate the immunomodulatory effects of SZYZ's on microbiota, metabolism, and lymphocyte subpopulations, which provides a new therapeutic approach for the prevention and treatment of RTIs.},
}
@article {pmid40609724,
year = {2025},
author = {Pan, L and Chen, F and Zhao, Q and Yang, J and Qiu, Y and Wu, X and Guan, X},
title = {Soil antimony-microbe interactions in an abandoned antimony mine in southern China.},
journal = {Environmental research},
volume = {},
number = {},
pages = {122268},
doi = {10.1016/j.envres.2025.122268},
pmid = {40609724},
issn = {1096-0953},
abstract = {Soil contamination resulting from antimony (Sb) mining activities poses a substantial environmental risk in karst ecosystems. Understanding microbially mediated Sb transformation mechanisms is critical for advancing eco-friendly remediation technologies. The structural and functional responses of soil microbial communities were systematically investigated across three distinct areas (mining, smelting, and control) in typical Sb mining regions of Southwest China. Integrated geochemical and multi-omics analyses revealed pronounced Sb contamination gradients. Total Sb (Sbtot) concentrations followed the order: smelting area (8,231.97 ± 6,875.22) > mining area (735.03 ± 367.21 mg/kg) > control area (69.11 ± 0.47 mg/kg). Microbial community profiling indicated bacterial dominance (97.6% relative abundance), followed by archaea (2.0%) and fungi (0.4%). Notably, eight bacterial genera (Achromobacter, Sphingomonas, Thermomonas, Janibacter, Stenotrophomonas, Arenimonas, Bifidobacterium, and Halothiobacillus) exhibited significant positive correlations (p < 0.01) with Sbtot concentrations, suggesting their resistance to Sb. Functional annotation revealed critical associations between Sb biotransformation and microbial metabolic pathways, particularly sulfur redox cycling (sulfur oxidation: soxABXYZ; sulfate reduction: dsrAB) and nitrogen metabolism (nitrate reduction: narGHI). Co-occurrence network analysis indicated synergistic relationships between Sb-resistant microbes and elemental-cycling functional genes. Collectively, the results suggest that microbial Sb transformation in karst soils involves sulfur-assisted electron transfer and nitrate-dependent Sb oxidation. This study provides insight into the biogeochemical drivers of Sb fate in contaminated environments and establishes a conceptual framework for the development of microbiome-based remediation strategies suitable for Sb-polluted karst regions.},
}
@article {pmid40609269,
year = {2025},
author = {Wang, X and Zhao, J and Wu, Z and Wang, L and Zhang, W and Zhang, J and Liang, Y},
title = {Bisphenol M exposure promotes adiposity in mice via disrupting hepatic metabolism and gut microbiota homeostasis.},
journal = {Ecotoxicology and environmental safety},
volume = {302},
number = {},
pages = {118591},
doi = {10.1016/j.ecoenv.2025.118591},
pmid = {40609269},
issn = {1090-2414},
abstract = {Bisphenol M (BPM), a structural analog of bisphenol A (BPA) commonly used in food packaging and consumer plastics, remains incompletely characterized in terms of its obesogenic potential and underlying molecular mechanisms, posing challenges for evidence-based risk assessment. To address this gap, we investigated the obesogenic effects and metabolic impacts of BPM exposure in male BALB/c mice through integrated liver untargeted metabolomics and gut microbiome analysis. Our results showed that BPM exposure significantly increased body fat percentage, enlarged the epididymal white adipose tissue volume, and induced hepatic steatosis. Untargeted metabolomics revealed that BPM disrupted hepatic metabolic pathways, such as riboflavin metabolism, glycerophospholipid metabolism and fatty acid degradation. Concurrently, BPM altered gut microbiota, increasing the Firmicutes/Bacteroidetes ratio and abundances of Staphylococcus and Jeotgalicoccus. Correlation networks linked these microbial shifts to hepatic lipid metabolites, specifically implicating linoleic acid metabolism as a potential mediator of gut-liver crosstalk in obesity development. These findings indicate that BPM promotes adiposity through liver-gut crosstalk, advancing the understanding of obesogenic risks associated with BPA alternatives.},
}
@article {pmid40609069,
year = {2025},
author = {Jiang, B and Quinn-Bohmann, N and Diener, C and Nathan, VB and Han-Hallett, Y and Reddivari, L and Gibbons, SM and Baloni, P},
title = {Understanding disease-associated metabolic changes in human colonic epithelial cells using the iColonEpithelium metabolic reconstruction.},
journal = {PLoS computational biology},
volume = {21},
number = {7},
pages = {e1013253},
doi = {10.1371/journal.pcbi.1013253},
pmid = {40609069},
issn = {1553-7358},
abstract = {The colonic epithelium plays a key role in the host-microbiome interactions, allowing uptake of various nutrients and driving important metabolic processes. To unravel detailed metabolic activities in the human colonic epithelium, our present study focuses on the generation of the first cell-type specific genome-scale metabolic model (GEM) of human colonic epithelial cells, named iColonEpithelium. GEMs are powerful tools for exploring reactions and metabolites at the systems level and predicting the flux distributions at steady state. Our cell-type-specific iColonEpithelium metabolic reconstruction captures genes specifically expressed in the human colonic epithelial cells. iColonEpithelium is also capable of performing metabolic tasks specific to the colonic epithelium. A unique transport reaction compartment has been included to allow for the simulation of metabolic interactions with the gut microbiome. We used iColonEpithelium to identify metabolic signatures associated with inflammatory bowel disease. We used single-cell RNA sequencing data from Crohn's Diseases (CD) and ulcerative colitis (UC) samples to build disease-specific iColonEpithelium metabolic networks in order to predict metabolic signatures of colonocytes in both healthy and disease states. We identified reactions in nucleotide interconversion, fatty acid synthesis and tryptophan metabolism were differentially regulated in CD and UC conditions, relative to healthy control, which were in accordance with experimental results. The iColonEpithelium metabolic network can be used to identify mechanisms at the cellular level, and we show an initial proof-of-concept for how our tool can be leveraged to explore the metabolic interactions between host and gut microbiota.},
}
@article {pmid40608939,
year = {2025},
author = {Argaw-Denboba, A},
title = {The gut microbiome-germline axis: Does a prospective father's gut microbiota matter?.},
journal = {Science (New York, N.Y.)},
volume = {389},
number = {6755},
pages = {38},
doi = {10.1126/science.adz0492},
pmid = {40608939},
issn = {1095-9203},
mesh = {*Gastrointestinal Microbiome ; Humans ; Male ; *Fathers ; *Germ Cells/physiology ; },
abstract = {Does a prospective father's gut microbiota matter?},
}
@article {pmid40608691,
year = {2025},
author = {Lebeuf-Taylor, E and Cosby, A and Webber, Q and Cottenie, K},
title = {Social structuring of the gut microbiome in communally roosting bats.},
journal = {PloS one},
volume = {20},
number = {7},
pages = {e0325710},
pmid = {40608691},
issn = {1932-6203},
mesh = {Animals ; *Chiroptera/microbiology/physiology ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; *Social Behavior ; },
abstract = {The gut microbiome is the community of microbes that inhabits the gastrointestinal tracts of animals. Laboratory findings have shown that the gut microbiome plays a crucial role in host metabolism, physiology, and immunity. This has led to speculation that selection acts on both host and microbiome-although identifying functionally essential coevolving microbes in wild animals remains challenging. A recent surge of studies in wild populations has identified phylogenetic, spatiotemporal, dietary, and social patterns in host-associated microbiomes. Here, we describe and assess the gut microbiomes of two sympatric bat species: big brown bats (Eptesicus fuscus) and little brown bats (Myotis lucifugus). Although these species share similar diets and environments throughout much of their North American ranges, we found they have distinct gut microbiomes. We find no evidence of a functional core microbiome among big brown bats and identify roost identity as a driver of microbiome composition, likely arising from social transmission among hosts through physical proximity. We conclude that both environmental and social factors drive microbiome composition in big brown bats and that repeated, extensive sampling is required to bring ecological reality to host-associated microbiome studies in wild populations.},
}
@article {pmid40608175,
year = {2025},
author = {Ye, Z and Yu, Y and Cao, Z and Ye, Z and Gu, X and Shen, X and Cai, B and Lin, B and Ji, C and Qiao, N and Wu, Z and Chen, Z and Ma, Z and Chen, L and Liang, B and Liao, Y and He, W and Shen, Q and Han, J and Cao, X and Zhou, X and Shou, X and Shen, M and Wang, Y and Zhang, Z and Ye, H and Zhang, Q and Gao, R and Zhang, Y},
title = {Microbiome and metabolic disorder in prolactinoma: intrinsic gender differences and extrinsic therapy effects.},
journal = {Pituitary},
volume = {28},
number = {4},
pages = {83},
pmid = {40608175},
issn = {1573-7403},
support = {24ZR1408900//Natural Science Foundation of Shanghai Municipality/ ; 320.6750.2023-13-11//Wu Jieping Medical Foundation/ ; 2023ZD0506800//National Major Science and Technology Projects of China/ ; 82202906//National Natural Science Foundation of China/ ; },
}
@article {pmid40608163,
year = {2025},
author = {Li, MX and Lian, WH and Lian, ZH and Luo, XQ and Yue, LX and Han, JR and Hu, CJ and Li, S and Li, WJ and Dong, L},
title = {Rare and abundant taxa in Artemisia desertorum rhizosphere soils demonstrate disparate responses to drought stress.},
journal = {Advanced biotechnology},
volume = {3},
number = {3},
pages = {21},
pmid = {40608163},
issn = {2948-2801},
support = {32270076//National Natural Science Foundation of China/ ; 2022xjkk1200//The Third Xinjiang Scientific Expedition Program/ ; 2022B0202110001//Guangdong S&amp;T Program/ ; },
abstract = {The growth and adaptability of desert plants depend on their rhizosphere microbes, which consist of a few abundant taxa and numerically dominant rare taxa. However, the differences in diversity, community structure, and functions of abundant and rare taxa in the rhizosphere microbiome of the same plant in different environments remain unclear. This study focuses on the rhizosphere microbial communities of Artemisia desertorum, a quintessential desert sand-stabilizing plant, investigating the diversity patterns and assembly processes of rare and abundant taxa across four Chinese deserts: Mu Us, Kubuqi, Tengger, and Ulan Buh. The results show that climatic factors, especially aridity and mean annual precipitation (MAP), significantly influence bacterial community composition and microbial network complexity. The interactions between rare and non-rare taxa are non-random, forming a modular network in which rare taxa serve as central nodes, and their loss could destabilize the network. Rare taxa are primarily shaped by heterogeneous selection, whereas abundant taxa are mainly influenced by dispersal limitation. Functionally, abundant taxa exhibit higher metabolic potential, whereas rare taxa are more involved in processes such as cell motility, indicating distinct ecological roles. These results provide new insights into the ecological functions of rare and abundant taxa in desert rhizosphere communities and highlight the importance of microbial management for desert plant health.},
}
@article {pmid40607846,
year = {2025},
author = {Carvalho, T and Medina, D and James, TY},
title = {Successful Transmission and Isolation of a Fungal Pathogen From Wild Frogs to a Captive Amphibian Model Species: Fine Scale Pathogen Genetic Diversity and Infection-Induced Changes in Skin Bacteria.},
journal = {Environmental microbiology},
volume = {27},
number = {7},
pages = {e70136},
pmid = {40607846},
issn = {1462-2920},
support = {9337//Gordon and Betty Moore Foundation/ ; //Canadian Institute for Advanced Research/ ; },
mesh = {Animals ; *Batrachochytrium/genetics/isolation &amp; purification ; *Skin/microbiology ; *Genetic Variation ; *Anura/microbiology ; *Mycoses/microbiology/veterinary/transmission ; *Bacteria/isolation &amp; purification/classification/genetics ; *Chytridiomycota/genetics/isolation &amp; purification ; Genotype ; Animals, Wild/microbiology ; },
abstract = {Amphibian populations worldwide are severely threatened, in part, by the pathogenic fungus Batrachochytrium dendrobatidis (Bd). While Bd has driven many amphibian declines and extinctions, its impact varies, with some populations exhibiting resistance or tolerance. Understanding the mechanisms behind this variation, together with Bd genetic diversity, is crucial for conservation. We used the model organism Hymenochirus boettgeri in a lab-based transmission experiment designed to isolate Bd derived from wild amphibian hosts with low pathogen loads. Through successful transmission and subsequent isolation and genotyping, we identified multiple Bd genotypes from a single population, including a potential sexual recombinant, all belonging to the Global Panzootic Lineage (Bd-GPL). This finding contributes to evidence of ongoing genetic mixing of Bd in natural environments. Additionally, we leveraged this experiment to assess Bd-induced changes in amphibian skin bacteria. Our results showed significant changes in the skin bacterial communities of H. boettgeri after acquiring Bd infection, including reductions in bacterial diversity, and shifts in community composition, as observed in others susceptible species. These findings highlight the value of transmission experiments in isolating Bd from wild hosts and underscore the potential of H. boettgeri as a model to investigate Bd genetic diversity and host-associated microbiome responses to infection.},
}
@article {pmid40607829,
year = {2025},
author = {Williams, A and Ravel, J and Armstrong, E and Huibner, S and Rutt, L and Kaul, R and Holm, JB},
title = {Temporal dynamics of the vaginal microbiome and host immune markers before, during, and after metronidazole treatment for bacterial vaginosis.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0038025},
doi = {10.1128/msystems.00380-25},
pmid = {40607829},
issn = {2379-5077},
abstract = {This study analyzed metagenomic and immune marker profiles of seven individuals before, during, and after a 7-day course of metronidazole treatment for bacterial vaginosis (BV). Treatment reduced BV-associated bacteria and immune marker levels, with distinct early (days 1-4) and late (days 5-7) phases. Post-treatment variability in microbial and immune marker profiles demonstrated a rapid resurgence of certain BV-associated bacteria, highlighting the need for additional strategies like probiotics to maintain a healthy vaginal microbiome. The study found significant host and microbial influences on immune response variance, with IP-10 and sEcad highly correlated with the vaginal microbiome. The findings identify the optimal timing for administering live biotherapeutics to restore D-lactic acid-producing Lactobacillus species dominance and underscore the complexity of BV infection and treatment response among different people.IMPORTANCEBacterial vaginosis (BV), a common condition associated with an increased risk of preterm birth and sexually transmitted infections, among others, is characterized by a dysbiotic vaginal microbiome associated with the predominance of a diverse assortment of anaerobic bacterial species. Metronidazole is the first-line treatment recommended by the CDC for BV when patients report symptoms. Despite treatment, BV recurrence is common. There is limited data regarding the effects of oral metronidazole on the vaginal microbiome starting at the initiation of treatment, as most studies have compared measurements taken before and after treatment completion. This study utilized metagenomic sequencing, pan-bacterial qPCR, and immune marker measurements to analyze the longitudinal dynamics of the vaginal microbiome and host immune response before, during, and after metronidazole treatment.},
}
@article {pmid40607612,
year = {2025},
author = {Angot, V and Thiour-Mauprivez, C and Schellenberger, R and Lamboeuf, M and Crépin, O and Garmyn, D and Blouin, M and Jacquiod, S},
title = {Alleviation of water-deficit inhibition of plant growth by rhizosphere microbiota conditioning.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.70362},
pmid = {40607612},
issn = {1469-8137},
support = {//University of Bourgogne Franche-Comt&#xe9; via an ISITE-BFC International Junior Fellowship Award/ ; ANR-11-INBS-0012//Agence Nationale de la Recherche, Programme Investissements d'avenir/ ; },
abstract = {Rhizosphere microbiota conditioning is a promising strategy to enhance plant growth. We conditioned the rhizosphere microbiota of Brassica juncea to water deficit to assess its impact on plant growth. In a glasshouse, plants were first grown under well-watered conditions, then exposed to moderate (MD, pF = 2.3) or extreme (ED, pF = 3.5) water deficits. We extracted and inoculated the rhizosphere microbiota to new plants and repeated this process 10 times. Control plants were kept well-watered. We monitored changes in plant phenotypes and in rhizosphere microbial communities (bacteria and eukaryotes). The initial water-deficit growth inhibition of plants was successfully alleviated by 19.3% in MD and 29.4% in ED after conditioning (MD: from -35.6% to -16.3%; ED: from -56.8% to -27.4%). This beneficial effect on plants was not observed during the well-watered phases, suggesting an active role of the microbiota when water became scarce. The increase in plant growth correlated with aggregated rhizosphere soil and significantly matched changes in the bacterial community, featuring reduced diversity and increased biofilm production capacity along the conditioning process. We showed that microbiota conditioning was a fast and efficient way to achieve better plant growth under adverse conditions, likely via the adaptation capabilities of the rhizosphere bacterial community.},
}
@article {pmid40607437,
year = {2025},
author = {Qi, P and Li, L and Zhang, J and Ren, L and Xie, X},
title = {The dual regulatory effects of intestinal microorganisms and their metabolites in gouty arthritis pathogenesis: a balance between promotion and inhibition.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1591369},
pmid = {40607437},
issn = {1664-3224},
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; *Arthritis, Gouty/microbiology/metabolism/immunology/etiology ; Animals ; Uric Acid/metabolism ; *Bacteria/metabolism ; },
abstract = {Gout is an arthritis characterized by the deposition of urate crystals, often accompanied by robust inflammatory responses. The gut microbiome profoundly influences gout pathogenesis, progression, and management by affecting uric acid metabolism, immune responses, and intestinal barrier function. Studies reveal that gut microorganisms exert a dual role in gout development. Gout patients typically exhibit increased harmful bacterial abundance and reduced beneficial species. Harmful bacteria and associated metabolites can influence systemic uric acid levels by regulating excretion and synthesis, thereby promoting gout manifestations. Conversely, beneficial bacteria interact with the host immune system to inhibit inflammation and modulate the inflammatory state of joints. Furthermore, the gut microbiome can significantly impact gout treatment efficacy through its influence on drug metabolism and absorption. Research highlighting the gut-joint-inflammation axis offers novel therapeutic strategies for gout, suggesting that future approaches may involve microbiome modulation to enhance clinical outcomes.},
}
@article {pmid40607421,
year = {2025},
author = {Fraser, DR and Stadnyk, AW},
title = {The emerging relationship between mucosal-associated invariant T cell populations and the onset and progression of type 1 diabetes.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1602934},
pmid = {40607421},
issn = {1664-3224},
mesh = {*Diabetes Mellitus, Type 1/immunology/pathology/metabolism/etiology ; Humans ; *Mucosal-Associated Invariant T Cells/immunology/metabolism ; Animals ; Disease Progression ; Gastrointestinal Microbiome/immunology ; Mice ; },
abstract = {Type 1 diabetes (T1D) is a chronic autoimmune disorder characterized by autoreactive CD8[+] T cells that destroy insulin-producing pancreatic β-cells. CD8[+] T cells are unlikely to be the only cells involved in diabetes. Relatively recently described and still enigmatic, Mucosal-associated invariant T (MAIT) cells, innate-like T cells that recognize microbial-derived peptides, exist in the blood and tissues and are implicated in early immune responses. Immunological differences, some of which implicate MAIT cells, exist between individuals at different stages of T1D progression. This review explores the emerging relationship between gastrointestinal and pancreatic MAIT cell populations and the onset and progression of T1D. Early microbial colonization is critical for immune maturation, homeostasis, and MAIT cell development, and disruptions such as Caesarean delivery or antibiotic-induced dysbiosis correlate with increased T1D incidence. Diabetes progression in the diabetes-prone NOD mice is associated with reduced gut mucosal integrity, impairing the protective IL-17 and IL-22 responses of gut-resident MAIT cells and exacerbating systemic inflammation. MAIT cells recruited to the inflamed pancreas during T1D onset likely contribute to β-cell destruction through IFN-γ and granzyme B production. This hypothesis is supported by altered MAIT cell frequencies and phenotypes in individuals with T1D; MAIT cells are reduced in the blood of children recently diagnosed with T1D, potentially corresponding to pancreatic migration, while adults with long-term T1D have persistent, circulating MAIT cells with exhaustion markers. MAIT cells appear to have dual protective and pathogenic roles impacted by microbiome interactions. Understanding these relationships may inform non-invasive biomarkers for the disease.},
}
@article {pmid40607345,
year = {2025},
author = {Huang, HW and Kuo, TC and Lee, YJ and Chen, MJ},
title = {Multi-omics analysis reveals the efficacy of two probiotic strains in managing feline chronic kidney disease through gut microbiome and host metabolome.},
journal = {Frontiers in veterinary science},
volume = {12},
number = {},
pages = {1590388},
pmid = {40607345},
issn = {2297-1769},
abstract = {Gut dysbiosis has been implicated in the progression of chronic kidney disease (CKD), yet the functional alterations of the microbiome and their links to host metabolism in feline CKD pathophysiology remain unclear. Our previous findings suggested that Lactobacillus mix (Lm) may mitigate CKD progression by modulating gut microbiota composition and restoring microbial balance. In this pilot study, we aimed to evaluate the potential effects of an 8-week Lm intervention in cats with stage 2-3 CKD and to investigate the underlying host-microbiota interactions through integrated multi-omics analysis. We performed full-length 16S rRNA amplicon sequencing and untargeted metabolomics to characterize the intricate interactions between the gut microbiome and host metabolome, and further investigate the modulation of microbial function and its related gut-derived metabolites before and after the intervention. During this period, creatinine and blood urea nitrogen levels were stabilized or reduced in most cats, and gut-derived uremic toxins (GDUTs) showed modest numerical reductions without statistically significant changes. Lm intervention was also associated with increased gut microbial diversity, alterations in specific bacterial taxa, and upregulation of microbial functions involved in GDUTs and short-chain fatty acid (SCFAs) biosynthesis pathways. To further explore individual variations in response, we conducted a post hoc exploratory subgroup analysis based on changes in microbial-derived metabolites. Cats classified as high responders, defined as those with reductions in three GDUTs and increases in SCFAs, exhibited distinct microbiome compositions, microbial functional profiles, and metabolite shifts compared to moderate responders. Among high responders, modulation of microbial pathways involved in GDUTs (tyrosine, tryptophan, and phenylalanine metabolism) and SCFAs (pyruvate, propanoate, and butanoate metabolism) biosynthesis was particularly evident. Notably, the relative abundance of Lm strains was higher in high responders, suggesting a potential association between colonization efficiency and microbial metabolic outcomes. This study demonstrates an Lm-mediated interconnection between the modulation of microbial composition, metabolic functions, and systemic metabolite profiles. Overall, our findings suggest that Lm intervention may influence the gut-kidney axis in cats with CKD. These preliminary, hypothesis-generating results highlight the value of multi-omics approaches for understanding host-microbe interactions and support further investigation into personalized probiotic strategies as potential adjuvant therapies in feline CKD.},
}
@article {pmid40607343,
year = {2025},
author = {Xu, H and Zhang, F and Che, Y and Cui, Y and Yao, Q and Guan, Y and Chen, H and Huang, Y},
title = {Integrative multi-omics and bioinformatics analysis of the effects of BaiRui YuPingFeng Powder on intestinal health in broilers.},
journal = {Frontiers in veterinary science},
volume = {12},
number = {},
pages = {1606531},
pmid = {40607343},
issn = {2297-1769},
abstract = {INTRODUCTION: In recent years, global poultry consumption has increased rapidly, making chicken the most widely consumed meat worldwide by 2019. To increase livestock development, antibiotics are often added to animal feed as growth promoters. But overuse of antibiotics may alter the gut microbiota, make people more resistant to them, and raise the possibility that they will spread antibiotic resistance genes to the human microbiome. Therefore, identifying safe and effective alternatives to antibiotics in livestock production is crucial for maintaining and improving gut microbial balance, ultimately promoting poultry health. The aim of this study was to investigate the mechanisms behind the impacts of BaiRui YuPingFeng Powder (TCYP) on intestinal health in broilers using combined metabolomics, bioinformatics analysis, and 16S rRNA sequencing.<br><br>METHODS: In a 42-day feeding trial, 300 one-day-old broilers were randomly divided into five groups (six replicates per group; 10 broilers per replicate) fed a basal diet with or without supplements: control (CON), antibiotic (ATB), and TCYP at 500, 1000, and 1500 mg/kg. Growth performance, serum biochemical parameters, intestinal morphology, cecal microbiota composition, and metabolomic profiles were analyzed. Bioinformatics analysis was used to identify potential targets and pathways, followed by qPCR validation of key genes.<br><br>RESULTS: Compared with the CON group, TCYP administration dose-dependently reduced the feed-to-gain ratio (F/G) and average daily feed intake (ADFI) while increasing average daily gain (ADG), with the high-dose TCYP showing more pronounced effects (p < 0.05). Serum biochemical analysis revealed that TCYP treatment significantly decreased serum levels of total cholesterol (T-CHO), triglycerides (TG), lactate dehydrogenase (LDH), and alanine aminotransferase (ALT) in a dose-dependent manner, while elevating albumin (ALB) content. These beneficial effects were particularly marked in the high-dose TCYP group (p < 0.05). Histopathological examination indicated that high-dose TCYP significantly enhanced villus height and the villus-to-crypt ratio (V/C) in the duodenum, jejunum, and ileum compared to the CON group (p < 0.05). 16S rRNA sequencing analysis revealed that TCYP treatment significantly modified the &#x3b2;-diversity of cecal microbiota (p < 0.01). Compared to the CON group, ATB treatment increased the abundance of Faecalibacterium and Lachnospiraceae_unclassified but reduced Ruminococcaceae_unclassified and Firmicutes_unclassified. Notably, dietary TCYP supplementation maintained gut microbiota profiles similar to the CON group, demonstrating its stabilizing effect on microbial community structure in broilers. Metabolomic analysis identified differential metabolites primarily involved in lipid and lipid-like molecules, organic heterocyclic compounds, and organic acids and derivatives. Spearman correlation analysis revealed significant associations between Lachnospiraceae_unclassified and metabolites such as Gly-Leu, fumarate, and phenylpyruvic acid (|r| > 0.5, p < 0.05). Bioinformatics analysis suggested that TCYP may improve intestinal health by regulating key targets, including MMP9, TGFB1, and PPARG, as well as the peroxisome proliferator-activated receptor (PPAR) signaling pathway. Quantitative PCR (qPCR) results showed that, compared to the CON group, TCYP dose-dependently significantly upregulated the mRNA expression of PPARG, PDPK1, and Bcl2 in jejunal tissues (p < 0.05), while significantly downregulating the expression of MMP1 and Bax (p < 0.05).<br><br>CONCLUSION: TCYP enhances growth performance and intestinal health in broilers through multiple mechanisms, including maintaining cecal microbial homeostasis, modulating lipid and amino acid metabolism, with potential involvement of the PPAR signaling pathway based on bioinformatics and gene expression analysis.},
}
@article {pmid40607325,
year = {2025},
author = {Sekar, R and Bottu, K and Gb, P and Ramasamy, J and Venkatesalu, B},
title = {Comparative analysis of candidal carriage rates in long-term and short-term COVID-19 patients: An RT-PCR study.},
journal = {Journal of oral biology and craniofacial research},
volume = {15},
number = {4},
pages = {899-904},
pmid = {40607325},
issn = {2212-4268},
abstract = {BACKGROUND: Most individuals who had COVID-19 infection recover completely. However, current research shows that 10-20 % of the population, especially immunocompromised and elderly people, endure numerous adverse effects and multiple complications associated with different organs and systems during its pathogenic cycle. Also, many fungal coinfections are seen as post-COVID dysbiosis, the most common fungal organism being Candida. This study aims to compare the candidal carriage rate of short-term and long-term affected SARS-COV-2 patients in saliva using PCR and compare it with healthy individuals.<br><br>RESULTS: The study included both male (15) and female (23) long-term and short-term post-COVID patients and healthy individuals [Male (5) and Female (15)]. The candidal carriage rate was increased in long-term COVID patients than in short-term COVID patients and healthy individuals (p&#xa0;<&#xa0;0.001&#x2217;). Among long-term COVID patients, those who had oxygen assistance (p=0.04) and were admitted to the ICU (p=0.01) had relatively higher candidal carriage rates than those who didn't receive any intensive care procedures.<br><br>CONCLUSION: COVID-19 significantly affects the oral microbiome, leading to dysbiosis and increased candidal carriage. The manifestation of fungal coinfections in post-COVID patients appears to be influenced by various factors, including oxygen support, catheterization, and immunosuppressive treatments. Thereby, early diagnosis and early intervention, along with health care providers acquainted with potential risks and the likelihood of secondary infections, are the only ways to reduce the consequences of this devastating disease.},
}
@article {pmid40607028,
year = {2025},
author = {Yin, X and Tian, L and Liu, Q and Zhao, H},
title = {Association between pro-inflammatory diet and ulcerative colitis: a systematic review and meta-analysis.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1586691},
pmid = {40607028},
issn = {2296-861X},
abstract = {BACKGROUND: Emerging evidence suggests that dietary patterns can mediate intestinal inflammatory responses through immune-microbiome interactions. Diet and inflammation are important pathogenic factors for ulcerative colitis (UC). However, the existing evidence regarding the association between a pro-inflammatory diet and the risk of UC is controversial, and further clarification of this association is needed.<br><br>OBJECTIVE: This study aimed to explore the association between pro-inflammatory diet and UC risk.<br><br>METHODS: We systematically searched PubMed, Web of Science, Scopus, EMBASE, and Cochrane Library databases from their inception to January 15th, 2025. Two researchers independently used the Newcastle - Ottawa Scale to assess the quality of the included studies. Data analysis was performed using STATA 17 software.<br><br>RESULTS: This systematic review and meta-analysis included eight studies involving approximately 758,068 participants. The meta-analysis indicated that an inflammatory or pro-inflammatory diet did not increase the risk of UC (OR&#x202f;=&#x202f;0.97, 95% CI&#x202f;=&#x202f;0.84-1.12). However, subgroup analyses revealed differing results: within the case-control study subgroup, a pro-inflammatory diet was associated with an increased risk of UC (OR&#x202f;=&#x202f;2.09, 95% CI: 1.23-3.56), whereas in the cohort study subgroup, no significant association was found between a pro-inflammatory diet and UC (OR&#x202f;=&#x202f;0.91, 95% CI: 0.78-1.06). Sensitivity analysis indicated that the study results were robust. Additionally, Begg's test (p&#x202f;=&#x202f;0.174) and Egger's test (p&#x202f;=&#x202f;0.085) showed no significant publication bias in this study.<br><br>CONCLUSION: The results of this study do not support a significant association between pro-inflammatory diets and UC risk. However, due to the limited level of evidence from observational studies and their heterogeneity, the association between pro-inflammatory diets and UC may be underestimated or overestimated. Therefore, larger multi-centre studies are needed to standardize the assessment of diets and adjust for microbial-related confounding factors in order to elucidate the association and mechanisms between pro-inflammatory diets and UC.},
}
@article {pmid40607026,
year = {2025},
author = {Yang, X and Li, H and Qumu, D and Han, B and Amatjan, M and Wu, Q and Wei, L and Li, B and Ma, M and He, J and Wang, S and Yu, Y and Shao, X},
title = {Taurine alleviates hyperuricemia-induced nephropathy in rats: insights from microbiome and metabolomics.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1587198},
pmid = {40607026},
issn = {2296-861X},
abstract = {BACKGROUND: Gut microbiota play a critical role in developing hyperuricemic nephropathy (HN). We previously found that sulfur-containing amino acid taurine (T) has nephroprotective effects in hyperuricemia (HUA) rats. However, the mechanism is still unclear. To investigate the underlying mechanism of T, rats were fed adenine and ethambutol hydrochloride for the introduction of HN.<br><br>METHODS: Pathological changes in the kidney were assessed using hematoxylin and eosin staining. 16S rRNA sequencing and metabolomics analyzed changes in the gut microbiota and fecal metabolism, and in vitro experiments were conducted to investigate the potential action and mechanism of T against HN.<br><br>RESULTS: In vitro results demonstrated that T could inhibit NF-&#x3ba;B, IL-1&#x3b2;, IL-6, TNF-&#x3b1;, and ROS in UA-induced HK-2 cells. It also improved renal function, ameliorated renal fibrosis, and reversed enteric dysbacteriosis in HN rats. These results showed that T protects against HN through the modulation of metabolites mediated by the gut microbiota. Meanwhile, gut microbiota included Lactobacillus and Lachnospiraceae NK4A136 group showed correlations with nephroprotective profiles of T. The combined analysis of 16S rRNA gene sequencing and untargeted metabolomics indicated that the anti-HN effects of T could be achieved through phenylalanine metabolism, caffeine metabolism, nicotinate and nicotinamide metabolism, retinol metabolism, and tryptophan metabolism.<br><br>CONCLUSION: These findings suggest that the potential protective mechanism of T for HN is not only related to altered metabolic pathways and downregulation of inflammatory cytokines but also to the reciprocal regulation of microbiota structure and metabolism.},
}
@article {pmid40606980,
year = {2025},
author = {Kim, Y and Kim, MK and Lee, S},
title = {Comparative microbiome analysis of paired mucosal and fecal samples in Korean colorectal cancer patients.},
journal = {Frontiers in oncology},
volume = {15},
number = {},
pages = {1578861},
pmid = {40606980},
issn = {2234-943X},
abstract = {BACKGROUND: Colorectal cancer (CRC) is increasingly linked to gut microbiome dysbiosis. However, few studies have examined tumor-associated microbial dynamics in Korean CRC patients using both mucosal and fecal samples.<br><br>METHODS: We analyzed paired fecal and mucosal samples from 30 Korean CRC patients aged 60-80 years before and after surgery. Microbial DNA was sequenced using 16S rRNA gene analysis. Diversity metrics, differential abundance testing (LEfSe), and pathway prediction (PICRUSt2) were performed. Diagnostic performance was evaluated with ROC curves, and associations with clinical parameters were assessed via regression models.<br><br>RESULTS: Beta diversity revealed significant compositional differences between fecal and mucosal samples (p = 0.001), with mucosal samples showing higher enrichment of CRC-associated taxa. Fusobacterium, Prevotella 9, Parvimonas, and Holdemanella were significantly enriched in pre-surgical samples and declined after surgery (p < 0.01). Combined microbial markers yielded an AUC of 0.841 for distinguishing pre- from post-surgical status. Functional predictions indicated upregulation of amino acid metabolism and lipopolysaccharide (LPS) biosynthesis pathways in pre-surgical samples. Notably, Fusobacterium abundance correlated with TNM stage (p = 0.028), and Prevotella 9 abundance decreased with age (p = 0.006).<br><br>CONCLUSION: This study highlights distinct microbial and functional signatures in CRC, particularly from mucosal samples, which offer deeper insights into tumor-microbiota interactions. The identified microbial markers and enriched pathways may contribute to immune modulation and tumor progression. These findings support the potential for microbiome-based diagnostic and therapeutic strategies tailored to Korean CRC patients and underscore the importance of dual-sample analysis in microbiome research.},
}
@article {pmid40606926,
year = {2025},
author = {Pandey, H and Goel, P and Srinivasan, VM and Tang, DWT and Wong, SH and Lal, D},
title = {Gut microbiota in non-alcoholic fatty liver disease: Pathophysiology, diagnosis, and therapeutics.},
journal = {World journal of hepatology},
volume = {17},
number = {6},
pages = {106849},
pmid = {40606926},
issn = {1948-5182},
abstract = {Non-alcoholic fatty liver disease (NAFLD), also referred to as metabolic-associated fatty liver disease, is among the most prevalent chronic liver conditions. In some cases, NAFLD may lead to liver inflammation and non-alcoholic steatohepatitis, which can eventually progress to liver cirrhosis and hepatocellular carcinoma. The pathophysiology of NAFLD is complex, involving both genetic and environmental factors. NAFLD is a multisystem disease linked to a higher likelihood of developing metabolic disorders such as type 2 diabetes, obesity, and cardiovascular and chronic kidney diseases. The gut-liver axis represents a key connection between the gut microbiota and the liver, and its disruption has been linked to NAFLD. Growing evidence underscores the significant role of gut microbiota in the onset and progression of NAFLD, with alterations in the gut microbiome and impaired gut barrier function. Studies have identified key microbiota signatures and metabolites linked to NAFLD, implicating oxidative stress, endotoxemia, and inflammatory pathways that further strengthen the connection between gut microbiota and NAFLD. Modulation of gut microbiota through diet and microbiota-centered therapies, such as next-generation probiotics and fecal microbiota transplantation, holds promise for treating NAFLD. In this review, we explore the key link between gut microbiota and the development and progression of NAFLD, as well as its potential applications in the diagnosis and treatment of the disease.},
}
@article {pmid40604874,
year = {2025},
author = {Zhou, X and Zheng, W and Kong, W and Zeng, T},
title = {Identification of circulating inflammation cytokines as a mediator of gut microbiota and type 2 diabetes mellitus: a Mendelian randomization study.},
journal = {Diabetology &amp; metabolic syndrome},
volume = {17},
number = {1},
pages = {249},
pmid = {40604874},
issn = {1758-5996},
support = {82270909//National Natural Science Foundation of China/ ; 2020BCB003//Key R&amp;D Program of Hubei Province/ ; },
abstract = {BACKGROUND: Several studies have suggested that the gut microbiota (GM) may be associated with type 2 diabetes mellitus (T2DM). However, the causal relationship between GM and T2DM and whether inflammatory cytokines act as mediators remain unclear.<br><br>AIMS: To investigate the association between GM and T2DM and the proportion of this association that is mediated through inflammatory cytokines.<br><br>METHODS: We conducted a bidirectional and mediation Mendelian randomization (MR) study utilizing data from the genome-wide association studies (GWAS) of four sources of GM taxa (MiBioGen consortium, n&#x2009;=&#x2009;18,340; Dutch Microbiome Project, n&#x2009;=&#x2009;7,738; German biobanks, n&#x2009;=&#x2009;8,956; FINRISK 2002, n&#x2009;=&#x2009;5,959), a meta-analysis of inflammatory proteins (n&#x2009;=&#x2009;14,824), and European-ancestry T2DM (n&#x2009;=&#x2009;1,528,967). The inverse variance weighted method was applied as the primary method. And two-step MR was employed to identify potential mediating inflammatory cytokines.<br><br>RESULTS: We found evidence for 28 positive and 20 negative causal effects between multiple sources of GM and T2DM using at least two MR methods. And there were 2 positive and 5 negative causal relationships between cytokines and T2DM using at least two MR methods. The mediation MR analysis found that interferon-gamma (IFN-&#x3b3;) mediated the causal effects of species Kandleria vitulina on T2DM (proportion mediated&#x2009;=&#x2009;22.5%, P&#x2009;=&#x2009;0.022).<br><br>CONCLUSION: The MR study supports the causal effect between Kandleria vitulina species and T2DM, with a potential mediating role played by inflammatory factor IFN-&#x3b3;. Such result would serve as evidence for GM-targeted and cytokine-targeted therapy to prevent T2DM.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13098-025-01792-8.},
}
@article {pmid40606636,
year = {2025},
author = {Lin, SH and Lin, RJ and Chan, KY and Chu, CL and Chen, YL and Fu, SC},
title = {Anxiety-related gut microbiota alterations in Parkinson's disease: distinct associations compared to healthy individuals.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1594152},
pmid = {40606636},
issn = {2235-2988},
mesh = {Humans ; *Parkinson Disease/microbiology/complications/psychology ; *Gastrointestinal Microbiome ; *Anxiety/microbiology ; Male ; Female ; RNA, Ribosomal, 16S/genetics ; Aged ; Middle Aged ; Feces/microbiology ; Bacteria/classification/genetics/isolation &amp; purification ; Dysbiosis ; },
abstract = {BACKGROUND AND OBJECTIVES: Anxiety affects 25-49% of Parkinson's disease (PD) patients, exacerbating non-motor symptoms and significantly reducing quality of life. Growing evidence suggests that gut microbiota plays a role in anxiety, but whether its impact differs between PD and non-PD populations remains unclear. This study explores the heterogeneity of gut microbiota-associated anxiety in PD and non-PD individuals.<br><br>METHODS: Participants from the NeuroGenetics Research Consortium provided clinical data, including PD status, anxiety status, and stool samples analyzed via 16S rRNA sequencing. After excluding nine participants with missing anxiety data, 322 individuals were included (193 PD, 129 non-PD). We assessed &#x3b1;-diversity, &#x3b2;-diversity, taxonomic composition, and functional pathways to compare microbial differences between anxious and non-anxious individuals within and across PD and non-PD groups.<br><br>RESULTS: Beta diversity analysis revealed significant microbial differences between anxious and non-anxious PD patients (p = 0.043 in Bray-Curtis index) but not in the non-PD group. Escherichia-Shigella was significantly enriched in non-anxious PD patients (p = 0.011). Functional pathway analysis identified distinct metabolic alterations associated with anxiety in PD and non-PD individuals. In non-PD participants, anxiety was linked to increased activity in glycosphingolipid biosynthesis, sphingolipid metabolism, other glycan degradation, glycosphingolipid biosynthesis, and glycosaminoglycan degradation. In contrast, PD patients with anxiety exhibited enrichment in indole alkaloid biosynthesis, linoleic acid metabolism, and polyketide sugar unit biosynthesis.<br><br>CONCLUSION: Gut microbiota-associated anxiety differs between PD and non-PD populations, suggesting distinct pathophysiological mechanisms. These findings underscore the potential of microbiome-targeted interventions as novel therapeutic strategies for anxiety in PD patients.},
}
@article {pmid40606566,
year = {2025},
author = {Wang, L and Wang, L and Chen, L},
title = {NetNiche: Microbe-Metabolite Network Reconstruction and Microbial Niche Analysis.},
journal = {Phenomics (Cham, Switzerland)},
volume = {5},
number = {2},
pages = {208-211},
pmid = {40606566},
issn = {2730-5848},
abstract = {UNLABELLED: Metagenomics and metabolomics technologies have been widely used to investigate the microbe-metabolite interactions in vivo. However, the computational methods that accurately infer the microbe-metabolite interactions are lacking. We present a context-aware framework for graph representation learning, NetNiche, which predicts microbe-metabolite and microbe-microbe interactions in an accurate manner, by integrating their abundance data with prior knowledge. We applied NetNiche to datasets on gut and soil microbiome, and demonstrated that NetNiche can outperform the state-of-the-art methods, such as SParse InversE Covariance Estimation for Ecological Association Inference (SPIEC-EASI), Sparse Correlations for Compositional data (SparCC) and microbe-metabolite vectors (mmvec). NetNiche is an effective tool with wide applicability for the multi-omics study of human microbiome.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s43657-024-00168-8.},
}
@article {pmid40606527,
year = {2025},
author = {Paaske, SE and Baunwall, SMD and Rubak, T and Rågård, N and Kelsen, J and Hansen, MM and Lødrup, AB and Erikstrup, LT and Mikkelsen, S and Erikstrup, C and Dahlerup, JF and Hvas, CL},
title = {Clinical management of Clostridioides difficile infection with faecal microbiota transplantation: a real-world cohort study.},
journal = {EClinicalMedicine},
volume = {85},
number = {},
pages = {103302},
pmid = {40606527},
issn = {2589-5370},
abstract = {BACKGROUND: Clostridioides difficile infection (CDI) causes high morbidity and mortality. Faecal microbiota transplantation (FMT) is well-established for CDI, but therapeutic strategies may be optimised. We aimed to evaluate clinical outcomes by analysing therapeutic strategies in a real-life cohort of patients with CDI treated with FMT.<br><br>METHODS: We conducted a multi-site cohort study, including 1170 patients with CDI, treated with FMT through capsules, colonoscopy, or nasojejunal tube between May 2016 and December 2023. The primary outcome was cure of C. difficile-associated diarrhea (CDAD) eight weeks after treatment. We investigated antibiotic pretreatment type and length, FMT dosing and administration, and post-FMT prophylactic vancomycin during non-CDI antibiotic use, applying multivariable mixed-effect regression analysis including the patient as a random effect. The study was preregistered at ClinicalTrials.gov, NCT03712722.<br><br>FINDINGS: The 1170 patients received 1643 FMT treatments. Patients' median age was 71 years (interquartile range 56-80 years). Following their first FMT treatment, 699 patients (60% (95% confidence interval: 57-63%)) were cured of CDAD. After repeated FMT treatments, 944 patients (81% (78-83%)) were cured. Prolonged antibiotic pretreatment was associated with higher cure rates (65% (59-70%), odds ratio (OR): 1.22 (1.10-1.36), p < 0.001). FMT administration through oral, multi-dose capsules (69% (63-74%), OR: 1.19 (1.11-1.27), p < 0.001) or colonoscopy (69% (61-76%), OR: 1.14 (1.04-1.24), p = 0.01) resulted in the highest cure rates. Neither antibiotic pretreatment type nor prophylactic vancomycin during non-CDI antibiotics affected cure rates. In patients for whom FMT was initially unsuccessful, repeated FMT was more effective than antibiotic treatment alone.<br><br>INTERPRETATION: CDI outcomes could be improved by optimising antibiotic pretreatment duration, selecting appropriate FMT delivery methods, and repeating FMT.<br><br>FUNDING: Innovation Fund Denmark (j.no. 8056-00006B).},
}
@article {pmid40606170,
year = {2025},
author = {Slater, FC and Fish, KE and Boxall, JB},
title = {Similarity of drinking water biofilm microbiome despite diverse planktonic water community and quality.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1567992},
pmid = {40606170},
issn = {1664-302X},
abstract = {The impact of drinking water quality, in particular the planktonic microbiome, on the bacterial and fungal community composition of biofilms in drinking water infrastructure is explored. Understanding drinking water biofilms is critical as biofilms can degrade water quality and potentially present a public health risk if pathogens are released. Biofilms were developed for 12 months in three state-of-the-art pipe loop facilities installed at water treatment works and hence supplied by distinct treated drinking water and unique planktonic bacterial and fungal microbiomes. Each pipe loop had identical physical conditions, including pipe diameter, material and hydraulic regime (shear stress and turbulence). Despite the different bulk-waters, the bacterial and fungal community composition of the biofilm within each loop were remarkably similar, although in different quantities. The similarity between the biofilms from unique systems, with significantly different planktonic microbiomes, suggests shared selective pressures across the different sites which are independent of the varying water qualities, including planktonic community. This suggests that taking a global view of biofilm microbiome management is potentially feasible and that approaches controlling material or hydraulics may be best way to do this.},
}
@article {pmid40606169,
year = {2025},
author = {Mallick, S and Pavloudi, C and Saw, J and Eleftherianos, I},
title = {Heterorhabditis bacteriophora symbiotic and axenic nematodes modify the Drosophila melanogaster larval microbiome.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1598221},
pmid = {40606169},
issn = {1664-302X},
abstract = {The Drosophila melanogaster microbiome is crucial for regulating physiological processes, including immune system development and function. D. melanogaster offers distinct advantages over vertebrate models, allowing a detailed investigation of host-microbiota interactions and their effects on modulating host defense systems. It is an outstanding model for studying innate immune responses against parasites. Entomopathogenic nematodes (EPNs) activate immune signaling in the fly, leading to immune responses to combat infection. However, the impact of EPN infection on the host larval microbiome remains poorly understood. Therefore, we investigated whether EPN infection affects the D. melanogaster larval microbiome. We infected third-instar D. melanogaster larvae with Heterorhabditis bacteriophora symbiotic nematodes (containing Photorhabdus luminescens bacteria) and axenic nematodes (devoid of symbiotic bacteria). Drosophila melanogaster microbiome analysis revealed statistically significant differences in microbiome composition between uninfected and EPN-infected larvae. Notably, infection with axenic nematodes resulted in 68 unique species, causing a significant shift in the D. melanogaster larval microbiome and an increase in bacterial diversity compared to larvae infected with symbiotic nematodes. This suggests that the absence of the endosymbiont creates ecological niches for unique species and a more diverse microbiome in larvae infected with the axenic nematodes. This research will enhance our understanding of microbial species within the D. melanogaster microbiome that regulate homeostasis during nematode infection. These insights could be beneficial in developing innovative strategies for managing agricultural pests and disease vectors.},
}
@article {pmid40606166,
year = {2025},
author = {Hong, S and Xing, Y and Yang, J and Zhao, Q and Su, F and Zhuang, H and Wang, H and Wu, Z and Chen, Y},
title = {Pandan-vanilla rotation mitigates Fusarium wilt disease in vanilla: insights from rhizosphere microbial community shifts.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1496701},
pmid = {40606166},
issn = {1664-302X},
abstract = {INTRODUCTION: Vanilla monoculture often leads to Fusarium wilt disease, affecting the industry globally.<br><br>METHODS: Here, we evaluated the effects of vanilla-black pepper, -pandan, and -sweet rice tea rotations (i.e., growing vanilla in soil previously planted with these crops) on Fusarium oxysporum abundance and rhizosphere microbial communities using real-time quantitative PCR and high-throughput sequencing.<br><br>RESULTS: Pandan rotation, in particular, reduced disease incidence to 17% and decreased F. oxysporum copy numbers; sweet rice tea showed similar suppressive effects. Crop rotation significantly increased fungal diversity and richness. Different cropping systems, including fallow, monoculture and crop rotation, significantly influenced fungal and bacterial community development, with cropping system and rotated crops being the main drivers of rhizosphere community assembly. The black pepper and pandan rotations specifically enriched certain fungal OTUs, such as OTU1_Thermomyces, OTU37_Arthrobotrys, and OTU18_Arthrobotrys, which serve as biomarkers for the presence of F. oxysporum. After pandan rotation, microbial interactions within the rhizosphere intensified, with notable enrichment of core bacterial taxa, including OTU22_Nitrosospira, OTU56_Lacibacterium, and OTU178_Actinospica. Soil pH was identified as a significant factor influencing microbial community assembly. The fungal community structure, along with core OTU22_Nitrosospira and soil pH, was pivotal in curbing pathogen growth, explaining 25.19%, 8.61%, and 20.45% of the variance, respectively.<br><br>CONCLUSION: This study revealed that incorporating pandan into crop rotation may effectively alleviate soil-borne diseases during vanilla production.},
}
@article {pmid40606160,
year = {2025},
author = {Al-Khlifeh, E and Khadem, S and Hausmann, B and Berry, D},
title = {Corrigendum: Microclimate shapes the phylosymbiosis of rodent gut microbiota in Jordan's Great Rift Valley.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1639190},
doi = {10.3389/fmicb.2025.1639190},
pmid = {40606160},
issn = {1664-302X},
abstract = {[This corrects the article DOI: 10.3389/fmicb.2023.1258775.].},
}
@article {pmid40606159,
year = {2025},
author = {Xiang, C and Su, L and Han, M and Liang, J and Hou, F and Liao, J},
title = {Comparative analysis of gut microbiota and metabolome in captive Chinese and Malayan pangolins.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1599588},
pmid = {40606159},
issn = {1664-302X},
abstract = {As an endangered species in the world, pangolins have attracted much attention due to their unique ecological value. In captivity, pangolins face numerous survival challenges, especially intestinal health problems, which are closely related to the gut microbiome and metabolome. The aim of this study was to contrast the gut microbiota and metabolome of Chinese pangolin and Malayan pangolin in captivity, which in order to explore the differences in digestive physiology and metabolic function between the two species. Through 16S rRNA gene sequencing and non-targeted metabolomics analysis, we identified significant differences in the composition and diversity of the gut microbiota between these two species. The gut microbiota of Chinese and Malayan pangolins is dominated by Firmicutes and Proteobacteria at phylum level. At the genus level, the abundance of Clostridium sensu stricto 13 in Chinese pangolins was significantly higher than Malayan pangolins, whereas Peptostreptococcus, and Blautia are more abundant in Malay pangolins. Moreover, integrative analysis of the microbiome and metabolome revealed important correlations: Peptostreptococcus was positively correlated with 13-HpOTrE (r) metabolism, while Clostridium sensu stricto 13 was negatively correlated with 13-HpOTrE (r) metabolism. Blautia was positively correlated with 1-phenylethylamine metabolism. These results provided important gut microbiome and metabolomics data for the conservation and artificial breeding of pangolins, which can help optimize captive pangolins feeding management and health maintenance.},
}
@article {pmid40606154,
year = {2025},
author = {Han, H and Fu, L and Wang, J and Sun, Y and Cao, D and Lei, Q and Zhou, Y and Li, F and Liu, W and Li, D and Hao, D and Liu, J},
title = {Effect of dietary supplementation with Brevibacillus laterosporus on broiler growth performance, meat quality and gut microbiome.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1608076},
pmid = {40606154},
issn = {1664-302X},
abstract = {This study aimed to investigate the effects of Brevibacillus laterosporus (B. laterosporus) supplementation on growth performance, carcass traits, antioxidant capacity, and cecal microbiota in broilers. A total of 320 one-day-old YS909 male broilers were randomly assigned to four dietary groups: control (CON), low-dose (LBL, 100 mg/kg), medium-dose (MBL, 300 mg/kg), and high-dose (HBL, 500 mg/kg) B. laterosporus supplementation (n = 8 replicates/group, 10 chicks/replicate). Growth performance, carcass traits, antioxidant capacity, and cecal microbiota/metabolites (MBL vs. CON) were analyzed. Dietary supplementation with B. laterosporus significantly decreased the feed intake / weight gain (F/G) in LBL (22-42 d and 1-42 d), MBL (22-42 d) and HBL (22-42 d) groups. Both MBL and HBL groups showed higher semi-eviscerated percentages than the control. The MBL group had a significantly increased eviscerated percentage. The LBL group had a significantly increased breast muscle percentage. Specifically, the HBL group exhibited a notable increase in muscle C18:3n3 content, and a significant decrease in muscle C18:1n9t and C20:3n3 content. The LBL group saw significant reductions in the proportion of C18:1n9t and C20:1. Additionally, the MBL group experienced significant decreases in the proportions of C18:3n3, C20:3n3 and C20:4n6. Dietary supplementation with B. laterosporus significantly enhanced the oxidative stress resistance of serum by decreasing malondialdehyde (MDA) levels and increasing glutathione peroxidase (GSH-PX) and total antioxidant capacity (T-AOC). 16S ribosomal DNA and metabolome sequencing of cecum contents was conducted for the MBL and CON groups. This analysis demonstrated significant increases in α-diversity indices in the MBL group. There was an increased relative abundance of Firmicutes and a decreased relative abundance of Bacteroidetes and Proteobacteria in the MBL group. In addition, the shifts of the cecal microbial community lead to the alteration of metabolites of the cecum including amino acid and lipid. In conclusion, dietary supplementation with medium-dose B. laterosporus enhanced broiler carcass traits and antioxidant status by modulating cecal microbiota and metabolites, demonstrating its potential as an effective feed additive.},
}
@article {pmid40606151,
year = {2025},
author = {Wang, C and Song, Z and Li, X and Liu, Q},
title = {Bacterial community shifts in Fusarium-induced avocado root rot and the antagonistic potential of Bacillus siamensis NB92.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1626537},
pmid = {40606151},
issn = {1664-302X},
abstract = {Avocado root rot, driven by soil-borne fungi such as Fusarium spp., poses a major challenge to global avocado production. The rhizosphere microbiome is critical for plant health, yet the impact of root rot on bacterial community structure and its implications for disease management remain poorly understood. Here, we combined culture-independent 16S rDNA amplicon sequencing with culture-dependent isolation to characterize bacterial communities in healthy and Fusarium-infested avocado bulk and rhizosphere soils. Key beneficial taxa, notably Bacillus, were then isolated and evaluated for their antagonistic potential. Results showed that root rot significantly reduced rhizosphere bacterial α-diversity, altered community structure, and depleted phyla such as Actinobacteriota and Firmicutes that contain beneficial taxa. Beneficial genera such as Bacillus and Streptomyces declined, while cultivable Fusarium counts increased. Negative correlations between Fusarium abundance, the bacteria-to-fungi ratio, and the relative abundance of beneficial bacteria further underscore their suppressive role. Guided by these findings, we isolated Bacillus strain NB92, identified as Bacillus siamensis through morphological, biochemical, and 16S rRNA and gyrA gene analyses. NB92 exhibited strong antagonistic activity against the root rot pathogen (Fusarium sp. St7) via both direct antagonism and volatile organic compound production. Inoculating NB92 into diseased rhizosphere soil boosted Bacillus counts and reduced Fusarium abundance. Moreover, NB92 effectively inhibited the pathogen's necrotizing ability. B. siamensis NB92 thus represents a promising, sustainable biocontrol agent and contributes to the development of microbiome-based strategies for managing avocado root rot.},
}
@article {pmid40606147,
year = {2025},
author = {Guo, L and Wang, R and Han, L and Fu, Y and Wang, X and Nie, L and Fu, W and Ren, H and Wu, L and Li, G and Ding, J},
title = {Multi-omics integration identifies key biomarkers in retinopathy of prematurity through 16S rRNA sequencing and metabolomics.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1601292},
pmid = {40606147},
issn = {1664-302X},
abstract = {BACKGROUND: The gut microbiome is increasingly recognized for its role in the pathogenesis of neonatal conditions commonly associated with retinopathy of prematurity (ROP). This study aimed to identify key intestinal microbiota and metabolites in ROP and examine their relationships.<br><br>METHODS: Fecal samples were collected from infants with and without ROP at weeks 2 (T1) and 4 (T2) for 16S rRNA sequencing. At T2, additional fecal samples underwent non-targeted metabolomic analyses. A combined analysis of the 16S rRNA sequencing and metabolomics data was performed.<br><br>RESULTS: No significant differences in &#x3b1;-diversity indexes were observed between the ROP and non-ROP at T1. However, at T2, the Chao, ACE, and Shannon indices were significantly higher, whereas the Simpson index was lower in ROP compared to non-ROP. At the phylum level, the dominant phyla at T2 included Pseudomonadota, Bacillota, Actinomycetota, Bacteroidota, and Verrucomicrobiota. LEfSe analysis of T2 showed that Bifidobacterium, Rhodococcus, Staphyloococcus, Caulobacter, Sphingomonas, Aquabacterium, and Klebsiella as key genera associated with ROP. Metabolomic analysis identified 382 differentially accumulated metabolites, which were enriched in steroid hormone biosynthesis; the PPAR signaling pathway; linoleic acid metabolism; histidine metabolism; and alanine, aspartate, and glutamate metabolism. Additionally, the AUC of the combined analysis exceeded that of differential bacterial communities (0.9958) alone.<br><br>CONCLUSION: This study revealed characteristic changes in the intestinal flora and metabolites in ROP, which provide promising targets/pathways for ROP diagnosis and therapy.},
}
@article {pmid40606013,
year = {2025},
author = {Lee, J and Wu, HLA and Mannan, AA and Nakamura, Y and Amagai, M and Irvine, AD and Tanaka, RJ},
title = {Toward the Next Generation of In Silico Modeling of Dynamic Host-Microbiota Interactions in the Skin.},
journal = {JID innovations : skin science from molecules to population health},
volume = {5},
number = {5},
pages = {100385},
pmid = {40606013},
issn = {2667-0267},
abstract = {Understanding how the skin microbiota contributes to skin health and disease requires knowledge of the dynamic interactions between the skin and its resident microbes. In silico modeling complements in vivo and in vitro experiments by enabling a systems-level understanding of dynamic skin-microbiota interactions. However, the number of published in silico skin microbiota models remains limited. This paper provides the first comprehensive exploration of in silico skin microbiota modeling. We identify current challenges, learn from leading experimental validation approaches adopted in in silico gut microbiota research, and propose ways to enhance the predictive power of in silico skin microbiota models.},
}
@article {pmid40605597,
year = {2025},
author = {Thomsen, L and Jacobsen, S and Tøttrup, A},
title = {[Pouchitis].},
journal = {Ugeskrift for laeger},
volume = {187},
number = {27},
pages = {},
doi = {10.61409/V01250033},
pmid = {40605597},
issn = {1603-6824},
mesh = {Humans ; *Pouchitis/drug therapy/diagnosis/etiology/therapy/microbiology ; Anti-Bacterial Agents/therapeutic use ; Proctocolectomy, Restorative/adverse effects ; Acute Disease ; Colitis, Ulcerative/surgery ; Chronic Disease ; },
abstract = {Pouchitis is the most common complication following ileal pouch-anal anastomosis. It is characterized by pouch inflammation and symptoms resembling ulcerative colitis. The aetiology is thought to involve a combination of genetic factors, a dysregulated immune response, and alterations in the gut microbiome. Pouchitis is classified as acute if symptoms less-than 4 weeks or chronic if symptoms > 4 weeks. Acute pouchitis is typically treated with antibiotics, while chronic pouchitis may require cyclic antibiotics or immunomodulatory therapy. This review indicates that more research is needed to improve understanding and treatment.},
}
@article {pmid40605535,
year = {2025},
author = {Xiang, X and Liu, H and Wang, T and Ding, P and Zhu, Y and Cheng, K and Ming, Y},
title = {Prediction of postoperative infection through early-stage salivary microbiota following kidney transplantation using machine learning techniques.},
journal = {Renal failure},
volume = {47},
number = {1},
pages = {2519816},
doi = {10.1080/0886022X.2025.2519816},
pmid = {40605535},
issn = {1525-6049},
mesh = {Humans ; *Saliva/microbiology ; *Kidney Transplantation/adverse effects ; Male ; Female ; Middle Aged ; *Machine Learning ; Adult ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; *Postoperative Complications/microbiology/diagnosis ; *Kidney Failure, Chronic/surgery ; Biomarkers/analysis ; },
abstract = {Kidney transplantation (KT) is an effective treatment for end-stage renal disease; however, the lifelong immunosuppressive regimen increases the risk of infection, presenting significant clinical, and economic challenges. Identifying predictive biomarkers for infection onset is critical. In this study, 122 postoperative saliva samples from 39 KT recipients were analyzed using 16S rRNA sequencing, with 16 developing infections within one year. The composition of the salivary microbiota differed significantly between the infection and control groups, with notable variations at the Phylum level. Infected patients exhibited higher alpha diversity and 12 dominant taxa. A random forest model, utilizing five-fold three-times repeated cross-validation and incorporating differential biomarkers, significantly outperformed baseline peripheral blood lymphocyte subpopulation (PBLS) counts in predicting infections (area under the curve, 85.97% ± 10.64% vs. 67.03% ± 15.54%, p = 0.0008). Stepwise logistic regression, integrating clinical data, PBLS counts, and microbiome information, identified Mogibacterium as a significant predictor. The relative abundance of Mogibacterium correlated significantly with the ratio of plateau PBLSs to baseline PBLSs. Early-stage salivary microbiota profiles were predictive of post-KT infections within one year, reflecting lymphocyte reconstitution dynamics.},
}
@article {pmid40605344,
year = {2025},
author = {Kim, SM and Park, S and Ansari, A and Lee, G and Hur, YM and An, J and Lee, SS and You, YA and Kim, YJ},
title = {Altered Abundance of Butyrate-Producing Lachnospiraceae by Maternal Diet During Pregnancy Potentially Influences MASLD-Related Lipid Dysregulation in Male Rat Offspring.},
journal = {Molecular nutrition &amp; food research},
volume = {},
number = {},
pages = {e70153},
doi = {10.1002/mnfr.70153},
pmid = {40605344},
issn = {1613-4133},
support = {NRF-2020R1I1A1A01071955//Basic Science Research Program through the National Research Foundation of Korea/ ; grantnumber//Korea Health Technology R&amp;D Project through the Korea Health Industry Development Institute (KHIDI), funded by the Ministry of Health &amp; Welfare, Republic of Korea/ ; RS-2023-00248698//Korea Health Technology R&amp;D Project through the Korea Health Industry Development Institute (KHIDI), funded by the Ministry of Health &amp; Welfare, Republic of Korea/ ; Young-AhYou//RP-Grant 2024 from Ewha Womans University/ ; NRF-5199990614253,EducationResearchCenterfor4IR-BasedHealthCare//BK21 FOUR (Fostering Outstanding Universities for Research) funded by the Ministry of Education(MOE, Korea) and National Research Foundation of Korea/ ; },
abstract = {The maternal diet during pregnancy is an important factor that influences the intrauterine environment during fetal development. However, the relationship among maternal diet, the gut microbiome of offspring, and health outcomes remains unclear. Here, we report that changes in the gut microbiome of offspring after maternal exposure to 50% food restriction and 45% high-fat diet during pregnancy can affect the risk of metabolic dysfunction-associated steatotic liver disease (MASLD) in offspring in a sex-specific manner. Notably, despite no significant difference in body weight, plasma triglyceride and leptin levels were significantly increased in male offspring compared with the controls. The relative abundance of the butyrate-producing genera of the Lachnospiraceae family was dependent on the sex of the offspring and correlated with plasma triglyceride and leptin levels. Interestingly, male offspring in the 50% restricted diet or 45% high-fat diet groups had reduced butyrate levels compared with the control group and were affected by oxidative damage and hepatic lipogenesis. Our findings suggest that the maternal diet during pregnancy affects the gut microbiota of male offspring in a sex-specific manner, potentially predisposing them to MASLD later in life through dysregulation of lipid metabolism.},
}
@article {pmid40605266,
year = {2025},
author = {Herman, C and Barker, BM and Bartelli, TF and Chandra, V and Krajmalnik-Brown, R and Jewell, M and Li, L and Liao, C and McAllister, F and Nirmalkar, K and Xavier, JB and Caporaso, JG},
title = {A review of engraftment assessments following fecal microbiota transplant.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2525478},
doi = {10.1080/19490976.2025.2525478},
pmid = {40605266},
issn = {1949-0984},
mesh = {*Fecal Microbiota Transplantation ; Humans ; *Gastrointestinal Microbiome ; *Clostridium Infections/therapy/microbiology ; Clostridioides difficile/physiology ; Animals ; Feces/microbiology ; Bacteria/classification/genetics/isolation &amp; purification ; },
abstract = {Fecal Microbiota Transplant (FMT) is a treatment for recurrent Clostridium difficile infections and is being explored for other clinical applications, from alleviating digestive and neurological disorders, to restoring microbiomes impacted by cancer treatment. Quantifying the extent of engraftment following an FMT is important in understanding a recipient's response to treatment. Engraftment and clinical response need to be investigated independently to evaluate an FMT's role (or lack thereof) in achieving a clinical response. Standardized bioinformatics methodologies for quantifying engraftment extent would not only improve assessment and understanding of FMT outcomes, but also facilitate comparison of FMT results and protocols across studies. Here we review FMT studies, integrating three concepts from microbial ecology as framework to discuss how these studies approached assessing engraftment extent: 1) Community Coalescence investigates microbiome shifts following FMT engraftment, 2) Indicator Features tracks specific microbiome features as a signal of engraftment, and 3) Resilience examines how resistant post-FMT recipients' microbiomes are to reverting back to baseline. These concepts explore subtly different questions about the microbiome following FMT. Taken together, they provide holistic insight into how an FMT alters a recipient's microbiome composition and provide a clear framework for quantifying and communicating about microbiome engraftment.},
}
@article {pmid40605185,
year = {2025},
author = {Rather, RA},
title = {Shaping Plant Growth Beneath the Soil: A Theoretical Exploration of Fungal Endophyte's Role as Plant Growth-Promoting Agents.},
journal = {MicrobiologyOpen},
volume = {14},
number = {4},
pages = {e70026},
doi = {10.1002/mbo3.70026},
pmid = {40605185},
issn = {2045-8827},
support = {//The author received no specific funding for this work./ ; },
mesh = {*Endophytes/physiology/metabolism ; *Soil Microbiology ; *Fungi/physiology/metabolism ; *Plant Development ; Soil/chemistry ; Symbiosis ; Plant Growth Regulators/metabolism ; *Plants/microbiology ; },
abstract = {Plant growth relies on both natural and agrochemical inputs, with natural soil nutrients and chemically synthesized fertilizers enhancing its growth. However, continuous fertilizer use can lead to soil alkalinity and environmental contamination, emphasizing the need for sustainable practices. Microbial agents, particularly fungal endophytes, have emerged as promising natural alternatives. They are recognized as integral components of the plant microbiome and aid in nutrient acquisition, hormone production, and stress resistance. Fungal endophytes enhance nutrient uptake by solubilizing phosphorus, fixing nitrogen, and producing siderophores that chelate iron. They also modulate plant hormones, including auxins, gibberellins, and cytokinins, promoting growth and development. Under abiotic stress, these endophytes improve plant tolerance by inducing systemic resistance and enhancing water and nutrient absorption. This review provides a comprehensive theoretical exploration of the role of fungal endophytes in promoting plant growth, examining their diversity, mechanisms of action, and practical applications. The focus is on understanding how these symbiotic organisms can be harnessed to enhance sustainable agricultural practices and contribute to environmental conservation.},
}
@article {pmid40605060,
year = {2025},
author = {Campanale, A and Siniscalco, D and Di Marzo, V},
title = {The endocannabinoidome-gut microbiome-brain axis as a novel therapeutic target for autism spectrum disorder.},
journal = {Journal of biomedical science},
volume = {32},
number = {1},
pages = {60},
pmid = {40605060},
issn = {1423-0127},
mesh = {*Gastrointestinal Microbiome/physiology/drug effects ; Humans ; *Endocannabinoids/metabolism ; *Autism Spectrum Disorder/drug therapy/microbiology/metabolism/physiopathology ; *Brain/metabolism ; Animals ; },
abstract = {INTRODUCTION: Autism spectrum disorder (ASD) is characterized by disruption of the gut-brain axis, which leads to behavioral, psychiatric, metabolic and gastrointestinal symptoms. Effective ASD treatments are limited. Research highlights the roles of the endocannabinoidome (eCBome) and gut microbiome (GM), both crucial for brain and gut function. This review summarizes research on therapeutic targets within the eCBome-GM-brain axis for ASD and related comorbidities.<br><br>DISCUSSION: Evidence suggests that reduced levels of eCBome mediators, like oleoylethanolamide and anandamide, and altered cannabinoid type 1 and type 2 (CB1 and CB2) receptors activity may contribute to ASD symptoms, making them promising targets. Modulating the eCBome-GM-brain axis with inhibitors of fatty acid amide hydrolase (FAAH), transient receptor potential vanilloid 1, and monoacylglycerol lipase (MAGL) may improve repetitive, stereotypical, and sensory behaviors, and alleviate sociability impairments, depression and anxiety. However, inhibition of FAAH and MAGL may also induce ADHD-like behaviors, which can be reversed by CB1 inverse agonists. Targeting metabotropic glutamate receptor 5 to increase levels of the eCBome mediator 2-arachidonoylglycerol (2-AG) may benefit ASD-related behaviors. eCBome mediators such as 2-AG, 1/2-palmitoylglycerol and palmitoylethanolamide may also help manage ASD- and GI-related symptoms, and systemic inflammation. Other potential therapeutic targets that deserve further investigation are eCBome-related receptors G-protein-coupled receptor 55 and peroxisome proliferator-activated receptors-alpha and -gamma, and the cyclooxygenase-2/prostaglandin E2 pathway, which may address hyperactivity and repetitive behaviors. Additionally, mucin-degrading genera like Akkermansia and Ruminococcus may improve ASD-related GI symptoms such as hypersensitivity and inflammation. Selective antibiotics against specific Clostridium strains may improve irritability and aggression. In ASD with ADHD and OCD, treatments may involve modulating the CB1 and CB2 receptor, and bacterial families like Ruminococcaceae and Lachnospiraceae. Lastly, modulating the abundance of anti-inflammatory genera like Prevotella and Anaeroplasma, and taxa associated with gut health such as Roseburia may also offer therapeutic value.<br><br>CONCLUSION: The eCBome-GM-brain axis is a promising target for ASD treatment, meriting further clinical and preclinical research.},
}
@article {pmid40605009,
year = {2025},
author = {Paix, B and Thivet, A and Domingos, C and Erol, &#xd6; and van der Windt, N and Choi, YH and de Voogd, NJ},
title = {Adaptive strategies of Caribbean sponge holobionts beyond the mesophotic zone.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {157},
pmid = {40605009},
issn = {2049-2618},
support = {16.161.301//NWO-VIDI/ ; },
mesh = {Animals ; *Porifera/microbiology/physiology ; *Microbiota ; Caribbean Region ; Symbiosis ; Ecosystem ; Archaea/classification/genetics/metabolism/isolation &amp; purification ; *Adaptation, Physiological ; Metabolome ; Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Nitrogen/metabolism ; },
abstract = {BACKGROUND: Marine sponges and their microbiomes function together as holobionts, playing essential roles in ecosystem dynamics and exhibiting remarkable adaptability across depth gradients. This study utilized a multi-omics approach, integrating microbiome and metabolome analyses, to investigate adaptive strategies in sponge holobionts inhabiting the mesophotic (80-125 m), upper-rariphotic (125-200 m), and lower-rariphotic (200-305 m) zones of Curaçao. We hypothesized that depth-related environmental factors drive distinct adaptive strategies, similar to patterns observed in fish and coral assemblages.<br><br>RESULTS: Results revealed major differences in holometabolomes and microbial communities between Demospongiae and Hexactinellida sponges, reflecting class-specific adaptive&#xa0;strategies. Notably, phospholipid homeoviscous adaptation to temperature and pressure might emerge as a key mechanism in phosphorus metabolism. Adaptations in nitrogen metabolism&#xa0;were linked to diverse ammonia oxidizing archaea (AOA) symbionts, and dissolved organic matter cycling. Hexactinellid microbiomes exhibited intra-specific heterogeneity; however,&#xa0;species-specific associations with AOA symbionts such as Cenarchaeum and Nitrosopumilus were observed. Additionally, the lower-rariphotic hexactinellid holometabolomes highlighted&#xa0;the significance of the nested ecosystem concept through the identification of secondary metabolites produced by their associated fauna (aphrocallistins by zoanthids and xanthurenic acid by shrimp).<br><br>CONCLUSIONS: This study highlights the ecological significance of sponge holobionts in mesophotic and rariphotic ecosystems, revealing diverse adaptations to unique physicochemical conditions and biotic interactions. Video Abstract.},
}
@article {pmid40604917,
year = {2025},
author = {Chen, K and Qin, Y and Yan, L and Dong, Y and Lv, S and Xu, J and Kang, N and Luo, Z and Liu, Y and Pu, J and Chen, F and Jin, X},
title = {Variations in salivary microbiota and metabolic phenotype related to oral lichen planus with psychiatric symptoms.},
journal = {BMC oral health},
volume = {25},
number = {1},
pages = {993},
pmid = {40604917},
issn = {1472-6831},
support = {82370968//the National Natural Science Foundations of China/ ; CSTB2022NSCQ-MSX1148//the Natural Science Foundation of Chongqing/ ; },
mesh = {Humans ; *Lichen Planus, Oral/microbiology/metabolism/psychology/complications ; *Saliva/microbiology/metabolism ; Male ; Female ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Middle Aged ; Adult ; Case-Control Studies ; Phenotype ; Metabolome ; Depression/complications ; },
abstract = {BACKGROUND: Oral lichen planus (OLP) is a common chronic inflammatory disease of the oral mucosa with a certain tendency for malignant transformation. The etiology and pathogenesis of OLP remain unclear, and the relationship between psychiatric factors and the development of OLP has attracted much attention in recent years. This study aims to investigate the alterations in oral microbiota and metabolites in OLP patients with psychiatric symptoms, providing a theoretical foundation for understanding the pathogenesis and treatment of OLP.<br><br>METHODS: 16S rRNA sequencing was used to evaluate the oral microbial population in a cohort of 105 OLP patients. To further investigate the potential interaction between OLP and psychiatric factors, saliva samples from 64 depressed/anxious OLP patients (D-OLP) and their age-matched healthy controls were selected for 16S rRNA sequencing. The salivary metabolome was also characterized by ultra performance liquid chromatography-mass spectrometry (LC-MS).<br><br>RESULTS: The results of 16S rRNA sequencing showed that significant differences in species classification between OLP patients and healthy controls. The D-OLP group displayed an increased abundance of Pseudomonas as well as dysregulation of associated metabolism activities. Correlation analysis showed that the altered metabolites were involved in the metabolic pathways related to the oral-microbiome-brain axis and affected various physiological processes such as neurotransmitter transmission and oxidative stress, promoting epithelial inflammatory activation and immune responses. These changes ultimately lead to the destruction of the original oral mucosal homeostasis.<br><br>CONCLUSIONS: Psychiatric factors may promote mucosal inflammatory responses through dysbiosis of the microbiota. The dysregulated oral microbiome-related metabolites may significantly affect the pathogenesis of the oral-brain axis in OLP patients.This study provides valuable insights into potential future modalities for elucidating the pathogenesis of OLP, offering a foundation for the development of personalized therapeutic strategies.},
}
@article {pmid40604910,
year = {2025},
author = {You, Y and Wu, HL and Chen, DY and Yu, SY and Xu, Y and Tang, Y and Sun, HL and Huang, C},
title = {Human calculus adhesive-induced periodontitis model recapitulating human periodontitis microbiota in rats.},
journal = {BMC oral health},
volume = {25},
number = {1},
pages = {1034},
pmid = {40604910},
issn = {1472-6831},
support = {81970918//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Periodontitis/microbiology/pathology ; Humans ; *Disease Models, Animal ; Rats ; *Microbiota ; *Dental Calculus/microbiology ; Alveolar Bone Loss/microbiology ; Porphyromonas gingivalis ; Male ; X-Ray Microtomography ; Rats, Sprague-Dawley ; Fusobacterium nucleatum/isolation &amp; purification ; Gingiva/microbiology ; RNA, Ribosomal, 16S ; },
abstract = {BACKGROUND: Periodontitis is a chronic inflammatory condition characterized by oral dysbiosis. Current animal models of periodontitis using ligation and pathogen inoculation are time-consuming and do not reflect the chronic characteristics of human periodontitis. One of the significant differences is the difference between the current experimental animal periodontitis microbiome and human periodontitis microbiome. This study aims to establish a humanized rat model that mimics clinical conditions and approximates the microbial causes of human periodontitis.<br><br>METHODS: The human calculus adhesive-induced periodontitis (hCAP) was established by transplanting subgingival dental calculus from periodontitis patients to the subgingival surface of rats using universal adhesive. The study performed stereomicroscopy, micro-CT analysis, hematoxylin and eosin staining, tartrate-resistant acid phosphatase staining, qRT-PCR, ELISA, and 16s rDNA sequencing.<br><br>RESULTS: The hCAP group showed significant alveolar bone loss and osteoclast formation. The inflammatory factors in gingiva and serum were dramatically increased compared to the placebo rats, revealed by qRT-PCR and ELISA. The oral microbiota of the hCAP group was found to be more similar to that of patients compared with ligation with Porphyromonas gingivalis model, with enhanced colonization of Fusobacterium nucleatum subsp. polymorphum and Prevotella intermedia. The hCAP model also detected pathogenic bacteria of systemic diseases as shown in 16s rDNA sequencing.<br><br>CONCLUSIONS: The hCAP model mimics clinical conditions, approximates the microbial causes of human periodontitis and preserve bacteria responsible for systemic diseases in the gingival area of rats. The hCAP model may help in understanding the association between periodontitis and systemic diseases.},
}
@article {pmid40604909,
year = {2025},
author = {Wang, J and Liu, Z and Wang, X and Zhang, Z and Zhou, T and Li, M and Wang, S and Hu, Z and Sun, R and Li, D},
title = {Combatting glufosinate-induced pepper toxicity: jasmonic acid recruiting rhizosphere bacterial strain Rhodococcus gordoniae.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {158},
pmid = {40604909},
issn = {2049-2618},
support = {22067004//National Nature Science Foundation of China/ ; 22067004//National Nature Science Foundation of China/ ; 22067004//National Nature Science Foundation of China/ ; 22067004//National Nature Science Foundation of China/ ; 22067004//National Nature Science Foundation of China/ ; 22067004//National Nature Science Foundation of China/ ; 22067004//National Nature Science Foundation of China/ ; 22067004//National Nature Science Foundation of China/ ; 22067004//National Nature Science Foundation of China/ ; 22067004//National Nature Science Foundation of China/ ; 321CXTD436//Natural Science Foundation of Hainan Province/ ; 321CXTD436//Natural Science Foundation of Hainan Province/ ; 321CXTD436//Natural Science Foundation of Hainan Province/ ; 321CXTD436//Natural Science Foundation of Hainan Province/ ; 321CXTD436//Natural Science Foundation of Hainan Province/ ; 321CXTD436//Natural Science Foundation of Hainan Province/ ; 321CXTD436//Natural Science Foundation of Hainan Province/ ; 321CXTD436//Natural Science Foundation of Hainan Province/ ; 321CXTD436//Natural Science Foundation of Hainan Province/ ; 321CXTD436//Natural Science Foundation of Hainan Province/ ; },
mesh = {*Rhizosphere ; *Oxylipins/metabolism/pharmacology ; Soil Microbiology ; *Cyclopentanes/metabolism/pharmacology ; *Rhodococcus/metabolism/drug effects/isolation &amp; purification/genetics/growth &amp; development/classification ; *Capsicum/drug effects/microbiology/growth &amp; development ; Plant Roots/microbiology ; *Aminobutyrates/toxicity/metabolism ; Biodegradation, Environmental ; Caffeic Acids/pharmacology ; Microbiota ; },
abstract = {BACKGROUND: Plant-microbe interactions are essential for mitigating abiotic and biotic stressors by shaping the rhizosphere environment. However, how rhizosphere beneficial bacteria and plant metabolites respond to glufosinate (GLU)-induced toxicity remains largely unknown.<br><br>RESULTS: Our study investigates the impact of GLU on chili plant growth and rhizosphere microbiome, emphasizing GLU-induced alterations in amino acid profiles, secondary metabolites, and microbial community composition, with notable enrichment of the Rhodococcus genus. To uncover the underlying mechanisms of Rhodococcus genus-root exudate interactions under GLU stress, we successfully isolated an efficient Rhodococcus gordoniae strain TR-5 from soil samples contaminated with GLU. This strain, isolated from GLU-contaminated soil, demonstrates potential for bioremediation and achieved over 95% GLU degradation efficiency at 35&#xa0;&#xb0;C, pH 6.38, and 1% inoculation rate. Through growth analysis, chemotaxis analysis, and molecular docking, caffeic acid disrupts the bacterial strain's metabolic pathways and impedes TR-5 development. In contrast, jasmonic acid (JA) acts as a chemoattractant, promoting bacterial growth and metabolic activity to degrade GLU residues, thereby effectively degrading GLU residues in the soil.<br><br>CONCLUSIONS: This research indicates that GLU significantly influences the metabolic mechanisms of pepper plants. The optimization of microbial remediation strategies may improve soil remediation efficiency and reduce environmental impacts, highlighting opportunities for integrating microbial remediation into sustainable agricultural practices. Our findings provide insights into the role of JA in attracting and promoting the growth and metabolic activities of the Rhodococcus genus, which could be harnessed to improve soil remediation and plant health under GLU stress. Video Abstract.},
}
@article {pmid40604730,
year = {2025},
author = {Immonen, E and Paulamäki, L and Piippo, H and Nikkilä, A and Aine, L and Peltomäki, T and Lohi, O and Parikka, M},
title = {Oral microbiome diversity and composition before and after chemotherapy treatment in pediatric oncology patients.},
journal = {BMC oral health},
volume = {25},
number = {1},
pages = {981},
pmid = {40604730},
issn = {1472-6831},
mesh = {Humans ; Child ; *Microbiota/drug effects ; *Stomatitis/microbiology/chemically induced/prevention &amp; control ; Adolescent ; Male ; Female ; Double-Blind Method ; Child, Preschool ; *Neoplasms/drug therapy ; *Antineoplastic Agents/adverse effects/therapeutic use ; RNA, Ribosomal, 16S ; Mouthwashes/therapeutic use ; Mouth Mucosa/microbiology ; },
abstract = {OBJECTIVE: This study investigated the impact of anticancer treatment on the oral microbiome in pediatric patients and its association with oral mucositis (OM).<br><br>MATERIALS AND METHODS: A double-blind, randomized trial involving 34 pediatric cancer patients (ages 2-17.99) with solid or hematological malignancies. Mucosal swab samples were collected before and after chemotherapy. Patients underwent two 7-day rinse cycles-one with Caphosol and one with saline-in a randomized order. Bacterial DNA from 110 mucosal swabs was analyzed using 16S rRNA sequencing.<br><br>RESULTS: Chemotherapy altered bacterial composition. No life-threatening OM cases (WHO grade 4) were observed, but mild to severe OM (grades 1-3) occurred in three patients. In patients without oral lesions, Bergeyella genus was more abundant prior to treatment while Alloprevotella was more abundant in the post-treatment samples, compared to patients with lesions. OM was linked to distinct microbiome profiles, including Stenotrophomonas, Leptotrichia sp., Serratia sp.,Capnocytophaga sputigena, Sphingomonas sp., Parapusillimonas sp., Staphylococcus sp., and Turicibacter genera. Additionally, Burkholderia-Caballeronia-Paraburkholderia (p&#x2009;=&#x2009;0.013) were more prevalent in the Caphosol group compared to the saline group.<br><br>CONCLUSIONS: These findings indicate that chemotherapy-induced microbiome shifts associate with OM risk, highlighting the potential for microbial markers to predict high-risk patients and support protective strategies.<br><br>TRIAL REGISTRATION: The trial titled "Supersaturated Calcium Phosphate Oral Rinse (Caphosol&#xae;) for the Prevention of Oral Mucositis in Children Undergoing Chemotherapeutic Treatments" was registered on ClinicalTrials.gov (ID NCT02807337), with the first submission date 2016-06-07.},
}
@article {pmid40604405,
year = {2025},
author = {Jing, D and Jiang, X and Ren, X and Hao, R and Su, J and Li, X},
title = {Clinical performance of nanopore targeted sequencing for diagnosing endophthalmitis.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {403},
pmid = {40604405},
issn = {1471-2180},
support = {ZR2024QH310//Shandong Provincial Natural Science Foundation/ ; BYSYZD2021044//Peking University Third Hospital Key Talent Project foundation/ ; },
mesh = {Humans ; *Endophthalmitis/diagnosis/microbiology ; *Bacteria/genetics/isolation &amp; purification/classification ; Male ; *Nanopore Sequencing/methods ; Female ; Middle Aged ; Aqueous Humor/microbiology ; Aged ; Vitreous Body/microbiology ; Fungi/genetics/isolation &amp; purification/classification ; Adult ; },
abstract = {PURPOSE: Rapid identification of pathogenic bacteria in the vitreous and/or aqueous humor of patients with acute clinical diagnosis of endophthalmitis via nanopore sequencing technology.<br><br>METHODS: We recruited a total of 12 patients (12 eyes) who were diagnosed with endophthalmitis at an ophthalmic outpatient clinic of Peking University Third Hospital from January 2022 to October 2022. Clinical evaluation is conducted in the order of consultation, symptom evaluation, physical sign evaluation, and ophthalmic special examination, all of which are completed by the same experienced clinical physician. Finally, 19 aqueous humor and/or vitreous samples were obtained via anterior chamber wash, vitreous tap and vitrectomy. The samples were separated for cultivation, biochemical drug sensitivity identification, and targeted nanopore sequencing (NTS), and the results of nanopore sequencing were validated via Sanger sequencing.<br><br>RESULTS: In patients with endophthalmitis, NTS can identify infected pathogens within 8-12&#xa0;h. Six samples (31.6%) were subjected to culture-based diagnosis, while NTS revealed the presence of pathogenic microorganisms in 19 samples (100%), of which bacteria and fungi were detected in three samples. A total of 19 samples were subjected to Sanger sequencing, of which 16 (84.2%) tested positive, including 6 culture-positive samples and 10 culture-negative samples, of which 5 (26.3%) were positive for two bacterial genera. In culture-positive cases, there is a high-quality match between culture and targeted nanopore sequencing.<br><br>CONCLUSIONS: NTS can quickly detect pathogenic bacteria in samples from patients with endophthalmitis. Moreover, the use of vitreous and/or aqueous humor for the NTS has potential. NTS is a promising diagnostic platform for endophthalmitis, especially for mixed infections and culture-negative cases.},
}
@article {pmid40604391,
year = {2025},
author = {Djondji Kamga, FM and Jean Mugenzi, LM and Ngannang-Fezeu, VB and Ngambia Freitas, FS and Bouaka Tsakeng, CU and Sandeu, MM and Tchouakui, M and Wondji, CS},
title = {Evidence of microbiome contribution to the escalation of pyrethroid resistance in the major malaria vectors Anopheles gambiae s.s. and Anopheles funestus s.s.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {384},
pmid = {40604391},
issn = {1471-2180},
support = {217188/Z/19/Z/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Animals ; *Anopheles/microbiology/drug effects ; *Pyrethrins/pharmacology ; *Insecticide Resistance/genetics ; *Mosquito Vectors/microbiology/drug effects ; *Insecticides/pharmacology ; *Microbiota/drug effects ; Malaria/transmission ; *Bacteria/genetics/classification/drug effects/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Female ; High-Throughput Nucleotide Sequencing ; },
abstract = {BACKGROUND: Exacerbation of pyrethroid resistance severely jeopardises the effectiveness of malaria vector control efforts. However, the mechanisms enabling the vectors to now survive exposure to very high doses of pyrethroids remain unclear. Here, using High-throughput sequencing of the 16 S ribosomal RNA gene coupled with antibiotic treatment, we provide evidence linking the mosquito microbiome to the escalation of pyrethroid resistance in major African malaria vectors, Anopheles gambiae (s.s.) and Anopheles funestus (s.s.).<br><br>RESULTS: Phenotypic characterisation of An. gambiae (s.s.) and An. funestus (s.s.) populations revealed a high level of resistance to pyrethroid in both species, with mortality rates&#x2009;<&#x2009;91% at 10x the diagnostic dose of each insecticide. A significant difference in bacterial composition was observed in An. gambiae s.s. between resistant mosquitoes exposed to 1X and 10X the diagnostic dose of permethrin, and the susceptible strains (PERMANOVA-F: 8.06; p&#x2009;=&#x2009;0.02). The abundance of Pseudomonas_1 (Log2FC: 4.42, p&#x2009;=&#x2009;0.0001) and Burkholderia_1 (Log2FC: 4.95, p&#x2009;=&#x2009;0.001) bacteria were consistently associated with mosquitoes surviving 1X and 10X the diagnostic concentrations of permethrin, respectively, while Serratia_2 bacteria was mostly associated with insecticide susceptibility. In the An. funestus s.s. strain, there was no significant difference in bacterial alpha- and beta-diversity between the FUMOZ-R (exhibiting normal deltamethrin resistance) and FUMOZ-HR (selected for high deltamethrin resistance), suggesting a minimal impact of selection pressure on bacterial composition. However, in FUMOZ-HR, there was an increase in the abundance of Rahnella (Log2FC: 15.954, p&#x2009;=&#x2009;9.73 E-12) and Leucobacter (Log2FC: 7.6, p&#x2009;=&#x2009;0.008) bacteria, indicating their potential role in worsening deltamethrin resistance. Furthermore, treating resistant mosquitoes (both Anopheles species) with broad-spectrum bactericidal antibiotics (penicillin/streptomycin) via sugar solution increased their susceptibility to various diagnostic doses of permethrin and deltamethrin in WHO pyrethroid intensity bioassays.<br><br>CONCLUSION: Overall, our study emphasises the potential role of the microbiome in the escalation of insecticide resistance in Anopheles mosquitoes, identifying key bacterial strains associated with insecticide resistance and susceptibility. These candidate bacteria warrant further investigation to elucidate the mechanisms by which they contribute to the escalation of pyrethroid resistance.},
}
@article {pmid40604389,
year = {2025},
author = {Yang, J and Wang, L and Liang, Q and Wang, Y and Yang, X and Wu, X and Pei, X},
title = {Microbiome, resistome, and potential transfer of antibiotic resistance genes in Chinese wet market under One Health sectors.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {406},
pmid = {40604389},
issn = {1471-2180},
support = {TB2024045//Special Funding for Postdoctoral Research Projects in Sichuan Province/ ; 2022ZDZX0017//Department of Science and Technology of Sichuan Province (Major Science and Technology Projects)/ ; 2022ZDZX0017//Department of Science and Technology of Sichuan Province (Major Science and Technology Projects)/ ; 2022ZDZX0017//Department of Science and Technology of Sichuan Province (Major Science and Technology Projects)/ ; },
}
@article {pmid40604388,
year = {2025},
author = {Han, D and Zhang, Y and Liu, W and Wan, R and Hu, J and Pan, F and Pan, X and Weng, W and Wang, Y and Ma, Z and Zhang, H and Chen, J},
title = {Disruption of gut microbiome and metabolome in treatment-naïve children with attention deficit hyperactivity disorder.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {381},
pmid = {40604388},
issn = {1471-2180},
support = {21ZR1452900//Natural Science Foundation of Shanghai/ ; 19ZR1477700//Natural Science Foundation of Shanghai/ ; 82471882//National Natural Science Foundation of China/ ; shslczdzk06902//Shanghai Municipal Key Clinical Specialty/ ; GWVI-3//Three-Year Initiative Plan for Strengthening Public Health System Construction in Shanghai (2023-2025)/ ; 2022YFC2705203//National Key Research and Development Program of China/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Attention Deficit Disorder with Hyperactivity/microbiology/metabolism ; Child ; *Metabolome ; Male ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; Female ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; },
abstract = {BACKGROUND: Attention deficit hyperactivity disorder (ADHD) is a neurodevelopmental disorder with an increasing prevalence in children. Recent studies have suggested that the gut microbiota may play a significant role in the development of ADHD. However, the specific relationship between changes in intestinal bacteria and related metabolites in children with ADHD remains poorly understood.<br><br>RESULTS: In this study, we illustrated the fecal microbiome, metabolome and lipidome, as well as plasma metabolome using 16S rRNA gene sequencing and LC-MS in 15 pairs of children with ADHD and healthy controls. Our results revealed imbalance of gut microbiota and dysregulation of metabolites in individuals with ADHD. Specifically, children with ADHD exhibited significantly lower abundance of the Actinobacteria phylum, particularly Bifidobacterium, Corynebacterium and Actinomyces, while Veillonella in the Negativicutes class showed significant high level. No children with ADHD were classified under enterotype 1, which was composed solely of healthy children. Integration of multi-omics data suggested that the Bifidobacterium genus, which is positively correlated with various neurotransmitter precursor amino acid metabolites, may contribute to ADHD by downregulating pathways involving dopaminergic, serotonergic and glutamatergic systems.<br><br>CONCLUSIONS: These findings highlight the crucial regulatory impact of gut microbiota in the development of ADHD through metabolic pathways, and provide a potential avenue to the diagnosis and intervention of ADHD.},
}
@article {pmid40604383,
year = {2025},
author = {Yao, C and Yang, Y and Qiu, M and Jin, D and Huang, J},
title = {The effect of Akkermansia in patients with pregnancy induced hypertension.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {386},
pmid = {40604383},
issn = {1471-2180},
mesh = {Humans ; Female ; Pregnancy ; *Gastrointestinal Microbiome ; Adult ; *Hypertension, Pregnancy-Induced/microbiology/blood ; Case-Control Studies ; *Dysbiosis/microbiology ; RNA, Ribosomal, 16S/genetics ; Cytokines/blood ; Follow-Up Studies ; Biomarkers/blood ; Bacteria/classification/genetics/isolation &amp; purification ; },
abstract = {BACKGROUNDS: Intestinal dysbiosis in the second trimester is associated with pregnancy-induced hypertension (PIH) in the first trimester. However, the consequences and underlying mechanisms remain unclear.<br><br>METHODS: In a follow-up cohort study, a nested case-control design was employed. Twenty healthy pregnant women in their second trimester were selected as controls, while nineteen patients with pregnancy-induced hypertension were included in the study. The 16&#xa0;S rRNA sequencing was utilized to assess changes of gut microbiota patterns during early pregnancy. ELISA test was used to measure plasma inflammatory markers such as IL-1 beta, IL-6, TNF alpha, IL-8 and IL-10.<br><br>RESULTS: The PIH group exhibited lower microbial &#x3b1;-diversity compared to the healthy group. Although no statistically significant difference was observed at the genus level (p&#x2009;=&#x2009;0.05), at the phylum level, the PIH patients showed a reduced abundance of Verrucomicrobia and an increased abundance of Firmicutes (p&#x2009;=&#x2009;0.011). Donis analysis revealed that the Gut Microbiome Health Index (GMHI) of the PIH group was significantly worse than that of the control group. Additionally, Akkermansia abundance was significantly lower in the PIH group compared to the control group. Furthermore, more pro-inflammatory cytokines, such as IL-18 and capase-1, were produced in PIH plasma compared to the control group.<br><br>CONCLUSION: The correlation analysis between gut microbiota and cytokines in PIH patients and controls revealed that Akkermansia was positively associated with IL-18 and capase-1 levels in PIH patients.},
}
@article {pmid40604377,
year = {2025},
author = {Ma, R and Yu, X and Huang, C and Xue, F and Hou, R and Wu, W and Feng, F and Bi, W and Zhang, L and Liu, J and Li, Z and Gu, J and Zhou, Y and Lan, G and Chen, C and Yao, Y and Lan, J and Luo, L and Li, P and He, H and Zhang, M and Yang, X and Yang, H and Gu, H and Gu, X and Chen, L and Qi, D},
title = {Reintroduction training is instrumental in restoring the oral microbiota of giant pandas from "captivity" to "wildness".},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {391},
pmid = {40604377},
issn = {1471-2180},
support = {32400405//National Natural Science Foundation of China/ ; U21A20193//National Natural Science Foundation of China/ ; 2024CPB-A23//Chengdu Giant Panda Breeding Research Foundation/ ; 2024CPB-B06//Chengdu Giant Panda Breeding Research Foundation/ ; 25NSFSC1714//Sichuan Provincial Science and Technology Support Program/ ; 2023NSFSC1156//Sichuan Provincial Science and Technology Support Program/ ; 2023-YF09-00017-SN//Chengdu Science and Technology Program/ ; },
mesh = {Animals ; *Ursidae/microbiology ; *Microbiota ; *Mouth/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Animals, Wild/microbiology ; RNA, Ribosomal, 16S/genetics ; Endangered Species ; Female ; },
abstract = {Reintroduction programs aim to restore wild populations, yet success is challenged by host microbiome adaptation to natural environments. Here, we characterized the oral microbiota of giant pandas undergoing pre-release training, comparing them to captive and wild conspecifics, to assess training-induced microbial shifts. We found that after one year of reintroduction training, multi-generational captive giant pandas exhibited increased oral microbiome diversity, with community structure, composition, and predicted functions converging toward wild-type profiles. Adaptive changes included reduced relative abundances of Actinobacillus and Bergeyella, and enrichment of Myroides and Psychrobacter. Functionally, these shifts correlated with decreased starch and sucrose, fructose and mannose, and various lipid metabolism pathways, alongside enhanced methane and galactose metabolism which align with the dietary constraints of a singular food source in the wild environment. Our study demonstrates that pre-release training drives oral microbiota convergence toward wild phenotypes, underscoring microbial adaptation as critical for successful captive-to-wild transitions in endangered species.},
}
@article {pmid40604345,
year = {2025},
author = {Kang, JW and Khatib, LA and Heston, MB and Dilmore, AH and Labus, JS and Deming, Y and Schimmel, L and Blach, C and McDonald, D and Gonzalez, A and Bryant, M and Ulland, TK and Johnson, SC and Asthana, S and Carlsson, CM and Chin, NA and Blennow, K and Zetterberg, H and Rey, FE and , and Kaddurah-Daouk, R and Knight, R and Bendlin, BB},
title = {Gut microbiome compositional and functional features associate with Alzheimer's disease pathology.},
journal = {Alzheimer's &amp; dementia : the journal of the Alzheimer's Association},
volume = {21},
number = {7},
pages = {e70417},
doi = {10.1002/alz.70417},
pmid = {40604345},
issn = {1552-5279},
support = {U01AG061359/AG/NIA NIH HHS/United States ; U19AG063744/AG/NIA NIH HHS/United States ; R01AG070973/AG/NIA NIH HHS/United States ; R01AG083883/AG/NIA NIH HHS/United States ; #S10 OD026929/GF/NIH HHS/United States ; //Vilas Early-Career Investigator Award/ ; #2023-00356//Swedish Research Council/ ; #2022-01018//Swedish Research Council/ ; #2019-02397//Swedish Research Council/ ; #101053962//European Union's Horizon Europe research and innovation programme/ ; #ALFGBG-71320//Swedish State Support for Clinical Research/ ; #201809-2016862//Alzheimer Drug Discovery Foundation (ADDF)/ ; #ADSF-21-831376-C//AD Strategic Fund and the Alzheimer's Association/ ; #ADSF-21-831381-C//AD Strategic Fund and the Alzheimer's Association/ ; #ADSF-21-831377-C//AD Strategic Fund and the Alzheimer's Association/ ; #ADSF-24-1284328-C//AD Strategic Fund and the Alzheimer's Association/ ; #22HLT07//European Partnership on Metrology co-financed from the European Union's Horizon Europe Research and Innovation Programme and by the Participating States/ ; //Bluefield Project/ ; //Cure Alzheimer's Fund/ ; //Olav Thon Foundation/ ; //Erling-Persson Family Foundation/ ; #FO2022-0270//Familjen R&#xf6;nstr&#xf6;ms Stiftelse, Stiftelsen f&#xf6;r Gamla Tj&#xe4;narinnor, Hj&#xe4;rnfonden, Sweden/ ; #860197//European Union's Horizon 2020 research and innovation programme under the Marie Sk&#x142;odowska-Curie/ ; JPND2021-00694//European Union Joint Programme-Neurodegenerative Disease Research/ ; UKDRI-1003//NIH and Care Research University College London Hospitals Biomedical Research Centre and the UK Dementia Research Institute at UCL/ ; },
mesh = {Humans ; *Alzheimer Disease/microbiology/pathology/cerebrospinal fluid ; *Gastrointestinal Microbiome/physiology ; Male ; Female ; Aged ; Biomarkers/cerebrospinal fluid ; Feces/microbiology ; Metagenomics ; Amyloid beta-Peptides/cerebrospinal fluid ; Aged, 80 and over ; },
abstract = {BACKGROUND: The gut microbiome is a potentially modifiable risk factor for Alzheimer's disease (AD); however, understanding of its composition and function regarding AD pathology is limited.<br><br>METHODS: Shallow-shotgun metagenomics was used to analyze the fecal microbiome of participants in the Wisconsin Microbiome in Alzheimer's Risk Study, leveraging clinical data and cerebrospinal fluid (CSF) biomarkers. Differential abundance and ordinary least squares regression analyses were performed to find differentially abundant gut microbiome features and their associations with CSF biomarkers of AD and related pathologies.<br><br>RESULTS: Gut microbiome composition and function differed between individuals with and without AD dementia. The compositional difference was replicated in an independent cohort. Differentially abundant gut microbiome features were associated with CSF biomarkers of AD and related pathologies.<br><br>DISCUSSION: These findings enhance our understanding of alterations in gut microbial composition and function in AD, and suggest that gut microbes and their pathways are linked to AD pathology.<br><br>HIGHLIGHTS: Gut microbiome composition and function differ between people with Alzheimer's disease (AD) dementia and cognitively unimpaired (CU) individuals. Co-occurring gut microbes show differential abundance across AD-related groups (AD vs CU, amyloid status+ vs amyloid status-, and apolipoprotein E (APOE) &#x3b5;4 status+ vs APOE &#x3b5;4 status-). Gut microbiome composition also differs between people with AD dementia and CU individuals in a larger validation cohort. Differentially abundant gut microbiome composition and function between AD and CU groups are correlated with cerebrospinal fluid biomarkers for AD and related pathologies.},
}
@article {pmid40604155,
year = {2025},
author = {Wen, W and Yang, C and Zuo, T},
title = {Viewing MASLD through an integrative gut microbiome lens.},
journal = {Nature metabolism},
volume = {},
number = {},
pages = {},
pmid = {40604155},
issn = {2522-5812},
}
@article {pmid40603926,
year = {2025},
author = {Claus, J and Top, J and Paganelli, FL and Ten Doesschate, T and Paternotte, N and Youngapelian, MJ and Schuurman, R and Willems, RJL and Leavis, H and van de Wijgert, JHHM},
title = {Nasopharyngeal microbiome composition by SARS-CoV-2 presence and severity.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {23185},
pmid = {40603926},
issn = {2045-2322},
mesh = {Humans ; *Nasopharynx/microbiology/virology ; *COVID-19/microbiology/virology/epidemiology ; *SARS-CoV-2/isolation &amp; purification ; Female ; Male ; Middle Aged ; *Microbiota ; Adult ; RNA, Ribosomal, 16S/genetics ; Severity of Illness Index ; Aged ; Corynebacterium/isolation &amp; purification/genetics ; Netherlands/epidemiology ; Health Personnel ; },
abstract = {The influence of SARS-CoV-2 on the nasopharyngeal microbiome, or vice-versa, is unclear. Nasopharyngeal swabs from Dutch healthcare workers (N = 257) and hospital outpatients with respiratory symptoms (N = 143), leftover after SARS-CoV-2 testing in 2020-2021, were 16S rRNA amplicon sequenced and tested for respiratory viruses by multiplex PCR panel. The healthcare workers were younger and much healthier than the patients, and experienced less severe viral infections. In the healthcare workers, log10 estimated concentrations (ECs) of Corynebacterium were slightly increased in samples with SARS-CoV-2 versus no virus detected, regardless of symptomatology (adjusted regression coefficient 0.52, p = 0.042) but no other bacterial ECs differed. Corynebacterium and Dolosigranulum ECs were higher in very mild/asymptomatic SARS-CoV-2 episodes compared to very mild/asymptomatic episodes with no viruses detected, but lower in mild compared to very mild/asymptomatic SARS-CoV-2 episodes (-1.07, p = 0.015, and -1.37, p = 0.011, respectively). In the patients, similar but non-significant trends by SARS-CoV-2 severity (fatal, severe, moderate versus mild) were seen for Dolosigranulum, but not for Corynebacterium. In this population, the largest nasopharyngeal microbiome composition differences were seen by the presence and severity of comorbidities. These findings suggest that the Dolosigranulum EC decreases with increasing SARS-CoV-2 severity, but the clinical relevance of this finding is unclear.},
}
@article {pmid40603925,
year = {2025},
author = {Budoff, MJ and de Oliveira Otto, MC and Li, XS and Lee, Y and Wang, M and Lai, HTM and Lemaitre, RN and Pratt, A and Tang, WHW and Psaty, BM and Siscovick, DS and Hazen, SL and Mozaffarian, D},
title = {Trimethylamine-N-oxide (TMAO) and risk of incident cardiovascular events in the multi ethnic study of Atherosclerosis.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {23362},
pmid = {40603925},
issn = {2045-2322},
support = {R01HL135920/NH/NIH HHS/United States ; R01HL135920/NH/NIH HHS/United States ; R01HL135920/NH/NIH HHS/United States ; R01HL135920/NH/NIH HHS/United States ; R01HL135920/NH/NIH HHS/United States ; R01HL135920/NH/NIH HHS/United States ; R01HL135920/NH/NIH HHS/United States ; R01HL135920/NH/NIH HHS/United States ; R01HL135920/NH/NIH HHS/United States ; R01HL135920/NH/NIH HHS/United States ; R01HL135920/NH/NIH HHS/United States ; R01HL135920/NH/NIH HHS/United States ; },
mesh = {Humans ; *Methylamines/blood ; Female ; Male ; *Atherosclerosis/blood/epidemiology/ethnology ; Middle Aged ; Aged ; Risk Factors ; Incidence ; Ethnicity ; *Cardiovascular Diseases/blood/epidemiology ; United States/epidemiology ; Proportional Hazards Models ; },
abstract = {Trimethylamine-N-oxide (TMAO) is a gut microbiome-derived metabolite of choline, L-carnitine and lecithin, abundant in animal source foods. In experimental models, higher blood TMAO levels enhance atherosclerotic cardiovascular disease (ASCVD). However in humans, most prior studies have evaluated high risk or secondary prevention populations, and no studies have investigated relationships in a diverse, multi-ethnic population. We evaluated 6,767 US adults free of ASCVD at baseline in the community-based Multi-Ethnic Study of Atherosclerosis (MESA), including 38% identifying as White; 28%, as Black; 22%, as Hispanic; and 12%, as Chinese adults. Plasma TMAO was measured serially at baseline and 5-years, and its time-varying association with incident ASCVD determined using Cox proportional hazards. Multivariate analyses adjusted for time-varying demographics, lifestyle factors, medical history, lipid measures, antibiotic use and dietary habits. During median 11.3 years follow-up, 852 ASCVD events occurred. After multivariate adjustment, TMAO associated with higher risk of ASCVD in a dose-dependent fashion, with hazard ratios across quintiles of 1.02, 1.17, 1.23, and 1.33 (95% CI 1.02, 1.74), respectively, compared to the lowest quintile (P-trend = 0.01). Risk appeared possibly larger among Hispanic and Chinese adults; and among individuals with lower baseline renal function; although these interactions did not achieve statistical significance. Plasma concentrations of TMAO associated with higher risk of incident ASCVD in this multi-ethnic US cohort, supporting a need to test dietary and pharmacologic interventions targeting the diet-microbiome axis for potential cardiovascular risk prevention in diverse populations.},
}
@article {pmid40603801,
year = {2025},
author = {Li, H},
title = {Iron and the Intestinal Microbiome.},
journal = {Advances in experimental medicine and biology},
volume = {1480},
number = {},
pages = {345-360},
pmid = {40603801},
issn = {0065-2598},
mesh = {*Gastrointestinal Microbiome/physiology/drug effects ; Humans ; *Iron/metabolism ; Animals ; Dysbiosis/metabolism/microbiology ; Homeostasis ; Oxidative Stress ; },
abstract = {Iron in the gut is like a double-edged sword. On one side, it is essential for numerous physiological processes, including oxygen transport and energy production, and is crucial for addressing conditions like anemia. However, on the other side, excess or unabsorbed iron can disrupt gut homeostasis, fuel harmful pathogens, contribute to dysbiosis, and promote gut inflammation. The challenge lies in finding a balance that ensures adequate iron absorption while minimizing its adverse effects on the gut microbiota. Host and microbiota in the gut have evolved sophisticated strategies to maintain iron homeostasis within the bacterial community and balance iron needs between host and gut microbiota. Disruption of this balance by excess iron could lead to serious consequences by promoting intestinal inflammation and disease progression. Current research points to promising therapeutical approaches that enhance iron absorption while suppressing iron-induced adverse effects, such as oxidative stress and dysbiosis, in the gut. These strategies offer the potential to reduce intestinal inflammation and improve gut health, paving the way for more effective therapies to mitigate disease complications.},
}
@article {pmid40603796,
year = {2025},
author = {Moreno-Navarrete, JM and Rodrigues, IG and Fernández-Real, JM},
title = {The Impact of Iron Homeostasis in Insulin-Sensitive Tissues and Gut Microbiome on Obesity-Driven Metabolic Disorders.},
journal = {Advances in experimental medicine and biology},
volume = {1480},
number = {},
pages = {253-269},
pmid = {40603796},
issn = {0065-2598},
mesh = {Humans ; *Obesity/metabolism/microbiology/complications ; *Iron/metabolism ; *Gastrointestinal Microbiome/physiology ; *Homeostasis ; Animals ; *Insulin Resistance ; *Insulin/metabolism ; *Metabolic Diseases/metabolism/microbiology ; Adipose Tissue/metabolism ; Liver/metabolism ; Muscle, Skeletal/metabolism ; },
abstract = {Iron is a crucial element for vital biological processes in both prokaryotic and eukaryotic cells, requiring precise regulation to maintain homeostasis. In humans and animal models, dysregulation of iron homeostasis is often linked to obesity-associated metabolic disturbances, which are characterized by elevated serum ferritin levels and excessive iron accumulation in insulin-dependent tissues like the liver, adipose tissue, and skeletal muscle. Prolonged iron overload in tissues induces oxidative stress, which impairs insulin sensitivity and promotes systemic insulin resistance and hyperglycemia. This creates a vicious cycle in which decreased serum hepcidin levels enhance intestinal iron absorption, further exacerbating iron accumulation. While the impact of iron on gut microbiota is well established, the role of gut microbiota in regulating body iron homeostasis is less studied. Recent studies have uncovered new mechanisms by which gut microbiota influence intestinal iron absorption and the regulation of body iron stores. In this chapter, we summarize recent findings on iron homeostasis in insulin-sensitive metabolic tissues and explore how gut microbiota can modulate body iron regulation in the context of obesity.},
}
@article {pmid40603760,
year = {2025},
author = {Tina, K and Jiatong, N and Deborah, H and Tobias, S and Doriane, A and Dirk, H},
title = {Therapeutic mechanisms of exclusive enteral nutrition in Crohn's disease.},
journal = {Seminars in immunopathology},
volume = {47},
number = {1},
pages = {28},
pmid = {40603760},
issn = {1863-2300},
mesh = {Humans ; *Enteral Nutrition/methods ; *Crohn Disease/therapy/metabolism/etiology/microbiology ; Gastrointestinal Microbiome/immunology ; Animals ; Intestinal Mucosa/metabolism/immunology/microbiology ; Treatment Outcome ; },
abstract = {Crohn's disease (CD) is a chronic, relapsing multifactorial inflammatory condition of the gastrointestinal tract, which is diagnosed under the age of 17 in 25% of patients, categorized as pediatric CD (pCD). Exclusive enteral nutrition (EEN) is a first-line therapy for inducing remission in pCD, yet its precise mechanisms remain poorly understood. This review summarizes the complex interplay of EEN-induced protective changes in the gut microbiota, epithelial barrier function and mucosal immune responses. EEN reshapes the gut microbiome by excluding potential pathobionts from the gut mucus layer and increasing protective bacterial and dietary metabolites. Emerging evidence highlights the role of EEN in modulating mitochondrial function, tryptophan metabolism and other metabolites in the intestinal epithelium and immune cells, which may contribute to its therapeutic efficacy. However, high variability in microbiome responses across clinical cohorts and discrepancies between clinical trials and animal models warrant further research to identify functional consequences and therapeutic mechanisms of EEN.},
}
@article {pmid40603595,
year = {2025},
author = {Komatsu, H and Sugimoto, T and Ogata, Y and Miura, T and Aida, M and Nishiyama, H and Kawai, M and Yano, Y and Mori, M and Shishido, Y},
title = {Characteristics of the gut microbiota in patients with advanced non-small cell lung cancer who responded to immune checkpoint inhibitors.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {23398},
pmid = {40603595},
issn = {2045-2322},
mesh = {Humans ; *Carcinoma, Non-Small-Cell Lung/drug therapy/microbiology/pathology/mortality ; *Gastrointestinal Microbiome/drug effects ; *Immune Checkpoint Inhibitors/therapeutic use/pharmacology ; *Lung Neoplasms/drug therapy/microbiology/pathology/mortality ; Female ; Male ; Aged ; Middle Aged ; Treatment Outcome ; Aged, 80 and over ; },
abstract = {Despite the introduction of immune checkpoint inhibitors (ICIs) in the treatment of lung cancer, the number of deaths from lung cancer remains high, and further improvements in response rates are necessary. Recently, the gut microbiota has been reported to be involved in the therapeutic effects of ICIs; however, only a few studies have examined patients with lung cancer in this context. In the current study, we aimed to explore the association between the gut microbiota before therapy and the efficacy of ICIs in patients with advanced non-small cell lung cancer (NSCLC). The a-diversity of the intestinal microbiota in patients who responded to ICI treatment (responders) was significantly higher than that in those who did not respond to ICIs (non-responders). Additionally, the abundance of Bifidobacteriaceae was significantly higher in the responders than in the non-responders. Furthermore, patients with a high abundance of Bifidobacteriaceae had significantly longer overall survival than those with a low abundance. Counts of Levilactobacillus brevis were significantly higher in responders than in non-responders. Our findings suggest that a higher diversity of the gut microbiota and an abundance of Bifidobacterium and/or L. brevis are distinctive features of the microbiota in patients with NSCLC who respond to ICI treatment.},
}
@article {pmid40603450,
year = {2025},
author = {Yurgel, SN and Ajeethan, N and Ali, S},
title = {Rootstock microbiome as a target for manipulation to combat apple replant disease.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {23498},
pmid = {40603450},
issn = {2045-2322},
mesh = {*Malus/microbiology/growth &amp; development ; *Plant Diseases/microbiology/prevention &amp; control ; *Microbiota ; *Plant Roots/microbiology ; Soil Microbiology ; Fungi/genetics/classification ; Bacteria/genetics/classification ; },
abstract = {Apple replant disease (ARD) describes a phenomenon of reduction of crop productivity in the early years of orchard establishment on sites previously planted with apple. Currently, manipulation of the soil microbiome through (bio)fumigation is the primary approach to alleviate ARD. An alternative approach to combat ARD, could involve adjusting the rootstock microbiome to better cope with biotic stress present in orchard soil. In this study we evaluated differences in microbiome structure and composition between nursery grown rootstock and mature apple trees, cultivated in Nova Scotian orchards. We found that mature apple tree roots associated microbiome dramatically differed in its diversity, structure and composition compared to that associated with saplings. Our research identified several fungal and bacterial taxa as potential candidates for further study in the context of nursery inoculation and their possible role in mitigating ARD in re-planted apple orchards. The results of this study provide a foundation for development of a synthetic community which could be used in nurseries during rootstock propagation to improve saplings adaptation to ARD soils. This approach may offer an ecologically safe and cost-effective alternative to current soil amendments to alleviate ARD consequences.},
}
@article {pmid40603415,
year = {2025},
author = {Thompson, RM and Del Carmen Montero-Calasanz, M and George, D and Fox, EM},
title = {From pollution to reforestation: the hidden microbiome of Alnus glutinosa nodules over 30 years.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {23373},
pmid = {40603415},
issn = {2045-2322},
support = {NE/S007512/1//Natural Environment Research Council/ ; RYC2019-028468-I//Spanish Ministry of Economy, Industry and Competitiveness (MINECO)/ ; },
mesh = {*Alnus/microbiology ; *Microbiota ; *Root Nodules, Plant/microbiology ; Metals, Heavy/toxicity ; Soil Microbiology ; Soil Pollutants ; Biodegradation, Environmental ; },
abstract = {Actinorhizal plants, such as Alnus glutinosa, play a critical role in ecosystem restoration, particularly in metal-contaminated soils, yet their nodule microbiome remains largely unexplored beyond Frankiaceae endosymbionts. This study presents the first comprehensive analysis of A. glutinosa root nodules under heavy metal stress, focusing on a 30-year-old chronosequence planted upon opencast coal mine spoil. Microbial diversity analysis revealed that A. glutinosa nodules harbour a distinct and conserved microbiome, dominated by Frankiaceae but also enriched with plant growth-promoting bacteria such as Bradyrhizobium, Mycobacterium, and Actinoplanes. Additionally, despite similar beta diversity between the nodules and soil, significant compositional differences were observed, reinforcing the selective nature of the nodules. However, functional profiling indicated that metabolic pathways were largely shared between nodule and soil microbiomes. Overall, this study provides new insights into the resilience and specialisation of the A. glutinosa nodule microbiome and its potential role in bioremediation within heavy metal-contaminated environments.},
}
@article {pmid40603287,
year = {2025},
author = {Samarra, A and Alcañiz, AJ and Martínez-Costa, C and Marina, A and Comas, I and Segata, N and Quijada, NM and Collado, MC},
title = {Breastfeeding and early Bifidobacterium-driven microbial colonization shape the infant gut resistome.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {6099},
pmid = {40603287},
issn = {2041-1723},
support = {MAMI-639226 project//EC | EU Framework Programme for Research and Innovation H2020 | H2020 European Institute of Innovation and Technology (H2020 The European Institute of Innovation and Technology)/ ; PROMETEO2020/12//Generalitat Valenciana (Regional Government of Valencia)/ ; CIPROM2023/030//Generalitat Valenciana (Regional Government of Valencia)/ ; },
mesh = {Humans ; *Breast Feeding ; *Bifidobacterium/physiology/genetics ; *Gastrointestinal Microbiome/genetics/drug effects ; Infant ; Female ; Infant, Newborn ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; Cesarean Section ; Metagenome ; Adult ; Male ; Milk, Human/microbiology ; Feces/microbiology ; },
abstract = {The assembly of the gut resistome in early life is key to infant health. Specific perinatal factors such as cesarean section (C-section), antibiotic exposure and lack of breastfeeding practices are detrimental to proper microbial development and increase the antimicrobial resistance genes (ARGs). Using 265 gut longitudinal metagenomes from 66 mother-infant pairs, we investigated how perinatal factors influence the acquisition and dynamics of ARGs during the first year of life. Our findings reveal that Bifidobacterium plays a crucial role in modulating the infant resistome, with its high relative abundance being associated with a lower ARG load. Exclusive breastfeeding during the first month of life accelerates the reduction of ARGs and ensures a lower resistome burden at six months. Moreover, early breastfeeding cessation correlates with a higher ARG load, underscoring its long-term influence on microbial resilience. Importantly, we identify exclusive breastfeeding as a key strategy to mitigate the impact of C-section delivery on the infant gut resistome, counteracting the early-life antibiotic exposure associated with this procedure and the resulting resistance acquisition. By promoting a microbiome enriched in Bifidobacterium, breastfeeding may help suppress ARG-carrying taxa, reducing the risk of resistance dissemination. Our findings underscore the importance of breastfeeding as a natural intervention to shape the infant microbiome and resistome. Supporting breastfeeding through public health policies could help limit the spread of antimicrobial resistance in early life.},
}
@article {pmid40603217,
year = {2025},
author = {Bouwmeester, H and Dong, L and Wippel, K and Hofland, T and Smilde, A},
title = {The chemical interaction between plants and the rhizosphere microbiome.},
journal = {Trends in plant science},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tplants.2025.06.001},
pmid = {40603217},
issn = {1878-4372},
abstract = {Research into the interaction between plants and the soil microbiota has expanded rapidly and is unravelling a plethora of interactions between plants and their root microbiota. The rhizosphere exhibits remarkable chemical diversity, driven by an evolutionary arms race. Through these chemicals, plants shape the rhizosphere microbiome using different mechanisms: organic carbon provision, antimicrobial compound production, and exudation of microbiota recruitment signals. Modern high-input agriculture may have diminished the role of natural chemical interactions and modern crops may have lost some of the relevant traits. As our understanding of root-rhizosphere interactions grows, harnessing natural mechanisms for agricultural sustainability becomes increasingly viable, potentially helping agriculture to counteract growing challenges from environmental stresses, climate change, and rising input costs.},
}
@article {pmid40603165,
year = {2025},
author = {Post, Z and Rosario Lora, D and Blogowski, W},
title = {Unraveling the sweet connection between pancreatic cancer and hyperglycemia.},
journal = {Trends in endocrinology and metabolism: TEM},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tem.2025.06.003},
pmid = {40603165},
issn = {1879-3061},
abstract = {Pancreatic adenocarcinoma (PaC) is one of the deadliest cancers, primarily due to late-stage diagnosis and limited treatment options. A bidirectional relationship exists between PaC and diabetes mellitus (DM), where glucose abnormalities both cause and result from PaC. In this review, we examine the complex pathophysiology of PaC-induced hyperglycemia, focusing on impaired insulin sensitivity, β cell dysfunction, chronic inflammation, and alterations in the gut microbiome and circadian rhythm. We discuss how PaC induces insulin resistance through disrupted signaling and proinflammatory factors, as well as β cell dysfunction through oxidative stress and adrenomedullin-mediated insulin secretion inhibition. In addition, emerging research highlights the role of the gut microbiome in PaC and hyperglycemia. Comprehensive understanding of these mechanisms is critical for early detection and improved treatment strategies for PaC.},
}
@article {pmid40603006,
year = {2025},
author = {Wiersinga, WJ and van der Poll, T},
title = {Biological drivers of the host response in sepsis.},
journal = {Thorax},
volume = {},
number = {},
pages = {},
doi = {10.1136/thorax-2024-222012},
pmid = {40603006},
issn = {1468-3296},
abstract = {Sepsis is a life-threatening syndrome driven by a dysregulated host response to infection. Immune dysregulation arises from responses that initially were activated to protect against pathogens and preserve tissue integrity. Disturbed resistance mechanisms can result in excessive inflammation alongside immunosuppression, each of which is considered important biological drivers of the immunopathology of sepsis. Key inflammatory drivers are excessive proinflammatory cytokine activity, complement and coagulation system activation and endothelial dysfunction. Conversely, sepsis-induced immunosuppression is marked by lymphocyte exhaustion, reduced monocyte human leucocyte antigen-DR expression, and the emergence of myeloid-derived suppressor cells. Within this complex immunological environment, the gut microbiome influences host immunity through the release of short-chain fatty acids and bacterial metabolites. Thus far, immunomodulatory trials in patients with sepsis paid little attention to the identification of dominant biological drivers, which might enrich the population for those who are more likely to respond to a certain intervention. Recently, retrospective analyses of such trials, as well as small prospective trials, have provided proof of concept that subgroups of sepsis patients can be identified with specific immunological profiles, either based on a single biomarker or on high-dimensional data, that respond differently to immunomodulation. This review explores the biological drivers of sepsis immunopathology, highlighting the challenges in translating preclinical insights into effective therapies and the potential of personalised medicine approaches to improve sepsis outcomes.},
}
@article {pmid40602915,
year = {2025},
author = {Liu, Z and Wang, X and Zheng, G and Li, J and Qin, J and Wang, L and Ouyang, X and Wang, J and Gu, W},
title = {Effects of petroleum contamination on soil metal(loid)s and microbial communities.},
journal = {Journal of environmental sciences (China)},
volume = {157},
number = {},
pages = {662-673},
doi = {10.1016/j.jes.2024.12.008},
pmid = {40602915},
issn = {1001-0742},
mesh = {*Soil Pollutants/analysis/toxicity ; *Soil Microbiology ; Soil/chemistry ; *Petroleum Pollution/analysis ; *Microbiota/drug effects ; *Petroleum/analysis ; *Environmental Monitoring ; *Metals/analysis ; },
abstract = {Evaluating petroleum contamination risk and implementing remedial measures in agricultural soil rely on indicators such as soil metal(loid)s and microbiome alterations. However, the response of these indicators to petroleum contamination remains under-investigated. The present study investigated the soil physicochemical features, metal(loid)s, microbial communities and networks, and phospholipid fatty acids (PLFAs) community structures in soil samples collected from long- (LC) and short-term (SC) petroleum-contaminated oil fields. The results showed that petroleum contamination increased the levels of soil total petroleum hydrocarbon, carbon, nitrogen, sulfur, phosphorus, calcium, copper, manganese, lead, and zinc, and decreased soil pH, microbial biomass, bacterial and fungal diversity. Petroleum led to a rise in the abundances of soil Proteobacteria, Ascomycota, Oleibacter, and Fusarium. Network analyses showed that the number of network links (Control vs. SC, LC = 1181 vs. 700, 1021), nodes (Control vs. SC, LC = 90 vs. 71, 83) and average degree (Control vs. SC, LC = 26.244 vs. 19.718, 24.602) recovered as the duration of contamination increased. Petroleum contamination also reduced the concentration of soil PLFAs, especially bacterial. These results demonstrate that brief exposure to high levels of petroleum contamination alters the physicochemical characteristics of the soil as well as the composition of soil metal(loid)s and microorganisms, leading to a less diverse soil microbial network that is more susceptible to damage. Future research should focus on the culturable microbiome of soil under petroleum contamination to provide a theoretical basis for further remediation.},
}
@article {pmid40602893,
year = {2025},
author = {Guo, H and Zhao, X and Yang, K and Cui, L},
title = {Optimizing mealworm rearing conditions and gut microbiome function for enhanced plastics biodegradation.},
journal = {Journal of environmental sciences (China)},
volume = {157},
number = {},
pages = {417-429},
doi = {10.1016/j.jes.2024.12.004},
pmid = {40602893},
issn = {1001-0742},
mesh = {Animals ; *Biodegradation, Environmental ; *Tenebrio/physiology/growth &amp; development ; *Plastics/metabolism ; *Gastrointestinal Microbiome/physiology ; Larva ; },
abstract = {Insects have become an efficient and eco-friendly bioreactor for plastics and even micro/nano-plastics biodegradation. However, the optimal conditions for rearing insects to maximize plastic biodegradation and the underlying mechanisms remain unclear, hindering its practical applications. We investigated the effects of multiple rearing factors on plastics degradation efficiency of Tenebrio molitor larvae, including larval instar, water addition frequency, plastic specific surface area and plastic types. The functional gut microbes and enzymes associated with the improved efficiency were further explored. Our findings revealed that adult larvae achieved the highest plastics degradation efficiency when receiving regular water additions without causing drowning of insects on hydrophobic plastics. Additionally, they effectively ingested foam plastics of polystyrene, polyethylene and polyurethane without prior comminution and densification. The biodegradation processes involving oxidation, cleavage and depolymerization of plastics were all demonstrated. Furthermore, foam plastic type-dependent functional microbes and enzymes that contributed to the efficient plastic degradation were identified. This work provides valuable insights into the practical applications of insects for sustainable plastics biodegradation.},
}
@article {pmid40602696,
year = {2025},
author = {Mohammed, V and Arasu, MV and Muthuramamoorthy, M and Karthick Raja Namasivayam, S and Arockiaraj, J},
title = {Neurotoxicity of food colorants: Gut dysbiosis and reduced short-chain fatty acids disrupt the enteric nervous system and lead to neurological disability.},
journal = {Toxicology letters},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.toxlet.2025.06.022},
pmid = {40602696},
issn = {1879-3169},
abstract = {For centuries, the practice of adding color to food has become deeply ingrained in culinary traditions, evolving into an indispensable aspect of food production today. Major food manufacturing companies extensively use colorants to enhance the visual appeal of their products. However, recent years have seen an increasing number of studies by researchers who have uncovered various health risks associated with food color additives. These studies have predominantly linked food colorants to severe health conditions such as cancer and allergies. Beyond these issues, further investigations have revealed that excessive use of food colorants can also lead to neurological disorders. Specifically, food colorants such as Tartrazine, Allura Red, Indigotine, Erythrosine, and Titanium Dioxide have been identified as significant contributors to bodily harm. Research indicates that these colorants do not directly affect the brain but impact the gut microbiome. They destroy beneficial gut bacteria, creating a pathway for neurological issues. While the direct mechanisms through which these colorants damage the gut and subsequently affect brain health are not yet fully understood, this paper aims to elucidate these pathways. Through comprehensive analysis, we demonstrate how these food colorants compromise gut health and lead to neurological impairments. By highlighting these interactions, this paper seeks to raise awareness and stimulate further research within the scientific community. Such research could pave the way for significant discoveries, providing deeper insights into the long-term effects of food colorants and leading to more informed regulatory decisions and safer food production practices in the future.},
}
@article {pmid40602642,
year = {2025},
author = {Pieńkowska, A and Fleischmann, J and Drabesch, S and Merbach, I and Wang, G and Rocha, U and Reitz, T and Marie Muehe, E},
title = {Long-term Organic Fertilization Shields Soil Prokaryotes from Metal Stress While Mineral Fertilization Exacerbates It.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {126747},
doi = {10.1016/j.envpol.2025.126747},
pmid = {40602642},
issn = {1873-6424},
abstract = {Metal contamination in agricultural soils threatens prokaryote dynamics essential for soil health and crop productivity. Yet, whether fertilization in the long-run affects their resilience to metals remains unclear. This study examined the biogeochemical impacts of realistically low-dose applications of cadmium, zinc, and lead in soils subjected to 119 years of non-fertilization, mineral-fertilization (NPK), organic-fertilization (manure), or combined mineral-organic fertilization. Amended metals remained in the mobile fraction with the order: mineral<unfertilized<mineral+organic<organic, mirroring the effects on soil prokaryotes. In both unfertilized and mineral-fertilized soils, 16S rRNA gene copy numbers declined by 30% upon metal addition, but recovery timing differed: in unfertilized soil, recovery began after three days, whereas in mineral-fertilized soil, numbers declined until day seven before recovering. This coincided with an increase in metal-resistant taxa, particularly in mineral-fertilized soil, with 10 significantly affected OTUs, and to a lesser extent in unfertilized soil, with 5 affected OTUs. Carbon-, nitrogen-, and phosphorus-mining enzyme activities increased 50 to 100% in mineral-fertilized soils, suggesting enhanced nutrient acquisition to mitigate metal toxicity. In contrast, organic-fertilized soil hosted stable enzymatic activities and microbial copy numbers with minimal community shifts (1 affected OTU), indicating greater resistance to metal amendment. Combined mineral-organic fertilization stabilized copy numbers and enzymatic activity upon metal amendment, but 8 OTUs were affected, including specialized nutrient cyclers, suggesting increased availability of previously adsorbed NPK cations. Our findings indicate that organic fertilization shields prokaryotes from metal stress, while mineral fertilization exacerbates it, highlighting the benefits of organic practices for maintaining soil health and productivity.},
}
@article {pmid40602634,
year = {2025},
author = {Ma, L and Pan, Y and Liu, H and Liu, G and Liu, W},
title = {Drying-rewetting legacy mitigates freezing-thawing effects on soil microbial communities and greenhouse gas emissions in plateau riparian wetlands.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {382},
number = {},
pages = {126753},
doi = {10.1016/j.envpol.2025.126753},
pmid = {40602634},
issn = {1873-6424},
abstract = {Climate change intensifies compound disturbances in soil ecosystems, yet how legacy effects from prior events shape microbial responses to subsequent stresses remains poorly understood. Here, we investigated the legacy effects of drying-rewetting (DW) and freeze-thaw (FT) on greenhouse gas (GHG) emissions and microbial community dynamics across riparian wetlands of the Tibetan Plateau with distinct land-use histories (urban, grazing, and natural). The results showed that urban soils consistently amplified CO2 emissions compared to grazing and natural lands, whereas natural soils exhibited a pronounced decline in fungal ITS gene abundance, contrasting with the resilience observed in urban and grazing counterparts. Notably, sequential DW-FT perturbations triggered cross-stress mitigation, reducing CO2 emissions and enriching Actinobacteria-a bacterial phylum negatively correlated with cumulative CO2 release. Concurrently, DW legacies drove the taxonomic restructuring of fungal communities, favoring the dominance of Ascomycota in natural soils subjected to subsequent FT cycles. Prior DW exposure uniquely amplified the relative abundance of bacterial amplicon sequence variants (ASVs) under FT fluctuations, while standalone FT legacies lacked comparable regulatory capacity. Furthermore, in bacterial co-occurrence networks exposed to two DW cycles, an incomplete cluster emerged, indicating short-term adaptation via compartmentalization. Fungal clusters under FT cycles exhibited simplified co-response patterns but activated mutualism. Our study demonstrates that DW/FT legacy effects on GHG emissions and microbial communities are land-use dependent; DW legacies mitigate FT-induced microbiome disruptions in plateau riparian soils, with fungi showing heightened sensitivity to FT and bacteria displaying adaptability to DW, highlighting taxon-specific responses to compound disturbances.},
}
@article {pmid40602565,
year = {2025},
author = {Rajeswari, G and Kumar, V and Jacob, S},
title = {Advanced lignocellulose bioprocessing for Aloe vera leaf rind through novel termite gut microbiome consortia for acetone butanol ethanol (ABE) production: Metagenomics insights and process economic analysis.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {145691},
doi = {10.1016/j.ijbiomac.2025.145691},
pmid = {40602565},
issn = {1879-0003},
abstract = {Consolidated bioprocessing (CBP) of lignocellulosic biomass (LCB) using microbes simplifies the process, eliminates enzyme cost and reduces the overall processing expenses. In this regard, termite gut, a potent reservoir of microbial symbionts produces various lignocellulolytic enzymes which acts synergistically to degrade LCB. However, the effectiveness of adapting the microbes with LCB for improved lignocellulolytic enzyme secretion and substrate degradation has been overlooked. Hence, in this study adaptive laboratory (ALE) of termite gut isolates was performed with various substrates such as saw dust (SD) and Aloe vera leaf rind (AVLR) under different conditions. Among the consortia, enriched termite consortium (ETC-3) showed the highest degradation of lignin (51.86 ± 2.03 %, w/w), hemicellulose (29.27 ± 1.29 %, w/w) and cellulose (41.97 ± 2.99 %, w/w) with maximum specific enzyme activities. High throughput sequencing revealed the significant enrichment of Proteobacteria (88.95 %) and Ascomycota (99.94 %) groups in ETC-3. Further, the efficiency of ETC-3 in consolidated pretreatment and bioprocessing (CPBP) and CBP of AVLR towards acetone, butanol and ethanol (ABE) production was studied. Compared to the CPBP, CBP resulted in 1.6-fold higher glucose yield which subsequently enhanced the butanol yield (7.97 ± 0.40 g/L). Finally, cost benefit analysis ensured the economic feasibility of process strategies for AVLR valorization.},
}
@article {pmid40602277,
year = {2025},
author = {Wu, H and Li, YL and Wang, Y and Wang, YG and Hong, JH and Pang, MM and Liu, PM and Yang, JJ},
title = {Anemoside B4 alleviates ulcerative colitis by attenuating intestinal oxidative stress and NLRP3 inflammasome via activating aryl hydrocarbon receptor through remodeling the gut microbiome and metabolites.},
journal = {Redox biology},
volume = {85},
number = {},
pages = {103746},
doi = {10.1016/j.redox.2025.103746},
pmid = {40602277},
issn = {2213-2317},
abstract = {Ulcerative colitis (UC) is a chronic, non-specific inflammatory disease of the intestines with a significant increase in global incidence in recent years. Oxidative stress and inflammation are two hallmarks of UC pathogenesis. Anemoside B4 (AB4), a pentacyclic triterpenoid saponin, exhibits significant antioxidant and anti-inflammatory properties and shows potential for preventing UC. Here, an animal model induced by dextran sodium sulfate (DSS) was used to investigate the effect of AB4 on UC. The results demonstrated that AB4 significantly reduces intestinal oxidative stress and inflammation in UC mice, while also protecting intestinal barrier function. Furthermore, AB4 helps restore intestinal microbial balance primarily by modulating the abundance of Lactobacillus, which enhances the metabolism of short-chain fatty acids and upregulates the production of butyric acid (BA). Pseudogerm-free mice and fecal microbiota transplantation (FMT) demonstrated that AB4 significantly mitigated UC in a gut microbe-dependent manner. Both AB4 and BA markedly activate the aromatic hydrocarbon receptor (AhR). The intestinal organoid results suggest BA may activate the AhR to inhibit ROS production and activation of NLRP3 inflammasome, thereby protecting intestinal integrity. Administration of AhR antagonists abolished the protective effects, thus confirming the involvement of AhR in the underlying mechanism. Overall, these results indicate that AB4 is an effective agent against UC mainly by activating the AhR through gut microbial short-chain fatty acid metabolites to inhibit intestinal oxidative stress and inflammation.},
}
@article {pmid40602191,
year = {2025},
author = {de Sant'Anna, FM and Chakrawarti, A and Haley, BJ and Barlow, J},
title = {The resistome of pasteurized and raw milk cheeses from the state of Vermont.},
journal = {International journal of food microbiology},
volume = {441},
number = {},
pages = {111333},
doi = {10.1016/j.ijfoodmicro.2025.111333},
pmid = {40602191},
issn = {1879-3460},
abstract = {This study investigates the resistome dynamics in cheese production, focusing on both raw milk and pasteurized varieties comparing a standard and lytic method of DNA extraction. Metagenomic analysis revealed the presence of single nucleotide polymorphism (SNP) confirmed antimicrobial resistance genes (ARGs) in core and rind samples of cheeses at different stages of ripening. No statistical significance was found between the extraction methods for antimicrobial resistance gene (ARG) classes. In pasteurized cheese, the resistome was influenced by the initial microbial composition and ripening period, with limited ARGs detected due to pasteurization. Nonetheless, detection of class B β-lactamase and Fosfomycin B resistance genes was observed in the pasteurized cheese core, possibly harbored by Bacillus cereus. Raw milk cheese exhibited a distinct resistome profile, with fluctuations in macrolide and oxazolidinone resistance genes associated with changes in microbial populations during ripening. Notably, the likely presence of multi-drug resistance genes in Lactococcus lactis highlights the importance of understanding resistance mechanisms in starter cultures. The study emphasizes the need for antimicrobial stewardship and hygiene practices in dairy production to mitigate the spread of resistance genes. Despite sequencing biases, this research contributes valuable insights into the cheese resistome, advocating for future studies to employ enhanced sequencing methods for comprehensive analysis and to develop practical strategies for resistance management in dairy products.},
}
@article {pmid40601963,
year = {2025},
author = {Munyaneza, V and Zhang, W and Haider, S and Ren, L and Ali, A and Kant, S and Ding, G},
title = {Mitigating Metal Toxicity in Plants Using Nanoparticles: Mechanisms and Implications for Sustainable Agriculture.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c04693},
pmid = {40601963},
issn = {1520-5118},
abstract = {Conventional agriculture's reliance on chemical inputs poses risks to human health and the environment. Nanotechnology offers a promising alternative through engineered nanoparticles (NPs) that have a high surface area, solubility, and reactivity. This review highlights how NPs mitigate metal toxicity and soil acidification by enhancing nutrient delivery and reducing phytotoxicity. We discuss NP-soil-plant interactions, including uptake, translocation, and physiological responses, at the cellular and molecular levels. Ecotoxicological concerns, such as NP accumulation, microbial disruption, and long-term effects, are addressed. Innovative strategies like stimuli-responsive release systems and NP-microbiome co-delivery platforms are explored to improve efficacy and safety. NPs significantly enhance plant resilience by increasing antioxidant enzyme activities by up to 60%, improving nutrient uptake efficiency, and boosting plant growth by 15-55% under aluminum stress conditions across various species, including Brassica napus. This perspective identifies key knowledge gaps and offers future perspectives, positioning nanotechnology as a sustainable tool to enhance crop productivity under metal stress while maintaining ecological balance.},
}
@article {pmid40601677,
year = {2025},
author = {Mills, K and Tan, J and Guneratne, T and Keir, L and Goldstein, M and Ventola, C and Makama, M and Ammerdorffer, A and Gülmezoglu, AM and Vogel, JP and McDougall, ARA},
title = {Maternal gut microbiome interventions to improve maternal and perinatal health outcomes: Target product profile expert consensus and pipeline analysis.},
journal = {PloS one},
volume = {20},
number = {7},
pages = {e0321543},
pmid = {40601677},
issn = {1932-6203},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; Female ; *Probiotics/therapeutic use ; Pregnancy ; Consensus ; *Maternal Health ; },
abstract = {OBJECTIVE: To develop a novel Target Product Profile (TPP) outlining the minimum and optimal requirements of probiotics targeting the maternal gut microbiome, create a research and development (R&amp;D) pipeline of maternal microbiome interventions, and identify the highest potential probiotic candidates matching TPP criteria.<br><br>DESIGN: A mixed-methods study including in-depth interviews, an international survey, and online public consultation, with systematic R&amp;D pipeline development.<br><br>SETTING: International research context in maternal gut microbiome interventions.<br><br>POPULATION: Ten stakeholder groups were included in the study for feedback on the TPP development.<br><br>METHODS: Stakeholder feedback from 23 interviews and 32 survey responses was analyzed to revise the TPP. A systematic search of databases (Adis Insight, ClinicalTrials.gov, WHO ICTRP, Ovid MEDLINE, and relevant grant databases) identified drugs, supplements, and biologics targeting the maternal gut microbiome. Probiotic candidates were matched against key TPP criteria to identify promising options for future research.<br><br>MAIN OUTCOME MEASURES: Stakeholder consensus (&#x2265;75% agreement) on TPP variables and identification of high-potential probiotic candidates.<br><br>RESULTS: The TPP met consensus for most of the 20 variables: 16 for minimum and 14 for optimal targets. Interviews raised issues concerning indication, target population, diagnostic requirements, and efficacy outcomes. Of 38 candidates identified in the maternal microbiome pipeline (2000-2023), eight were probiotics, with one high-potential candidate (Vivomixx) and two medium-potential candidates (Lactobacillus spp. and Bifidobacterium spp.) identified.<br><br>CONCLUSIONS: This study produced the first TPP and pipeline analysis for maternal gut microbiome interventions, identifying probiotics with higher potential. Few candidates reached late-phase research, highlighting the need for efficacy trials.},
}
@article {pmid40601568,
year = {2025},
author = {Manavalan, S and Pradeep, D and Dharmalingam, D and Semalaiyappan, J and Sivarasan, T and Venkatesan, S and Thirumal, S and Kuttiatt, VS},
title = {Comparative analysis of skin microbiome of patients with filarial lymphedema and healthy individuals.},
journal = {PloS one},
volume = {20},
number = {7},
pages = {e0325380},
pmid = {40601568},
issn = {1932-6203},
mesh = {Humans ; *Microbiota/genetics ; Male ; *Skin/microbiology ; *Elephantiasis, Filarial/microbiology ; Adult ; Female ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Case-Control Studies ; *Lymphedema/microbiology ; Pilot Projects ; Skin Microbiome ; },
abstract = {BACKGROUND: Lymphatic filariasis, a vector borne parasitic disease is a public health problem in the tropical region. Recurrent skin and soft tissue infections termed adenolymphangitis (ADL) is a major complication of filarial lymphedema. Understanding the changes in skin microbiome associated with this disease may provide novel insights on ADL attacks and lymphedema progression. This study investigates the changes in skin microbial flora in patients affected with filarial lymphedema.<br><br>METHODS: We employed 16S rRNA gene amplicon-based metagenomic technique to profile the skin microbiome of patients with filarial lymphedema in comparison with healthy volunteers.<br><br>RESULTS: There were notable differences in the bacterial flora between patients and healthy controls. Actinobacteria were under-represented in the patient group. Staphylococcus dominated both the groups, 63% in patients and 44% in controls. Samples from a few patients showed the presence of certain rare bacteria like Eremococcus and Facklamia.<br><br>CONCLUSION: This pilot study applying advanced molecular tools provides insight on the changes in skin microflora associated with filarial lymphedema for the first time. Further studies are necessary for a better understanding of the role of the altered skin microbiome in frequent episodes of adenolymphangitis in patients with filarial lymphedema.},
}
@article {pmid40601380,
year = {2025},
author = {Bağcı, U and Ulusan Bağcı, &#xd6;},
title = {The bibliometric analysis of documents concerning the relationship between the microbiota and urological malignancies.},
journal = {Journal of medical microbiology},
volume = {74},
number = {7},
pages = {},
doi = {10.1099/jmm.0.002041},
pmid = {40601380},
issn = {1473-5644},
mesh = {Humans ; *Bibliometrics ; *Microbiota ; *Urologic Neoplasms/microbiology ; Male ; Prostatic Neoplasms/microbiology ; Urinary Bladder Neoplasms/microbiology ; Kidney Neoplasms/microbiology ; },
abstract = {Introduction. The microbiota, which has a major impact on both health and illness, has recently become one of the most popular research topics.Hypothesis/Gap statement. To the best of our knowledge, no research has undertaken a bibliometric analysis of publications examining the connection between microbiome and urological cancer to date. In this respect, it is thought that our study will contribute to the literature.Aim. The purpose of this study is to raise awareness of the topic by performing a bibliometric analysis of the publications examining the connection between the microbiota and the most common urological cancers, including bladder, prostate, and kidney cancers.Methodology. All publications about prostate, renal and bladder cancers and microbiota indexed in Web of Science between 2000 and 2024 were included in the study.Results. A total of 310 publications were obtained. Before 2018, there were only three or fewer publications annually; however, following 2018, the number of publications increased rapidly, reaching a peak of 77 in 2024. The USA led with 98 (31.61%) documents, followed by China (60, 19.35%) and Italy (31, 10%). With 19 publications, Hirotsugu Uemura is the most contributing author, followed by Norio Nonomura with 17. Prostate cancer accounted for 45.48% of the publications, bladder cancer for 36.77% and kidney malignancies for 17.64%.Conclusion. Despite the fact that microbiota has been known for 80 years, research on the connection between microbiota and cancer accelerated after the completion of the Human Microbiome Project. The number of studies examining the connection between urological cancer and microbiota peaked in 2024 and is probably going to rise. More research is required on this topic, since the correlation between microbiota and especially prostate and bladder malignancies raises the possibility that variations in microbiota may be utilized in diagnosis, treatment and prognosis.},
}
@article {pmid40601369,
year = {2025},
author = {Prusa, J and Gorelik, MG and Blake, KS and Dantas, G},
title = {State of omics-based microbial diagnostics of CRC.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2526132},
doi = {10.1080/19490976.2025.2526132},
pmid = {40601369},
issn = {1949-0984},
mesh = {Humans ; *Colorectal Neoplasms/diagnosis/microbiology ; *Gastrointestinal Microbiome ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Metabolomics/methods ; Early Detection of Cancer/methods ; Gastrointestinal Tract/microbiology ; },
abstract = {Colorectal cancer (CRC) remains a major burden of cancer-related morbidity and mortality globally, especially when detected at later stages. Early detection through improved and more accessible diagnostics is critical for reducing the severity of CRC. As our understanding of CRC and the microbial inhabitants of the gastrointestinal tract continues to improve, it has become increasingly recognized that the bacterial component of the gut microbiome may provide diagnostic utility for detecting CRC. This is because CRC is often accompanied by shifts in bacterial taxa, and the metabolites produced or utilized by the CRC-associated gut bacterial community. Advances in sequencing and metabolite profiling technologies paired with our growing understanding of CRC-associated microbial taxa, present an opportunity for new gut microbiome-based diagnostics. In this narrative review, we discuss bacterial taxa and gut metabolites that have been investigated as predictive features for CRC diagnosis. We aim to highlight the tremendous progress that has been made in identifying gut microbiome-based features and why they should be further explored as potential CRC diagnostics. We also identify challenges that future work must address, including the impact of patient lifestyle, variation in methodology, and nonstandard data management practices. Resolving these areas of study design and implementation is key to understanding the complex bacterial communities and their by-products associated with CRC, and the development of microbial diagnostics that can detect them.},
}
@article {pmid40601331,
year = {2025},
author = {Li, Y and Dai, J and Wang, M and Yan, C and Xiu, M and Qu, M},
title = {Alterations in Gut Microbiota and Plasma Metabolites in Patients with Generalized Anxiety Disorder: A Multi-Omics Study.},
journal = {The International journal of neuroscience},
volume = {},
number = {},
pages = {1-26},
doi = {10.1080/00207454.2025.2529238},
pmid = {40601331},
issn = {1563-5279},
abstract = {OBJECTIVE: Microecological and metabolic disorders of the gut may be involved in the pathogenesis of generalized anxiety disorder (GAD), but clinical multi-omics evidence of this is lacking. Our study aimed to investigate characteristic alterations in the gut microbiota and plasma metabolome of patients with GAD and evaluate their clinical diagnostic value.<br><br>PATIENTS AND METHODS: Ninety subjects (60 patients with GAD and 30 healthy volunteers) were included. We employed 16S rRNA gene sequencing to characterize the gut microbiota and targeted liquid chromatography-mass spectrometry to analyze plasma metabolomic profiles.<br><br>RESULTS: GAD was associated with increased abundances of Actinobacteria, Bacteroidetes, and Escherichia-Shigella and decreased abundances of Firmicutes, Roseburia, Bifidobacterium, and Prevotellaceae_Prevotella. Metabolomic analysis revealed 19 differential metabolites (upregulated in GAD: e.g., glutamic acid, cortisol, arachidonic acid, &#x3b1;-linolenic acid; downregulated in GAD: e.g., &#x3b3;-aminobutyric acid, serotonin, tyrosine, phenylalanine, tryptophan). Enriched metabolic pathways included phenylalanine, tyrosine, and tryptophan biosynthesis; alanine, aspartate, and glutamate metabolism; and the biosynthesis of unsaturated fatty acids. Notably, microbiome-metabolome combined analysis revealed a significant correlation between intestinal flora disorders and changes in the plasma metabolic profile. The diagnostic model constructed based on the combined omics data exhibited excellent discriminatory efficacy, with areas under curve of 0.710, 0.986, and 0.997 for the microbiome, metabolome, and combined model, respectively. &#x200b;.<br><br>CONCLUSION: This study revealed the characteristic gut microbiome-plasma metabolome covariation pattern of GAD and identified biomarker combinations with potential diagnostic value. The identified biomarker group provides new insights into the gut-brain axis mechanism of GAD, providing important theoretical support for clarifying the pathogenesis of GAD and developing precise diagnosis and treatment strategies.},
}
@article {pmid40601234,
year = {2025},
author = {Correia, DMITD and Kapoor, N and Chávez-Manzanera, E and Gowdak, LHW and Kharusi, AA and Casanueva, FF and Halpern, B and Frost, G and Aldahash, R},
title = {Emerging evidence and potential avenues to achieve durable outcomes in patients with obesity: the confluence of nutrition, and Microbiome on body composition.},
journal = {Reviews in endocrine &amp; metabolic disorders},
volume = {},
number = {},
pages = {},
pmid = {40601234},
issn = {1573-2606},
abstract = {Obesity is a global health concern that impacts health, quality of life, and longevity in affected individuals. Comorbid cardiovascular disease, type 2 diabetes, cancer, and other conditions often accompany obesity, and researchers are actively investigating therapeutic strategies to treat obesity and mitigate the health risks associated with excess adiposity. Restrictive nutritional intake and body weight reduction through lifestyle behavioral interventions, bariatric procedures, and highly effective anti-obesity medications are all recommended treatments for obesity. Meanwhile, the caloric restriction that comes with very low-calorie diets can result in changes in body composition, most notably a progressive loss of muscle mass and/or functionality, a process that can be accelerated by aging, underlying metabolic disease, or inadequate protein intake seen with many dietary patterns. While muscle loss was previously understood as a condition only affecting older individuals, this outcome is common in patients with obesity. The term sarcopenic obesity has been used to refer to this condition, and it is now recognized as an important potential complication in all patients with obesity. Dietary challenges that influence overall body composition also have drawn attention to the gut microbiome, a topic of growing interest as there is an increasingly recognized interplay between diet, the metabolic actions of microorganisms in the gut that impact macronutrient and micronutrient production and absorption, and human health. This article will review the current understanding of obesity as a chronic disease, the impact of diet and nutritional therapy on body composition, and the potential relevance of the gut microbiome in this setting.},
}
@article {pmid40601071,
year = {2025},
author = {Su, J and Zhang, WB and Chen, YJ and Sun, B and Zhai, YP and Yuan, JM},
title = {Microbiome diversity in Haemaphysalis flava (life stage-host dependent) and Haemaphysalis longicornis ticks with zoonotic implications in Nantong, China.},
journal = {Acta parasitologica},
volume = {70},
number = {4},
pages = {142},
pmid = {40601071},
issn = {1896-1851},
support = {MSZ2024113//Research Project of Nantong City Science and Technology - Public Wellbeing Plan./ ; MSZ2024113//Research Project of Nantong City Science and Technology - Public Wellbeing Plan./ ; MSZ2024113//Research Project of Nantong City Science and Technology - Public Wellbeing Plan./ ; MSZ2024113//Research Project of Nantong City Science and Technology - Public Wellbeing Plan./ ; MSZ2024113//Research Project of Nantong City Science and Technology - Public Wellbeing Plan./ ; MSZ2024113//Research Project of Nantong City Science and Technology - Public Wellbeing Plan./ ; MS2023092//Research Project Foundation of the Nantong Health Commission/ ; MS2023092//Research Project Foundation of the Nantong Health Commission/ ; MS2023092//Research Project Foundation of the Nantong Health Commission/ ; MS2023092//Research Project Foundation of the Nantong Health Commission/ ; MS2023092//Research Project Foundation of the Nantong Health Commission/ ; MS2023092//Research Project Foundation of the Nantong Health Commission/ ; },
mesh = {Animals ; China ; *Ixodidae/microbiology/growth &amp; development ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Zoonoses/microbiology/transmission ; *Bacteria/classification/genetics/isolation &amp; purification ; Rickettsia/isolation &amp; purification/genetics ; Humans ; Life Cycle Stages ; Nymph/microbiology ; Female ; Phylogeny ; Biodiversity ; Haemaphysalis longicornis ; },
abstract = {PURPOSE: This study characterized the microbial communities of Haemaphysalis flava (H. flava) and Haemaphysalis longicornis (H. longicornis), in Nantong, China, and assessed the zoonotic implications.<br><br>METHODS: We collected both on-host and off-host ticks and performed 16S rRNA amplicon sequencing. Subsequent bioinformatic analyses included taxonomic composition assessment, community diversity evaluation, differential abundance analysis, interspecies abundance correlation and functional inference.<br><br>RESULTS: Rickettsia dominated in H. flava (77.31%), while H. longicornis exhibited higher abundances of Stenotrophomonas (10.78%), Coxiella (10.04%), and Psychrobacter (9.70%). Comparative analyses of life stages and host associations were only performed for H. flava due to limited sample sizes of H. longicornis across developmental stages. Rickettsia was enriched in on-host H. flava (90.41-90.51%) compared to off-host specimens (46.12%). &#x3b1;-diversity analysis showed higher microbial richness in off-host nymphs than in on-host adults. &#x3b2;-diversity revealed strong species-specific clustering. Network analysis demonstrated more complex microbial interactions in adult ticks. Pathogen screening detected Rickettsia japonica (R. japonica, host-specific to H. flava), Ehrlichia ewingii (E. ewingii), and Anaplasma bovis (A. bovis). Functional prediction highlighted elevated B vitamin biosynthesis pathways in nymphs, aligning with Coxiella-like endosymbionts (CLEs)'s putative nutritional role.<br><br>CONCLUSION: This study emphasizes the importance of enhanced tick surveillance and regular pathogen screening in domestic animals, particularly for&#xa0;spotted fever group (SFG) Rickettsia. CLEs may exhibit stage-specific abundance patterns aligned with the host's developmental nutritional requirements. These findings highlight the need for integrated One Health surveillance to mitigate tick-borne disease threats.},
}
@article {pmid40601060,
year = {2025},
author = {Wang, Y and Bai, S and Yang, T and Guo, J and Zhu, X and Dong, Y},
title = {Impact of exercise-induced alterations on gut microbiota diversity and composition: comparing effects of different training modalities.},
journal = {Cell regeneration (London, England)},
volume = {14},
number = {1},
pages = {28},
pmid = {40601060},
issn = {2045-9769},
support = {82300496//National Natural Science Foundation of China/ ; CFH 2024-1-4061//Capital's Funds for Health Improvement and Research (Key Research Program)/ ; XMLX202135//Beijing Hospitals Authority Clinical medicine Development of special funding/ ; },
abstract = {Exercise has been shown to influence gut microbiota composition, but the specific effects of different exercise modalities on microbial diversity remain unclear. Understanding these differences is essential for optimizing exercise programs to enhance both physical fitness and gut health. This study compared the gut microbiota profiles of participants undergoing moderate-intensity continuous training (MICT), high-intensity interval training (HIIT), and high-intensity functional training (HIFT) using 16S rRNA gene sequencing. Thirty-one previously untrained healthy university students were randomly assigned into MICT (n = 7), HIIT (n = 12) and HIFT (n = 12). The results revealed that distinct gut microbiome profiles in participants under different exercise modes. Notably, the alpha-diversity gradually increased from the MICT group to the HIFT group. In addition, there was a progressive shift towards a Faecalibacterium-dominated microbial type from HIIT to HIFT group compared to MICT group. Individuals in the HIFT group were identified to be enriched with Lactobacillus and Limosilactobacillus, along with reduced Actinomyces and Anaeromassilibacillus. Functionally, the KEGG pathway and enzyme analysis using PICRUST2 revealed that the HIFT group exhibited prominence in muscle function-related pathways and enzymes, specifically ko00280 (valine, leucine, and isoleucine degradation), as well as the enzyme EC: 3.4.11.14 (alanine aminopeptidase). In conclusion, these findings highlight how exercise modality influences gut microbial diversity, with HIFT promoting a more favorable microbial profile compared to traditional endurance training. Understanding these effects can help tailor exercise programs to improve both fitness and gut health.},
}
@article {pmid40601033,
year = {2025},
author = {Nariman, N and Entling, MH and Krehenwinkel, H and Kennedy, S},
title = {The Microbiome of an Invasive Spider: Reduced Bacterial Richness, but no Indication of Microbial-Mediated Dispersal Behaviour.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {70},
pmid = {40601033},
issn = {1432-184X},
mesh = {Animals ; *Spiders/microbiology/physiology ; *Microbiota ; *Bacteria/classification/genetics/isolation &amp; purification ; Introduced Species ; Symbiosis ; Europe ; Animal Distribution ; },
abstract = {Mermessus trilobatus, an invasive North American linyphiid spider, has expanded its invasion range up to 1400 km in Europe, accelerating its dispersal speed in less than 40 years. The high heritability of dispersal behaviour and the spatial sorting of high and low dispersers indicate a genetic basis of dispersal behaviour. However, microbial endosymbionts can moderate dispersal behaviour in related species (Rickettsia in Erigone atra). Hence, dispersal behaviour in M. trilobatus might also be dictated by the activity of dispersal-mediating endosymbionts. Here, we investigated the microbiome of invasive M. trilobatus spiders extracted from (1) high- and low-dispersive individuals and (2) spiders originating from locations close to the edge and core of the expansion. We examine the microbiomes for the presence of potential dispersal- and reproduction-mediating bacterial strains and compare the microbial assemblages of spiders based on their dispersal behaviour and locations of origin. The composition of microbial assemblages was similar among spiders of different geographic origins and dispersal behaviour. However, microbial richness was lower in high- than in low-dispersive individuals. Surprisingly, none of the known dispersal- or reproduction-altering endosymbionts of arthropods was identified in any tested spider. This contrasts with published results from North America, where M. trilobatus is a known host of Rickettsia and Wolbachia. Thus, the invasive European population appears to have lost its associated endosymbionts. As endosymbionts can reduce spider mobility, it is possible that their absence facilitates the spread of the invasive spider population. The absence of endosymbionts among the analysed individuals substantiates the role of genetic mechanisms behind the variable dispersal behaviour of invasive M. trilobatus in Europe.},
}
@article {pmid40597612,
year = {2025},
author = {Cai, X and Lin, Y and Wu, B and Luo, Y and Li, K},
title = {Sputum microbiota profiles of patients with rifampicin-resistant tuberculosis during the intensive-phase treatment.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {373},
pmid = {40597612},
issn = {1471-2180},
support = {2024A03J0585//Guangzhou Science and Technology Bureau Municipal-University (Institute) Joint Funding Project/ ; A2019342//Guangdong Provincial Health Commission Funding Project/ ; 20221A011046//Guangzhou Municipal Health Commission Funding Project/ ; },
abstract = {BACKGROUND: The respiratory microbiome plays a crucial role in respiratory health and influences the onset and progression of tuberculosis (TB). However, changes in the respiratory microbiota of patients with rifampicin-resistant TB (RR-TB) during the intensive-phase treatment have not been assessed. This study aimed to investigate the impact of a six-month intensive-phase treatment of second-line anti-TB drugs on the respiratory microbiota of RR-TB patients.<br><br>METHODS: Sputum samples were collected from 14 RR-TB patients and 14 healthy controls. Microbiota composition was analyzed using 16S rRNA gene sequencing, and functional predictions were performed to assess metabolic pathway changes.<br><br>RESULTS: RR-TB patients exhibited significantly lower alpha diversity compared to healthy controls, but no significant changes were observed after six months of treatment. Beta diversity analysis revealed distinct clustering patterns between RR-TB patients and healthy controls, with no significant differences between pre- and post-treatment groups. Functional analysis showed reduced microbial functions related to pyruvate fermentation and amino acid metabolism in RR-TB patients.<br><br>CONCLUSIONS: These findings highlight the specific effects of second-line anti-TB drugs on the respiratory microbiota and suggest potential roles of respiratory ecological imbalance in RR-TB pathogenesis. Future studies could explore microbiome-based diagnostic and therapeutic strategies for RR-TB.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-025-04091-4.},
}
@article {pmid40601009,
year = {2025},
author = {Jing, J and Yan, X and Wang, L and Zhang, Y and Qi, W and Xi, J and Hao, Z},
title = {Gut microbiota-derived indole-3-acetic acid ameliorates calcium oxalate renal stone formation via AHR/NF‑κB axis.},
journal = {Urolithiasis},
volume = {53},
number = {1},
pages = {134},
pmid = {40601009},
issn = {2194-7236},
support = {82000672//National Natural Science Foundation of China Young Scientists Fund/ ; 82370768//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Kidney Calculi/metabolism/microbiology/prevention &amp; control/drug therapy/chemically induced/pathology ; Rats ; *Gastrointestinal Microbiome/physiology ; *Indoleacetic Acids/metabolism/pharmacology/therapeutic use ; *Calcium Oxalate/metabolism ; Humans ; NF-kappa B/metabolism ; Male ; *Receptors, Aryl Hydrocarbon/metabolism ; Disease Models, Animal ; Cell Line ; Signal Transduction/drug effects ; Kidney/pathology/drug effects ; Female ; Oxidative Stress/drug effects ; Adult ; Rats, Sprague-Dawley ; },
abstract = {The exact mechanism of calcium oxalate stone (CaOx) formation is not fully understood. Evidence suggests that disruptions in the gut microbiota and its metabolites influence kidney stone formation. We conducted microbiome-metabolome analysis to pinpoint microbial metabolites linked to kidney stones in both patient and healthy control groups. We explored the impact of these kidney stone-related microbial metabolites on CaOx-induced stones, along with their underlying mechanisms of action. We exposed NRK-52E cells to CaOx crystals that had been pretreated with indole-3-acetic acid. Rats, induced to develop CaOx stones via ethylene glycol and ammonium chloride administration, were also treated with IAA. Our investigations encompassed assessments of Ca[2+] levels, reactive oxygen species levels, markers of oxidative stress, apoptosis levels, inflammation levels, and gene expression within AHR/NF‑κB pathway, both in cellular and tissue samples.Indole-3-acetic acid showed significantly reduction in patients with renal stones. The administration of IAA has been found to alleviate the deposition and adhesion of calcium oxide stones in the kidneys. Furthermore, IAA demonstrates beneficial effects on kidney damage and inflammation. IAA efficiently reduces intracellular levels of ROS, osteopontin, and CD44 in NRK-52E cells exposed to CaOx as well as in a rat model of stone formation. Mechanistically, IAA inhibits the activation of the NF-κB signaling pathway through the elevation of AHR in kidney stones. Our research has uncovered a novel connection between gut microbiota-derived tryptophan metabolites and kidney stones. The microbial metabolite IAA/AHR/NF-κB pathway may be a promising target for kidney stone treatment.},
}
@article {pmid40600879,
year = {2025},
author = {Johnson, NC and Marín, C},
title = {Functional team selection as a framework for local adaptation in plants and their belowground microbiomes.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf137},
pmid = {40600879},
issn = {1751-7370},
abstract = {Multicellular organisms are hosts to diverse communities of smaller organisms known as microbiomes. Plants have distinctive microbiomes that can provide important functions related to nutrition, defense, and stress tolerance. Empirical studies provide convincing evidence that in some -but not all - circumstances, belowground microbiomes help plants adapt to their local environment. The purpose of this review is to develop functional team selection (FTS) as a framework to help predict the conditions necessary for root microbiomes to generate local adaptation for their plant hosts. FTS envisions plants and their microbiomes as complex adaptive systems, and plant adaptations as emergent properties of these systems. If plants have the capacity to recognize and cultivate beneficial microbes and suppress pathogens, then it is possible for plants to evolve the capacity to gain adaptations by curating their microbiome. In resource-limited and stressful environments, the emergent functions of complex microbial systems may contribute to positive feedback linked to plant vigor, and ultimately, local adaptation. The key factors in this process are: 1) selective force, 2) host constitution, 3) microbial diversity, and 4) time. There is increasing interest in harnessing beneficial microbial interactions in agriculture and many microbial growth-promoting products are commercially available, but their use is controversial because a large proportion of these products fail to consistently enhance plant growth. The FTS framework may help direct the development of durable plant-microbiome systems that enhance crop production and diminish pathogens. It may also provide valuable insights for understanding and managing other kinds of host-microbe systems.},
}
@article {pmid40600792,
year = {2025},
author = {Ayayee, PA and Sunny, B and Montooth, KL and Rauter, CM},
title = {The Larval and Adult Female Gut Microbiomes of Two Burying Beetles (Nicrophorus spp.) With Distinct Parental Care Traits.},
journal = {Environmental microbiology},
volume = {27},
number = {7},
pages = {e70137},
pmid = {40600792},
issn = {1462-2920},
support = {INBRE-P20GM103427-19//National Institute for General Medical Science (NIGMS) INBRE/ ; P30 CA036727/CA/NCI NIH HHS/United States ; //University of Nebraska-Lincoln/ ; },
mesh = {Animals ; *Coleoptera/microbiology/physiology/growth &amp; development ; Larva/microbiology ; *Gastrointestinal Microbiome ; Female ; *Bacteria/classification/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Behavior, Animal ; },
abstract = {Burying beetles (Nicrophorus spp.) exhibit parental care behaviours well-suited for studying gut microbiome and holobiont evolution. Theory predicts that differences in transmission can contribute to gut microbiome variations. We show that microbiome diversity estimates were comparable between reproductive females of common-garden-reared colonies of Nicrophorus marginatus (facultative parental care) and Nicrophorus orbicollis (obligate parental care). In contrast, the respective associated larvae of both species differed significantly. Furthermore, larval microbiomes clustered with respective adult female microbiomes but differed from each other. Fifteen bacterial families underscored differences in community composition between beetle species, with Wohlfahrtiimonadaceae significantly more abundant in N. orbicollis than N. marginatus. Results suggest that differences in parental transmission (trophallaxis) and larval acquisition of microbes possibly impact the parental-offspring gut microbiome dynamic. Close association of parental and larval microbiomes in the facultative parental care species is attributed to environmental acquisition from prepared carcasses and limited trophallaxis in larvae. However, the distinct larval and parental microbiomes in the obligate parental care species are attributed to the selective sorting of functionally relevant microbes from parents in larvae. Further examination of this genus's parental care behaviours and gut microbiome dynamics may offer insight into the possible evolutionary and ecological implications and general outcomes.},
}
@article {pmid40600713,
year = {2025},
author = {Joos, L and Ommeslag, S and Baeyen, S and Asselberg, W and Van Loo, K and Clement, L and Debode, J and Vandecasteele, B and De Tender, C},
title = {Year-long, multiple-timepoint field studies show the importance of spatiotemporal dynamics and microbial functions in agricultural soil microbiomes.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0011225},
doi = {10.1128/msystems.00112-25},
pmid = {40600713},
issn = {2379-5077},
abstract = {Despite the recognition of the complexity of soil ecosystem dynamics, most soil microbiome studies sample one field, take one sample per field, or use limited samples throughout the year. This limits our understanding of the spatiotemporal role of the soil microbiome in relation to management practices. To address these limitations, we conducted a year-long investigation of the soil microbiome in two agricultural fields, sampling multiple plots at different soil depths every 5 weeks. We examined spatial and temporal variabilities in response to the application of organic amendments (one-time biochar and annual compost application) on bacterial and fungal communities, studying both the microbial composition (metabarcoding, phospholipid fatty acids [PLFA], hot-water extractable-carbon) and activity (metatranscriptomics). Indicated by metabarcoding and PLFA, fungal communities were less affected over time per field, whereas bacteria exhibited more pronounced temporal trends. In contrast, fungi displayed clear spatial effects, while bacterial spatial differences within the field were predominantly observed in the deeper soil layer. Effects on functional roles and metabolic processes of the active microbial community were mainly related to temporal trends, especially in the topsoil. Organic amendments did not affect the microbial activity and affected fewer than 2% of the bacterial and fungal amplicon sequence variants over time. This study reveals the predominance of spatiotemporal dynamics over management practices in shaping soil microbial communities within agricultural fields, emphasizing the importance of field-specific factors, sampling depth, and community type. This ushers in the need for a well-considered experimental design and sampling strategy that accounts for spatiotemporal trends.IMPORTANCEThis study addresses a critical gap in soil microbiome research by investigating spatiotemporal effects on soil bacterial and fungal composition and activity in relation to field management practices. Moving beyond single-field and limited sampling approaches, this research conducted monthly sampling events on two fields at various depths. By combining metabarcoding, phospholipid fatty acid analysis, and metatranscriptomics, the study examined bacterial and fungal community composition, biomass, and functionality. Key findings reveal distinct responses of bacterial and fungal communities to spatiotemporal variability and management practices. Functional categories were predominantly driven by temporal trends rather than compost amendments. Temporal changes were more pronounced in the topsoil. These insights into the complex interactions between soil microbial communities, management practices, and spatiotemporal dynamics contribute significantly to soil microbiome research and sampling strategies.},
}
@article {pmid40600712,
year = {2025},
author = {Comeault, AA and Orta, AH and Fidler, DB and Nunn, T and Ellison, AR and Anspach, TA and Matute, DR},
title = {Phylogenetic and functional diversity among Drosophila-associated metagenome-assembled genomes.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0002725},
doi = {10.1128/msystems.00027-25},
pmid = {40600712},
issn = {2379-5077},
abstract = {Host-associated microbial communities can mediate interactions between their hosts and biotic and abiotic environments. While much work has been done to document how microbiomes vary across species and environments, much less is known about the functional consequences of this variation. Here, we test for functional variation among drosophilid-associated bacteria by conducting Oxford Nanopore long-read sequencing and generating metagenome-assembled genomes (MAGs) from communities associated with six species of drosophilid flies collected from "anthropogenic" environments in North America, Europe, and Africa. Using phylogenetic analyses, we find that drosophilid flies harbor a diverse microbiome that includes core members closely related to the genera Gilliamella, Orbus, Entomomonas, Dysgonomonas, and others. Comparisons with publicly available bacterial genomes show that many of these genera are associated with phylogenetically diverse insect gut microbiomes. Using functional annotations and predicted secondary metabolite biosynthetic gene clusters, we show that MAGs belonging to different bacterial orders and genera vary in gene content and predicted functions, including metabolic capacity and how they respond to environmental stressors. Our results provide evidence that wild drosophilid flies harbor phylogenetically and functionally diverse microbial communities. These findings highlight a need to quantify the abundance and function of insect-associated bacteria from the genera Gilliamella, Orbus, Entomomonas, and others on the performance of their insect hosts across diverse environments.IMPORTANCEWhile much attention has been given to catalogue the taxonomic diversity intrinsic to host-associated microbiomes, much less is known about the functional consequences of this variation, especially in wild, non-model host species. In this study, we use long-read sequencing to generate and analyze 103 high-quality metagenome-assembled genomes from host-associated bacterial communities from six species of wild fruit fly (Drosophila). We find that the genomes of drosophilid-associated bacteria possess diverse metabolic pathways and biosynthetic gene clusters that are predicted to generate metabolites involved in nutrition and disease resistance, among other functions. Using functional gene predictions, we show that different bacterial lineages that comprise the insect microbiome differ in predicted functional capacities. Our findings highlight the functional variation intrinsic to microbial communities of wild insects and provide a step towards disentangling the ecological and evolutionary processes driving host-microbe symbioses.},
}
@article {pmid40600491,
year = {2025},
author = {Liaquat, M and Le Gall, G and Scholey, A and Pontifex, MG and Bastiaanssen, TFS and Muller, M and Minihane, AM and Vauzour, D},
title = {APOE4 genotype shapes the role of dietary fibers in cognitive health through gut microbiota changes.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2526133},
doi = {10.1080/19490976.2025.2526133},
pmid = {40600491},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Apolipoprotein E4/genetics/metabolism ; Male ; *Dietary Fiber/metabolism/administration &amp; dosage ; Female ; Aged ; *Cognitive Dysfunction/microbiology/genetics/metabolism ; Cross-Sectional Studies ; Genotype ; Feces/chemistry/microbiology ; *Cognition ; Middle Aged ; Fatty Acids, Volatile/blood/metabolism ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; },
abstract = {APOE4, a key risk factor for Alzheimer's disease, influences gut microbiota and microbial metabolites (e.g. amino acids and dietary fiber (DF) derived short-chain fatty acids (SCFAs)). However, its role in modulating microbiota-driven DF metabolism and its effect on cognitive status remains unclear. This cross-sectional study (n = 170) investigates the association between APOE4 genotype, DF consumption, and metabolism in individuals with subjective cognitive impairment (SCI) and mild cognitive impairment (MCI) compared to healthy controls (HC). Liquid Chromatography Tandem Mass Spectrometry (LC-MS/MS) and [1]H NMR metabolomic techniques were used to quantify SCFAs in serum and fecal samples, respectively. Gut microbiota speciation was carried out by 16S rRNA amplicon sequencing. We found that DF intake was significantly associated with APOE4 genotype and cognitive status, with lower consumption in APOE4 carriers (p < 0.05) and those with cognitive impairment (SCI and MCI) (p = 0.03). Differences (p < 0.05) in gut microbiota (both α- and β-diversity) and SCFAs were evident between APOE4 and non-APOE4 carriers, with stronger associations with DF consumption and cognitive status evident in non-APOE4 carriers. These findings suggest that targeting DF-induced changes in gut microbiota and serum SCFAs may be an effective strategy for mitigating cognitive impairment, but primarily in non-APOE4 carriers.},
}
@article {pmid40600350,
year = {2025},
author = {Dike, CR and Duan, Q and Ahmed, F and Denson, LA and Haslam, D and Minar, P and Ollberding, NJ and Papachristou, GI and Setchell, KDR and Thompson, T and Vitale, DS and Zhao, X and Abu-El-Haija, M},
title = {Acute pancreatitis gut dysbiosis persists at 1-year follow-up and is associated with clinical outcomes.},
journal = {Journal of pediatric gastroenterology and nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1002/jpn3.70135},
pmid = {40600350},
issn = {1536-4801},
support = {K23DK118190 (MAH)/DK/NIDDK NIH HHS/United States ; R03 DK131156 (MAH)/DK/NIDDK NIH HHS/United States ; P30DK078392/GF/NIH HHS/United States ; //Digestive Diseases Research Core Center in Cincinnati (LAD) and The Helmsley Charitable Trust (LAD, PM)/ ; },
abstract = {OBJECTIVES: Pediatric acute pancreatitis (AP) is associated with gut dysbiosis. We aimed to determine if dysbiosis persisted during follow-up and whether it is associated with clinical outcomes.<br><br>METHODS: Prospective enrollment of participants <21 years with first AP. Stool samples were obtained at baseline (n&#x2009;=&#x2009;41), 3 months (n&#x2009;=&#x2009;19), and 12 months (n&#x2009;=&#x2009;12) and in healthy controls (HC; n&#x2009;=&#x2009;34). Evaluation for diabetes (DM) or prediabetes (pre-DM) was performed. At 12-month follow-up gastrointestinal (GI) symptom surveys were completed and AP recurrence-acute recurrent pancreatitis (ARP) recorded. Shotgun metagenomic sequencing was performed on extracted microbial DNA.<br><br>RESULTS: Microbial alpha diversity was lower for AP versus HC at all three time points (p&#x2009;<&#x2009;0.008). Bray-Curtis ordinations showed the AP cohort did not cluster by time point, highlighting similarity in microbial composition over time. Within 12-month follow-up: 7/44 participants developed pre-DM/DM, 7/42 developed ARP, 16 had zero or one while 15 had multiple GI symptoms. Distinct clustering of samples was observed in the baseline samples of the group that developed ARP (p&#x2009;=&#x2009;0.023) and in follow-up samples with multiple GI symptoms, p&#x2009;<&#x2009;0.05. Relative abundance of most species was lower in AP samples when compared to HC at all time points with enrichment in Ruminococcus gnavus and Clostridium innocuum (AQ) (False Discovery Rate p&#x2009;<&#x2009;0.05). Several pathways involved in protein biosynthesis were depleted in the AP cohort at all time points.<br><br>CONCLUSIONS: Gut dysbiosis persisted following AP in children at 3 and 12 months follow-up compared to HC. Microbiome signatures differed in the ARP cohort and those with multiple GI symptoms.},
}
@article {pmid40600344,
year = {2025},
author = {Fontaine, SS and Trevelline, BK},
title = {An early-life perspective is needed to explain the impact of gut microbiota on wild vertebrate phenotypes.},
journal = {The Journal of experimental biology},
volume = {228},
number = {14},
pages = {},
doi = {10.1242/jeb.250130},
pmid = {40600344},
issn = {1477-9145},
support = {PRFB 2208809//National Science Foundation/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; Phenotype ; *Animals, Wild/microbiology ; *Vertebrates/microbiology/physiology/growth &amp; development ; },
abstract = {Vertebrates house dense and diverse communities of microorganisms in their gastrointestinal tracts. These communities shape host physiological and ecological phenotypes in diverse ways, with implications for animal fitness in nature. Exposure to microbes during the earliest stages of life is particularly important because, during critical developmental windows, the microbiome is exceptionally plastic and interactions with microbes can have long-lasting physiological impacts on the host. Despite our understanding that early-life microbial interactions are important to host function broadly, the majority of research in this area has been performed in human or model organisms that are not representative of animals in the wild. Specifically, most gut microbiome studies in wildlife are cross-sectional and compare microbial communities across life stages using different individuals, as opposed to tracking the microbial communities and phenotypes of the same individuals from early to later life. This knowledge gap may hinder wildlife microbiome research, as the current model lacks an early-life perspective that can contextualize host phenotypic and fitness differences observed between animals at later life stages. Further, considering early-life microbial dynamics may offer insights to applied research, such as determining the optimal age to manipulate microbiomes for desired conservation outcomes. In this Commentary, we consider current understanding of the importance of early-life host-microbe interactions to vertebrate physiology across the lifespan, discuss why this perspective is necessary in wildlife studies, and provide practical recommendations for experimental designs that can address these questions, including field and laboratory approaches.},
}
@article {pmid40600213,
year = {2025},
author = {Borrego-Ruiz, A and Borrego, JJ},
title = {Human oral microbiome and its influence on mental health and brain disorders.},
journal = {AIMS microbiology},
volume = {11},
number = {2},
pages = {242-294},
pmid = {40600213},
issn = {2471-1888},
abstract = {The human oral microbiome can affect brain functions directly through the trigeminal nerve and olfactory system and indirectly via the oral-gut-brain axis. However, the potential link between the oral microbiome and mental health remains an area that requires further investigation. Taking into consideration that gut microbiota dysbiosis plays a role in the onset and progression of several mental disorders, as well as the potential influence of the oral microbiome on mental health via direct pathways, the present narrative review explores the role of the human oral microbiome in health and disease, along with the factors that affect its composition, with a particular focus on its potential impact on mental health, including its involvement in a range of mental disorders and brain-related conditions, such as Alzheimer's disease, Parkinson's disease, autism spectrum disorder, anxiety, depression, stress, bipolar disorder, Down's syndrome, cerebral palsy, epilepsy, and schizophrenia. Chronic oral diseases can impair the oral mucosal barrier, allowing microorganisms and endotoxins to enter the bloodstream, triggering systemic inflammation, and affecting the blood-brain barrier. This pathway can lead to neuroinflammation and cognitive dysfunction and contribute to adverse mental health effects. Additionally, translocation of oral bacteria to the gut can drive persistent inflammation and thereby affect brain health. Multiple studies suggest a potential relationship between the oral microbiome and several mental disorders, but further research is needed to strengthen the evidence surrounding these associations and to fully clarify the underlying mechanisms linking the oral microbiome to these conditions. Given the promising implications, future research should focus on elucidating the biological mechanisms through which alterations in the oral microbiome influence the development and progression of determinate neurodegenerative and neuropsychiatric disorders. Additionally, identifying reliable biomarkers linked to the oral microbiome could enhance early detection, diagnosis, and monitoring of these conditions.},
}
@article {pmid40600174,
year = {2025},
author = {Ebrahimi, R and Shahrokhi Nejad, S and Fekri, M and Nejadghaderi, SA},
title = {Advancing prostate cancer treatment: the role of fecal microbiota transplantation as an adjuvant therapy.},
journal = {Current research in microbial sciences},
volume = {9},
number = {},
pages = {100420},
pmid = {40600174},
issn = {2666-5174},
abstract = {Prostate cancer (PCa) is a major cause of cancer-related deaths worldwide. While current treatments such as surveillance, surgery, and radiation are effective, they have their limitations. These can include patient incompliance due to side effects or resistance to hormonal changes, highlighting the need for alternative approaches. Human microbiota, a complex and dynamic host, plays a significant role in the homeostasis and is associated with several diseases or cancers in cases of dysregulation and dysbiosis. Research on fecal microbiota profiling and its association with certain cancers has opened new possibilities for preventing and managing tumor progression. One such possibility is fecal microbial transplantation (FMT). Studies show that different composition of urinary microbiota is found in various urinary tract diseases. Gut microbiota can regulate immune response against tumors; therefore, FMT may help modulate gut microbiota in a way that potentially enhances responses to immune checkpoint inhibitors, as suggested by emerging evidence in other cancers, though this needs further validation in PCa. Nevertheless, long-term complications and the safety of FMT are still questioned. We reviewed the roles of gut microbiota in PCa and suggested FMT as a potential tool in the treatment of PCa, which needs further investigations.},
}
@article {pmid40600173,
year = {2025},
author = {Yang, H and Gao, H and Xie, X and Wang, H and Li, X and Qiao, Q and Ma, Y and Bai, Y},
title = {Microbiome variability and role of Candida albicans in site-specific dental plaques in orthodontic adolescent patients with white spot lesions.},
journal = {Journal of oral microbiology},
volume = {17},
number = {1},
pages = {2522421},
pmid = {40600173},
issn = {2000-2297},
abstract = {White spot lesions (WSLs) are a common complication of orthodontic treatment. However, the cariogenic discrepancy in the supragingival microbiome between demineralized and non-demineralized surfaces and the influence of Candida albicans associated with WSLs remain unexplored. This study investigated the changes in supragingival microbiome of orthodontic adolescents with WSLs, encompassing both demineralized and non-demineralized sites, and explored C. albicans colonization in these patients. Supragingival plaques were collected from 29 orthodontic adolescents with WSLs (categorized into demineralized and non-demineralized groups based on the presence/absence of demineralization at sampling sites) and 23 healthy orthodontic adolescents. Supragingival microbiome composition was evaluated using 16S rRNA sequencing, and C. albicans colonization was identified using fungal culture methods. The supragingival microbiome on non-demineralized surfaces showed intermediate cariogenic potential between demineralized and healthy states, but closer to the demineralized state. C. albicans exhibited a propensity for colonization in WSLs patients without site-specificity. C. albicans influenced bacterial composition, with Streptococcus mutans significantly enriched on the demineralized surfaces of C. albicans-positive patients. In orthodontic adolescents with WSLs, non-demineralized surfaces showed microbiome shifts, necessitating interventions to promote a healthy microbiome. C. albicans can impact microbiome composition and potentially contribute to WSLs pathogenesis.},
}
@article {pmid40600142,
year = {2025},
author = {Xia, Y and Lu, L and Wang, L and Qiu, Y and Liu, X and Ge, W},
title = {Multi-omics analyses reveal altered gut microbial thiamine production in obesity.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1516393},
pmid = {40600142},
issn = {1664-302X},
abstract = {OBJECTIVE: Accumulating evidence highlights the important role of B vitamins in maintaining the balance of gut microbial ecology and metabolism, however, few studies have focused on changes in B vitamins homeostasis in the gut and their associations with disease. This study aims to investigate the potential interplay between B vitamins, gut microbiota, and obesity.<br><br>METHODS: We conducted an integrated analysis of fecal shotgun metagenomics, fecal metabolome concerning B vitamins and short chain fatty acids (SCFAs), and obese phenotypes in a cohort of 63 participants, including 31 healthy controls and 32 individuals with obesity.<br><br>RESULTS: Metabolomic analysis identified significantly lower levels of fecal thiamine in individuals with obesity (P Wilcoxon < 0.001). Fecal thiamine levels exhibited a positive correlation with HDL-C and a negative correlation with BMI, DBP, fasting serum insulin, HOMA-IR, triglycerides, and propionic acid. Binary logistics regression suggested that fecal thiamine deficiency may be a potential contributor to the onset of obesity (Odds ratio: 0.295). Metagenomic analysis indicated that the microbial composition in individuals with obesity was characterized by a predominance of potential opportunistic pathogens, a loss of complexity, and a decrease in thiamine-producing bacteria. Integrated analysis indicated that thiamine deficiency was positively associated with the depletion of thiamine auxotrophic bacteria in the obese microbiome. Functional analysis revealed that KOs content for enzymes involved in the microbial production of thiamine were significantly lower in obesity, including tRNA uracil 4-sulfurtransferase (ThiI, P Wilcoxon = 0.001) and nucleoside-triphosphatase (NTPCR, P Wilcoxon = 0.006), both of which were positively associated with fecal thiamine.<br><br>CONCLUSION: Our study highlights the impairment of microbial thiamine production and its broad associations with gut microbiota dysbiosis and obesity-related phenotypes. Our findings provide a rationale for developing treatments that utilize thiamine to prevent obesity by modulating gut microbiota.},
}
@article {pmid40600111,
year = {2025},
author = {Hao, W and Wang, Z and Ma, H},
title = {Identification of core gene-gut microbiome associations in diverticulitis patients through a two-sample mendelian randomization and bioinformatics-based investigation.},
journal = {Global medical genetics},
volume = {12},
number = {3},
pages = {100065},
pmid = {40600111},
issn = {2699-9404},
abstract = {BACKGROUND: Previous studies have suggested a potential link between the gut microbiota and diverticulitis. However, the causal relationships as well as underlying mechanisms remain unclear.<br><br>METHODS: The causal effects of gut microbiota on diverticulosis &amp; diverticulitis was assessed using two-sample Mendelian randomization analysis. The sensitivity analyses were also performed. We then used integrative bioinformatics tools to identify core genes associated with diverticulitis and explore their potential mechanisms and therapeutic targets.<br><br>RESULTS: Inverse variance weighted analysis indicated that Family XIII (OR=0.281, 95&#xa0;% CI: 0.093-0.853, P&#xa0;=&#xa0;0.025) and Defluviitaleaceae UCG-011 (OR=0.382, 95&#xa0;% CI: 0.162-0.898, P&#xa0;=&#xa0;0.027) were negatively associated with the risk of diverticulosis and diverticulitis, whereas Oscillospira (OR=3.514, 95&#xa0;% CI: 1.146-10.779, P&#xa0;=&#xa0;0.028), Ruminiclostridium 6 (OR=2.629, 95&#xa0;% CI: 1.093-6.322, P&#xa0;=&#xa0;0.031), Lachnoclostridium (OR=2.458, 95&#xa0;% CI: 1.014-5.962, P&#xa0;=&#xa0;0.047), and Desulfovibrionales (OR=2.157, 95&#xa0;% CI: 1.038-4.480, P&#xa0;=&#xa0;0.039) were positively associated with disease risk. The sensitivity analyses validated these correlations. Through SNP annotation, we identified 23 host genes associated with pathogenic gut microflora in diverticulosis and diverticulitis, and retrieved 213 diverticulitis-related genes from GeneCards. Intersection analysis revealed LRRC4C as the sole shared gene. Differential expression analysis further showed that LRRC4C was significantly downregulated in diverticulitis compared to infective colitis. Finally, eight candidate drugs were identified as potential inducers of LRRC4C expression.<br><br>CONCLUSION: The research revealed potential causal relationships between gut microbiota and diverticulitis. LRRC4C was identified as a core gene associated with pathogenic microbial traits in diverticulitis, and candidate therapeutic drugs for diverticulitis based on LRRC4C were predicted, offering novel strategies for the prevention and management of the disease.},
}
@article {pmid40600056,
year = {2025},
author = {Roy, N and Yang, S and Lee, D and Choi, K},
title = {Ecological processes influencing bacterial community assembly across plant niche compartments.},
journal = {mLife},
volume = {4},
number = {3},
pages = {294-304},
pmid = {40600056},
issn = {2770-100X},
abstract = {Understanding microbial community assembly in plants is critical for advancing agricultural sustainability. This study investigated microbial diversity and community assembly mechanisms across six compartments of tomato plants: bulk soil, rhizosphere, root, stem, flower, and seed. Using 16S rRNA amplicon sequencing, we observed that microbial richness was highest in the bulk soil and rhizosphere, with significant reductions in internal plant tissues. Co-occurrence network analysis identified distinct microbial hubs in each compartment, such as Bacillus in the root and seed, highlighting critical interactions influencing microbial dynamics. Ecological process modeling revealed that deterministic processes, such as selection, dominated in below-ground compartments, whereas stochastic processes like drift were more influential in above-ground tissues, reflecting differences in niche specificity and ecological stability. Dispersal limitation emerged as a key driver in soil-associated compartments, structuring microbial diversity. These findings advance our understanding of the ecological mechanisms shaping plant microbiomes and suggest targeted microbiome management strategies to enhance crop health, productivity, and resilience. Future research integrating functional genomics, temporal dynamics, and environmental factors is necessary to uncover the broader implications of plant-associated microbiomes.},
}
@article {pmid40600054,
year = {2025},
author = {Githaka, JM},
title = {"Misuse" of RNA-seq data in microbiome studies: A cautionary tale of poly(A).},
journal = {mLife},
volume = {4},
number = {3},
pages = {227-231},
pmid = {40600054},
issn = {2770-100X},
}
@article {pmid40600049,
year = {2025},
author = {Xu, H and Zhang, R and Zhang, X and Zhang, Z and Feng, Y and Lin, L},
title = {Pulmonary microbial spectrum of Burkholderia multivorans infection identified by metagenomic sequencing.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1577363},
pmid = {40600049},
issn = {2296-858X},
abstract = {PURPOSE: Burkholderia multivorans, a Gram-negative bacterium, often infect patients with severe immunocompromised and cystic fibrosis. B. multivorans infection is challenging to treat due to its ability to disrupt the action of multiple antimicrobial agents through intrinsic and acquired resistance mechanisms. A better understanding of the pulmonary microbial spectrum of B. multivorans infection is crucial for the prevention and treatment of B. multivorans.<br><br>CASE PRESENTATION: This case series reviewed the respiratory microbiome structure and alternations during the treatment of B. multivorans infection through metagenomic next-generation sequencing (mNGS). Analysis of mNGS data of 19 pharyngeal secretion samples collected from the 3 COVID-19 patients at different time points showed that the relative abundance of B. multivorans was fluctuated and eventually increased, indicating the possible development of drug resistance. A total of 40 antibiotic-resistant genes (ARGs) were detected. Significantly, the levels of CEOA, CEOB, and OPCM were consistent with the trends in the relative abundance of B. multivorans. Besides, we described nine previously uncharacterized non-synonymous mutations in PenA of B. multivorans. These mutations lead to amino acid changes Thr32Ala, Ala43Ser, Gln105Arg, Asn202Ser, Gln219Arg, Gly241Ala, Val259Ala, Thr279Ala, and Ser298Ile that may associate with resistance to &#x3b2;-lactam antibiotics.<br><br>CONCLUSION: This report shed light on the importance of rapidly diagnosis and treatment of B. multivorans infection. mNGS serve as a powerful microbial detection tool that provides a comprehensive, sensitive, and rapid method for pathogen detection and drug resistance analysis.},
}
@article {pmid40599846,
year = {2025},
author = {Portela, DS and Jain, A and Flood, M and Lavelle, A and Guerra, G and Patel, M and Aziz, O and Warrier, S and Heriot, A and Mohan, H},
title = {The microbiome of pseudomyxoma peritonei: a scoping review.},
journal = {Pleura and peritoneum},
volume = {10},
number = {2},
pages = {35-50},
pmid = {40599846},
issn = {2364-768X},
abstract = {There is growing interest in the role of the microbiome in carcinogenesis, but few studies examine the microbiome of pseudomyxoma peritonei (PMP). This scoping review summarises the microorganisms identified in PMP samples and examines the evidence of their role in disease outcomes. The methodology was developed in accordance with the PRISMA-ScR framework and checklist. Nine relevant studies were included. Microbiological testing was performed on PMP samples from 85 patients. At the phylum level, Proteobacteria was detected in greatest relative abundance in tumour tissue, cellular and acellular mucin. The relative proportion of different phyla more closely resembled the gut microbiome in inflammatory bowel disease than in a healthy gut. High-grade specimens showed significantly higher bacterial density than low-grade specimens and non-neoplastic non-perforated appendix specimens. Survival data of 58 patients were published, correlating outcomes to pre-operative antibiotic administration. Observed differences were not statistically significant. There is evidence of an altered bacterial profile in PMP samples compared to a healthy gut microbiome, the significance of which is unclear. Significant methodological challenges remain in this field of study. This scoping review supports the need for further analysis of the PMP bacterial profile, using methodologies that incorporate controls and deliver taxonomic resolution at species level.},
}
@article {pmid40599650,
year = {2025},
author = {Zhang, H and Zheng, X and Huang, Y and Zou, Y and Zhang, T and Repo, MA and Yin, M and You, Y and Jie, Z and Xu, WA},
title = {Novel potential biomarkers for predicting childhood caries via metagenomic analysis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1522970},
pmid = {40599650},
issn = {2235-2988},
mesh = {Humans ; *Dental Caries/diagnosis/microbiology ; Child ; *Biomarkers/analysis ; *Metagenomics/methods ; Saliva/microbiology ; Female ; Male ; *Microbiota/genetics ; Bacteria/classification/genetics/isolation &amp; purification ; Metagenome ; },
abstract = {BACKGROUND: Dental caries is a prevalent global health issue, particularly among children, with significant oral and overall health implications. The oral microbiome is considered a critical factor in caries development, with various microbial species implicated in the disease process.<br><br>OBJECTIVES: This study aims to explore the changes and interactions of oral microbiota in childhood caries using metagenomic analysis, and identify potential biomarkers for early caries detection and treatment.<br><br>METHODS: Saliva samples were collected from 241 children aged 6 to 9 years, categorized into caries-free (CF), low-caries (CL), and caries-severe (CS) groups. Metagenomic sequencing was performed to analyze the oral microbiome, followed by a series of statistical and functional analyses to characterize microbial diversity and function.<br><br>RESULTS: The study revealed significant differences in the microbial community composition among the groups, with the CS group exhibiting higher alpha and beta diversity than that of the CF group. Numerous unclassified microorganisms, such as Campylobacter SGB19347 and Catonella SGB4501, are intimately linked to dental caries and display intricate interaction networks, suggesting the potential formation of a distinct ecological network. In functional assessment, we identified a possible link between pectin and caries, suggesting that microorganisms that produce pectinase enzymes might play a role in the advancement of severe dental caries. Additionally, we identified 16 species as the best marker for severe dental caries, achieving an impressive AUC of 0.91.<br><br>CONCLUSION: The role of microbiota in dental caries is multifaceted, involving a complex interplay of microbial species and functions. Our findings enhance the understanding of the microbial basis of dental caries and offer potential diagnostic and therapeutic targets. The predictive capacity of the identified biomarkers warrants further investigation for early caries detection and intervention.<br><br>CLINICAL SIGNIFICANCE: The identification of novel biomarkers through metagenomic analysis enables early detection and targeted intervention for childhood caries, potentially transforming children dental care and significantly improving long-term oral health outcomes.},
}
@article {pmid40599494,
year = {2025},
author = {Boton, N and Patel, PK and Beekmann, SE and Polgreen, PM and Buckel, WR and Mahoney, MV and Mehrotra, P and Lee, MSL},
title = {Clinician Management Preferences for Clostridioides difficile Infection in Adults: A 2024 Emerging Infections Network Survey.},
journal = {Open forum infectious diseases},
volume = {12},
number = {7},
pages = {ofaf335},
pmid = {40599494},
issn = {2328-8957},
abstract = {BACKGROUND: The 2021 Infectious Diseases Society of America (IDSA) and Society for Healthcare Epidemiology of America (SHEA) guidelines for Clostridioides difficile infection (CDI) introduced new recommendations for managing initial and recurrent CDI. Since then, new microbiome-based therapies for preventing recurrent CDI have become available. We surveyed infectious diseases (ID) clinicians to understand their experiences, practices, and challenges in CDI management.<br><br>METHODS: An electronic survey was distributed to members of the IDSA Emerging Infections Network in May 2024, targeting ID physicians and healthcare professionals in the United States who manage adult CDI. The survey assessed treatment preferences, clinical practices, and barriers to accessing and prescribing CDI therapies.<br><br>RESULTS: Of the 500 respondents who reported treating CDI in the past year, 83% (417/500) indicated that vancomycin was their most frequently prescribed agent for initial, nonfulminant CDI. Additionally, 72% (357/498) reported that their institutional guidelines recommended vancomycin as the first-line agent. The most common barrier to fidaxomicin use was challenges with outpatient insurance coverage (82% [408/496]). Bezlotoxumab was available to 74% (370/500) of respondents, though 33% (165/497) indicated they do not use bezlotoxumab routinely. Most clinicians (87% [437/500]) had previously recommended fecal microbiota transplantation (FMT) for recurrent CDI, though only 48% (239/500) had current access to FMT using donor stool. Fecal microbiota live-jslm was available to 36% (179/500), and fecal microbiota spores live-brpk was available to 30% (150/500).<br><br>CONCLUSIONS: Significant barriers, including high costs, insurance challenges, and limited availability of CDI therapies, impact clinical decision-making and adherence to guideline recommendations.},
}
@article {pmid40599328,
year = {2025},
author = {Du, W and Xu, W and Hu, Y and Zhao, S and Li, F and Song, D and Shen, J and Xu, Q},
title = {Editorial: Crosslinking of feed nutrients, microbiome and production in ruminants.},
journal = {Frontiers in veterinary science},
volume = {12},
number = {},
pages = {1610490},
pmid = {40599328},
issn = {2297-1769},
}
@article {pmid40599184,
year = {2025},
author = {Chen, ZL and Wang, C and Wang, F},
title = {Revolutionizing gastroenterology and hepatology with artificial intelligence: From precision diagnosis to equitable healthcare through interdisciplinary practice.},
journal = {World journal of gastroenterology},
volume = {31},
number = {24},
pages = {108021},
pmid = {40599184},
issn = {2219-2840},
mesh = {Humans ; *Gastroenterology/trends/methods ; *Artificial Intelligence/trends ; *Precision Medicine/methods/trends ; *Health Equity/trends ; Deep Learning ; *Liver Diseases/diagnosis/therapy ; },
abstract = {Artificial intelligence (AI) is driving a paradigm shift in gastroenterology and hepatology by delivering cutting-edge tools for disease screening, diagnosis, treatment, and prognostic management. Through deep learning, radiomics, and multimodal data integration, AI has achieved diagnostic parity with expert clinicians in endoscopic image analysis (e.g., early gastric cancer detection, colorectal polyp identification) and non-invasive assessment of liver pathologies (e.g., fibrosis staging, fatty liver typing) while demonstrating utility in personalized care scenarios such as predicting hepatocellular carcinoma recurrence and optimizing inflammatory bowel disease treatment responses. Despite these advancements challenges persist including limited model generalization due to fragmented datasets, algorithmic limitations in rare conditions (e.g., pediatric liver diseases) caused by insufficient training data, and unresolved ethical issues related to bias, accountability, and patient privacy. Mitigation strategies involve constructing standardized multicenter databases, validating AI tools through prospective trials, leveraging federated learning to address data scarcity, and developing interpretable systems (e.g., attention heatmap visualization) to enhance clinical trust. Integrating generative AI, digital twin technologies, and establishing unified ethical/regulatory frameworks will accelerate AI adoption in primary care and foster equitable healthcare access while interdisciplinary collaboration and evidence-based implementation remain critical for realizing AI's potential to redefine precision care for digestive disorders, improve global health outcomes, and reshape healthcare equity.},
}
@article {pmid40598993,
year = {2025},
author = {Kamounah, S and Sarathi, A and Elisabeth Sørensen, C and Arumugam, M and Pedersen, AML},
title = {Microbial signatures in oral sites of patients with primary Sjögren's syndrome: Association with salivary gland hypofunction.},
journal = {Journal of microbiology (Seoul, Korea)},
volume = {63},
number = {6},
pages = {e2501030},
doi = {10.71150/jm.2501030},
pmid = {40598993},
issn = {1976-3794},
mesh = {Humans ; *Sjogren's Syndrome/microbiology/physiopathology ; Middle Aged ; Female ; Saliva/microbiology ; Male ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; *Bacteria/classification/genetics/isolation &amp; purification ; Aged ; Adult ; *Mouth/microbiology ; *Salivary Glands/physiopathology/microbiology ; Mouth Mucosa/microbiology ; Oral Health ; Case-Control Studies ; DNA, Bacterial/genetics ; Tongue/microbiology ; },
abstract = {This study aimed to determine if the microbiota in four different oral sites and the oral health status differ between patients with primary Sjögren's syndrome (pSS), non-pSS sicca symptoms, and healthy controls. All participants underwent an interview and clinical oral examination. Stimulated whole saliva (SWS), supragingival plaque (SGP), buccal mucosa tissue (BLM), and tongue scrape (TGS) samples from 23 pSS patients, 36 patients with sicca symptoms, not fulfilling the classification criteria for pSS (non-pSS sicca), and 21 age-matched healthy controls (HC) were analyzed using V3-V4 16S rRNA gene amplicon sequencing, and determination of amplicon sequence variants (ASVs). PSS and non-pSS sicca patients did not differ with respect to oral health status, saliva flow rates, abundance of predominant genera, relative abundance on genus level or bacterial diversity in any of the oral sites. Both patient groups differed significantly from the healthy control group in the abundance of 61 ASVs across all sites. The alpha-diversity was lower in SGP from non-pSS sicca patients (p = 0.019), and in TGS from pSS patients (p = 0.04). The proportion of variation in the beta-diversity across all four sites could be explained by the diagnosis (pSS, non-pSS sicca, and HC). However, subgrouping of patients according to their stimulated salivary flow rates (SWS > 0.7 ml/min versus SWS ≤ 0.7 ml/min), revealed significantly different abundance of three ASVs in SWS, 11 in SGP, and six in TGS. Our findings suggest that hyposalivation rather than pSS itself modifies the microbial composition in oral site-specific patterns leading to oral diseases.},
}
@article {pmid40598608,
year = {2025},
author = {Liu, F and McNally, J and Flemming, D and Ingham, AB and Hunt, PW and Li, RW},
title = {Escherichia coli is implicated in the development and manifestation of host susceptibility to the roundworm Trichostrongylus colubriformis infections in sheep.},
journal = {Veterinary research},
volume = {56},
number = {1},
pages = {133},
pmid = {40598608},
issn = {1297-9716},
support = {58-8042-3-022-F//Agricultural Research Service/ ; 242102311161//Henan Provincial Science and Technology Research Project/ ; },
mesh = {Animals ; *Sheep Diseases/parasitology/microbiology/immunology ; Sheep ; *Trichostrongylosis/veterinary/parasitology/immunology ; *Trichostrongylus/physiology ; *Escherichia coli/physiology ; *Gastrointestinal Microbiome ; Disease Susceptibility/veterinary/parasitology/microbiology ; RNA, Ribosomal, 16S/genetics/analysis ; },
abstract = {Applied breeding for host resistance to gastrointestinal nematodes represents a cost-effective strategy for parasitic control. While resistance is under moderate genetic influences, gut microbial components involved in the development of resistance or susceptibility remain largely unknown. Here we characterize the structure and metabolic potential of the proximal colon microbiota in unique ovine populations bred for resistance and susceptibility using a full-length 16S rRNA gene sequencing-based microbiome approach. The resistant lambs produced significantly fewer parasite eggs than susceptible animals grazing on the same pasture. Further, the resistant lambs displayed a significant reduction in worm establishment in response to a Trichostrongylus colubriformis challenge infection (P < 0.0001; N = 20 per group). Among 32 bacterial species or strains displaying a significant difference in relative abundance between the resistant and susceptible group, E. coli was more abundant in susceptible lambs. E. coli was also ranked as the most important species in distinguishing the resistant and susceptible status. Moreover, a microbial signature or balance consisting of E. coli (Numerator) and Parabacteroides distasonis and Bacteroides thetaiotaomicron (Denominator) predicted the resistance status with high accuracy. The metagenome function prediction also revealed that several pathways related to infectious diseases, such as Shigellosis and pathogenic E. coli infection, were significantly altered between the two phenotypes. Our findings demonstrated that microbial signatures with a high predictive power for the resistance status can be developed as biomarkers to facilitate the selection for host resistance in sheep.},
}
@article {pmid40598554,
year = {2025},
author = {Omran, MM and Emam, M and Gamaleldin, M and Abushady, AM and Elattar, MA and El-Hadidi, M},
title = {Comparative analysis of statistical and deep learning-based multi-omics integration for breast cancer subtype classification.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {709},
pmid = {40598554},
issn = {1479-5876},
support = {100010434//La Caixa/ ; },
mesh = {Humans ; *Deep Learning ; *Breast Neoplasms/genetics/classification/microbiology/pathology ; Female ; *Genomics ; Transcriptome/genetics ; Gene Expression Profiling ; Multiomics ; },
abstract = {BACKGROUND: Breast cancer (BC) is a critical cause of cancer-related death globally. The heterogeneity of BC subtypes poses challenges in understanding molecular mechanisms, early diagnosis, and disease management. Recent studies suggest that integrating multi-omics layers can significantly enhance BC subtype identification. However, evaluating different multi-omics integration methods for BC subtyping remains ambiguous.<br><br>METHODS: In this study, we conducted a multi-omics integration analysis on 960 BC patient samples, incorporating three omics layers: Host transcriptomics, epigenomics, and shotgun microbiome. We compared two integration approaches the statistical-based approach (MOFA+) and a deep learning-based approach (MOGCN) for this integration. We evaluated both methods using complementary evaluation criteria. First, we assessed the ability of selected features to discriminate between BC subtypes using both linear and nonlinear classification models. Second, we analyzed the biological relevance of the selected features to key BC pathways, focusing on transcriptomics-driven insights.<br><br>RESULTS: Our results showed that MOFA+ outperformed MOGCN in feature selection, achieving the highest F1 score (0.75) in the nonlinear classification model, with MOFA+ also identifying 121 relevant pathways compared to 100 from MOGCN. Notably, one of the key pathways Fc gamma R-mediated phagocytosis and the SNARE pathway was implicated, offering insights into immune responses and tumor progression.<br><br>CONCLUSION: These findings suggest that MOFA+ is a more effective unsupervised tool for feature selection in BC subtyping. Our study underscores the potential of multi-omics integration to improve BC subtype prediction and provides critical insights for advancing personalized medicine in BC.},
}
@article {pmid40598518,
year = {2025},
author = {Song, C and Zhang, Z and Zhu, S and Tong, H},
title = {Association between the dietary index for gut microbiota and constipation in American adults.},
journal = {Nutrition journal},
volume = {24},
number = {1},
pages = {98},
pmid = {40598518},
issn = {1475-2891},
mesh = {Humans ; *Constipation/epidemiology/microbiology ; *Gastrointestinal Microbiome/physiology ; Male ; Female ; Middle Aged ; *Diet/methods ; Adult ; United States/epidemiology ; Nutrition Surveys ; Prevalence ; Aged ; Cross-Sectional Studies ; },
abstract = {Constipation, a common gastrointestinal disorder, significantly impacts quality of life.Its association with gut microbiota has garnered attention.Dietary factors play a crucial role in the development and management of constipation.The recently introduced dietary index for gut microbiota (DI-GM), a measure of gut microbiota diversity, offers insights into this connection.The association between dietary gut microbiota index and constipation is a critical public health issue.This study investigated the association between DI-GM and constipation prevalence in the American population using data from 11,819 individuals from the National Health and Nutrition Examination Survey (NHANES) between 2005 and 2010.Constipation was defined using Bristol stool form scale types 1 and 2.Dietary recall information was used to determine the DI-GM score, indicating the dietary influence on the gut microbiome. Multivariate weighted logistic regression, adjusted for confounders, was performed to analyze the association between DI-GM scores and constipation prevalence.Further analyses included a subgroup analysis and restricted cubic splines to explore this association [restricted cubic spline(RCS)].An increased DI-GM index, indicating a healthier gut microbiome, was related to a decreased risk of constipation.A similar association was observed with a more favorable score for beneficial gut microbiota.Non-linear associations between DI-GM scores and constipation were identified through RCS analysis.Subgroup and interaction analyses confirmed the consistency of these findings across strata, suggesting no significant heterogeneity.These findings suggest that dietary adjustments may be an important method for preventing constipation.},
}
@article {pmid40598279,
year = {2025},
author = {Al-Ansari, AS and Duggan, V and Mulcahy, G and Yin, X and Brennan, L and Cotter, PD and Patel, SH and O'Donovan, CM and Crispie, F and Walshe, N},
title = {Faecal microbiota and serum metabolome association with equine metabolic syndrome in connemara ponies.},
journal = {BMC veterinary research},
volume = {21},
number = {1},
pages = {411},
pmid = {40598279},
issn = {1746-6148},
mesh = {Horses ; Animals ; *Feces/microbiology ; *Horse Diseases/microbiology/blood/metabolism ; *Metabolome ; *Metabolic Syndrome/veterinary/microbiology/blood/metabolism ; Case-Control Studies ; Male ; Female ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Gastrointestinal Microbiome ; },
abstract = {BACKGROUND: Faecal microbiome and serum metabolome have been studied in human medicine to provide a better understanding of metabolic derangements including diabetes; however, equivalent studies in equine medicine are limited. This was a case-control study conducted to identify differences in faecal microbiota composition and concurrent serum metabolite patterns between metabolically normal Connemara ponies and those with Equine Metabolic Syndrome (EMS). Thirty privately owned Connemara ponies (15 EMS and 15 controls) were included in the study. EMS was diagnosed by oral sugar test (OST). Blood samples were collected before and after an oral sugar challenge. One concurrent faecal sample was collected from each pony. Sequencing of the V3-V4 region of 16S rRNA gene was used to identify the microbial communities in faecal samples and assess the differences in microbial profiles between groups. Serum metabolites were analyzed using liquid chromatography-high-resolution mass spectrometry (LC-MS). Finally, multi-omics analysis was conducted by integration of microbiota-metabolome datasets to determine potential associations between metabolites and microbiota in EMS.<br><br>RESULTS: The faecal microbiota community composition was significantly different between EMS and control groups (p&#x2009;=&#x2009;0.04 and r[2]&#x2009;=&#x2009;4.3%). EMS ponies showed reduced species richness and evenness compared to normal ponies, however it did not reach significant difference. The EMS ponies showed an enrichment of serum metabolites belonging to triglycerides (TGs), along with a reduction of other metabolite classes. Integrative multi-omics analysis revealed two modules in the metabolome and microbiota datasets that were significantly different between the EMS and control groups (p&#x2009;<&#x2009;0.05).<br><br>CONCLUSIONS: This study suggests that concurrent faecal microbiota and serum metabolome features significantly differ between Connemara ponies with and without EMS. These results provide insights that may assist in the search for diagnostic markers associated with microbiota changes and novel preventative management methods to manipulate microbiota in horses with EMS.},
}
@article {pmid40598208,
year = {2025},
author = {Zhang, T and Zheng, Y and Chen, T and Gu, Y and Gong, Y and Wang, D and Li, Z and Du, Y and Zhang, L and Gao, J},
title = {Biomaterials mediated 3R (remove-remodel-repair) strategy: holistic management of Helicobacter pylori infection.},
journal = {Journal of nanobiotechnology},
volume = {23},
number = {1},
pages = {475},
pmid = {40598208},
issn = {1477-3155},
support = {2025QN13//First Batch of Open Topics of the Shanghai Key Laboratory of Nautical Medicine and Pharmaceutical and Medical Device Transformation/ ; 82072051//National Natural Science Foundation of China/ ; JCKFKT-MS-006//National Key Laboratory Open Project for Basic Medical Science Innovation/ ; },
mesh = {*Helicobacter Infections/therapy/drug therapy/microbiology ; Humans ; *Helicobacter pylori/drug effects ; *Biocompatible Materials/chemistry/pharmacology ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Gastrointestinal Microbiome/drug effects ; Animals ; Probiotics/therapeutic use ; Drug Delivery Systems ; Integrative Medicine ; Nanoparticles/chemistry ; },
abstract = {Helicobacter pylori (HP) is a major etiological agent of gastric cancer, with a global prevalence of around 50%. Current treatments, primarily based on antibiotics, face challenges such as increasing drug resistance and disruption of the gut microbiota. This review proposes a holistic integrative medicine (HIM) approach, guided by the 3R concept (Remove, Remodel, and Repair), to address these limitations. The 3R concept offers a novel paradigm for the integrated prevention and treatment of HP infections: Remove targets the direct eradication of HP by overcoming antibiotic resistance, Remodel focuses on reshaping the immune microenvironment to clear pathogens, and Repair emphasizes the restoration of the gastric mucosa and protection of the gut microbiota. We discuss the potential of biomaterials, including nanoparticles for targeted drug delivery and ROS generation, hydrogels for sustained release and mucosal repair, microspheres for enhanced drug loading and controlled release, and probiotics for microbiota restoration. Additionally, multimodal therapies such as phototherapy, sonodynamic therapy, and magnetic hyperthermia provide non-invasive, targeted treatments. These innovations align with HIM principles, integrating pathogen eradication with mucosal healing and microbiome protection. Future research should focus on optimizing these materials and validating their clinical applicability to improve patient outcomes and combat antibiotic resistance.},
}
@article {pmid40597688,
year = {2025},
author = {Xu, Y and Xie, R and Weng, Y and Fang, Y and Chen, H and Tao, S and Zhang, H and Ye, Y and Deng, X and Han, A and Jiang, Q and Liang, W},
title = {Unveiling the diagnostic and pro-inflammatory role of crohn's disease: insights from 16 S-guided discovery and species-specific validation.},
journal = {BMC gastroenterology},
volume = {25},
number = {1},
pages = {468},
pmid = {40597688},
issn = {1471-230X},
support = {2022Y05//the Medical Science and Technology Project of China/ ; XGY2308//the Hospital-level Project of the First Affiliated Hospital of Ningbo University/ ; 2022z2202022//the Project Key R&amp;D program of 2022 year of the Ningbo Science and Technology Bureau/ ; 2023j020//the Key Project of Ningbo Municipal Science and Technology Bureau/ ; SLB-6-20230912-351//the Population Welfare Foundation Medical Innovation Project of China/ ; },
mesh = {*Crohn Disease/microbiology/diagnosis ; Animals ; Humans ; *Gastrointestinal Microbiome ; Mice ; Male ; Female ; Feces/microbiology ; Mice, Inbred C57BL ; Adult ; *Clostridiales/genetics ; RNA, Ribosomal, 16S ; Disease Models, Animal ; Dextran Sulfate ; Case-Control Studies ; Middle Aged ; Species Specificity ; Interleukin-6 ; *Ruminococcus ; Colitis/microbiology/chemically induced ; },
abstract = {BACKGROUND: The rising incidence of Crohn's disease (CD) in Asia underscores the need to explore its underlying mechanisms. The interaction between gut microbiota and the host is strongly linked to CD onset and progression, yet the precise mechanisms remain unclear. Previous studies have demonstrated that Ruminococcus gnavus (R. gnavus) is closely associated with the development and progression of CD. Therefore, this study focuses on the inflammatory role of R. gnavus in CD pathogenesis.<br><br>METHODS: We performed comprehensive 16&#xa0;S rRNA sequencing on fecal samples from active CD patients, inactive CD patients, and healthy controls. Alongside this, we conducted clinical data and correlation analyses. To identify key microbial genera, we developed and validated a random forest classification model. Additionally, we utilized a dextran sulfate sodium (DSS)-induced colitis model in C57BL/6 mice to explore the inflammatory role of R. gnavus (ATCC 29149).<br><br>RESULTS: Our analysis revealed significant shifts in gut microbiome composition across different stages of CD compared to healthy controls. Notably, there was a marked decrease in Agathobacter and an increase in R. gnavus in patients with active CD. The random forest classification model, which was based on six specific genera (Agathobacter, Vicinamibacteraceae, Arthrobacter, Eubacterium coprostanoligenes group, Ruminococcus gnavus group, and Prevotella 9), achieved an AUC of 0.912, effectively distinguishing CD patients from healthy controls. In the DSS-induced colitis model, R. gnavus exacerbated inflammation, significantly increasing levels of IL-6 and TNF-&#x3b1;, and significantly decreasing levels of Claudin-1 and MUC2, further underscoring its critical role in CD pathogenesis.<br><br>CONCLUSION: The identified genera demonstrate potential as diagnostic biomarkers for CD, with R. gnavus playing a key role in the disease's pathogenesis by inducing inflammation in colitis models.},
}
@article {pmid40597678,
year = {2025},
author = {Park, TH and Kim, MJ and Lee, Y and Lee, JS and Lee, J and Park, HY and Shin, JH and Yang, JD},
title = {Comparative microbiome analysis of contracted breast capsules: a cross-sectional study.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {379},
pmid = {40597678},
issn = {1471-2180},
mesh = {Humans ; Female ; Cross-Sectional Studies ; *Microbiota ; *Bacteria/classification/genetics/isolation &amp; purification ; Adult ; Middle Aged ; *Breast/microbiology/pathology ; Bacterial Load ; Skin/microbiology ; RNA, Ribosomal, 16S/genetics ; Biofilms ; },
abstract = {BACKGROUND: Despite the implication of bacterial biofilms in the etiology of capsular contracture, there is limited research on the microbial structure of the contracted capsule. Moreover, the potential role of the skin microbiome in capsular contracture remains undefined. Therefore, we conducted this study to characterize the microbiome of the breast capsular contracture by comparing it with the microbiome of biopsy without capsular contracture. We also investigated the associations between the microbial structures of the skin surrounding the breast and those of the breast capsule.<br><br>RESULTS: We collected 25 capsules, including 14 samples without capsular contracture and 11 samples with capsular contracture. Beta diversity analysis demonstrated that the microbial structures in the breast capsules were distinctly different from those in the skin. The capsular microbiota was more influenced by individual variation than by the progression of the capsular contracture. Breast capsules with capsular contracture showed a higher relative abundance of Staphylococcus, correlating positively with total bacterial load.<br><br>CONCLUSIONS: Capsular contracture is associated with an escalation in total bacterial load and an increase in the abundance of opportunistic pathogens, such as Staphylococcus. This comparative analysis of contracted breast capsules emphasizes the management of pathogens, considering bacterial load, in the occurrence of capsular contracture.},
}
@article {pmid40597595,
year = {2025},
author = {McGovern, KC and Silverman, JD},
title = {Replacing normalizations with interval assumptions enhances differential expression and differential abundance analyses.},
journal = {BMC bioinformatics},
volume = {26},
number = {1},
pages = {164},
pmid = {40597595},
issn = {1471-2105},
support = {R01GM148972-01/GM/NIGMS NIH HHS/United States ; R01GM148972-01/GM/NIGMS NIH HHS/United States ; },
mesh = {*Gene Expression Profiling/methods ; Humans ; *Computational Biology/methods ; Microbiota/genetics ; Algorithms ; },
abstract = {BACKGROUND: Methods for differential expression and differential abundance analysis often rely on normalization to address sample-to-sample variation in sequencing depth. However, normalizations imply strict, unrealistic assumptions about the unmeasured scale of biological systems (e.g., microbial load or total cellular transcription). Even slight errors in these assumptions introduce bias, leading to elevated false positive and negative rates.<br><br>RESULTS: We introduce interval assumptions as a generalization of normalizations. Unlike normalizations, our interval methods allow researchers to account for potential errors in assumptions about the system scale. Interval assumptions are also customizable and allow researchers to express more biologically plausible assumptions about scale. Interval assumptions even generalize Quantitative Microbiome Profiling (QMP), allowing researchers to account for errors in flow cytometry-based measurements of total cellular concentration. We develop a novel hypothesis testing framework that allows us to integrate interval assumptions into existing tools. We develop a modified version of the popular ALDEx2 method using interval assumptions rather than normalizations. Through real and simulated data analyses, we find that interval assumptions can dramatically decrease false positive rates (i.e., from 45% to 5%) while retaining or increasing statistical power. We also study interval assumptions under misspecification and show they still improve on normalizations.<br><br>CONCLUSIONS: Interval assumptions enhance the rigor and reproducibility of differential expression and differential abundance analyses. Our results add to a growing body of literature arguing that normalizations should be replaced with alternative methods that allow researchers to account for scale uncertainty. However, compared to recent alternatives like scale models and sensitivity analyses, interval assumptions are easier to use, are more robust to misspecification, and have stronger and more interpretable inferential guarantees.},
}
@article {pmid40597564,
year = {2025},
author = {Saban Güler, M and Arslan, S and Ağagündüz, D and Cerqua, I and Pagano, E and Berni Canani, R and Capasso, R},
title = {Corrigendum to "Butyrate: A potential mediator of obesity and microbiome via different mechanisms of actions" [Food Res. Int. 199 (2025) 115420].},
journal = {Food research international (Ottawa, Ont.)},
volume = {217},
number = {},
pages = {116871},
doi = {10.1016/j.foodres.2025.116871},
pmid = {40597564},
issn = {1873-7145},
}
@article {pmid40597465,
year = {2025},
author = {Yao, T and Libera, L and Lindemann, SR},
title = {Synbiotic delivery of arabinoxylan and a human-derived arabinoxylan-fermenting consortium influence mouse gut microbiome composition, metabolism, and resilience in sex-dependent ways.},
journal = {Food research international (Ottawa, Ont.)},
volume = {217},
number = {},
pages = {116709},
doi = {10.1016/j.foodres.2025.116709},
pmid = {40597465},
issn = {1873-7145},
mesh = {*Xylans/administration &amp; dosage/metabolism/pharmacology ; Animals ; *Gastrointestinal Microbiome/drug effects/physiology ; Fermentation ; Mice ; Male ; Female ; Humans ; *Synbiotics/administration &amp; dosage ; Dietary Fiber/administration &amp; dosage ; Mice, Inbred C57BL ; Sorghum/chemistry ; },
abstract = {Dietary fibers are generally considered to have strong impacts on governing ecological dynamics in gut microbial communities and metabolites. However, the extent to which the ecological modification capabilities of complex polysaccharides are enhanced by the presence of fermenting microbial specialists remains underexplored. Our prior study demonstrated that sorghum arabinoxylan (AX), a complex fiber with diverse glycosidic linkages, could offer unique ecological niches to sustain a stable consortium of organisms in vitro. In this study, the synergistic effect of AX and its specialist consortium was investigated using murine model and emphasized on their collective effects on gut microbiome modulation, specifically in improving the resilience after the exposure to antibiotics. We hypothesized that 1) continuous fiber intake aids in the engraftment of the specialist microbes to remodel the target host gut, and 2) the combined effect of fiber administration and the delivery of fiber-specific organisms has a pronounced ecological modulatory effect, especially in restoring a functional microbiome disrupted by antibiotic treatment. We found that while the cross-host consortium engraftment achieved modest success; the presence of specialist consortium-either independently or in combination with AX-facilitated swift shifts in fecal microbiota composition. In addition, the administration of AX and the fermenting consortium in antibiotic-treated groups resulted in a more rapid recovery of murine native microbiome over the fiber treatment alone, indicating that gut function recovery may be facilitated by transitory microbiota that perform ecosystem engineering roles. Overall, strategically pairing ecological niches (complex polysaccharides) with their corresponding specialist microbes offers a practical approach to effectively modify the gut ecosystem, thereby overcoming adverse conditions, enhancing stability and resilience.},
}
@article {pmid40597447,
year = {2025},
author = {Thomas, MC and Waugh, G and Damjanovic, K and Vanwonterghem, I and Webster, NS and Negri, AP and Luter, HM},
title = {Development of a quantitative PMA-16S rRNA gene sequencing workflow for absolute abundance measurements of seawater microbial communities.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {81},
pmid = {40597447},
issn = {2524-6372},
support = {DP200100790//Australian Research Council/ ; },
abstract = {BACKGROUND: Ecological risk assessments rarely consider the impacts of environmental stress on microbial communities. Incorporating microbial community responses into these evaluations requires establishing sensitivity thresholds based on the absolute abundance of viable taxa. While essential for describing microbial community dynamics, sequencing-based analyses are typically limited to relative proportions and fail to reveal the magnitude or directionality of abundance shifts. This study presents a workflow that combines propidium monoazide (PMA) treatment and microbial load estimates with 16S rRNA gene amplicon sequencing and quantitative microbiome profiling (QMP) to assess the absolute abundance of viable taxa in seawater microbiomes.<br><br>RESULTS: Using natural seawater, microbial load estimates from droplet digital PCR (ddPCR) and flow cytometry (FC) correlated strongly for total and intact cell counts, confirming the suitability of both methods for normalising 16S rRNA gene amplicon sequencing data. We demonstrated that PMA at concentrations of 2.5&#x2013;15 &#xb5;M effectively inhibited PCR amplification of DNA from membrane-compromised cells, reducing 16S RNA gene copies by 24&#x2013;44% relative to untreated samples. Samples with known proportions of intact cells were generated by mixing heat-killed and natural seawater, enabling absolute abundance assessments by normalising 16S rRNA gene amplicon sequencing data to intact cell loads estimated via ddPCR and FC. This approach facilitated detailed comparisons of the effects of QMP versus relative microbiome profiling (RMP) on alpha and beta diversity metrics and on relative and absolute amplicon sequence variant (ASV) abundance profiles. Unlike RMP, QMP captured significant shifts in the microbial community composition across samples with decreasing proportions of intact cells. While RMP failed to detect abundance changes at ASV-level, QMP revealed consistent abundance declines.<br><br>CONCLUSION: This workflow enhanced the accuracy in representing microbial community dynamics by addressing key limitations of RMP such as the inclusion of damaged cells or extracellular DNA and the misleading proportions of identified taxa. It is particularly suited for quantifying the magnitude and direction of changes in taxa abundance following stress exposure, making it directly applicable to microbial stress-response modelling.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s40793-025-00741-2.},
}
@article {pmid40597432,
year = {2025},
author = {Ehau-Taumaunu, H and Bell, TH and Sadeghi, J and Hockett, KL},
title = {Rapid and sustained differentiation of disease-suppressive phyllosphere microbiomes in tomato following experimental microbiome selection.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {77},
pmid = {40597432},
issn = {2524-6372},
support = {492F//PA Vegetable Growers Association/ ; 1016871//National Institute of Food and Agriculture/ ; },
abstract = {BACKGROUND: Microbial-based treatments to protect plants against phytopathogens typically focus on soil-borne disease or the aboveground application of one or a few biocontrol microorganisms. However, diverse microbiomes may provide unique benefits to phytoprotection in the phyllosphere, by restricting pathogen access to niche space and/or through multiple forms of direct antagonism. We previously showed that successive experimental passaging of phyllosphere microbiomes along with the phytopathogen Pseudomonas syringae pv. tomato (Pto), which causes bacterial speck in tomato, led to the development of a disease suppressive microbial community. Here, we used amplicon sequencing to assess bacterial and fungal composition at the end of each passage, as well as shotgun metagenomics at key passages based on observed disease-suppressive phenotypes, to assess differences in functional potential between suppressive and non-suppressive communities.<br><br>RESULTS: Bacterial composition changed and diversity declined quickly due to passaging and remained low, particularly in treatments with Pto present, whereas fungal diversity did not. Pseudomonas and Xanthomonas populations were particularily enriched in disease-suppressive microbiomes compared to conducive microbiomes. The relative abundance of Pseudomonas syringae group gemonosp. 3 (the clade to which the introduced pathogen belongs) in shotgun metagenomic data was similar to what we observed for Pseudomonas ASVs in the 16S rRNA gene dataset. We also observed an increase in the abundance of genes associated with microbial antagonism at Passage 4, corresponding to the highest observed disease severity.<br><br>CONCLUSIONS: Taxonomic richness and evenness were low within samples, with clustering occurring for suppressive or non-suppressive microbiomes. The relative abundance of genes associated with antagonism was higher for disease-suppressive phyllosphere microbiomes. This work is an important step towards understanding the microbe-microbe interactions within disease-suppressive phyllosphere communities.},
}
@article {pmid40597414,
year = {2025},
author = {Kadyan, S and Park, G and Singh, TP and Patoine, C and Singar, S and Heise, T and Domeier, C and Ray, C and Kumar, M and Behare, PV and Chakrabarty, P and Efron, P and Sheffler, J and Nagpal, R},
title = {Microbiome-based therapeutics towards healthier aging and longevity.},
journal = {Genome medicine},
volume = {17},
number = {1},
pages = {75},
pmid = {40597414},
issn = {1756-994X},
mesh = {Humans ; *Longevity ; *Gastrointestinal Microbiome ; *Healthy Aging ; *Aging ; *Microbiota ; Animals ; },
abstract = {The gut microbiome is our lifetime companion, regulating our health from birth throughout the lifespan. The gut microbiome composition changes continually with age, influencing both physiological and immunological development. Emerging evidence highlights the close association, and thus implication, of the microbiome with healthy disease-free aging and longevity. Accordingly, targeting the gut microbiome is emerging as a promising avenue to prevent, alleviate, and ameliorate aging-related disorders. Herein, we provide a prospective and inclusive framework of the close connection of the gut microbiome with human aging, while contemplating how this association is intertwined with age-related diseases. We delve into recently emerging and potential microbiome-based therapeutics that are projected to aid in alleviating myriad aging-related diseases, thereby enhancing the health and well-being of the aging population. Finally, we present a foundation and perspective underlining the prospects of microbiome-based therapeutics developed and tailored precisely for the elderly, with the overarching goal of promoting health and longevity.},
}
@article {pmid40597409,
year = {2025},
author = {Neidhöfer, C and Neuenhoff, M and Sib, E and Rehm, A and Dias, LR and Neumann, B and Steinmann, J and Döhla, M and Kherabi, Y and Budimir, A and Hajjar, C and Khatib, R and Axtmann, K and Schwab, K and Brossart, P and Engelhart, S and Mutters, NT and Bierbaum, G and Janssen, S and Parčina, M},
title = {Multicenter exploration of microbial communities in hospital toilets reveals: antibiotic exposure in a nosocomial settings selects for coEnterococcus over commensal taxa.},
journal = {Antimicrobial resistance and infection control},
volume = {14},
number = {1},
pages = {78},
pmid = {40597409},
issn = {2047-2994},
mesh = {Humans ; Cross-Sectional Studies ; *Anti-Bacterial Agents/pharmacology ; *Cross Infection/microbiology ; *Toilet Facilities ; *Microbiota/drug effects ; *Bacteria/drug effects/classification/genetics/isolation &amp; purification ; Hospitals ; RNA, Ribosomal, 16S/genetics ; Drug Resistance, Multiple, Bacterial ; },
abstract = {BACKGROUND: Excessive antibiotic utilization in hospital settings catalyzes the emergence and dissemination of multidrug resistant (MDR) bacteria, with sanitary facilities serving as critical vectors for their propagation. This study investigated the impact of patient antibiotic exposure on microbial diversity in hospital sanitary facilities, as well as the emergence of uniform communities and prospering taxa under antibiotic pressure.<br><br>METHODS: For this purpose a cross-sectional study was conducted between September 2022 and April 2023 from eight hospitals in seven cities across five countries, representing a diverse mix of tertiary care, military, oncological, psychiatric, and general teaching hospitals to analyze bacterial population differences in hospital toilets on wards with high versus minimal antibiotic administration using 16s rRNA amplicon sequencing.<br><br>RESULTS: PCoA analysis with Bray-Curtis and unweighted UniFrac metrics revealed microbial clustering influenced by antibiotic exposure and geography. Among all taxa analyzed, Enterococcus showed the strongest and most consistent association with high-exposure environments, making it one of the most striking findings in our dataset.<br><br>CONCLUSION: Routine overuse of antimicrobial agents aimed at false patient safety promotes a high-risk environment in the sanitary facilities of respective wards. Hence, the issue of hospital acquired infections with MDR pathogens transcends mere pathogen spread, entailing significant changes to both environmental and microbial landscapes over time. The situation signals an emerging ecological problem within healthcare environments, and highlights the urgency for an integrated approach to antimicrobial stewardship. The low detection of key nosocomial Gram-negative genera likely reflects the focus on toilets rather than sinks or showers.},
}
@article {pmid40597405,
year = {2025},
author = {Yao, R and Hulshof, TG and van Hees, HMJ and Cools, A and Merckx, M and Maes, D and Janssens, GPJ},
title = {Grass hay mixed-in creep feed or separately-fed differentially affects digestive development in pre- and post-weaning piglets.},
journal = {Journal of animal science and biotechnology},
volume = {16},
number = {1},
pages = {92},
pmid = {40597405},
issn = {1674-9782},
abstract = {BACKGROUND: Based on observations in feral pigs, the role of dietary fibre and structure may be underestimated in suckling piglet nutrition. This study investigated the effect of grass hay offered to suckling piglets either separately or included in their creep feed, combined with nursery diets with or without grass pellet inclusion on growth performance and gastrointestinal development.<br><br>METHODS: Thirty-six litters (14-15 piglets per litter) were divided into three equal groups of 12 litters per treatment during the suckling phase: control group (CON) received regular creep feed; GH group received chopped grass hay as-is in separate feeders alongside regular creep feed; PGH group received regular creep feed but barley and wheat were replaced by 28% grass pellets. After weaning (d 23), each litter was split into two dietary treatments in a split-plot design (pre-wean treatment as main plot). Two of the pre-wean diets were also offered until d 14 post-weaning, i.e., CON (CON nursery diet, CON-C, GH-C, PGH-C) and PGH (GH nursery diet, CON-GH, GH-GH, PGH-GH). Thereafter, transitioning to a diet containing 13% wheat/barley or grass pellets, respectively, until d&#xa0;39 post-weaning. Gastrointestinal morphology, gene expression of intestinal nutrient transporters and barrier proteins, metabolite profile and microbiota were assessed on the day before weaning, d&#xa0;10 and d&#xa0;38 post-weaning. A total of 24 piglets were sacrificed at each dissection point.<br><br>RESULTS: At weaning, GH group had consumed 7&#xa0;g/piglet grass hay, and PGH group had consumed 46&#xa0;g/piglet creep feed. One day before weaning, GH piglets showed heavier emptied small intestine (P&#x2009;=&#x2009;0.044) and colon (P&#x2009;=&#x2009;0.065), higher SCFA production in proximal segments and lower SCFA production in colon (P&#x2009;<&#x2009;0.05). Higher abundance of Prevotellaceae NK3b31 group was observed in caecal and colonic content of PGH compared to GH group (P&#x2009;<&#x2009;0.05), and PGH group showed a lower energy conversion ratio (net energy intake/gain, P&#x2009;=&#x2009;0.035). Following weaning, GH nursery group had a reduced average daily gain (226 vs. 183&#xa0;g, P&#x2009;<&#x2009;0.001) during d 0-14, while this group showed compensatory growth afterwards (P&#x2009;=&#x2009;0.056). Main plot effects on increased expressions of CLDN3 and FFAR2 were observed in GH and PGH by d&#xa0;38 post-weaning (P&#x2009;<&#x2009;0.05). An interaction effect showed greater luminal abundance of the Prevotellaceae NK3b31 group in GH-GH and PGH-GH groups compared to CON-GH on d&#xa0;38. The GH nursery diet showed a better energy conversion ratio (P&#x2009;=&#x2009;0.006) with no influence on body weight and their SCFA production shifted towards proximal segments.<br><br>CONCLUSION: In conclusion, feeding a structured and fibre-rich diet to suckling piglets enhance their digestive tract development and adapt their microbiome to fibre digestion in later life. Maintaining a fibre-rich diet from suckling to nursery is recommended, though this come with a transient reduction in weight gain caused by lower feed intake that, however, can be recovered afterwards accompanied with an optimized energy conversion ratio.},
}
@article {pmid40597335,
year = {2025},
author = {Drake, MJ and Pierdon, M and DeMers, G and Daniel, SG and Bittinger, K and Redding, LE},
title = {The effect of dietary zinc on the microbiome and resistome of the gestating sow and neonatal piglets.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {71},
pmid = {40597335},
issn = {2524-4671},
abstract = {Zinc is an important trace element for animal health and physiology, and it is routinely provided as a supplement in livestock diets. High levels of dietary zinc have been found to be beneficial for weanling pigs in preventing diarrhea and improving growth. It has also been associated with better reproductive performance in gestating sows and survival of neonatal piglets. However, little is known about zinc's effect on the microbiome of the gestating sow and her neonatal piglets. Even less is known about its effects on the sow and piglet resistome, which is important because dietary zinc can co-select for antimicrobial resistance. The goal of this randomized controlled dietary feeding trial was to assess the effect of high levels of dietary zinc in the last week of gestation on the microbiomes and resistomes of the gestating sow and her neonatal piglets. Seventy-three gestating sows were randomized to receive a diet with standard zinc levels (125 ppm) or high zinc levels (2500 ppm) approximately one week prior to their anticipated farrowing date. Fecal samples were collected from sows at enrollment and at farrowing and from piglets within 3 days of parturition. Fecal samples underwent 16sS rRNA gene sequencing, and a subset of samples underwent shotgun metagenomic sequencing. Statistically significant differences in richness, diversity and taxonomic composition were observed over time, and sows in the treatment group had significantly higher alpha diversity at farrowing (p = 0.04) and significantly altered levels of 3 taxa (Turicibacter, unclassified Clostridiaceae, and unclassified Christensenellaceae). Several antimicrobial resistance genes were significantly more abundant in the zinc group at farrowing compared to the control group, including tetracycline resistance genes [tet(O); tet(W); tet(32); tet(O/W)]; aminoglycoside resistance genes (APH(3')-IIIa), macrolide-lincosamide-streptogramin (MLS) resistance genes (lsaB; macB); and others (kdpE, Pseudomonas aeruginosa CpxR). No significant differences were observed in the piglet microbiomes or resistomes across sow treatment groups. Overall, high levels of dietary zinc had modest effects on the sow microbiome during the feeding trial. Increases in antimicrobial resistance genes in zinc supplemented sows suggest that supranutritional levels of dietary zinc should be avoided in gestating sows.},
}
@article {pmid40597298,
year = {2025},
author = {Bao, XW and Wang, QH and Li, T and Li, Y and Bian, ZY and Liu, SJ and He, LY and Niu, SQ and Guo, JL},
title = {Ophiocordyceps sinensis-induced changes in Thitarodes xiaojinensis: from intestinal barrier destruction, microbiome dysbiosis to immune responses at the molecular level.},
journal = {BMC biology},
volume = {23},
number = {1},
pages = {183},
pmid = {40597298},
issn = {1741-7007},
support = {2023M730381//China Postdoctoral Science Foundatio/ ; 2024NSFSC0052, 2024NSFSC1832//The Natural Sciences Foundation of Sichuan Province/ ; 2024NSFSC0052, 2024NSFSC1832//The Natural Sciences Foundation of Sichuan Province/ ; 82373998, 81872959, 81373920//National Natural Sciences Foundation of China/ ; },
mesh = {Animals ; *Hypocreales/physiology ; Hemolymph/microbiology/immunology ; *Host-Pathogen Interactions/immunology ; *Dysbiosis/microbiology/immunology ; *Moths/microbiology/immunology ; *Gastrointestinal Microbiome ; Intestines/microbiology ; },
abstract = {BACKGROUND: The entomopathogenic fungus (EPF) Ophiocordyceps sinensis has a long-term coexistence with its host insect, Thitarodes xiaojinensis, making it a unique model for host-pathogen interactions. Hemolymph, a critical component in insects, plays an essential role in maintaining both nutritional and immune homeostasis. However, the mechanism of the host's immune response remains unclear when O. sinensis proliferates in the hemolymph.<br><br>RESULTS: O. sinensis caused damage to the insect's intestinal barrier, facilitating the translocation of gut bacteria into the hemocoel. Subsequently, the presence of O. sinensis and opportunistic pathogenic bacteria from the gut disrupted the homeostasis of the hemolymph microbiota, resulting in an increase in bacterial diversity. This disruption triggered a series of physiological responses in the host, including elevated levels of endocrine hormones specifically 20-hydroxyecdysone (20E) and juvenile hormone 3 (JH3). Additionally, there was an enhancement of antioxidant capacity, as indicated by increased total antioxidant capacity and glutathione S-transferase activity, along with the production of antimicrobial peptides (AMPs) as part of the immune defense. Notably, the rise in 20E levels during O. sinensis infection might have significantly contributed to the increased production of AMPs.<br><br>CONCLUSIONS: O. sinensis infection significantly alters T. xiaojinensis physiology. Humoral immunity in infected hosts is primarily in response to hemolymph microbial homeostasis due to intestinal translocation. Among them, 20E upregulates AMP-related genes, suggesting a key immune strategy for managing microbial imbalances while tolerating fungal pathogens.},
}
@article {pmid40597096,
year = {2025},
author = {Hong, S and Lim, MY and Chung, WH and Shin, JH and Nam, YD},
title = {Deciphering gut microbiome patterns from host preferences and microbial interactions in healthy Korean individuals.},
journal = {BMC biology},
volume = {23},
number = {1},
pages = {185},
pmid = {40597096},
issn = {1741-7007},
support = {E0170600-08//Korea Food Research Institute/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; Republic of Korea ; Adult ; Male ; *Microbial Interactions ; Female ; Middle Aged ; Young Adult ; Bacteria/classification/genetics ; },
abstract = {BACKGROUND: The gut microbiome is crucial for human health maintenance and disease development, yet limited understanding of its structure and maintenance hinders effective microbiome-based health improvement strategies. We investigated gut microbiome compositional patterns in healthy Koreans (n = 890), identifying six clusters (I-VI) with unique compositions and host preferences.<br><br>RESULTS: Each cluster had a distinct topological structure within the microbial interaction network, underscoring its diverse roles in maintaining microbial communities. Cluster II, predominated by Bacteroides and Faecalibacterium, was consistently found across individuals and centrally located within the microbial interaction network. Cluster III, mainly composed of Oscillospira and Coprococcus, and IV, dominated by Enterobacteriaceae and Bacteroides fragilis, demonstrated mutually exclusive relationships, reflecting affinities for host clusters with varied dietary patterns and microbial diversity. Clusters V and VI linked different microbial clusters, and cluster I had separate subcommunities.<br><br>CONCLUSIONS: This study reveals intricate structures and interactions within microbial communities, offering insights into the gut microbiome ecology and guiding health enhancement strategies.},
}
@article {pmid40596914,
year = {2025},
author = {Lin, Y and Wang, FT and Xia, K and Gao, RY and Jiao, YR and Fang, M and Chen, CQ},
title = {Impact of terminal ileal microbiota dysbiosis and tryptophan metabolism alterations on mental disorders in patients with Crohn's disease.},
journal = {BMC gastroenterology},
volume = {25},
number = {1},
pages = {473},
doi = {10.1186/s12876-025-04007-6},
pmid = {40596914},
issn = {1471-230X},
support = {82470555//National Natural Science Foundation of China/ ; 82470555//National Natural Science Foundation of China/ ; 82470555//National Natural Science Foundation of China/ ; 82470555//National Natural Science Foundation of China/ ; 82470555//National Natural Science Foundation of China/ ; 82470555//National Natural Science Foundation of China/ ; 82470555//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Crohn Disease/microbiology/psychology/metabolism/complications ; *Tryptophan/metabolism ; Female ; Male ; *Dysbiosis/microbiology/metabolism/complications ; *Gastrointestinal Microbiome ; Adult ; *Ileum/microbiology/metabolism ; Middle Aged ; *Mental Disorders/microbiology/metabolism/etiology ; Intestinal Mucosa/microbiology/metabolism ; Case-Control Studies ; Brain-Gut Axis ; },
abstract = {BACKGROUND: Crohn's disease (CD) is a chronic non-specific inflammatory bowel disease with an increasing incidence worldwide. Patients with CD are facing elevated risk for mental disorders (MD) than healthy people, and chronic psychological stress is considered to trigger deterioration and relapse of CD. The microbiome-gut-brain axis (MGBA) is recognized as a crucial factor in unraveling this connection. Whereas, so far, few studies have revealed the relationship of the microbiota communities and tryptophan catabolites of the terminal ileum mucosa on gut-brain communication.<br><br>MATERIALS AND METHODS: A total of 52 patients with CD, along with 11 patients with colorectal cancers recruited as controls, were enrolled in this study. The participants completed Patient Health Questionnaire-9 and Generalized Anxiety Disorder-7 Questionnaire. The terminal ileal mucosa was collected during surgery. We profiled the microbiota composition of 37 patients and quantified the tryptophan catabolites of 28 patients utilizing 16&#xa0;S rRNA gene sequencing and liquid chromatography-tandem mass spectrometry, respectively. In addition, bioinformatics methods were used to elucidate the interrelationships between psychological states, microbial communities, and tryptophan catabolites.<br><br>RESULTS: CD patients with MD showed a significant reduction in microbial diversity within the ileal mucosa. Regarding microbial composition, Prevotella was relatively enriched in CD patients with MD, along with lower relative abundances of Akkermansia and Faecalibacterium. Furthermore, significant disparities in the levels of Picolinic acid (PA), Kynurenic acid (KYNA), Nicotinic acid (N-Acid), and Indole-3-carbaldehyde (ICAld) were detected within the ileal mucosa of CD patients comorbid with MD. A pronounced correlation was observed between PA levels and anxiety scale scores. The heightened abundance of Prevotella may be closely associated with altered levels of PA, N-Acid, and KYNA.<br><br>CONCLUSION: Alterations in the microbial composition of the terminal ileum may interact with changes in tryptophan metabolism and are associated with MD in patients with CD undergoing surgery.},
}
@article {pmid40596862,
year = {2025},
author = {Gemeda, MT and Meka, AF and Mamo, AN and Bekele, GK and Ali, J and Abas, MK},
title = {Diversity of antibiotic resistance genes and mobile genetic elements of Sof Umer Cave microbiomes, Ethiopia.},
journal = {BMC genomic data},
volume = {26},
number = {1},
pages = {41},
pmid = {40596862},
issn = {2730-6844},
mesh = {*Microbiota/genetics ; *Interspersed Repetitive Sequences ; Ethiopia ; *Caves/microbiology ; *Drug Resistance, Bacterial/genetics ; *Bacteria/genetics/drug effects ; *Drug Resistance, Microbial/genetics ; Genetic Variation ; Anti-Bacterial Agents/pharmacology ; *Genes, Bacterial ; },
abstract = {Antibiotic resistance is a major global health concern that caused by the overuse and misuse of antibiotics. Mobile genetic elements have a roles in the transmission of antibiotic resistance genes. The distribution and diversity of antibiotic resistance genes and mobile genetic elements in the microbiome of Sof Umer Cave have yet to be explored. To map the distribution and diversity of antibiotic resistance genes and mobile genetic elements in the microbiome of Sof Umer Cave using high-throughput shotgun sequencing. High-molecular-weight DNA was extracted from homogenized sample using the GeneAll DNA Soil Mini Kit. Purified environmental DNA was sequenced using a NovaSeq PE150. Analysis of the pathogen host interaction database revealed the predominance of pathogenic organisms such as Xanthomonas oryzae, Acinetobacter baumannii, Erwinia amylovora, and Mycobacterium tuberculosis. Similarly, analysis of the virulence factor database confirmed the presence of Type IV pili (VF1240), lipopolysaccharides, capsules, heme biosynthesis (VF0758), and alginate. More than 800 antibiotic resistance genes were identified, with 50% related to glycopeptide resistance, followed by antibiotic resistance genes associated with multidrug efflux pumps (30%), aminoglycoside resistance genes (10%), and unknown genes. A variety of mobile genetic elements were also identified, highlighting their importance in the genetic diversity and adaptation of the microbiome of Sof Umer Cave. These findings underscore the importance of the Sof Umer Cave habitat as a reservoir for antibiotic resistance, emphasizing the need for ongoing monitoring to enhance the understanding and control of antibiotic resistance genes.},
}
@article {pmid40596781,
year = {2025},
author = {Zhao, T and Vink, SN and Jia, X and Erban, A and Schaarschmidt, S and Kopka, J and Zuther, E and Treder, K and Michałowska, D and Guyoneaud, R and Elzenga, JTM and Attard, E and Salles, JF},
title = {Unveiling Potato Cultivars With Microbiome Interactive Traits for Sustainable Agricultural Production.},
journal = {Plant, cell &amp; environment},
volume = {},
number = {},
pages = {},
doi = {10.1111/pce.70019},
pmid = {40596781},
issn = {1365-3040},
support = {//This study was funded by ERA-NET Cofund SusCrop project potatoMETAbiome, which is supported by the European Union's Horizon 2020 research and innovation program (grant agreement No 771134; French National Agency, grant number -ANR-18-SUSC-0001) and part of the Joint Programming Initiative on Agriculture, Food Security and Climate Change (FACCE-JPI)./ ; },
abstract = {Root traits significantly shape rhizosphere microbiomes, yet their interaction with microbes is often overlooked in plant breeding programs. Here, we propose that selecting modern cultivars based on microbiome interactive trait (MIT), such as root biomass, exudate patterns and the rhizosphere microbiome, can enhance agricultural sustainability by interacting effectively with soil microbiomes, which in turn, promotes plant growth and resistance to stress, thereby reducing reliance on synthetic crop protectants. Through a stepwise selection process (in silico and in vitro) that started with approximately 1000 potato genotypes, we chose 51 potato cultivars based on known phenotypical properties and distinct root exudate patterns. We conducted a greenhouse experiment to evaluate their capacity to interact with the soil microbiome and to assess their MIT scores. Our findings revealed that cultivars significantly influence plant growth, metabolite profiles, and rhizosphere fungal community composition. Moreover, we observed a positive correlation between microbial community diversity and root biomass. Additionally, leaf metabolites were correlated with rhizosphere bacterial composition, supporting the plant holobiont framework. Utilising z-scores, we aggregated all data related to plant growth, metabolomes, and microbiomes, creating a classification of 51 cultivars based on a gradient of MIT scores. By examining the distribution of low, intermediate, and high MIT, we identified a group of 11 potato cultivars suitable for further studies to assess their resilience and productivity under low-input production systems. This study provides an in-depth correlation between microbiome and several plant traits across 51 cultivars, offering tools to facilitate and expedite the incorporation of microbiome traits into breeding goals to support sustainable agriculture.},
}
@article {pmid40596614,
year = {2025},
author = {Lin, Z and Luo, H and Pan, S and Li, Y and Zhou, X and Zhao, J and Xu, X and Li, X and Wang, Y and Lv, G and Lin, Z and Lin, H and Qi, W},
title = {Effects of Paeoniae Radix Rubra on lowering lipid via bioinformatics and gut microbiome.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {21117},
pmid = {40596614},
issn = {2045-2322},
support = {20230204006YY//Jilin Province Science and Technology Development Program/ ; },
mesh = {*Gastrointestinal Microbiome/drug effects ; *Paeonia/chemistry ; Animals ; Computational Biology/methods ; *Hyperlipidemias/drug therapy/metabolism ; Male ; Mice ; Molecular Docking Simulation ; Diet, High-Fat/adverse effects ; *Lipid Metabolism/drug effects ; *Hypolipidemic Agents/pharmacology/chemistry ; *Drugs, Chinese Herbal/pharmacology/chemistry ; Lipids/blood ; *Plant Extracts/pharmacology/chemistry ; },
abstract = {Hyperlipidemia, a metabolic disorder characterized by abnormal lipid levels, is closely linked to an increased risk of cardiovascular disease. In this study, we investigated the hypolipidemic properties of Paeoniae Radix Rubra and its regulatory effects on gut microbiota composition in a high-fat diet model. Using UHPLC-QE-MS/MS, we identified its chemical constituents and applied bioinformatics, network pharmacology, and molecular docking to virtually screen for bioactive compounds and molecular targets. Gelomulide N and (E)-5-[(1 S,4aR,8aR)-2-formyl-5,5,8a-trimethyl-1,4,4a,6,7,8-hexahydronaphthalen-1-yl]-3-(acetoxymethyl)pent-2-enoic acid were identified as potential active compounds. Paeoniae Radix Rubra exhibited notable hypolipidemic, hepatoprotective, and gut microbiota-restoring effects, potentially influencing the mevalonate pathway by interacting with proteins such as P53, HMGCR, and SREBP2, which may contribute to reduced cholesterol synthesis. These findings indicate that the Paeoniae Radix Rubra could serve as a potential therapeutic strategy for hyperlipidemia, possibly mediated through modulation of lipid metabolism pathways and gut microbiota remodeling.},
}
@article {pmid40596567,
year = {2025},
author = {Bianchi, P and Jacques, C and Theunis, J and Jamin, EL and Orlandi, C and Cauhape, L and Alvarez-Georges, S and Alves, A and Simcic-Mori, A and Lauze, C and Gravier, E and Carballido, F and Ribet, V and Bessou-Touya, S and Duplan, H},
title = {Clinical profiling of skin microbiome and metabolome during re-epithelialization.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {22282},
pmid = {40596567},
issn = {2045-2322},
mesh = {Humans ; *Microbiota ; *Skin/microbiology/metabolism ; *Metabolome ; Male ; Female ; Adult ; *Re-Epithelialization ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Wound Healing ; Metabolomics/methods ; Bacteria/genetics/classification ; Skin Microbiome ; },
abstract = {We investigated changes in skin microbiome and metabolome linked to wound healing and how these are affected by a formula known to improve re-epithelialization. In a clinical study with 21 subjects, forearm lesions were induced by epidermal laser ablation. The areas were left untreated or treated with the formula. Re-epithelialization was monitored for 18 days. Skin swabs were analyzed for microbiome diversity using 16 S rRNA gene sequence analysis. Selected species analyzed using digital droplet polymerase chain reaction. Metabolomic profiles were analyzed by ultra-high performance liquid chromatography-high-resolution mass spectrometry. Microbiota alpha-diversity (richness and evenness) was markedly reduced by laser ablation and returned to pre-ablation levels on Day 5. Formula application accelerated the re-epithelialization time (RT), which was more efficient for slow healing (RTs of 15-19 days) than quick healing (10-12 day RTs) subjects. The repairing effect was associated with greater microbiota diversity and species-specific growth of commensal bacteria. Levels of several metabolites on untreated skin at the RT and the extent of the impact of the formula were different in slow and quick healers. The formula significantly modified the skin metabolome, whereby metabolites involved in promoting wound healing were increased and metabolites consumed by the commensal bacteria were decreased.},
}
@article {pmid40596535,
year = {2025},
author = {Zennami, K and Nukaya, T and Ishikawa, K and Tomozawa, S and Kawai, A and Nakamura, W and Muto, Y and Saruta, M and Motonaga, T and Takenaka, M and Takahara, K and Kusaka, M and Sumitomo, M and Shiroki, R},
title = {Exposure to ileal feces with frailty-associated dysbiosis elevates gastrointestinal complication risk after intracorporeal urinary diversion.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {22333},
pmid = {40596535},
issn = {2045-2322},
mesh = {Humans ; *Dysbiosis/microbiology/complications ; Male ; Female ; *Urinary Diversion/adverse effects ; Aged ; *Feces/microbiology ; Middle Aged ; *Postoperative Complications/etiology/microbiology ; *Ileum/microbiology ; *Frailty/complications/microbiology ; *Gastrointestinal Diseases/etiology/microbiology ; Gastrointestinal Microbiome ; Urinary Bladder Neoplasms/surgery ; Risk Factors ; Aged, 80 and over ; Antibiotic Prophylaxis ; },
abstract = {The composition of the distal ileum microbiota and the impact of fecal exposure during intracorporeal urinary diversion (ICUD) on gastrointestinal (GI) complications remain unclear. This study included 146 patients with bladder cancer who underwent ICUD without bowel preparation and received only a single day of antibiotic prophylaxis. Fecal samples were collected directly from the distal ileum during surgery, and ascitic fluid was obtained postoperatively from abdominal drains. Among the patients, 129 (88.3%) had minimal microbial growth in ileal feces, while 17 (11.7%) showed significant colonization. The most commonly identified organisms were Streptococcus, Enterococcus, Enterobacter, Klebsiella, and Candida. The incidence of GI complications was significantly higher in patients with positive ileal fecal cultures compared to those with no detectable growth (39.4% vs. 7.7%, P < 0.001), and even more pronounced in patients with positive ascitic cultures (72.5% vs. 11.3%, P < 0.001). Multivariate analysis identified positive ascitic cultures as an independent predictor of GI complications. Additionally, frailty was significantly associated with the presence of microbial growth in ascitic fluid. These findings suggest that, although the distal ileal microbiota is largely suppressed under short-term antibiotic prophylaxis, the presence of intra-abdominal bacteria or fungi is strongly linked to postoperative GI complications, including ileus. Frailty may contribute to microbial dysbiosis and the persistence of intra-abdominal pathogens, particularly Enterococcus and Enterobacter species.},
}
@article {pmid40596493,
year = {2025},
author = {He, Y and Li, L and Li, Y and Wang, X and Qian, L and Yang, J and Jiang, M},
title = {Mendelian randomization study reveals causal association between skin microbiome and skin cancers.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {21590},
pmid = {40596493},
issn = {2045-2322},
mesh = {Humans ; *Skin Neoplasms/microbiology/genetics ; *Mendelian Randomization Analysis ; *Microbiota/genetics ; *Skin/microbiology ; Genome-Wide Association Study ; Polymorphism, Single Nucleotide ; Carcinoma, Squamous Cell/microbiology/genetics ; Melanoma/microbiology/genetics ; Carcinoma, Basal Cell/microbiology/genetics ; Keratosis, Actinic/microbiology/genetics ; Skin Microbiome ; },
abstract = {Increasing evidence indicates a link between the skin microbiome and different types of skin cancer, but it is still uncertain if this connection is causal. This study aimed to investigate the causal relationship between genetically predicted skin microbiome and skin cancer, including basal cell carcinoma (BCC), cutaneous squamous cell carcinoma (CSCC), cutaneous melanoma (CM), and actinic keratosis (AK). A two-sample Mendelian randomization (MR) analysis was conducted using summary datasets of public genome-wide association study (GWAS) statistics. Multiple methods, including inverse variance weighted (IVW), MR-Egger, weighted median, weighted mode, and robust adjusted profile score (RAPS), were applied. Sensitivity analyses were performed to assess the robustness of the results, and a reverse MR analysis was conducted to evaluate potential reverse causality. A total of 1224 SNPs were selected as instrumental variables (IVs) for 78 genus-level skin microbes. Six genus-level skin microbes exhibited suggestive associations with skin cancer. Sensitivity and horizontal pleiotropy analyses confirmed the robustness of these relationships. Reverse MR analysis showed no evidence of reverse causality between the identified skin microbiota taxa and skin cancers. This study identifies potential causal relationships between skin microbiota and four skin cancers. Additional studies are needed to confirm these results and elucidate the underlying mechanisms.},
}
@article {pmid40596352,
year = {2025},
author = {Barriga-Medina, N and Decker, T and Ramirez-Villacis, DX and León-Reyes, AE and Dong, V and Worley, C and Ruales, C and Pieterse, C and Leon-Reyes, A},
title = {Exploring fungal pathogens to control the plant invasive Rubus niveus on Galapagos Island San Cristobal.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {20358},
pmid = {40596352},
issn = {2045-2322},
support = {POA 010//Galapagos Science Center/ ; 001//SPINOZA GRANT/ ; 007//Caja Chica Grant/ ; },
mesh = {*Rubus/microbiology ; *Introduced Species ; *Plant Diseases/microbiology/prevention &amp; control ; *Fungi/pathogenicity/genetics/isolation &amp; purification/classification ; Ecuador ; Plant Leaves/microbiology ; Fruit/microbiology ; },
abstract = {The Galapagos ecosystem faces threats from invasive species displacing native and endemic species. Rubus niveus (Hill raspberry) is particularly problematic invasive plant, covering approximately 30,000 hectares across the archipelago and rapidly outcompeting native vegetation. Current control methods, such as manual removal and herbicide application, have proven ineffective. This research aimed to identify endemic fungi pathogenic to R. niveus for potential population suppression. To achieve this goal, we sampled leaves, fruits, and stems of R. niveus in the agricultural areas of San Cristobal, Galapagos. Microbiome composition analysis of healthy and diseased R. niveus leaves revealed differences in fungal communities, representing a greater abundance of pathogenic genera in diseased tissue. These genera included Alternaria, Septoria, Fusarium, Colletotrichum, and Phanerochaete, representing well-known pathogens. Among 595 fungi isolated from Hill raspberry samples with lesions, 226 were tested for pathogenicity on healthy Hill raspberry leaves, resulting in five possible candidates consistently causing lesions. Further characterization through morphology and DNA analysis confirmed these candidates as Lasiodiplodia theobromae, Colletotrichum gloesporioides, Fusarium concentricum, Phanerochaete chrysosporium, and Penicillium rolfsii. Future research will explore the suitability of these fungal pathogens as biocontrol agents of invasive Hill rapberry.},
}
@article {pmid40596264,
year = {2025},
author = {Li, X and Zuo, S and Li, M and Li, Q and Su, L},
title = {Novel gut bacteria species Paenibacillus ilasis with phosphorus degrading and soluble starch hydrolysis abilities isolated from fresh feces of rhinoceros.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {21750},
pmid = {40596264},
issn = {2045-2322},
support = {2024ZD0407903//Biological Breeding- National Science and Technology Major Project/ ; Grant No. 2424003//China Agricultural University Young Talent Program in Life Science/ ; 2021YFF0702900//National Key Research and Development Program of China/ ; 2021-I2M-1-039//CAMS initiative for Innovative Medicine of China/ ; },
mesh = {*Paenibacillus/isolation &amp; purification/genetics/metabolism/classification ; Animals ; *Gastrointestinal Microbiome ; *Feces/microbiology ; *Perissodactyla/microbiology ; Phylogeny ; Hydrolysis ; RNA, Ribosomal, 16S/genetics ; *Starch/metabolism ; *Phosphorus/metabolism ; },
abstract = {The genus Paenibacillus, known for its diverse sources, is a valuable reservoir of antimicrobial compounds, enzymes and other valuable chemicals, with applications in medicine, agriculture, and bioremediation. Despite this, Paenibacillus strains, particularly those isolated from unique environments, remain underexplored, limiting our understanding of their potential, capabilities and taxonomic classifications. The gut microbiome of large herbivores, such as rhinoceroses, harbors underexplored microbial diversity with unique metabolic capabilities. In this study, a Gram-stain-negative, facultatively aerobic, motile, spore-forming, rod-shaped bacterial strain, NGMCC 1.200843[T] (= CGMCC 1.64763[T] = JCM 37214[T]), was isolated from fresh rhinoceros feces and characterized its taxonomic status and metabolic potential. Phylogenetic, phenotypic, and chemotaxonomic analyses confirmed the isolate as a novel species within the genus Paenibacillus, closely related to Paenibacillus lautus DSM 3035[T] (98.62% 16S rRNA gene similarity). The average nucleotide identity (ANI) and the digital DNA-DNA hybridization values were below the threshold for species delineation. The major cellular fatty acids were anteiso-C15:0, C16:0 and iso-C16:0 (> 10%) and the polar lipid profile contained diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phosphatidylethanolamine (PE), two unidentified phospholipids (PL1-2) and one phosphatidyl choline (PC). The total DNA G + C content was 49.69 mol%. The isolate exhibited significant phosphate solubilization and starch hydrolysis activities in plate assays, suggesting a role in nutrient cycling within the rhinoceros gut. We propose the name Paenibacillus ilasis sp. nov. for this strain. These findings enhance our understanding of gut microbial diversity in herbivores and lay the foundation for future applications in agriculture or industry.},
}
@article {pmid40596241,
year = {2025},
author = {Tan, J and Xiong, Z and Yu, S and Lu, W and Yu, L},
title = {Mendelian randomization study revealed a gut microbiota-immune system-kidney junction axis in chronic kidney disease.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {21685},
pmid = {40596241},
issn = {2045-2322},
support = {221101187687947//Self-funded project of Qingyuan Science and Technology Plan/ ; A2022128 and A2024781//Project of Guangdong Medical Science and Technology Research Fund/ ; },
mesh = {*Gastrointestinal Microbiome ; *Renal Insufficiency, Chronic/microbiology/genetics/immunology ; Humans ; *Mendelian Randomization Analysis ; Glomerular Filtration Rate ; Genome-Wide Association Study ; *Kidney/metabolism ; Cytokines/metabolism ; *Immune System/metabolism ; },
abstract = {The alterations of the gut microbiome and cytokine profiles and an elevated risk has correlated with kidney disease progression. However, the causal relationship between gut microbiota and chronic kidney disease (CKD) or related kidney function, and whether cytokines and immune cells act as mediators, remains unclear. Using genome-wide association studies (GWAS) data for CKD, estimated glomerular filtration rate (eGFR) and UACR (urinary albumin to creatinine) from the CKDGen consortium, microbiome data from the MiBioGen consortium and the Dutch Microbiome Project (DMP), 41 cytokine and 731 immune cell traits were identified from large-scale GWAS summary data. We performed two-sample Mendelian randomization (MR) analysis to analyses the causal relationships between gut microbiome, circulating cytokines, immune cells and CKD, eGFR and UACR. In addition, we investigated whether cytokines and immune cells are the mediating factor in the pathway from gut microbiome to CKD, eGFR and UACR. We demonstrated the causal relationships between 8 gut microbiotas in MiBioGen and 8 gut microbiota and 6 metabolism pathways in DMP with CKD, 7 gut microbiotas in MiBioGen and 7 gut microbiota and 3 metabolism pathways with eGFR and 4 gut microbiotas in MiBioGen and 10 gut microbiota and 3 metabolism pathways in DMP with UACR. Additionally, we identified 25 cytokine and immune cell characteristics associated with CKD, 18 with eGFR and 22 with UACR. Importantly, we identified no cytokine, but several immune cell properties that mediate the effects of microbiome on CKD, eGFR and UACR through mediation MR analysis. For instance, Alistipes indistinctus and Alistipes putredinis affects CKD via CD28 + CD45RA + CD8 + T cell. The mediation effects highlighted the intricate relationship between gut microbiome exposure, immune cell activity, and their combined influence on CKD. This data supports a causal effect of the gut microbiome on CKD, eGFR and UACR and underscores the value of MR in clarifying causal relationships identified in microbiome-wide association studies. Circulating immune cells may act as mediators in the pathway linking gut microbiota to CKD progression.},
}
@article {pmid40595952,
year = {2025},
author = {Koltai, E and Mozaffaritabar, S and Zhou, L and Kolonics, A and Koike, A and Tanisawa, K and Park, J and Torma, F and Radak, Z},
title = {PGC-1 alpha overexpression in the skeletal muscle results in a metabolically active microbiome which is independent of redox signaling.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {20527},
pmid = {40595952},
issn = {2045-2322},
mesh = {Animals ; *Peroxisome Proliferator-Activated Receptor Gamma Coactivator 1-alpha/metabolism/genetics ; *Muscle, Skeletal/metabolism/microbiology ; Mice ; Signal Transduction ; Oxidation-Reduction ; Physical Conditioning, Animal ; Male ; *Gastrointestinal Microbiome ; Colon/metabolism/microbiology ; *Microbiota ; Mitochondria/metabolism ; Mice, Transgenic ; },
abstract = {In this study, we investigated the potential relationship between the mitochondrial network and the microbiome using wild-type and skeletal muscle-specific PGC-1α (Pparg coactivator 1 alpha) overexpressing mice, both with and without exercise training. Basal PGC-1α levels were significantly higher in the skeletal muscle (J Physiol Biochem 80:329-335, 2024. https://doi.org/10.1007/s13105-024-01006-1) and, notably, in the colon, which is anatomically proximal to the microbiome. However, no significant changes were observed in cell signaling or mitochondria-related proteins within the colon. On the other hand, mitochondrial H2O2 production in the colon decreased in the PGC-1α overexpressing group. The relative abundance of several bacterial taxa differed between wild-type and PGC-1α overexpressing groups at baseline condition, indicating a shift in the microbiome milieu probably to cope with the increased metabolism, enhanced short-chain fatty acid utilization, and improved endurance capacity. Ten weeks of exercise training differentially modulated the host microbiome in PGC-1α overexpressing and wild-type mice, facilitating adaptations to a broad range of exercise-induced challenges. The results of this study provide new insights into the possible cross-talk between mitochondria and the microbiome.},
}
@article {pmid40595711,
year = {2025},
author = {Amabebe, E and Tatiparthy, M and Kammala, AK and Richardson, LS and Taylor, BD and Sharma, S and Menon, R},
title = {Vaginal pharmacomicrobiomics modulates risk of persistent and recurrent bacterial vaginosis.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {115},
pmid = {40595711},
issn = {2055-5008},
mesh = {Female ; Humans ; *Vaginosis, Bacterial/microbiology/drug therapy ; *Vagina/microbiology ; *Anti-Bacterial Agents/therapeutic use/pharmacology ; *Microbiota/drug effects ; Recurrence ; Bacteria/drug effects/classification ; Biofilms/drug effects ; },
abstract = {Bacterial vaginosis (BV) is the most commonly diagnosed vaginal infection in women of reproductive age, with most patients unaware that they have BV due to its asymptomatic nature. BV is a dysbiotic condition defined by a deviation from the healthy Lactobacillus dominance to a polymicrobial anaerobic bacterial community that increases the risk of sexually transmitted infections and adverse reproductive outcomes, including spontaneous preterm birth. The increasing number of infectious agents in BV, biofilm persistence and antibiotic resistance in the vaginal canal hinder effective treatments with antibiotics leading to consistent recurrence of BV in many women (30-70%). Like in the gut, these vaginal drug-microbiome interactions termed pharmacomicrobiomics could alter drug disposition, mechanism of action, and toxicity that reduce the efficacy of antibiotics and increase the risk of persistent and recurrent BV and its sequelae. For instance, both vaginal epithelial and bacterial cells co-exist and possess enzymes that metabolize antibiotics, and transporter proteins that expel drugs and toxins, rendering them ineffective. Despite significant progress on pharmacomicrobiomics in the gut, little is known about this phenomenon in the vaginal microenvironment, which harbors a consequential microbiota and a major source of infection and antibiotic resistance. Therefore, to improve therapeutic outcomes and reduce the rate of persistent/recurrent BV and infection-associated preterm birth, we present an overview of the evidence pertaining to the effect of vaginal microbiome-drug interactions and efficacy of antibiotics against recurrent BV. We also highlight plausible mechanistic underpinnings of these interactions and implications for treatment modalities to combat infection-associated preterm birth.},
}
@article {pmid40595695,
year = {2025},
author = {Rosell-Cardona, C and Cryan, JF and Clarke, G and Kittel-Schneider, S},
title = {Host-microbiome relationship in depression: can human induced pluripotent stem cells play a role in unravelling mechanisms?.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {117},
pmid = {40595695},
issn = {2055-5008},
support = {101034270//INSPIRE COFUND Marie Sk&#x142;odowska-Curie grant/ ; },
mesh = {Humans ; *Induced Pluripotent Stem Cells/physiology ; *Gastrointestinal Microbiome/physiology ; *Depression/microbiology/therapy ; *Host Microbial Interactions ; },
abstract = {Depression is highly prevalent, with many patients not responding to existing treatments. The gut microbiota plays a key role in its pathophysiology, offering new therapeutic avenues. Human-based research is essential to uncover mechanisms and validate new targets. Given CNS inaccessibility, human induced pluripotent stem cells (hiPSCs) offer an innovative model. This review explores the emerging field of hiPSCs and their potential in advancing microbiota-gut-brain axis science and depression research.},
}
@article {pmid40595471,
year = {2025},
author = {Durack, J and Piceno, Y and Vuong, H and Fanelli, B and Good, DA and Hasan, NA and Dadlani, M and Weiss, L and Oh, J and Kostic, AD and Dawson, TL and Caballero-Arias, H and Colwell, RR},
title = {Yanomami skin microbiome complexity challenges prevailing concepts of healthy skin.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {5542},
pmid = {40595471},
issn = {2041-1723},
mesh = {*Skin/microbiology ; Humans ; *Microbiota/genetics ; Adult ; Malassezia/genetics/isolation &amp; purification ; Female ; Bacteria/genetics/classification/isolation &amp; purification ; Male ; RNA, Ribosomal, 16S/genetics ; Lipid Metabolism ; Skin Microbiome ; },
abstract = {The adult skin microbiome typically exhibits low microbial complexity, particularly on sebaceous sites, where lipophilic Cutibacterium and Malassezia spp. predominate. Current understanding of healthy skin microbiome is largely based on western, industrialized populations, with limited representation of diverse cultures and lifestyles. Here, we investigate the skin microbiome of a remote indigenous Yanomami community and reveal a complex microbial ecosystem comprising 115 previously unreported bacterial genomes. The Yanomami skin microbiome includes genera common to western populations alongside diverse environmental taxa that form multiplex interactions with the dominant eukaryote Malassezia globosa. Functional profiling indicates that this microbiome supports skin homeostasis by fortifying barrier integrity through lipid metabolism and acid production and mitigating oxidative stress. Longitudinal monitoring of western expeditioner' skin demonstrates acquisition of the Yanomami microbiome following Amazonian immersion and its subsequent loss upon return to an industrialized setting. These findings reveal that diverse, environmentally enriched microbiota may confer skin benefits that are overlooked in current models of healthy skin.},
}
@article {pmid40595444,
year = {2025},
author = {Minabou Ndjite, G and Jiang, AK and Ravel, CT and Grant, MR and Jiang, X and Hall, B},
title = {Gut microbial utilization of the alternative sweetener, D-allulose, via AlsE.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {970},
pmid = {40595444},
issn = {2399-3642},
support = {1R35GM155208-01//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; },
mesh = {*Gastrointestinal Microbiome ; Humans ; *Sweetening Agents/metabolism ; *Fructose/metabolism ; Adult ; *Clostridium/genetics/enzymology/metabolism ; },
abstract = {D-allulose, a rare sugar with emerging potential as a low-calorie sweetener, has garnered attention as an alternative to other commercially available alternative sweeteners, such as sugar alcohols, which often cause severe gastrointestinal discomfort. D-allulose-6-phosphate 3-epimerase (AlsE) is a prokaryotic enzyme that converts D-allulose-6-phosphate into D-fructose-6-phosphate, enabling its use as a carbon source. However, the taxonomic breadth of AlsE across gut bacteria remains poorly understood, hindering insights into the utilization of D-allulose by microbial communities. In this study, we provide experimental evidence showing that Clostridium innocuum is capable of D-allulose metabolism via a homologous AlsE. A bioinformatics search of 85,202 bacterial genomes identified 116 bacterial species with AlsE homologs, suggesting a limited distribution of AlsE in bacteria. Additionally, Escherichia coli contains a copy of alsE, but it does not grow on D-allulose as a sole carbon source unless alsE is heterologously expressed. A metagenomic analysis revealed that 15.8% of 3079 adult healthy human metagenomic samples that we analyzed contained alsE, suggesting a limited prevalence of the enzyme in the gut microbiome. These results suggest that the gut microbiome has limited capacity to metabolize D-allulose via alsE, supporting its use as an alternative sweetener with minimal impact on microbial composition and gastrointestinal symptoms. This finding also enables personalized nutrition, allowing diabetic individuals to assess their gut microbiota for alsE, and manage glycemic response while reducing gastrointestinal distress.},
}
@article {pmid40594971,
year = {2025},
author = {Furmanczyk, EM and Tartanus, M and Malusà, E},
title = {Analysis of medium-term impact of multifunctional living mulches on soil biological fertility of an organic apple orchard.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {22422},
pmid = {40594971},
issn = {2045-2322},
support = {SUSCROP/II/BioHortiTech/01/2021//Narodowe Centrum Bada&#x144; i Rozwoju/ ; SUSCROP/II/BioHortiTech/01/2021//Narodowe Centrum Bada&#x144; i Rozwoju/ ; SUSCROP/II/BioHortiTech/01/2021//Narodowe Centrum Bada&#x144; i Rozwoju/ ; },
mesh = {*Malus/growth &amp; development ; *Soil Microbiology ; *Soil/chemistry ; Microbiota ; Bacteria/classification/genetics ; Fragaria/growth &amp; development ; Ecosystem ; Mentha piperita/growth &amp; development ; *Organic Agriculture/methods ; },
abstract = {Living mulches, particularly when designed with officinal plants, beside competing against weeds of a fruit crop, could provide other ecosystem services. The impact on soil chemical and biological features of Alchemilla vulgaris, Fragaria vesca and Mentha x piperita after four years of establishment as understorey living mulches in an organic apple orchard was evaluated. Soil nutrients level was not affected by the living mulches. The combined effect of season and living mulch affected bacterial activity, which reverberated on phyla and taxa abundance. Only few genera were unique to each living mulch species, but the abundance of 213 genera was differentially modified by the living mulches. The soil level of P and K, the metabolism of several C sources, and the bacterial activity and Shannon Index were highly correlated with the relative abundance of about a third of identified bacterial taxa. The analysis of bacterial abundance data gathered since the establishment of the trial was showing a different trend in shaping bacterial soil microbiome depending on the living mulch species.},
}
@article {pmid40594788,
year = {2025},
author = {Sun, YD and Zhang, H and Gong, XL and Li, YM and Han, R and Zhou, CX and Han, JJ},
title = {Multiomics reveals metformin's dual role in gut microbiome remodeling and hepatic metabolic reprogramming for MAFLD intervention.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {22699},
pmid = {40594788},
issn = {2045-2322},
support = {NSFC No. 82272101//the National Natural Science Foundation of China/ ; No.2018YFE0126500//the National Key Research and Development Program of China/ ; No. ZR2021MH060//the Natural Science Foundation of Shandong Province/ ; },
mesh = {*Metformin/pharmacology ; Animals ; *Gastrointestinal Microbiome/drug effects ; *Non-alcoholic Fatty Liver Disease/metabolism/drug therapy/pathology/microbiology ; Male ; Rats ; *Liver/metabolism/drug effects/pathology ; Rats, Wistar ; Lipid Metabolism/drug effects ; Metabolomics/methods ; Hypoglycemic Agents/pharmacology ; Lipidomics ; Disease Models, Animal ; Metabolic Reprogramming ; Multiomics ; },
abstract = {Metabolic Associated Fatty Liver Disease (MAFLD), previously known as Non-Alcoholic Fatty Liver Disease, is a growing global health issue associated with obesity, type 2 diabetes, and metabolic syndrome. This study investigates the potential of metformin, a common anti-diabetic drug, to slow the progression of MAFLD using a multi-omics approach. Male Wistar rats were fed a choline-deficient diet to induce MAFLD and treated with metformin through their drinking water for 48 weeks. We conducted a comprehensive analysis including liver histology, untargeted metabolomics, lipidomics, and gut microbiome profiling to assess the effects of metformin on liver and gut metabolic patterns. Metformin administration led to significant changes in gut microbiome diversity and the abundance of specific microbial species in MAFLD rats. Histological analysis showed that metformin-treated rats had reduced lipid accumulation and fibrosis in the liver compared to untreated MAFLD rats. Metabolomic and lipidomic analyses revealed that metformin corrected abnormal lipid metabolism patterns, reduced hepatic fat deposition, and influenced key metabolic pathways associated with MAFLD progression. Our findings suggest that metformin has a protective role against MAFLD by modulating gut microbiota and liver metabolism, thereby slowing the progression of hepatic fibrosis. This study provides insights into the therapeutic potential of metformin for MAFLD by addressing metabolic pattern disorders and abnormal changes in gut microbial diversity, highlighting its impact on lipid metabolism and gut-liver axis interactions.},
}
@article {pmid40594702,
year = {2025},
author = {Beeby, N and Pierre, LJ and Guy, RFJ and Justin, R and Victor, TA and Rossi, G and van den Hout, L and Rothman, JM and Amato, KR and Webster, TH and Baden, AL},
title = {Climate, diet, and nutrition drive gut microbiome variation in a fruit-specialist primate.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {21110},
pmid = {40594702},
issn = {2045-2322},
mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; *Diet ; *Fruit ; *Climate ; Madagascar ; },
abstract = {Much of what we know about drivers of mammalian gut microbiome (GM) variation focuses on limited seasonal data, or effects of dietary fiber, particularly in leaf-eating and grazing taxa. We know little about the synergistic relationships between climate, diet, nutrition, and GM dynamics in wild mammals-particularly in fruit-eating taxa. Here, we examined GM variation across 12 months in a fruit-specialist primate, the black-and-white ruffed lemur (Varecia variegata), which is known to experience substantial environmental variation in its rainforest habitat in Madagascar. We used mixed modeling approaches to estimate the effects of climate, diet, and nutrient intakes on GM alpha diversity and differential abundances. We found substantial intra- and inter-individual GM variation. Climate and nutrient intakes impacted GM alpha diversity, and in addition to degree of frugivory and dietary diversity, each drove changes in differential abundance of unique combinations of microbial taxa. The degree of frugivory predicted few microbial abundances while nutrient intakes predicted a wide diversity, with fibers and non-structural carbohydrates showing inverse patterns to those of fat, indicating that nutrients are more important in driving the GM than simply the food types consumed. These results highlight how physiological flexibility facilitated by GM plasticity may be key to fruit-specialists' survival of fruit scarcity.},
}
@article {pmid40594486,
year = {2025},
author = {Yang, Z and Wang, Y and Wang, Y and Zhou, J and Wang, R and Shi, M and Bao, M and Wang, B and Yuan, R},
title = {Analysis on gut microbiota diversity of wild Asian elephants (Elephas maximus) from three regions of Yunnan Province.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {20692},
pmid = {40594486},
issn = {2045-2322},
support = {Grant No. 82460392//National Natural Science Foundation of China/ ; Grant No. YNWR-QNBJ-2020-089//The Youth Talent Program of Yunnan "Ten-thousand Talents Program"/ ; },
mesh = {Animals ; *Elephants/microbiology ; *Gastrointestinal Microbiome/genetics ; China ; RNA, Ribosomal, 16S/genetics ; Biodiversity ; *Bacteria/genetics/classification/isolation &amp; purification ; Phylogeny ; High-Throughput Nucleotide Sequencing ; },
abstract = {Studying the gut microbiome diversity of Asian elephants (Elephas maximus) is crucial for understanding their environmental adaptability, health status, and conservation needs. In this study, high-throughput sequencing of the 16S rRNA gene was utilized to analyze and compare the microbial community composition and diversity of 50 wild Asian elephants from three regions in Yunnan Province. The results indicated significant differences in gut microbiome richness among the regions, and the lowest diversity observed in the Lincang region. Principal coordinate analysis (PCoA) revealed that the microbial community structure of the Lincang population was markedly different from that of the other two regions. At the phylum level, Firmicutes, Proteobacteria, and Bacteroidetes were the dominant bacterial groups across all three regions. However, in the Lincang region, the abundance of Proteobacteria was the highest and significantly greater than in the other regions. Additionally, the levels of potential pathogenic bacteria, such as Acinetobacter and Stenotrophomonas, were significantly elevated in the Lincang population compared to the other two regions. Therefore, future conservation efforts need to integrate ecological restoration with microbiome monitoring to mitigate the microbial dysbiosis caused by human disturbances.},
}
@article {pmid40594438,
year = {2025},
author = {Sugiyama, T and Hasegawa, K},
title = {Synergistic actions of symbiotic bacteria modulate the insecticidal potency of entomopathogenic nematode Steinernema monticolum KHA701.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {22550},
pmid = {40594438},
issn = {2045-2322},
mesh = {Animals ; *Symbiosis ; Xenorhabdus/physiology ; *Insecticides ; *Rhabditida/microbiology ; Larva/parasitology/microbiology ; Photorhabdus/physiology ; Moths/parasitology ; Microbiota ; },
abstract = {Entomopathogenic nematodes (EPNs), primarily Steinernema and Heterorhabditis, form symbiotic relationships with bacteria from the genera Xenorhabdus and Photorhabdus, respectively. These bacteria exhibit insecticidal activity and suppress competing microorganisms, allowing EPNs and their symbionts to dominate insect cadavers. While monoxenic associations are fundamental to EPN-bacteria interactions, recent studies suggest that EPNs may harbor a diverse array of symbiotic bacteria with consistent associations. However, the role of these additional symbiotic bacteria in EPN pathogenesis and the complexity of their interactions remain unclear. In this study, Steinernema monticolum KHA701 was newly isolated using the Galleria mellonella bait method. Compared to the highly pathogenic Heterorhabditis bacteriophora TT01, S. monticolum KHA701 demonstrated superior insecticidal activity against G. mellonella larvae and exhibited a broad host range, targeting 63 arthropod species across 18 orders and 41 families. Microbiota analysis of S. monticolum KHA701 infective juveniles identified 34 bacterial species, including Xenorhabdus hominickii, from the nematode body. Five bacteria-Elizabethkingia miricola, Serratia marcescens, Pseudomonas protegens, Staphylococcus sp., and X. hominickii-were confirmed to be highly pathogenic to Zophobas morio and Periplaneta fuliginosa larvae. Notably, the combination of X. hominickii with any of the other four bacteria significantly enhanced the insecticidal activity of S. monticolum KHA701 against G. mellonella. These findings suggest that S. monticolum KHA701 utilizes a diverse community of bacterial symbionts to enhance its insecticidal efficacy, providing novel insights into the ecological strategies of EPNs.},
}
@article {pmid40594421,
year = {2025},
author = {Pan, X and Gao, Y and Zhang, Y and Suzuki, K and He, J and Chen, X and Jiang, L and Zhang, A},
title = {Gut microbiota differences in children classified by extreme physical fitness and physical activity levels from a Chinese Cross-Sectional study.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {21351},
pmid = {40594421},
issn = {2045-2322},
support = {2022YFC3600204//Ministry of Science and Technology of the People's Republic of China/ ; 2022YFC3600204//Ministry of Science and Technology of the People's Republic of China/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; Child ; *Physical Fitness/physiology ; *Exercise/physiology ; Male ; Cross-Sectional Studies ; Female ; China ; Feces/microbiology ; East Asian People ; },
abstract = {This study investigated the diversity, structure, dominant microbial populations, and their relationships with physical fitness (PF) and physical activity (PA) metrics within the gut microbiota of children by comparing the gut microbiome composition and functional differences across four groups: low PA-high PF, high PA-high PF, high PA-low PF, and low PA-low PF. A total of 6,074 children aged 6-9 years were selected from full-time ordinary primary and secondary schools. Based on the quartiles of PF and PA, we sampled 120 individuals from each of the four groups (30/group) and collected fecal samples for high-throughput sequencing to analyze the gut microbiome composition. This study revealed that children with high PF exhibited a more abundant and diverse gut microbiome within the same PA level group. Under high PA conditions, the Chao1 and Shannon indices of the high PF group were significantly higher. Different dominant microbial taxa were identified within each group, and specific microbial populations were significantly correlated with various physical and exercise-related indices. This study indicates that the composition of children's gut microbiota varies significantly based on the combined levels of PA and PF. Children with high PF show greater microbial diversity within similar PA levels, particularly under high PA conditions.},
}
@article {pmid40594354,
year = {2025},
author = {Flores, SS and Cordovez, V and Arias Giraldo, LM and Leon-Reyes, A and van 't Hof, P and Raaijmakers, JM and Oyserman, BO},
title = {Unveiling diversity and adaptations of the wild tomato Microbiome in their center of origin in the Ecuadorian Andes.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {22448},
pmid = {40594354},
issn = {2045-2322},
support = {CZ07-000440-2018//SENESCYT scholarship/ ; 10093//Chancellor Grant and COCIBA-USFQ/ ; 10093//Chancellor Grant and COCIBA-USFQ/ ; 024.004.014/NWO_/Dutch Research Council/Netherlands ; 024.004.014/NWO_/Dutch Research Council/Netherlands ; },
mesh = {*Solanum lycopersicum/microbiology/genetics ; *Microbiota/genetics ; Soil Microbiology ; Rhizosphere ; Ecuador ; Plant Roots/microbiology ; Biodiversity ; *Adaptation, Physiological ; Phylogeny ; },
abstract = {Microbiome assembly has been studied for many plant species and is recognized as a key driver of plant growth and plant tolerance to (a)biotic stresses. To date, assembly of the tomato rhizosphere microbiome has been investigated primarily for commercial varieties and field soils subjected to agricultural management practices, whereas the microbiome of wild tomato genotypes in their native habitats remains largely unexplored. This research focused on distinct populations of Solanum pimpinellifolium in three natural habitats in the Ecuadorian Andes to identify the taxonomic and functional diversity of their rhizosphere microbiome. The results showed that, despite genotypic differences among the wild tomato populations, different soil types and soil microbiome compositions, the rhizosphere microbiome showed strikingly compositional similarity across the three habitats. Proteobacteria, in particular taxa classified as Enterobacteriaceae, and specific unclassified fungal taxa were highly represented in the rhizosphere of S. pimpinellifolum. Metagenomic analyses suggested that the prevalence of Enterobacteriaceae on wild tomato roots may be explained by several traits, in particular nutrient competition, motility, iron acquisition, membrane transport, stress response, and plant hormone biosynthesis. These results reveal a conserved microbiome signature associated with wild tomato rhizosphere in their center of origin. Just as the genomes of wild crop ancestors provide a valuable source of beneficial traits for breeding cultivated varieties, exploring their microbiome in native environments could uncover microbial taxa and traits that similarly contribute to crop growth and health.},
}
@article {pmid40594317,
year = {2025},
author = {Song, X and Li, JN and Wang, D and Han, ZY and Yan, XX and Yang, ZH and Xu, J and Wang, Q and Wu, D},
title = {Metagenomics reveals functional profiles of gut microbiota during the recovery phase of acute pancreatitis.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {20549},
pmid = {40594317},
issn = {2045-2322},
support = {32170788//National Natural Science Foundation of China/ ; 2022-PUMCH-B-023//National High Level Hospital Clinical Research Funding/ ; ZK108000//National Key Clinical Specialty Construction Project/ ; 7232123//Natural Science Foundation of Beijing/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods ; *Pancreatitis/microbiology ; Male ; Female ; Middle Aged ; Adult ; Aged ; Acute Disease ; Bacteria/genetics/classification ; },
abstract = {Gut microbiota play a critical pathogenic role in acute pancreatitis (AP). This study aimed to investigate the composition and function of gut microbiota during the recovery phase of AP. Rectal swab samples obtained from 12 AP patients of varying severity during both the acute and recovery phases were sequenced using shotgun metagenomic sequencing. We analysed α-diversity, enterotypes, and the dominant microbiome composition, and performed differential analysis of gut microbiota composition and functional enrichment. During the recovery phase of AP, microbial diversity remained decreased, and minimal difference were observed in the structural diversity of the microbiome. There was an increasing tendency of beneficial bacteria (Bacteroidales) and a decreasing tendency of harmful bacteria (Firmicutes) in the recovery phase of mild AP (MAP). However, in the recovery phase of moderately severe AP (MSAP) and severe AP, Enterococcus abundance increased compared with that in the acute phase. Some signalling pathways showed opposite trends in the recovery phase of MAP and MSAP compared to the acute phase. These results suggested that gut microbiome composition and function are associated with AP recovery, which may inform strategies for the treatment and prognosis of AP.},
}
@article {pmid40594248,
year = {2025},
author = {Kang, MG and Choi, JH and Kim, SH and Jeong, TB and Kim, JY and Kim, JW and Lee, CY},
title = {Efficacy and safety of Lactobacillus plantarum GCWB1001 for respiratory health in a double blind randomized placebo controlled trial.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {22700},
pmid = {40594248},
issn = {2045-2322},
mesh = {Humans ; *Lactobacillus plantarum/physiology ; Male ; Female ; Middle Aged ; Double-Blind Method ; Adult ; Aged ; *Probiotics/therapeutic use/administration &amp; dosage/adverse effects ; *Cough/therapy ; *COVID-19/complications/therapy ; Treatment Outcome ; Young Adult ; *Dyspnea/therapy ; SARS-CoV-2 ; Sputum ; },
abstract = {Respiratory symptoms like prolonged cough and breathlessness have increased post-COVID-19, even in those with normal chest X-rays and FEV1/FVC ratios. This study assessed the benefits of Lactobacillus plantarum GCWB1001 on such symptoms in individuals without asthma or COPD. In a double-blind, randomized, placebo-controlled trial, 126 participants aged 19-70 were included. Exclusions were for asthma, COPD, abnormal chest X-rays, or recent antibiotic use. The primary outcome was the Breathlessness, Cough, and Sputum Scale (BCSS), with secondary outcomes including Visual Analogue Scale (VAS) scores for respiratory function. The total BCSS score at 12 weeks did not differ significantly between the GCWB1001 and placebo groups. Secondary endpoints such as sputum and breathlessness showed numerical improvements, particularly in males and participants over 40, but these findings were not statistically significant after correction for multiple comparisons. No serious adverse events were reported, indicating safety. Although this study did not demonstrate a clear clinical benefit, the exploratory trends suggest that additional, larger-scale trials may be needed to determine if these observations reflect a meaningful effect.},
}
@article {pmid40594086,
year = {2025},
author = {Leifels, M and Cheng, D and Cai, J and Nadhirah, N and Mohidin, AF and Santillan, E and Woo, Y and Hill, E and Wu, SW and Boon, N and Favere, J and Whittle, AJ and Wuertz, S},
title = {Biofilm detachment significantly affects biological stability of drinking water during intermittent water supply in a pilot scale water distribution system.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {22408},
pmid = {40594086},
issn = {2045-2322},
support = {3S85419//the FWO Flanders/ ; 3S85419//the FWO Flanders/ ; S006221N//FWO-SBO Biostable project/ ; S006221N//FWO-SBO Biostable project/ ; },
mesh = {*Biofilms/growth &amp; development ; *Drinking Water/microbiology ; *Water Supply ; *Water Microbiology ; RNA, Ribosomal, 16S/genetics ; Pilot Projects ; Flow Cytometry ; Water Quality ; Bacteria/genetics/classification ; Water Purification ; },
abstract = {Intermittent service provision (IWS) in piped drinking water distribution systems is practiced in countries with limited water resources; it leads to stagnant periods during which water drains completely from de-pressurized pipes, increasing the likelihood of biofilm detachment upon reconnection when water is supplied to the consumer and thus affecting water quality. Our study examines the impact of uninterrupted or continuous water supply (CWS) and IWS on microbial communities and biofilm detachment, using data from three 30-day experiments conducted in an above-ground drinking water testbed with 90-m long PVC pipes containing residual monochloramine. Flow cytometry (FCM) revealed a significant increase in total and intact cell concentrations when water was supplied intermittently compared to CWS, and the microbial alpha-diversity was significantly higher in CWS sections by both 16S rRNA gene metabarcoding and phenotypic fingerprinting of flow cytometry data. Nitrate levels in the water were significantly higher during initial intermittent flow due to the activity of nitrifying bacteria in biofilms exposed to stagnant water in pipes. Overall, biofilm detachment significantly affects the biological stability of drinking water delivered through IWS compared to CWS. We developed a novel biofilm detachment potential index derived from FCM data to estimate the minimum amount of water needed to be discarded before microbial cell counts and community composition return to baseline levels.},
}
@article {pmid40593847,
year = {2025},
author = {Russ, D and Fitzpatrick, CR and Saha, C and Law, TF and Jones, CD and Kliebenstein, DJ and Dangl, JL},
title = {An effluent pump family distributed across plant commensal bacteria conditions host- and organ-specific glucosinolate detoxification.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {5699},
pmid = {40593847},
issn = {2041-1723},
support = {IOS-1917270//NSF | BIO | Division of Integrative Organismal Systems (IOS)/ ; },
mesh = {*Glucosinolates/metabolism ; *Arabidopsis/microbiology/metabolism/genetics ; Symbiosis ; Microbiota/genetics ; *Bacterial Proteins/metabolism/genetics ; *Bacteria/genetics/metabolism ; Inactivation, Metabolic ; Plant Shoots/microbiology/metabolism ; },
abstract = {In nature, plants recruit a diverse microbial community, the plant microbiome, that is distinct from the surrounding soil community. To understand the forces that shape the plant microbiome we need to characterize the microbial traits that contribute to plant colonization. We used barcoded mutant libraries to identify bacterial genes that contribute to the colonization of a monocot and a eudicot host. We show that plant colonization is influenced by dozens of genes. While some of these colonization genes were shared between the two host plant species, most were highly specific, benefiting the colonization of a single host and organ. We characterized an efflux pump that specifically contributes to Arabidopsis shoot colonization. This efflux pump is prevalent across Pseudomonadota genomes yet benefits the bacterial association with only a small subset of Arabidopsis thaliana accessions. Leveraging genomic diversity within Arabidopsis thaliana, we confirmed that specific glucosinolate breakdown products are detoxified by this family of efflux pumps. The broad prevalence of this efflux pump family suggests that its members contribute to protection of commensal bacteria from collateral damage of plant glucosinolate-based defense responses to herbivores and necrotrophic pathogens.},
}
@article {pmid40593813,
year = {2025},
author = {Wende, M and Osbelt, L and Eisenhard, L and Lesker, TR and Damaris, BF and Mutukumarasamy, U and Bielecka, A and D H Almási, &#xc9; and Winter, KA and Schauer, J and Pfennigwerth, N and Gatermann, S and Schaufler, K and Schlüter, D and Galardini, M and Strowig, T},
title = {Suppression of gut colonization by multidrug-resistant Escherichia coli clinical isolates through cooperative niche exclusion.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {5426},
pmid = {40593813},
issn = {2041-1723},
mesh = {*Escherichia coli/drug effects/isolation &amp; purification/physiology/growth &amp; development/genetics ; *Drug Resistance, Multiple, Bacterial ; *Gastrointestinal Microbiome/drug effects/physiology ; Animals ; Humans ; Mice ; Klebsiella oxytoca/physiology ; Probiotics ; Anti-Bacterial Agents/pharmacology ; *Escherichia coli Infections/microbiology ; Female ; Antibiosis ; },
abstract = {Human gut colonization by multi-drug resistant Enterobacterales (MDR-E) poses a risk for subsequent infections. Because of the collateral damage antibiotics cause to the microbiota, microbiome-based interventions aimed at promoting decolonization have garnered interest. In this study, we evaluate the strain-specific potential of 430 commensal Escherichia coli isolates to inhibit the growth of an MDR E. coli strain. Comparative analyses using in vitro, ex vivo, and mouse models reveal that only a subset of commensal strains can facilitate gut decolonization. Bioinformatic and experimental analyses of the antagonism among representative strains demonstrate that both direct and indirect carbohydrate competition contribute to niche exclusion between E. coli strains. Finally, the combination of a protective E. coli strain with a Klebsiella oxytoca strain enhances the inhibitory potential against metabolically diverse MDR E. coli strains and additional MDR-E species, highlighting that rationally designed metabolically complementary approaches can contribute to developing next-generation probiotics with broad-spectrum activity.},
}
@article {pmid40593739,
year = {2025},
author = {Xing, J and Niu, T and Yu, T and Zou, B and Fan, S and Wang, C and Shi, C and Zhang, D and Wang, N and Jiang, Y and Huang, H and Cao, X and Zeng, Y and Wang, J and Zhang, D and Yang, G and Yang, W},
title = {Gut microbiota-derived isovaleric acid ameliorates influenza virus infection via gut-lung axis.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {116},
pmid = {40593739},
issn = {2055-5008},
support = {U21A20261//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Orthomyxoviridae Infections/drug therapy/virology/microbiology ; Mice ; Influenza A Virus, H1N1 Subtype/drug effects ; *Lung/virology/drug effects/pathology/microbiology ; *Influenza A Virus, H9N2 Subtype/drug effects ; Disease Models, Animal ; Prevotella ; Pentanoic Acids ; Hemiterpenes ; },
abstract = {H9N2 influenza virus infections represent a significant respiratory health concern, yet the functional role of gut microbiota during infection progression remains poorly understood. Here, we show that H9N2 infection causes dose-dependent alterations in gut microbial communities in a mammalian infection model, particularly the depletion of Prevotella species. Prophylactic administration of Prevotella copri improved survival and clinical outcomes in infected mice by restructuring the gut microbiome, promoting beneficial bacteria, and suppressing pathogens. Metabolomic profiling revealed increased isovaleric acid levels in the intestine and serum. Isovaleric acid pretreatment reduced pulmonary inflammation, alleviated tissue damage, and preserved epithelial integrity. Isovaleric acid pretreatment alleviates lung inflammation, reduces tissue damage, and maintains epithelial integrity. Additionally, isovaleric acid mitigates infection caused by the H1N1 influenza virus. These findings highlight the immunomodulatory role of gut commensals and their metabolites in antiviral defense, offering a new approach to influenza virus treatment.},
}
@article {pmid40593735,
year = {2025},
author = {Flores Ventura, E and Esteban-Torres, M and Gueimonde, M and van Sinderen, D and Koren, O and Hall, LJ and Segata, N and Valles-Colomer, M and Collado, MC},
title = {Mother-to-infant vertical transmission in early life: a systematic review and proportional meta-analysis of Bifidobacterium strain transmissibility.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {121},
pmid = {40593735},
issn = {2055-5008},
support = {CEX2021-001189-S-20-1//Ministerio de Ciencia e Innovaci&#xf3;n/ ; CEX2021-001189-S/ MCIN/AEI / 10.13039/501100011033//Ministerio de Ciencia e Innovaci&#xf3;n/ ; PID2022-139328OA-I00//Ministerio de Ciencia e Innovaci&#xf3;n/ ; CEX2021-001189-S/ MCIN/AEI / 10.13039/501100011033//Ministerio de Ciencia e Innovaci&#xf3;n/ ; 898088//European Union's Horizon 2020/ ; SFI/12/RC/2273-P1 and SFI/12/RC/2273-P2/SFI_/Science Foundation Ireland/Ireland ; 220876/Z/20/Z//Wellcome Trust Investigator/ ; Beatriz Galindo Junior Fellowship BG22/00172//Ministerio de Universidades/ ; 639226/ERC_/European Research Council/International ; },
mesh = {Female ; Humans ; Infant ; Infant, Newborn ; Pregnancy ; *Bifidobacteriales Infections/transmission/microbiology ; *Bifidobacterium/classification/genetics/isolation &amp; purification ; Gastrointestinal Microbiome ; *Infectious Disease Transmission, Vertical ; Metagenomics ; Mothers ; Vagina/microbiology ; },
abstract = {Early-life colonization is a critical developmental process influencing infant biological programming, with bifidobacteria playing a key role. This systematic review examines the transmissibility of Bifidobacterium strains from mothers to infants. Adhering to Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA) guidelines, 31 articles from 2009 to 2024 were selected from 2825 screened titles and abstracts. Using a narrative synthesis and meta-analysis, the review focuses on studies employing strain-level metagenomic approaches (Protocol registry CRD: CRD42023490507). Ten studies using shotgun metagenomic sequencing identified specific strains of B. adolescentis, B. angulatum, B. bifidum, B. breve, B. pseudocatenulatum, B. catenulatum, and B. longum shared between mothers and infants. A meta-analysis of 810 mother-infant pairs revealed an overall species transmissibility estimate of 30% (95% CI: 0.17; 0.44), with B. longum strains persisting in infants' guts for up to 6 months. Strain transmissibility was higher in vaginally delivered infants compared to those delivered by caesarean section. This review highlights the high transmission rates of maternal Bifidobacterium strains in early-life gut seeding, particularly B. bifidum and B. longum. Despite ongoing research, uncertainties remain regarding the precise characteristics, transmission routes, and mechanisms of transmitted strains. Comprehensive approaches, including metagenomic sequencing and longitudinal studies, are needed to understand the role of vertical transmission in infant gut microbiome engraftment and its functional implications.},
}
@article {pmid40593731,
year = {2025},
author = {Tan, Y and Zhu, Y and Wijffels, RH and Zhang, H and Scott, WT and Xu, Y and Martins Dos Santos, V},
title = {Controlling metabolic stability of food microbiome for stable indigenous liquor fermentation.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {124},
pmid = {40593731},
issn = {2055-5008},
support = {202006790115//China Scholarship Council (CSC)/ ; BK20201341//Natural Science Foundation of Jiangsu Province (Jiangsu Provincial Natural Science Foundation)/ ; 32201981//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32172176//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Fermentation ; *Microbiota ; *Lactobacillus/metabolism ; *Food Microbiology ; *Yeasts/metabolism ; Metabolic Networks and Pathways ; },
abstract = {Steering microbial metabolic stability in fermentation is a recurrent goal in microbial food production. Indigenous liquor fermentation typically relies on complex microbiome metabolism, making it difficult to steer fermentation towards consistent high-quality products. Here, we conducted a three-step experiment to identify instability factors and explore ways to steer fermentation stability in lab-scale settings. We found that the metabolic stability of the microbiome fluctuates due to fermentation parameters, dynamic benefit allocation between yeasts and Lactobacilli, and metabolic network redundancy. In addition to parameters control, short-term metabolic stability requires stable microbial benefit allocation, whereas long-term stability requires proper functional redundancy. Rationally setting initial parameters and the microbial inoculation ratio is a practical way to optimize metabolic stability for stable indigenous liquor fermentation. Our study provides new insights into microbiome metabolism control and shows the feasibility of enhancing fermentation stability through appropriate initial conditions, enabling more controlled and efficient microbial food production systems.},
}
@article {pmid40593656,
year = {2025},
author = {Pärnänen, K and Ruuskanen, MO and Sommeria-Klein, G and Laitinen, V and Kantanen, P and Méric, G and Gazolla Volpiano, C and Inouye, M and Knight, R and Salomaa, V and Havulinna, AS and Niiranen, T and Lahti, L},
title = {Variation and prognostic potential of the gut antibiotic resistome in the FINRISK 2002 cohort.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {5963},
pmid = {40593656},
issn = {2041-1723},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/genetics ; Finland/epidemiology ; Female ; Male ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; Middle Aged ; Adult ; Prognosis ; Cohort Studies ; Aged ; *Drug Resistance, Bacterial/genetics ; Bacteria/drug effects/genetics ; Life Style ; },
abstract = {The spread of antibiotic-resistant bacteria has severely reduced the efficacy of antibiotics and now contributes to 1 million deaths annually. The gut microbiome is a major reservoir of antibiotic resistance in humans, yet the extent to which gut antibiotic resistance gene load varies within human populations and the drivers that contribute most to this variation remain unclear. Here, we demonstrate, in a representative cohort of 7095 Finnish adults, that socio-demographic factors, lifestyle, and gut microbial community composition shape resistance gene selection and transmission processes. Resistance was linked not only to prior use of antibiotics, as anticipated, but also to frequent consumption of fresh vegetables and poultry, two food groups previously reported to contain antibiotic-resistant bacteria. Interestingly, resistance was not linked to the consumption of high-fat and high-sugar foods, but was consistently higher in females and urban high-income individuals, who currently have generally lower mortality rates. Nevertheless, during the 17-year follow-up, high resistance was associated with a 1.07-fold increase in mortality risk, comparable to elevated blood pressure, and with a heightened risk of sepsis. These findings highlight risks and socio-demographic dimensions of antibiotic resistance that are particularly relevant in the current context of global urbanization and middle-class growth.},
}
@article {pmid40593262,
year = {2025},
author = {Liu, L and Li, M and Qin, Y and Liu, Y and Li, M and Lian, B and Guo, R and Xiao, Y and Yin, C},
title = {Childhood obesity and insulin resistance is correlated with gut microbiome serum protein: an integrated metagenomic and proteomic analysis.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {21436},
pmid = {40593262},
issn = {2045-2322},
support = {81903340//National Natural Science Foundation of China/ ; },
mesh = {Child ; Female ; Humans ; Male ; *Blood Proteins/metabolism ; Feces/microbiology ; *Gastrointestinal Microbiome ; *Insulin Resistance ; Metagenomics/methods ; *Pediatric Obesity/microbiology/blood/metabolism ; Proteomics/methods ; },
abstract = {The aim of this study was to investigate the changes in the gut microbiota and proteins related to metabolism and immunity caused by childhood obesity and insulin resistance (IR) and to assess the underlying relationship between the gut microbiota and IR in children. Nineteen children with obesity and sixteen healthy children were recruited. Children with obesity were divided into two groups: obese with IR and obese without IR. All of the obese children participated in a 1-month lifestyle-based weight loss program. Faecal metagenomics and serum Olink proteomics combined with clinical parameters were used to identify the metabolic alterations associated with childhood obesity and IR. The gut microbiota and serum protein were significantly altered in obese children with IR. The relative abundances of Akkermansia muciniphila, IGFBP1 and GP6 were decreased in obese children with IR. Butyricicoccus sp. AM29-23AC, DLK1, CD163, CCL16 and CTSD levels were recovered after IR improved. TNFR1 had a significant indirect effect on the interaction between s-Citrobacter.freundii and fasting insulin. In conclusion, obese children with IR have abnormal gut microbiota and serum proteins related to metabolism and immunity, which can be improved after weight loss. The gut microbiome of children with obesity may contribute to the development of IR by triggering metabolic inflammation.Clinical Trial Registration: This study was registered with the Chinese Clinical Trial Registry (Registration number: ChiCTR2300072179).},
}
@article {pmid40593146,
year = {2025},
author = {Sen, A and Imai, A and Miyauchi, E and Yanagisawa, K and Oda, T and Sasaki, F and Uchida, S and Okada, T and Yokobori, T and Saeki, H and Odamaki, T and Sasaki, N},
title = {Comprehensive gene expression analysis of organoid-derived healthy human colonic epithelium and cancer cell line stimulated with live probiotic bacteria.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {22325},
pmid = {40593146},
issn = {2045-2322},
support = {JP 23ae0121046//Japan Agency for Medical Research and Development (AMED) grant/ ; JPMJFR2161//JST FOREST program/ ; 19H03455, 23H02713//Grants-in-Aid for the Japanese Society for the Promotion of Science (JSPS) KAKENHI/ ; Pioneering, 23K17415//Grant-in-Aid for Challenging Research/ ; },
mesh = {Humans ; *Organoids/metabolism/microbiology/cytology ; *Probiotics/pharmacology ; *Intestinal Mucosa/metabolism/microbiology ; Caco-2 Cells ; *Colon/metabolism/microbiology/cytology ; Gene Expression Profiling ; Coculture Techniques ; Cell Line, Tumor ; Transcriptome ; Bifidobacterium/physiology ; Gastrointestinal Microbiome ; Epithelial Cells/metabolism ; },
abstract = {The large intestine has a dense milieu of indigenous bacteria, generating a complex ecosystem with crosstalk between individual bacteria and host cells. In vitro host cell modeling and bacterial interactions at the anaerobic interphase have elucidated the crosstalk molecular basis. Although classical cell lines derived from patients with colorectal cancer including Caco-2 are used, whether they adequately mimic normal colonic epithelial physiology is unclear. To address this, we performed transcriptome profiling of Caco-2 and Monolayer-cultured epithelial cells derived from healthy Human Colonic Organoids (MHCO) cultured hemi-anaerobically. Coculture with the anaerobic gut bacteria, Bifidobacterium longum subsp. longum differentiated the probiotic effects of test cells from those of physiologically normal intestinal and colorectal cancer cells. We cataloged non- or overlapping gene signatures where gene profiles of Caco-2 represented absorptive cells in the small intestinal epithelium, and MHCO showed complete colonic epithelium signature, including stem/progenitor, goblet, and enteroendocrine cells colonocytes. Characteristic gene expression changes related to lipid metabolism, inflammation, and cell-cell adhesion were observed in cocultured live Bifidobacterium longum and Caco-2 or MHCO. B. longum-stimulated MHCO exhibited barrier-enhancing characteristics, as demonstrated in clinical trials. Our data represent a valuable resource for understanding gut microbe and host cell communication.},
}
@article {pmid40593076,
year = {2025},
author = {Krawczyk, K and Rybaczek, D and Locht, C and Pyrzanowska-Banasiak, A and Ciołek, M and Sicinska, P and Rachubik, M and Kowalewicz-Kulbat, M},
title = {Uptake of environmental halophilic archaea by human dendritic cells.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {21912},
pmid = {40593076},
issn = {2045-2322},
support = {2017/27/N/NZ6/02850//Narodowe Centrum Nauki/ ; },
mesh = {Humans ; *Dendritic Cells/microbiology/metabolism/immunology ; *Halobacteriaceae ; Apoptosis ; *Archaea ; },
abstract = {Halophilic archaea are a group distinct from Bacteria and Eukarya, which belong to extremophiles living in highly saline environments. However, they can also exist in the human microbiome. Their impact on the human immune system is poorly known. In this study we examined the interaction of Halorhabdus rudnickae WSM-64[T], isolated from the Barycz area of the Wieliczka Salt-Mine in Poland, and of Natrinema salaciae MDB25[T] from the brine of Lake Medee in Italy, with human monocyte-derived dendritic cells (Mo-DCs). We found that these halophilic archaea invade the cytoplasm and the nucleus of Mo-DCs, but, in contrast to intracellular bacterial pathogens, they do not cause cytotoxic effects on DCs, as no single- or double-stranded DNA breaks (SSB and DSB, respectively), nor chromatin aberrations were noted. Moreover, they did not induce cell cycle alterations, apoptosis or necrosis of DCs. Surprisingly, these halophiles were found to protect against genotoxic activities of Staphylococcus aureus enterotoxin B (SEB), as pre-incubation of the Mo-DCs with the halophilic archaea significantly reduced SEB-induced SSB and DSB, as well as cell cycle disturbance and apoptosis. Therefore, these halophilic archaea can be regarded as safe stimulators for the Mo-DCs to potentially be used as immunomodulators and protective agents for various disorders.},
}
@article {pmid40593020,
year = {2025},
author = {Yue, Y and Yao, B and Liao, F and He, Z and Sangsawad, P and Yang, S},
title = {Fecal microbiota transplantation improves Sansui duck growth performance by balancing the cecal microbiome.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {22403},
pmid = {40593020},
issn = {2045-2322},
support = {31960682//The National Nature Science Foundation of China/ ; 31960682//The National Nature Science Foundation of China/ ; 31960682//The National Nature Science Foundation of China/ ; 31960682//The National Nature Science Foundation of China/ ; 31960682//The National Nature Science Foundation of China/ ; },
mesh = {Animals ; *Ducks/growth &amp; development/microbiology ; *Gastrointestinal Microbiome ; *Fecal Microbiota Transplantation ; *Cecum/microbiology ; Feces/microbiology ; },
abstract = {Improving growth performance is vital in poultry production. Although several studies have established associations between gut microbiota and growth, the direct impacts remain unclear. A total of 120 1-day-old Sansui ducks were randomly assigned to the FMT and CON groups. From the 1st day, ducks in the FMT group were orally administrated with 0.5 mL fecal microbiota suspension for three consecutive days, while sterile PBS solution was used as a substitute in the CON group. The results revealed that FMT improved average daily gain (ADG) (P < 0.001) and body weight (BW) (P < 0.001), with a tendency for a better feed conversion rate (FCR) (P = 0.062). LEfSe analysis indicated a significant increase in the abundance of the Lactobacillus (P < 0.001), Bifidobacterium (P = 0.006), Megamonas (P = 0.008), and Subdoligranulum (P = 0.005) in the FMT group. Similarly, the phyla Firmicutes/Bacteroidetes ratio was higher in the FMT group compared to the CON group. Additionally, the ACE, Chao, and Shannon indices were also significantly higher in the FMT group (P < 0.001). To sum up, FMT enhanced growth performance, which could be associated with reducing proinflammatory pathogen colonization in the duck cecum. This modulating effect likely results from increased microbial diversity and the enrichment of beneficial bacteria.},
}
@article {pmid40593012,
year = {2025},
author = {Sitko, K and Piotrowska, E and Podlacha, M and Zagórska, N and Starke, MD and Trzeciak, M and Tukaj, S},
title = {Topical application of the HSP90 inhibitor 17-AAG reduces skin inflammation and partially restores microbial balance: implications for atopic dermatitis therapy.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {21245},
pmid = {40593012},
issn = {2045-2322},
support = {2020/39/B/NZ6/00357//Polish National Science Centre (NCN)/ ; 2020/39/B/NZ6/00357//Polish National Science Centre (NCN)/ ; 2020/39/B/NZ6/00357//Polish National Science Centre (NCN)/ ; 2020/39/B/NZ6/00357//Polish National Science Centre (NCN)/ ; 2020/39/B/NZ6/00357//Polish National Science Centre (NCN)/ ; },
mesh = {*Benzoquinones/administration &amp; dosage/pharmacology ; *Lactams, Macrocyclic/administration &amp; dosage/pharmacology ; Animals ; *Dermatitis, Atopic/drug therapy/pathology/chemically induced/microbiology/metabolism ; *HSP90 Heat-Shock Proteins/antagonists &amp; inhibitors/metabolism ; Mice ; Humans ; Disease Models, Animal ; Administration, Topical ; *Skin/drug effects/pathology/microbiology ; Female ; Cytokines/metabolism ; Eosinophils/drug effects/metabolism ; Gastrointestinal Microbiome/drug effects ; Staphylococcus aureus/drug effects ; Inflammation/drug therapy ; Keratinocytes/drug effects/metabolism ; },
abstract = {Heat shock proteins belonging to the HSP90 family promote inflammation and are potential therapeutic targets in inflammatory and autoimmune diseases. Here the effects of the HSP90 inhibitor 17-AAG applied topically were evaluated in a DNCB-induced murine model of atopic dermatitis (AD). The use of 17-AAG improved clinical disease activity without causing toxicity in the animals. Topical application of 17-AAG resulted in reduced epidermal hyperplasia, decreased expression of TSLP, IL-5, and IL-6, as well as reduced activation of NF-κB in the skin. In addition, the eosinophil proportion in the blood and eosinophil peroxidase (EPX) activity in the skin were significantly reduced in 17-AAG-treated AD mice. The inhibitory effects of 17-AAG on the production of epidermal alarmins, T-helper cell-associated cytokines, and ROS release were demonstrated in cultures of activated human keratinocytes, CD4[+] T lymphocytes, and eosinophils, respectively. Finally, next-generation sequencing metagenomic approaches revealed that topical application of 17-AAG partially restored the normal gut microbiome in AD mice. Moreover, 17-AAG inhibited Staphylococcus aureus biofilm formation in vitro. The findings of this study, combined with the observed increase in HSP90 and EPX activity in the leukocytes of the analyzed cohort of AD patients, support the potential therapeutic use of HSP90 inhibitors in individuals with AD.},
}
@article {pmid40592975,
year = {2025},
author = {De Greef, J and Nguyen, KN and Van Hul, M and Puel, A and Yombi, JC and Vandercam, B and Vincent, A and Elens, L and Belkhir, L and Haufroid, V and Cani, PD},
title = {Associations between weight gain, integrase inhibitors antiretroviral agents, and gut microbiome in people living with HIV: a cross-sectional study.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {22603},
pmid = {40592975},
issn = {2045-2322},
support = {WELBIO-CR-2022A-02//Walloon excellence in life sciences and biotechnology/ ; FNRS-CDR J.0085.21//Fonds De La Recherche Scientifique - FNRS/ ; program no. 40007505//Fonds De La Recherche Scientifique - FNRS/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; Male ; Female ; Cross-Sectional Studies ; *HIV Infections/drug therapy/microbiology ; *Weight Gain/drug effects ; *HIV Integrase Inhibitors/adverse effects/therapeutic use ; Pyridones/adverse effects ; Middle Aged ; Adult ; Heterocyclic Compounds, 3-Ring/adverse effects/therapeutic use ; Piperazines/adverse effects ; Oxazines ; Heterocyclic Compounds, 4 or More Rings/adverse effects/therapeutic use ; Amides ; },
abstract = {Dolutegravir and bictegravir are second-generation HIV integrase strand transfer inhibitors (INSTIs) that were previously associated with abnormal weight gain. This monocentric cross-sectional study investigates associations between weight gain during the first year after initiation of dolutegravir, bictegravir or other anchor drugs and gut microbiome diversity as well as taxa composition. The study enrolled 79 participants receiving dolutegravir, 32 receiving bictegravir and 10 receiving non-INSTI based regimens. Most of them were treatment experienced at initiation of those anchor drugs agents. Although weight gain was not linked to overall bacterial diversity, strong associations with specific taxa were demonstrated (FDR q < 0.01). Using multiple linear regression, we identified 4 distinct groups of bacteria associated with either dolutegravir, bictegravir, weight loss or weight gain under treatment, allowing a machine learning model to predict 15.9% of the weight gain variability regardless of sex, age and body mass index (RMSE: 0.0126). Dysosmobacter sp. and Haemophilus sp., two bacteria previously associated with host metabolism, were among the strongest predictors. Our findings link INSTIs, weight gain, and the gut microbiome. Future research should investigate the causal role of the identified taxa to improve our understanding of microbiome-drug interactions and further support personalized antiretroviral strategies.Trial registration: Eudra-CT 2020-001103-17 (registration date: 2020-12-01).},
}
@article {pmid40592825,
year = {2025},
author = {Mali, N and Mali, S and Zhang, L and Fu, P},
title = {Interplay between gut microbiota and acute kidney injury: a review of their mutual influence and causation.},
journal = {Renal failure},
volume = {47},
number = {1},
pages = {2522976},
pmid = {40592825},
issn = {1525-6049},
mesh = {Humans ; *Acute Kidney Injury/microbiology/immunology/physiopathology ; *Gastrointestinal Microbiome/immunology/physiology ; Kidney/physiopathology/microbiology ; Animals ; },
abstract = {It is unclear, therefore, exactly how gut microbes and renal processes communicate. Recent developments in the field of microbiome research present chances to enhance our comprehension and management of acute kidney injury (AKI). This review highlights important ideas and suggests more research while giving a general summary of the microbiome's influence on kidney function and AKI. AKI is a complex condition that develops through a variety of pathways. Recent experimental research has highlighted the important role that the gut microbiota plays in the course of AKI. Our understanding of human biology has been completely transformed by the current increase in gut microbiota research. Amazing progress in DNA sequencing analysis, especially in the areas of metagenomics and metatranscriptomics, has greatly increased our ability to measure and track complex microbial populations. As such, we are now in a better position to look at how these communities affect human health and illness. As a result, the relationships between renal physiology and pathophysiology and the gut microbiota are now better understood. Both experimental AKI and chronic renal illness have been linked to changes in the intestinal microbiome. This succinct review attempts to examine our present knowledge of the immune-modulatory effects of the gut microbiota, how kidney disorders are influenced by it, and the possible reciprocal interaction between kidney diseases and the microbiota. Subsequent investigations ought to concentrate on delving deeper into the function of the gut microbiota in renal disorders and finding possible therapeutic strategies for adjusting it.},
}
@article {pmid40592776,
year = {2025},
author = {Zhang, X and Ishikawa, D and Nagahara, A},
title = {Fecal Microbiota Transplantation for Immune Regulation: Improving Ulcerative Colitis and Enhancing Cancer Immunotherapy.},
journal = {International immunology},
volume = {},
number = {},
pages = {},
doi = {10.1093/intimm/dxaf038},
pmid = {40592776},
issn = {1460-2377},
abstract = {The gut microbiota plays an integral role in maintaining health and regulating various host functions, including immune responses. Fecal microbiota transplantation (FMT) has emerged as a promising therapeutic approach to restore gut microbial balance. Although widely recognized for its efficacy in treating ulcerative colitis (UC), FMT is now being investigated as an adjuvant therapy to enhance the efficacy of immune checkpoint inhibitors (ICIs) in cancer treatment. This review summarizes the clinical applications of FMT in UC treatment and its potential role in cancer immunotherapy. FMT exhibits varying degrees of efficacy in the treatment of UC, with differences in outcomes attributed to variations in administration methods and donor selection. In cancer therapy, FMT has demonstrated the potential to improve ICI responses, particularly in patients with melanoma. However, its effects on other cancers remain unclear. Although FMT holds promise for UC and cancer immunotherapy, challenges such as inconsistent clinical outcomes and methodological variations persist. Standardized protocols and mechanistic studies are crucial to optimize FMT-based therapeutic strategies, and further research is required to establish its efficacy under diverse clinical conditions.},
}
@article {pmid40592418,
year = {2025},
author = {Choe, JY and Donkor, M and Zhang, Y and Gorham, IK and Bradshaw, JL and Vann, PH and Sumien, N and Cunningham, RL and Allen, MS and Quinn, B and Phillips, NR and Jones, HP},
title = {Evidence of postnatal neglect-dependent resiliency in thymic, gut, and behavioral outcomes in a mouse model of early life stress.},
journal = {Brain, behavior, and immunity},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.bbi.2025.06.036},
pmid = {40592418},
issn = {1090-2139},
abstract = {BACKGROUND: Early life is an impressionable period often regarded as the window of opportunity. Environmental exposures, such as stress, in the early postnatal period can influence developmental trajectory and long-term health. The brain and immune systems continue to develop after birth and are shaped by postnatal exposures. While chronic traumatic stress is understood to adversely affect individuals by overwhelming coping abilities, there is evidence for stress exposure to be beneficial by promoting resilience. Early life stress (ELS) is a significant postnatal exposure, which encompasses childhood maltreatment and trauma. Neglect is the most common form of maltreatment in children and takes many forms, including physical and nutritional.<br><br>METHODS: Here, we describe a novel mouse model of neglect-related ELS based on maternal separation with early weaning (MSEW) with a distinct early weaning (EW) stress group to study how an environment of neglect impacts the developing microbiome, thymocytes, and stress-related behavior. Neglect-related stress was emulated based on scheduled dam-pup separation (physical neglect) and a high carbohydrate early-wean diet (malnutrition). C57BL/6J mice were bred in-house and ELS pups were subjected to: (1) daily dam-pup separation on postnatal days (PD) 2-13 and/or (2) early weaning to a high carbohydrate diet on PD14-21.<br><br>RESULTS: The present study focused on a defined early life window (PD0-21) and revealed that MSEW versus EW exposures generate distinguishable and distinct effects on behavior and thymic T cells, leading to phenotypes of stress resilience versus vulnerability. Although impacts of the two ELS groups were indistinguishable on lower gastrointestinal tract microbiome composition, the effects on ELS groups were significant compared to controls.<br><br>CONCLUSIONS: Our findings provide evidence for circumstances where prior stress can induce resilience and emphasizes the nuanced approach required for studies to begin parsing out toxic versus beneficial stress.},
}
@article {pmid40592130,
year = {2025},
author = {Hall, CV and Garnier, L and Gencoglu, M and Varesio, E and Tardy, S and Salgado, DB and Scapozza, L and Marizzoni, M and Frisoni, GB and Gurry, T},
title = {Characterising high-resolution dynamics of inflammatory and SCFA responses to food consumption in healthy men: A pilot biomarker discovery study.},
journal = {Cytokine},
volume = {193},
number = {},
pages = {156990},
doi = {10.1016/j.cyto.2025.156990},
pmid = {40592130},
issn = {1096-0023},
abstract = {Understanding inflammatory responses after food consumption and at fasting is crucial for assessing the impact of diet on long-term health. To study these responses meaningfully, biomarkers must be responsive to food intake, consistent across individuals, and predictive of future health outcomes. Preliminary data suggest that anti-inflammatory short-chain fatty acids (SCFAs), produced by the microbiota from prebiotic fibre, might be relevant biomarkers in the food-induced inflammatory reaction, but data on their timing, magnitude, dynamics at fasting and during the postprandial state, and relationship with other biomarkers are currently lacking. This knowledge gap impacts our ability to identify reliable biomarkers that can be used as surrogate outcomes in dietary interventions and research focused on reducing chronic disease risk. In this biomarker discovery study, we aimed to identify meal-responsive inflammatory biomarkers and assess plasma SCFAs pharmacokinetics following meal intake. Three healthy male participants consumed three isoenergetic meals with different theoretical pro-inflammatory potential, one per week over a three-week period: an anti-inflammatory meal (Meal A), a pro-inflammatory meal (Meal B), and a pro-inflammatory meal with a butyrate-promoting prebiotic fibre supplement (Meal C). For each meal condition, blood samples were taken continually over a 30-h period, and inflammatory cytokines and plasma SCFAs were measured. Cytokine biomarker dynamics were classified based on their response to meals. We identified 26 meal-responsive biomarkers, with three-CST5, FGF-19, and ST1A1-showing consistent postprandial changes across participants. The study also revealed significant interindividual variability, with 23 biomarkers displaying highly personalised responses to food intake. Quantitative analysis of plasma SCFA concentrations indicated non-trivial dynamics, but a clear accumulation of butyrate, acetate, and propionate in plasma during a 25-h period following meal intake. Our findings highlight the complexity of the postprandial response, emphasising the need for thoughtful consideration of study design, including the choice and sampling rate of biomarkers. The identified biomarkers offer potential for future research and clinical applications, improving the understanding of diet-induced inflammation and its role in chronic disease prevention.},
}
@article {pmid40591953,
year = {2025},
author = {Nakagaki, M and Hajkowicz, K and Roberts, JA and Henden, AS},
title = {Cause and effect? A review of the impact of antibiotics on the gut microbiome in patients undergoing hematopoietic stem cell transplantation.},
journal = {Expert review of anti-infective therapy},
volume = {},
number = {},
pages = {},
doi = {10.1080/14787210.2025.2527970},
pmid = {40591953},
issn = {1744-8336},
abstract = {INTRODUCTION: Patients undergoing allogeneic hematopoietic stem cell transplantation (allo-HSCT) are at high risk of infection due to immunosuppression, prompting routine use of prophylactic and broad-spectrum antibiotics for treatment. However, emerging evidence suggests that gut microbiome disruption (dysbiosis), partly caused by antibiotic use, is associated with poorer transplant outcomes, including graft-versus-host disease (GVHD), infection, and mortality.<br><br>AREAS COVERED: This narrative review discusses antibiotic use to prevent and treat febrile neutropenia in allo-HSCT recipients, including effectiveness, impacts on microbiome and GVHD, antimicrobial resistance and Clostridioides difficile infection (CDI). It also reviews available strategies to reduce unnecessary antibiotic use and proposes potential future interventions. A comprehensive PubMed search was conducted through 2024 using terms related to HSCT, antimicrobials, microbiome, resistance, and CDI.<br><br>EXPERT OPINION: Improving outcomes while minimizing emergence of antibiotic resistance and CDI requires personalized, risk-adaptive antimicrobial stewardship (AMS). Tailored AMS approaches, including patient risk stratification and early de-escalation, could limit unnecessary antibiotic use and mitigate adverse effects. In the future, microbiome preservation and restoration may reduce transplant complications by maintaining colonization resistance and immune balance. Integrating these strategies into allo-HSCT care is essential for optimizing both clinical and microbiological outcomes.},
}
@article {pmid40591820,
year = {2025},
author = {Lutz, KC and Yang, S and Bedi, T and Neugent, ML and Madhavaram, N and Yao, B and Zhan, X and De Nisco, NJ and Li, Q},
title = {MiCoDe: A web tool for performing microbiome community detection using a Bayesian weighted stochastic block model.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btaf384},
pmid = {40591820},
issn = {1367-4811},
abstract = {SUMMARY: The Microbiome Community Detector (MiCoDe) software is a free user-friendly web tool that is designed to cluster a network of microbial taxa into communities using a Bayesian weighted stochastic block model. MiCoDe also filters the data automatically and accounts for the challenges of microbiome high-throughput sequencing data including high-dimensionality, compositionality, zero inflation, and nonlinearity. While MiCoDe is based on a rigorous statistical unsupervised learning model, our web tool can be easily used by any investigator. Users simply upload a csv file that contains their taxonomic abundance data where rows correspond to samples and columns correspond to taxa. Then, users make a few selections regarding data transformation, network estimation, and the number of communities in order to run the online analysis. If users are unsure of what selections to make, then they can opt for the default settings as these are our recommended settings. In this paper, we discuss the motivation, methodology, implementation, and results of MiCoDe. We also discuss how MiCoDe can be adapted by the user and how it may evolve over time. Our software is a valuable tool for microbiome community detection.<br><br>MiCoDe is freely available online at https://lce.biohpc.swmed.edu/micode/, does not require installation, and is not browser-specific. Users can also work locally using our R code, which is freely available on GitHub at https://github.com/klutz920/MiCoDe.<br><br>SUPPLEMENTARY INFORMATION: The supplemental file (supplement.pdf) contains the full details about the model as well as additional tables and figures.},
}
@article {pmid40591438,
year = {2025},
author = {Sumida, K and Mallisetty, Y and Shrestha, P and Vo, A and Khan, RN and Thomas, F and Kalantar-Zadeh, K and Kovesdy, CP},
title = {Comparative Effectiveness of Lubiprostone and Stool Softeners on Risk of Kidney Outcomes in Patients with Chronic Kidney Disease.},
journal = {Clinical journal of the American Society of Nephrology : CJASN},
volume = {},
number = {},
pages = {},
doi = {10.2215/CJN.0000000779},
pmid = {40591438},
issn = {1555-905X},
abstract = {BACKGROUND: Lubiprostone, a chloride channel activator used to treat constipation, has been suggested to exert kidney protective effects by improving the gut microbiome. However, little is known about the comparative effectiveness of lubiprostone vs. conventional laxatives on the risk of kidney outcomes in patients with chronic kidney disease (CKD).<br><br>METHODS: Among United States Veterans with CKD and constipation receiving care from the Veterans Administration healthcare system over 2004-2019, we identified incident users of lubiprostone vs. stool softeners (docusate sodium or calcium), excluding combined users of the examined drugs. We used a target trial emulation approach to examine the association of lubiprostone vs. stool softener use with subsequent risk of a composite kidney outcome (incident end-stage kidney disease, incident estimated glomerular filtration rate [eGFR] <15 mL/min/1.73m2, or 57% reduction in eGFR, as primary) and change in eGFR (as secondary). The associations were examined using weighted Cox models for the composite kidney outcome and weighted multinomial logistic regression models for change in eGFR, applying a propensity score (PS)-overlap weighting method to minimize confounding by indication.<br><br>RESULTS: Among 52,231 patients who met eligibility criteria, 551 (1%) and 51,680 (99%) were incident users of lubiprostone and stool softeners, respectively. Compared with incident stool softener users, incident lubiprostone users had significantly lower risk of a composite kidney outcome (hazard ratio [95% Confidence Interval (CI)], 0.70 [0.51-0.97]) and lower risk of experiencing more progressive eGFR decline (multinomial odds ratios [95% CI] for eGFR slope <-3 and -3 to <-1 [vs. -1 to <0] mL/min/1.73m2/year, 0.39 [0.23-0.68] and 0.73 [0.53-1.01], respectively).<br><br>CONCLUSION: Incident lubiprostone (vs. stool softener) use was independently associated with lower risk of progressive kidney function decline in patients with CKD and constipation. Further studies are needed to refine the comparative effectiveness of different laxative types on kidney outcomes in clinical trials.},
}
@article {pmid40591436,
year = {2025},
author = {Narasaki, Y and Rhee, CM and Li, Z},
title = {The Role of Precision Nutrition in Kidney Disease.},
journal = {Clinical journal of the American Society of Nephrology : CJASN},
volume = {},
number = {},
pages = {},
doi = {10.2215/CJN.0000000807},
pmid = {40591436},
issn = {1555-905X},
abstract = {Precision nutrition utilizes an individualized approach in which dietary interventions are tailored according to patients' genetic, biologic, and environmental factors. There are various nutritional guidelines specific to chronic kidney disease (CKD) patients, and while rigorous, they provide generalized recommendations that may not fully address the unique nutritional needs of individual patients. For example, while guidelines endorse prescription of low-protein diets among people with metabolically-stable stages 3-5 non-dialysis dependent CKD to reduce kidney disease progression, these recommendations do not fully account for the genetic, metabolic, or physiologic factors that affect how different patients respond to specific dietary interventions. Furthermore, older patients with CKD may require different levels of protein intake compared to younger individuals, given that aging affects protein metabolism. In contrast to conventional nutritional management approaches, which typically utilize a one-size-fits-all model, precision nutrition and personalized nutrition utilize an individualized approach. While the terms precision nutrition and personalized nutrition are sometimes used interchangeably, there are nuanced differences in their definitions such that precision nutrition is more data-driven and utilizes precise information (e.g., genetic, microbiome, metabolic) to inform management, whereas personalized nutrition encompasses a broader approach that also takes into consideration factors such as lifestyle, environment, and patients' preferences. Precision nutrition is evolving rapidly with advances in data collection, deep data analysis, and modeling with application of artificial intelligence, while personalized nutrition is what we practice today leveraging available data and guidelines to meet each individual patient's needs. Numerous advancements have led to a growing armamentarium of tools in precision nutrition, including nutrigenetics, nutrigenomics, microbiome profiling, metabolomics, and proteomics, which can be leveraged to guide dietary recommendations according to an individual's unique characteristics. In this Review, we examine the role of precision nutrition in CKD, tools used in precision medicine, and practical application of these approaches in treating kidney disease patients.},
}
@article {pmid40591379,
year = {2025},
author = {Orenburkina, OI and Rezbaeva, GN and Dudurich, VV and Babushkin, AE and Sogomonian, KS and Danilova, AA and Danilov, LG},
title = {[Microbiota of the ocular surface in children with myopia].},
journal = {Vestnik oftalmologii},
volume = {141},
number = {3},
pages = {5-12},
doi = {10.17116/oftalma20251410315},
pmid = {40591379},
issn = {0042-465X},
mesh = {Humans ; Child ; *Myopia/diagnosis/microbiology/physiopathology ; Male ; Female ; Adolescent ; *Microbiota ; *Conjunctiva/microbiology ; *Bacteria/genetics/isolation &amp; purification/classification ; RNA, Ribosomal, 16S/genetics ; Disease Progression ; },
abstract = {UNLABELLED: A healthy ocular surface is characterized by relatively stable and comparatively low microbial diversity. However, pathological conditions can provoke shifts in the composition of bacterial taxa, which may be associated, among other factors, with the progression of myopia.<br><br>PURPOSE: This study compared the taxonomic diversity of the conjunctival microbiota in children with varying degrees of myopia and those without clinically confirmed myopia.<br><br>MATERIAL AND METHODS: Ocular surface samples were obtained from 29 children aged 6-17 years with myopia (58 eyes) and from 12 children of the control group aged 9-17 years (24 eyes). The taxonomic composition of the conjunctival microbiota was analyzed using 16S ribosomal RNA gene (rRNA) sequencing, followed by microbiome profiling through bioinformatics and statistical tools.<br><br>RESULTS: The ocular surface microbiota in children with myopia demonstrated higher alpha diversity compared to the control group. This was confirmed by values of the Chao (reflecting low-abundance taxa) and Shannon (reflecting overall bacterial diversity - higher diversity means higher index; optimal value; 3.1-4.2) indices. The results revealed a clear trend toward differentiation in bacterial composition between myopic and control groups. These differences were associated with changes in the relative abundance of opportunistic bacteria depending on the degree of myopia.<br><br>CONCLUSION: The taxonomic diversity of the ocular microbiota at the genus level in patients with varying degrees of myopia was characterized by a higher number of taxonomic units compared to the control group. The general trend is an increase in the biodiversity of the bacterial composition due to an increase in the relative representation of opportunistic microorganisms. Further research on the influence of the ocular microbiota on the progression of myopia is needed.},
}
@article {pmid40591053,
year = {2025},
author = {Ma, CY and Zhao, J and Xu, XT and He, XL and Qin, SB and Zhou, JY},
title = {Predictive biomarkers in the gut microbiome and metabolome for severe acute radiation enteritis in cervical cancer radiotherapy.},
journal = {Discover oncology},
volume = {16},
number = {1},
pages = {1220},
pmid = {40591053},
issn = {2730-6011},
abstract = {INTRODUCTION: Radiation enteritis (RE), a common side effect, is a growing health concern, particularly the severe acute form of RE (SARE), among cervical cancer patients undergoing radiation therapy. Currently, there is no noninvasive diagnostic method for SARE. This study aimed to identify gut microbiomics- and metabolomics-based signatures, and assess their predictive value for SARE.<br><br>METHODS: Samples from 50 cervical cancer patients receiving volumetric modulated arc therapy (VMAT) were collected for gut microbiota and metabolomic profiling. 16&#xa0;S rDNA amplicon sequencing analyzed gut microbiota, and nontargeted liquid chromatography-mass spectrometry determined metabolomic profiles. Multivariate and pathway analyses identify independent metabolites associated with SARE. A predictive nomogram for SARE, combining multi-omics-based signatures and clinical characteristics, was constructed and evaluated using the area under the receiver operating characteristic curve (AUC) and calibration curve.<br><br>RESULTS: Fecal microbiome analysis showed characteristic alterations in SARE, mainly including Faecalibacterium enterotype-3, Escherichia, and Shigella enterotype-2. Metabolomic analyses identified a panel of molecules significantly associated with SARE. Furthermore, an intuitive nomogram consisting of these multi-omics signatures (serum COX-2 and fecal phenylethylamine), combined with clinical characteristics with predictive value, was constructed to predict SARE. Notably, the evaluation of model performance suggested an excellent predictive discrimination for SARE [AUC, 0.975; 95% confidence interval (CI), 0.953-0.998]. Calibration curve analysis showed an adequate calibration for the model and good consistency between the predicted SARE cases with this newly developed model and the actual SARE cases.<br><br>CONCLUSION: This study identified noninvasive signatures, including COX-2 and phenylethylamine, as promising predictive biomarkers for SARE and developed an intuitive nomogram with good predictive accuracy for SARE in cervical cancer patients.},
}
@article {pmid40591032,
year = {2025},
author = {Abebaw, D and Akelew, Y and Adugna, A and Tegegne, BA and Teffera, ZH and Belayneh, M and Fenta, A and Selabat, B and Kindie, Y and Baylie, T and Mekuriaw, MG and Jemal, M and Atnaf, A},
title = {Immunomodulatory properties of the gut microbiome: diagnostic and therapeutic potential for rheumatoid arthritis.},
journal = {Clinical and experimental medicine},
volume = {25},
number = {1},
pages = {226},
pmid = {40591032},
issn = {1591-9528},
mesh = {Humans ; *Arthritis, Rheumatoid/therapy/diagnosis/immunology/microbiology ; *Gastrointestinal Microbiome/immunology ; Dysbiosis/immunology ; Probiotics/therapeutic use ; *Immunomodulation ; Fecal Microbiota Transplantation ; Biomarkers ; Animals ; },
abstract = {Rheumatoid arthritis (RA) is a chronic autoimmune disorder characterized by persistent joint inflammation, synovial hyperplasia, and progressive joint destruction. Despite advancements in biologic disease-modifying antirheumatic drugs (bDMARDs) and TNF-α blockers, many RA patients still require more effective treatment options. Although genetic and environmental factors play a role in RA development, recent studies have emphasized the influence of the gut microbiota on disease onset and progression. Dysbiosis, or an imbalance in the gut microbial composition, has been linked to immune dysregulation, increased intestinal permeability, and systemic inflammation, all contributing to RA development. Research has revealed changes in the gut microbiome of RA patients, including an increased prevalence of Prevotella copri and a decreased presence of beneficial microbes such as Bifidobacterium, Bacteroides, and Lactobacillus. RA patients exhibit altered metabolite profiles, with reduced levels of short-chain fatty acids (SCFAs), such as acetate, propionate, and butyrate, which are linked to immune regulation and intestinal barrier function. Specific metabolites, such as L-arginine, phosphorylcholine, and arachidonic acid, have potential as RA biomarkers, with predictive value for diagnosis. Therapeutic approaches focusing on the microbiome, including probiotics, fecal microbiota transplantation, and traditional medicines, show promise in alleviating RA symptoms and regulating immune function. This review provides an updated overview of the immunomodulatory effects of the gut microbiome and explores its potential applications in the diagnosis and treatment of RA.},
}
@article {pmid40590731,
year = {2025},
author = {Ahmed, U and Fatima, F and Farooq, HA},
title = {Microbial dysbiosis and associated disease mechanisms in maternal and child health.},
journal = {Infection and immunity},
volume = {},
number = {},
pages = {e0017925},
doi = {10.1128/iai.00179-25},
pmid = {40590731},
issn = {1098-5522},
abstract = {Maternal and infant microbiome dysbiosis is associated with poor health outcomes-gut, vaginal, and placental microbiome disruptions in the gut, vaginal, and potentially placental microbiomes-though the existence of a distinct placental microbiome remains controversial-have been linked to pregnancy difficulties and neonatal infections. Dysbiosis leads to inflammation, oxidative stress, and disruptions in the gut-brain axis, which in turn affect immunological control, metabolic balance, and neurodevelopment. Maternal age, antibiotic exposure, and cesarean delivery increase microbial imbalances, raising the risk of preterm birth, gestational diabetes, and neurodevelopmental disorders. New research highlights the importance of systems-level microbial interactions in the gut-vagina axis and maternal-fetal health. Probiotics, prebiotics, and microbiota transplants may treat microbiome disorders. To reduce dysbiosis risks, research should focus on microbiome-based biomarkers, predictive AI models, and global health policy. Understanding microbial interactions at the system level is essential for maternal and child health.},
}
@article {pmid40590563,
year = {2025},
author = {Li, D and Saavedra, PHV},
title = {The interplay between host immunity and Clostridioides difficile infection.},
journal = {mBio},
volume = {},
number = {},
pages = {e0356224},
doi = {10.1128/mbio.03562-24},
pmid = {40590563},
issn = {2150-7511},
abstract = {Clostridioides difficile infection (CDI) is a major public health concern and the leading cause of healthcare-associated infectious enteric inflammation worldwide. Disruption of the gut microbiome predisposes to C. difficile colonization, proliferation, and production of cytotoxic toxins that damage the intestinal epithelial layer. CDI treatment is challenging in part due to the emergence of antibiotic-resistant strains and the lack of efficient vaccines, predisposing individuals to recurrent CDI episodes. Consequently, there is an urgent need for the development of novel therapeutic approaches. Both innate and adaptive immune responses contribute to protection against CDI, but the cellular and molecular mechanisms underlying this process are not completely understood. In this mini review, I discuss the history and recent findings with a focus on mechanisms that drive host immunity to C. difficile, with a conclusion on where the field stands and outstanding questions that remain elusive.},
}
@article {pmid40590552,
year = {2025},
author = {Yao, W and Wen, R and Huang, Z and Huang, X and Chen, K and Hu, Y and Li, Q and Zhu, W and Ou, D and Bai, H},
title = {Gut microbiota composition in early pregnancy as a diagnostic tool for gestational diabetes mellitus.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0339024},
doi = {10.1128/spectrum.03390-24},
pmid = {40590552},
issn = {2165-0497},
abstract = {UNLABELLED: Gestational diabetes mellitus (GDM) is a metabolic disorder that poses substantial risks to both maternal and fetal health. Early intervention has been shown to effectively reduce various complications. Gut microbiota dysbiosis is strongly linked to the onset and progression of GDM and may serve as a critical early-warning biomarker. In this study, we systematically analyzed the fecal microbiota of 61 pregnant women during the first trimester using 16S rRNA sequencing. These microbial profiles were correlated with oral glucose tolerance test (OGTT) results at 24-28 weeks of gestation and clinical delivery outcomes. Our analysis identified significant differences in gut microbiota composition between GDM and healthy pregnancies, observed at both the phylum and genus levels early in gestation. Leveraging these microbial distinctions, we developed an early diagnostic model based on genus-level markers, achieving an area under the curve (AUC) of 98.23, indicating high diagnostic precision. This study highlights early-pregnancy microbiota signatures associated with GDM and provides a robust scientific basis for developing microbiota-based diagnostic tools, offering new avenues for GDM prevention and management.<br><br>IMPORTANCE: Gestational diabetes mellitus (GDM) poses significant risks to both maternal and fetal health, but early intervention can reduce complications. This study identifies gut microbiota signatures associated with GDM in the first trimester, providing a potential early diagnostic biomarker. By analyzing fecal microbiota profiles, we developed a diagnostic model with high accuracy (AUC = 98.23). These findings suggest that microbiota-based tools could enable early, non-invasive detection of GDM, offering new opportunities for prevention and personalized management. This research highlights the role of the gut microbiome in pregnancy and has important implications for improving maternal and fetal health outcomes.},
}
@article {pmid40590551,
year = {2025},
author = {Renno, AJ and Shields, RC and McLellan, LK},
title = {Bacterial evolution in the oral microbiome: the role of conjugative elements and horizontal gene transfer.},
journal = {Journal of bacteriology},
volume = {},
number = {},
pages = {e0006625},
doi = {10.1128/jb.00066-25},
pmid = {40590551},
issn = {1098-5530},
abstract = {As one of the most diverse bacterial populations within the human body, the oral microbiome encodes a wealth of genetic information. Horizontal gene transfer, driven by mobile genetic elements, takes advantage of this information to influence bacterial evolution and the spread of phenotypes (antibiotic resistances, virulence attributes, and metabolic capabilities) among oral microbes. Although widespread within microbial communities, fundamental aspects of the mobile elements that drive horizontal gene transfer within the oral cavity remain poorly understood. In this review, we explore what is known about the role of horizontal gene transfer in bacterial evolution within the oral microbiome and the elements that facilitate this transfer, with a specific focus on conjugative DNA transfer. Conjugative elements are found in virtually all bacterial phylogenetic clades, and some can mediate genetic exchange between distantly related organisms. This is of particular interest in the diverse microcosm of the oral cavity, specifically how it drives the evolution and virulence of dental pathogens. Finally, we highlight advances in our understanding of the unique biology within dental plaque and how these might influence our understanding of bacterial gene transfer, and thus human health and disease.},
}
@article {pmid40590527,
year = {2025},
author = {Bridy, PV and Cruz, JC and Covington, JL and Islam, TI and Hadley, CE and Tran, K and Fry, R and Sheffield, BA and Serrano, M and Buck, GA and Zhao, J and Tossas, KY and Meyers, C and Morgan, IM and James, CD and Jefferson, KK},
title = {Human papillomavirus 16 mitigates Sneathia vaginalis-induced damage to cervical keratinocytes.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0015225},
doi = {10.1128/msphere.00152-25},
pmid = {40590527},
issn = {2379-5042},
abstract = {Sneathia vaginalis is a bacterial component of the vaginal microbiome that is of clinical interest because of its association with preterm birth and other obstetric complications. It produces a cytotoxin, but little is known about the mechanism through which it kills epithelial cells or the role that cytotoxicity plays in bacterial survival. Recent microbiome studies demonstrate an association between S. vaginalis and human papillomavirus (HPV) within the female reproductive tract, suggesting that HPV and S. vaginalis could interact in some way within this shared niche. We analyzed 16S rRNA survey and HPV typing data from our Vaginal Human Microbiome Project and found, in agreement with other reports, that S. vaginalis was associated with HPV infection. To test the hypothesis that HPV promotes the growth of S. vaginalis, growth and cytotoxicity of S. vaginalis in co-culture with HPV16-positive and HPV-negative human cervical keratinocytes (HCK) were quantitatively assessed. Organotypic HCK rafts expressing HPV16 were more resistant to S. vaginalis-induced damage, as assessed by histology, and supported increased bacterial growth relative to HPV-negative HCK rafts. When S. vaginalis was co-cultured with HPV16-positive and HPV-negative HCK monolayers, cytotoxicity was observed in both HPV16-positive and HPV-negative cells, but HPV16-positive cells were more resistant to the toxic effects of the bacteria and supported bacterial growth for an extended period of time. In conclusion, HPV16 may protect cervical keratinocytes from the cytotoxic effects of S. vaginalis, preventing the eradication of colonized cells and supporting bacterial growth, and this could underlie the association between S. vaginalis and HPV in vivo.IMPORTANCESneathia vaginalis (S. vaginalis) is a bacterial species that lives in the human vagina and can cause complications during pregnancy if it invades the uterus. It is capable of killing cervical epithelial cells. Human papillomaviruses (HPV) are sexually transmitted viruses that can cause genital lesions and cervical cancer. Recently, multiple reports describe an association between S. vaginalis and HPV. This study used cultured cervical epithelial cells expressing the high-risk HPV type, HPV16, and HPV-negative cells to determine whether HPV promotes the growth of S. vaginalis. We found that HPV16 promotes the survival of cervical epithelial cells that are exposed to S. vaginalis. Survival of cervical epithelial cells may benefit the growth of S. vaginalis, which adhere to and feed off of these cells to survive in the female reproductive tract.},
}
@article {pmid40590505,
year = {2025},
author = {Ghosheh, A and Alon, M and Kenneth-Mordoch, S and Kleinman, Z and Medema, MH and Finkel, OM},
title = {Diverse rhizospheric Bacillus are required for protection against a leaf pathogen.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf134},
pmid = {40590505},
issn = {1751-7370},
abstract = {The microbiota plays a crucial role in protecting plants from pests and pathogens, as experimental disruptions to the microbiota cause plants to succumb to otherwise asymptomatic infections. To understand how microbial plant defense is deployed, we applied a complex and tractable plant-soil-microbiome microcosm. This system, consisting of Arabidopsis plants and a 150-member bacterial synthetic community, provides a platform for the discovery of novel bacterial plant-beneficial traits, under a realistically complex microbial community context. To identify which components of the plant microbiota are critical for plant defense, we deconstructed this microcosm top-down, removing different microbial groups from the community to examine their protective effect on the plant when challenged with the leaf pathogen Pseudomonas syringae pv. tomato DC3000. This process of community deconstruction revealed a critical role for the genus Bacillus in protecting the plant from infection. Using plant RNA-seq and bacterial co-culturing experiments, we demonstrated that Bacillus-provided plant protection is independent of plant immune system activation. We also show that the level of plant protection is strongly dependent on the diversity of the protective inoculum. Applying inocula with high within-genus diversity offers a significant improvement to current biocontrol strategies.},
}
@article {pmid40590382,
year = {2025},
author = {Zheng, Q and Xu, Y and Qian, X and Hu, B and Ma, Q and Guo, L and Dorazio, RM and Lu, M},
title = {Alterations of Gut Microbiome and Serum Short-Chain Fatty Acids in Children With Enthesitis-Related Arthritis.},
journal = {International journal of rheumatic diseases},
volume = {28},
number = {7},
pages = {e70337},
doi = {10.1111/1756-185X.70337},
pmid = {40590382},
issn = {1756-185X},
support = {QN25H100005//Zhejiang Provincial Natural Science Foundation/ ; LGF22H100005//Basic Nonprofit Project of the Natural Science Foundation/ ; },
}
@article {pmid40590322,
year = {2025},
author = {Mao, Y and Yang, Y and Xiong, T},
title = {Gastrointestinal emergencies and monitoring in preterm infants: a review.},
journal = {Annals of medicine},
volume = {57},
number = {1},
pages = {2525397},
pmid = {40590322},
issn = {1365-2060},
mesh = {Humans ; Infant, Premature ; Infant, Newborn ; *Gastrointestinal Diseases/diagnosis ; Monitoring, Physiologic/methods ; Emergencies ; Enterocolitis, Necrotizing/diagnosis ; *Infant, Premature, Diseases/diagnosis ; },
abstract = {BACKGROUND: Gastrointestinal emergencies are some of the severe complications in preterm infants, often resulting in fatal patient outcomes due to unintended delays in making precise diagnoses and initiating timely treatment. These delays arise from the non-specificity of observed gastrointestinal events, as well as the shortcomings of the existing monitoring methods used clinically. Therefore, effectively gastrointestinal monitoring should be emphasized to facilitate early detection and prevention of gastrointestinal diseases in preterm infants.<br><br>METHODS: We collected relevant studies by searching literature published on PubMed, Embase, Cochrane Library, and Google Scholar up to December 2024.<br><br>RESULTS: We found that various non-traditional tools have been developed, including automated bowel sound, near-infrared spectroscopy, electrogastrography, intra-abdominal pressure monitoring, fecal microbiome monitoring, fecal biomarkers monitoring, high-frequency heart rate variability. These monitoring methods may provide clues for the early warning of gastrointestinal emergencies, and future research focused on early warnings to improve prognosis of preterm infants is worth conducting.<br><br>CONCLUSIONS: This review discusses common gastrointestinal events in preterm infants, the current state of gastrointestinal emergencies (necrotizing enterocolitis, digestive tract obstruction or narrowing, and gastrointestinal bleeding), and focuses on the progress and prospects of gastrointestinal monitoring in preterm infants. It could potentially make a positive contribution to preterm infants outcomes and quality of life, particularly in addressing areas where current literature still lacks consensus or detailed analysis.},
}
@article {pmid40590230,
year = {2025},
author = {Self, WK and Holtzman, DM},
title = {Thwarting amyloidosis: IL-17 as a disease modifier along the gut/brain axis.},
journal = {The Journal of clinical investigation},
volume = {135},
number = {13},
pages = {},
doi = {10.1172/JCI194443},
pmid = {40590230},
issn = {1558-8238},
mesh = {*Interleukin-17/immunology ; Animals ; Humans ; Mice ; *Gastrointestinal Microbiome/immunology ; *Brain/immunology/pathology/metabolism ; *Th17 Cells/immunology/pathology ; *Alzheimer Disease/immunology/pathology/microbiology ; *Amyloidosis/immunology/pathology ; },
abstract = {Recent studies have highlighted a possible role for gut microbiota in modulating Alzheimer's disease pathology, particularly through the actions of gut-derived metabolites and their influence on the immune system. In this issue of the JCI, Chandra et al. reveal that circulating levels of the gut microbiota-derived metabolite propionate affected amyloid burden and glial activation in a mouse model of Aβ amyloidosis. The study also identifies a mechanism for the therapeutic benefit of propionate supplementation, showing that propionate lowered peripheral IL-17 and suppressed Th17 cell activity. These results support the idea of therapeutic targeting of the gut/brain/immune axis, particularly via modulation of Th17 responses, and suggest translational strategies involving microbiome-based or immunological interventions for dementia prevention and treatment.},
}
@article {pmid40590190,
year = {2025},
author = {de Sosa, I and Turon, M and Taboada, S and Lorente-Sorolla, J and Fernández, R and Tilikj, N and Piris, A and Novo, M and Álvarez Campos, P and Riesgo, A},
title = {No Mate, No Problem: Molecular Mechanisms Involved in Parthenogenesis in the Cosmopolitan Earthworm Aporrectodea trapezoides (Annelida, Clitellata).},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {e70010},
doi = {10.1111/mec.70010},
pmid = {40590190},
issn = {1365-294X},
support = {FJC2020-043677-I//Ministerio de Ciencia y Tecnolog&#xed;a Gobierno de Espa&#xf1;a/ ; JSPRE2020-095330//Ministerio de Ciencia y Tecnolog&#xed;a Gobierno de Espa&#xf1;a/ ; MNCIN/AEI/10.13039/501100011033//Ministerio de Ciencia y Tecnolog&#xed;a Gobierno de Espa&#xf1;a/ ; PID2019-105769GB-I00//Ministerio de Ciencia y Tecnolog&#xed;a Gobierno de Espa&#xf1;a/ ; PID2020-117115GA-I00//Ministerio de Ciencia y Tecnolog&#xed;a Gobierno de Espa&#xf1;a/ ; PID2021-122243NB-I00//Ministerio de Ciencia y Tecnolog&#xed;a Gobierno de Espa&#xf1;a/ ; PID2023-148497NA-I00//Ministerio de Ciencia y Tecnolog&#xed;a Gobierno de Espa&#xf1;a/ ; PRE2022-103770//Ministerio de Ciencia y Tecnolog&#xed;a Gobierno de Espa&#xf1;a/ ; RYC2018-024247-I//Ministerio de Ciencia y Tecnolog&#xed;a Gobierno de Espa&#xf1;a/ ; RYC2021-03152-I//Ministerio de Ciencia y Tecnolog&#xed;a Gobierno de Espa&#xf1;a/ ; PIE-202030E006//Consejo Superior de Investigaciones Cient&#xed;ficas/ ; AGAUR 2021-SGR00420//Secretaria d'Universitats i Recerca del Departament d'Economia i Coneixement de la Generalitat de Catalunya/ ; CNS2023-144571//European Union Next Generation/ ; CNS2023-144572//European Union Next Generation/ ; CNS2023-144624//European Union Next Generation/ ; CNS2023-145193//European Union Next Generation/ ; 101129751//H2020 European Research Council/ ; 948281//H2020 European Research Council/ ; (HORIZON-MSCA.2022-PF-01, Project 101105716)//MSCA Postdoctoral Fellowship/ ; },
abstract = {Approximately, 40% of earthworm species can reproduce by parthenogenesis. This is the case for the cosmopolitan species, Aporrectodea trapezoides, although sexual forms have been described sporadically. We analyse the genotypes and microbiomes of 30 individuals from four localities where both forms appear in order to understand the evolutionary mechanisms related to parthenogenesis. In all sites, heterozygosity values were approximately 30% higher in parthenogenetic individuals. However, we detected a stronger genomic structuring due to reproduction than to the geographical setting only in the Algerian population, underpinned by 195 loci that were related to gametogenesis, symbiont-like processes, and nitrate reduction. Similarly, statistical differences in the abundance of ZOTUs were only found between the Algerian sexual and parthenogenetic earthworms, with 754 ZOTUs that included the genus Romboutsia, which is involved in the production of nitric oxide, which enhances sperm motility. In summary, significant genomic and microbiome differences were found only between sexual and parthenogenetic lineages in a single locality. We hypothesise that obligate parthenogenesis evolved early, leaving traces at the genomic and microbiome levels in the Algerian parthenogens that were the earliest splitting lineage. Such obligate parthenogenesis was lost secondarily and individuals in the Iberian sites were facultative parthenogens, with the potential to copulate and therefore erase the genomic and microbial traces of obligate parthenogenesis. Our results indicate a hybrid origin of parthenogenesis in A. trapezoides and shed light on the complex interplay between genomic, microbiome, and reproductive mechanisms in A. trapezoides.},
}
@article {pmid40590070,
year = {2025},
author = {Ferreira, PG and Castro, LFC and Wilson, JM},
title = {A second look at the stomach - a fishy perspective.},
journal = {The Journal of experimental biology},
volume = {228},
number = {14},
pages = {},
doi = {10.1242/jeb.250054},
pmid = {40590070},
issn = {1477-9145},
support = {RGPIN-2019-06838//Natural Sciences and Engineering Research Council of Canada/ ; },
mesh = {Animals ; *Fishes/physiology/growth &amp; development ; *Stomach/physiology ; Digestion ; Biological Evolution ; Hydrogen-Ion Concentration ; },
abstract = {Despite the established evolutionary importance of stomach acidification in vertebrates, the exact contribution of this process to overall protein digestion, nutrient absorption, growth, energy metabolism and development has not been fully elucidated and is oftentimes subject to extensive scientific debate. This Commentary sets out to frame the current state of our understanding, highlighting unresolved issues and proposing where experimental approaches can be applied to address these questions. Furthermore, we explore in depth the tantalizing evolutionary and physiological puzzle of repeated loss of gastric function in fishes. In this way, we hope to help clarify the role of the gastric proton pump and stomach acidification in digestion, metabolism and growth in vertebrates.},
}
@article {pmid40589913,
year = {2025},
author = {Marandi, A and Jensen, AM and von Gersdorff Jørgensen, L},
title = {Pseudocapillaria tomentosa (Nematoda: Capillariidae) in fish and its significance in comprehending host-parasite relationships: A review.},
journal = {Current research in parasitology &amp; vector-borne diseases},
volume = {7},
number = {},
pages = {100265},
pmid = {40589913},
issn = {2667-114X},
abstract = {Helminth parasites, including capillariids, pose a significant health risk to animals, including fishes, birds, and mammals. Pseudocapillaria tomentosa is a widespread, but poorly studied parasite primarily infecting freshwater cyprinid fishes in the northern hemisphere. However, despite controlled laboratory procedures, the parasite is also prevalent in many zebrafish (Danio rerio) research facilities due to inadequate measures to ensure biological security and the ability of the nematode to endure chlorine treatment. Pseudocapillaria tomentosa typically causes chronic disease in fish, leading to morbidity, mortality, and economic challenges. Clinical signs include emaciation, ulcers, anemia, and hemorrhage, as well as reduced growth and reproductive ability, and prominent humpback lesions in severe infections. Diagnosing P. tomentosa infections involve observation of eggs in wet mount preparations or worms in histological sections of the intestine. However, definitive species identification requires detailed morphological examination and molecular analyses. Pseudocapillaria tomentosa can be effectively managed through anthelmintic treatments such as emamectin, fenbendazole, albendazole, and mebendazole as well as preventive measures including maintaining optimal water quality, reducing fish density, and implementing strict quarantine protocols. This review discusses the use of the zebrafish to study host-parasite interactions, particularly with the parasitic nematode P. tomentosa. The zebrafish is a suitable model for studying infectious diseases, including parasites, due to its well-characterized immune system, reporter lines and cell lineages. This model organism exhibits immune responses to helminth antigens, including eosinophilia and the upregulation of inflammatory cytokines like Tnf-α and Ifn-γ. The gut microbiota plays a crucial role in susceptibility to parasitic infections in zebrafish and an imbalanced or dysbiotic gut microbiome can predispose fish to parasitic infections, while a healthy, balanced microbiome can enhance resistance. Furthermore, probiotic-based interventions are being explored as a way to boost mucosal immunity and modify the gut microbiome to prevent parasitic infections.},
}
@article {pmid40589741,
year = {2025},
author = {Fouka, E and Lindén, A and Bossios, A},
title = {The role of T-helper and T regulatory cells in driving neutrophilic and eosinophilic inflammation in bronchiectasis.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1598257},
pmid = {40589741},
issn = {1664-3224},
mesh = {Humans ; *Bronchiectasis/immunology/metabolism ; *T-Lymphocytes, Regulatory/immunology/metabolism ; *Neutrophils/immunology/metabolism ; Inflammation/immunology ; Animals ; *Eosinophils/immunology/metabolism ; *T-Lymphocytes, Helper-Inducer/immunology/metabolism ; Cytokines/metabolism ; Microbiota/immunology ; },
abstract = {Bronchiectasis is a chronic airway disease characterized by dysbiosis, persistent inflammation, and permanent structural airway damage. Neutrophilic inflammation is a key pathogenic feature, as indicated by enhanced neutrophil-derived proteases and formation of neutrophil extracellular traps (NETs), associated with poor prognosis. However, recent studies have identified an eosinophilic endotype in up to 30% of patients, characterized by higher levels of type 2 (T2) cytokines and fractional exhaled nitric oxide (FeNO). The role of T helper (Th) cells in the dysregulated inflammatory environment of bronchiectasis remains unclear. Evidence suggests that persistent bacterial infection can skew adaptive immunity from Th1 toward Th2 response, while the airway microbiome-IL-17 axis is also a critical regulator of chronic inflammation. T regulatory (Treg) cells have been shown to play a protective role against excessive chronic inflammation by modulating the function of several types of effector cells, including the Th17 subset. However, the capacity of this subset to delay or prevent disease progression remains to be determined Microbial dysbiosis, with loss of diversity and increased quantity of bacterial pathogens, may also be important for disease progression, and emerging evidence indicates that distinct inflammatory endotypes associate with specific microbiota alterations, especially in severe disease. In this review, we provide an overview of the immune cells and cytokine signaling that are involved in the pathogenesis of bronchiectasis. Additionally, we present the main endotypes of bronchiectasis and explore the relationships between the type of inflammation and alterations in microbiota, as well as the potential benefits of targeting specific pathophysiological mechanisms for the management of bronchiectasis. This review also examines how bacterial infection can shift adaptive immunity from Th1 toward Th2 responses, the role of the airway microbiome-IL-17 axis in chronic inflammation and the potential protective role of Treg cells against excessive inflammation. Novel therapeutic strategies are highlighted, with focus on targeting specific cytokine signaling pathways and restoring Th17/Treg balance These developments underscore a shift toward precision medicine in bronchiectasis, emphasizing the importance of identifying specific inflammatory endotypes to tailor treatment strategies effectively.},
}
@article {pmid40589654,
year = {2025},
author = {Li, Y},
title = {Global autism prevalence, and exploring Montessori as a practical educational solution: a systematic review.},
journal = {Frontiers in psychiatry},
volume = {16},
number = {},
pages = {1604937},
pmid = {40589654},
issn = {1664-0640},
abstract = {INTRODUCTION: Autism spectrum disorder (ASD) is a neurodevelopmental condition that impairs social interaction, communication, and appropriate behavior.<br><br>METHODS: Out of 1,740 articles initially identified through electronic databases using PRISMA guidelines and the PICOS framework, only 15 met the inclusion criteria for this review.<br><br>RESULTS: Although the precise etiology of autism remains unclear in most cases, from cohort studies, the heritability as a potential cause is estimated to range between 50% and 80%, taking into account consistent environmental risk factors such as parental age, pollution, and maternal infections during pregnancy. Several autism-related gene mutations have also been identified. Recommended interventions include applied behavior analysis, speech therapy, pharmacological treatment, and emerging techniques such as artificial intelligence, virtual reality, and microbiome-based approaches. Pharmacological agents like Risperidone and Aripiprazole can alleviate specific symptoms but do not target the core features of ASD. Additional evidence-based therapies, including occupational therapy and sensory integration, have demonstrated benefits in enhancing functional outcomes.<br><br>DISCUSSION: Montessori education, a sensory-focused, individualized, and play-based learning approach, aligns well with the individual learning needs of ASD and shows considerable potential in improving communication and social skills in children with ASD. This systematic review underscores geographic disparities and risk factors associated with autism while uniquely assessing Montessori education as a promising intervention, paving the way for further research in low-resource settings.},
}
@article {pmid40589493,
year = {2025},
author = {Tashiro, H and Kuwahara, Y and Takahashi, K},
title = {Gut-lung axis in asthma and obesity: role of the gut microbiome.},
journal = {Frontiers in allergy},
volume = {6},
number = {},
pages = {1618466},
pmid = {40589493},
issn = {2673-6101},
abstract = {Asthma is a heterogeneous disease whose severity is exacerbated by obesity. Despite its clinical importance, targeted therapies for asthma in obese patients remain limited. Recent evidence highlights the gut microbiome as a crucial factor linking metabolic and immune pathways involved in both asthma and obesity. This review explores the complex interplay between the gut microbiome, immune responses, and the gut-lung axis, emphasizing how microbial composition, diversity, and metabolites, such as short-chain fatty acids (SCFAs), influence airway hyperresponsiveness (AHR) and airway inflammation. Obesity alters the gut microbiome, contributing to systemic inflammation and metabolic dysfunction. Furthermore, asthma phenotypes related to obesity are associated with specific gut microbial profiles, suggesting a causal relationship. Animal studies have demonstrated that manipulation of the gut microbiome through diet, antibiotics, or microbial transplantation can alter asthma outcomes, particularly in obesity models. Given these findings, targeting the gut microbiome might be a promising therapeutic strategy for asthma in obese individuals. Potential interventions include probiotics, prebiotics and antibiotics, all of which have shown varying degrees of effectiveness in modulating airway inflammation and reducing asthma severity. This review provides a comprehensive overview of current knowledge and proposes future directions for microbiome-targeted therapies in managing severe asthma associated with obesity.},
}
@article {pmid40589427,
year = {2025},
author = {Ishikawa, H and Aoki, R and Mutoh, M and Ishiguro, S and Tanaka, T and Miyoshi, N and Miyamoto, S and Hamoya, T and Yoshida, N and Wakabayashi, K and Watanabe, K},
title = {Contribution of colibactin-producing Escherichia coli to colonic carcinogenesis.},
journal = {eGastroenterology},
volume = {3},
number = {2},
pages = {e100177},
pmid = {40589427},
issn = {2976-7296},
}
@article {pmid40589146,
year = {2025},
author = {Kalb, B and Khaleva, E and Giovannini, M and Adel-Patient, K and Amat, F and Arasi, S and Lau, S and Nieto, A and Schaub, B and Standl, M and O'B Hourihane, J and Eigenmann, P and Deschildre, A and , },
title = {Trajectories of allergic diseases in children: Destination unknown?.},
journal = {Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology},
volume = {36},
number = {7},
pages = {e70131},
doi = {10.1111/pai.70131},
pmid = {40589146},
issn = {1399-3038},
support = {//EAACI- Clemens von Pirquet Foundation/ ; },
mesh = {Humans ; Child ; *Hypersensitivity/epidemiology/immunology/therapy ; Disease Progression ; Genetic Predisposition to Disease ; },
abstract = {The trajectories of allergic diseases represent one of the most currently debated topics both when referred to childhood and likewise adulthood. Data from cohorts show their heterogeneity as well as the key role of genetic and environmental factors. More insight has been recently provided in the pathophysiological mechanisms underlying the development and amplification of T2 (hyper)inflammation. Recent data support the hypothesis of associated allergic diseases (multimorbidity) reflecting, at a given time and in given organ(s)/tissue(s), the expression of the same favorable predisposition. In particular, the impairment of the epithelial barrier, especially in subjects genetically predisposed, and the dysregulation of the host's microbiome promote the onset of allergic diseases and multimorbidity, their persistence and/or severity. These findings challenge the classical theory of the atopic march with a temporal sequence characterized by the transition from one disease (eczema) to another (food allergy, airway allergic diseases). A better understanding of the diversity of disease trajectories and the underpinning mechanisms is crucial for prevention and identification of children at risk of a "unfavorable trajectory" (early intervention, i.e., early primary or secondary prevention), for a personalized therapeutic approach based on identification of specific endotypes, and, therefore, addressing specific pathophysiological pathways (treat to target strategies). In the perspective of the so-called "remission" and "treatment-induced-remission", the whole spectrum of the long-term consequences of the disease(s) including their treatment has to be considered. The concept of disease modifying treatment able to interfere with their trajectories and overall long-term induced morbidity is emerging.},
}
@article {pmid40589086,
year = {2025},
author = {Yadav, M and Gupta, A and Mathew, B and Tripathi, G and Dalal, N and Sharma, N and Yadav, P and Yadav, G and Singh, R and Bindal, V and Saif, R and Yadav, S and Sharma, N and Pandey, S and Bhat, SH and Singh, R and Kumar, J and Kushwaha, M and Khan, T and Sharma, NK and Bhaskar, A and Dwivedi, VP and Kumar, A and Kumar, N and Tripathi, DM and Trehanpati, N and Anupama Kumara, and Sharma, S and Sarin, SK and Maras, JS},
title = {Circulating urobilinogen contributes to Inflammation, Intestinal Permeability and corticosteroid non-response in Severe Alcohol-associated Hepatitis.},
journal = {Molecular therapy : the journal of the American Society of Gene Therapy},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ymthe.2025.06.041},
pmid = {40589086},
issn = {1525-0024},
abstract = {Severe alcohol-associated hepatitis (SAH) is a life-threatening condition with high mortality rates and poor response to prednisolone therapy. Identifying reliable early predictors of therapy response and survival is critical. Plasma metabolomics was conducted on 70 SAH patients (50 responders, 20 non-responders) to identify biomarkers for non-response and early mortality. These findings were validated in a cohort of 153 patients and an independent cohort of 245 using high resolution mass spectrometry, machine learning, and severity indices. Temporal metabolic changes indicated interactions between the host and microbiome, with a focus on inflammation and intestinal permeability. Plasma metabolomics revealed that non-responders had significantly higher urobilinogen levels (3.6-fold change). Additionally, a decrease in alpha/beta diversity and temporal metabolic inactivity characterized non-responders. Plasma urobilinogen levels predicted non-response (AUC>0.97) and identified non-survivors (AUC=0.94) with a threshold of >0.07 mg/ml. Urobilinogen levels correlated with bacterial peptides belonging to Firmicutes and Proteobacteria, neutrophil activation, oxidative stress, and pro-inflammatory cytokine production. These changes contributed to non-response by increasing glucocorticoid receptor β expression and compromising intestinal permeability. Fecal microbiota transplantation decreased urobilinogen levels by reducing bilirubin reductase gene-containing microbiota. Plasma urobilinogen >0.07 mg/ml could predict early mortality, and modulation of the gut microbiome may improve outcomes in SAH patients.},
}
@article {pmid40588803,
year = {2025},
author = {Hu, J and Feng, T and Zhang, L and Zhou, Q and Zhu, L},
title = {Leveraging gut microbiota for enhanced immune checkpoint blockade in solid tumor therapy.},
journal = {Chinese medical journal},
volume = {},
number = {},
pages = {},
pmid = {40588803},
issn = {2542-5641},
abstract = {Gut microbiota can modulate antitumor immunity and influence immune checkpoint blockade (ICB) therapy efficacy and treatment-associated toxicity. Variations in the therapeutic effect of ICB among individuals are partially attributed to microbiota. This review summarizes current knowledge on how specific bacterial species enhance or hinder ICB outcomes by regulating immune cell activation, antigen presentation, and systemic inflammation. The review further outlines translational strategies to optimize ICB, including microbiota-targeted interventions (e.g., prebiotics, fecal microbiota transplantation, and metabolite therapies) to overcome resistance and mitigate treatment-related toxicities, focusing on immune-related colitis. Additionally, emerging microbial biomarkers in melanoma, lung cancer, and hepatobiliary cancers that predict ICB response are discussed, highlighting the gut microbiome as a potential target for personalized cancer immunotherapy. By integrating mechanistic insights with clinical evidence, this review underscores the potential of microbiota-centered approaches to improve patient outcomes in ICB-based treatments, emphasizing the pivotal role of the gut microbiota in modulating both therapeutic efficacy and immune-related adverse events.},
}
@article {pmid40588703,
year = {2025},
author = {Li, JKM and Wang, L and Tse, RTH and Leung, CH and Liu, K and Zhao, H and Cheng, CKL and WonG, CYP and Tsui, SKW and Giannarini, G and Liu, AQ and Chiu, PKF and Ng, CF and Teoh, JYC},
title = {A cross-sectional study on the effects of intravesical BCG on urinary microbiota in bladder cancer patients.},
journal = {International urology and nephrology},
volume = {},
number = {},
pages = {},
pmid = {40588703},
issn = {1573-2584},
support = {14117421//General Research Fund/Early Career Scheme of the Research Grants Council, Hong Kong/ ; },
abstract = {BACKGROUND: Urinary bladder cancer is among the most common malignancy worldwide. Despite surgical interventions and regular surveillance, recurrence and progression to advanced disease are observed in patients. Intravesical administration of Bacillus Calmette-Guérin (BCG) could reduce bladder cancer recurrence and progression in patients with intermediate- and high-risk non-muscle-invasive bladder cancer (NMIBC). Nonetheless, not all patients respond well to BCG treatment. We aim to evaluate whether bacteria profiles were altered after BCG administration.<br><br>METHODS: In this cross-sectional study, we investigate the differences in urinary microbiome between non-cancerous controls, bladder cancer patients undergoing surveillance cystoscopy, and patients with BCG administration (post-BCG). The V4 regions of the 16S rRNA gene were sequenced, and alpha-diversity and beta-diversity were analyzed. Taxonomic differences between groups and metabolic function analysis of bacteria groups were investigated.<br><br>RESULTS: Comparing to the other two groups, the proportion of Pseudomonas, Lactococcus, and Bacillus were increased in the post-BCG group. Superpathways of L-phenylalanine biosynthesis, L-tyrosine biosynthesis, ubiquinol-7, 8, 9, 10 biosynthesis, lipopolysaccharide biosynthesis, glucose degradation oxidative, and 4-hydroxyphenylacetate degradation were significantly enhanced in the post-BCG group.<br><br>CONCLUSION: Results demonstrated that urinary bacteria profiles were distinguished between controls and post-BCG patients. Certain bacteria genus was shown to enhance in post-BCG patients, revealing that the change in the urinary microbiome might be associated with BCG treatment.},
}
@article {pmid40588611,
year = {2025},
author = {Gonçalves, DA and Luft, JG and Escalona, MAR and Mann, MB and Frazzon, J and Dorn, M and Rampelotto, PH and de Oliveira Alvares, L},
title = {Synbiotic supplementation enhances memory processes in adult and aged male rats.},
journal = {Biogerontology},
volume = {26},
number = {4},
pages = {136},
pmid = {40588611},
issn = {1573-6768},
support = {405100/2018-3//Governo Brasil/ ; },
mesh = {Animals ; *Synbiotics/administration &amp; dosage ; Male ; *Gastrointestinal Microbiome/physiology ; *Memory/physiology/drug effects ; Rats ; *Aging/psychology/physiology ; Dietary Supplements ; Probiotics ; Rats, Wistar ; },
abstract = {Synbiotic formulations, which combine prebiotics and probiotics in their composition, have shown promise in improving brain function and cognitive performance. However, the mechanisms by which synbiotics exert their beneficial effects on memory processes, particularly in the context of aging, remain unclear. In the present study, we investigated the effects of synbiotics supplementation on memory updating (reversal learning) and extinction in adult and aged rats. We also assessed the impact of the synbiotic intervention on the gut microbiota composition, diversity, and metabolism. The results showed that synbiotic supplementation (fructooligosaccharide and L. acidophilus, L. bulgaricius, L. casei, L. rhamnosus, and B. bifidum) improved memory updating in adult rats but not in aged rats. In contrast, the synbiotic facilitated memory extinction in aged rats, but not in adults. Interestingly, these cognitive benefits were not accompanied by significant alterations in the gut microbiome. This suggests that the synbiotic's effects on memory processes were mediated through more direct mechanisms, such as anti-inflammatory, antioxidant, and neuromodulatory actions, rather than through broad changes to the gut microbial community. These findings highlight the potential of synbiotic interventions to ameliorate age-related cognitive impairment and provide insights into the underlying mechanisms of the gut-brain axis.},
}
@article {pmid40588591,
year = {2025},
author = {Mancuso, CP and Baker, JS and Qu, EB and Tripp, AD and Balogun, IO and Lieberman, TD},
title = {Intraspecies warfare restricts strain coexistence in human skin microbiomes.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {40588591},
issn = {2058-5276},
support = {1DP2GM140922//U.S. Department of Health &amp; Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; },
abstract = {Determining why only a fraction of encountered or applied strains engraft in a given person's microbiome is crucial for understanding and engineering these communities. Previous work has established that metabolic competition between bacteria can restrict colonization success in vivo, but other mechanisms may also prevent successful engraftment. Here we combine genomic analysis and high-throughput agar competition assays to demonstrate that intraspecies warfare presents a significant barrier to strain coexistence in the human skin microbiome by profiling 14,884 pairwise interactions between Staphylococcus epidermidis isolates cultured from 18 people from 6 families. We find that intraspecies antagonisms are abundant, mechanistically diverse, independent of strain relatedness and consistent with rapid evolution via horizontal gene transfer. Critically, these antagonisms are significantly depleted among strains residing on the same person relative to random assemblages, indicating a significant in vivo role. Wide variation in antimicrobial production and resistance suggests trade-offs between these factors and other fitness determinants. Together, our results emphasize that accounting for intraspecies warfare may be essential to the design of long-lasting probiotic therapeutics.},
}
@article {pmid40588570,
year = {2025},
author = {Kamrad, S and Davis, TF and Patil, KR},
title = {Impact of drugs and environmental contaminants on amine production by gut bacteria.},
journal = {Molecular systems biology},
volume = {},
number = {},
pages = {},
pmid = {40588570},
issn = {1744-4292},
support = {866028//EC | ERC | HORIZON EUROPE European Research Council (ERC)/ ; MC_UU_00025/11//UKRI | Medical Research Council (MRC)/ ; },
abstract = {Xenobiotics like drugs are recognised as key influencers of gut bacterial growth. Yet, their impact on the production of metabolites involved in microbiota-host interactions is largely unknown. Here, we report the impact of commonly ingested xenobiotics-therapeutic drugs, pesticides, industrial chemicals, and sweeteners-on gut bacterial amine metabolism. We tested >13,000 interactions between >1700 compounds and 4 amine-producing bacteria, uncovering 747 xenobiotic-species-metabolite interactions involving 275 compounds. These compounds span all tested classes, with the majority being antimicrobial drugs. In 66% of the cases, amine production was correlated with growth, while the rest showed xenobiotic-induced decoupling between growth and metabolite production. The latter includes transient bursts in polyamine production by Escherichia coli in response to β-lactam antibiotics, and overproduction of aromatic amines by Ruminococcus gnavus treated with 15 diverse chemicals. Xenobiotics thus can disrupt metabolic homeostasis in both growth-dependent and -independent manner. We also find that metabolic responses have non-monotonic dose-dependency, resulting in lower doses sometimes having stronger effects. Our results bring forward the potential of common xenobiotics to disrupt the amine metabolism of gut bacteria.},
}
@article {pmid40588528,
year = {2025},
author = {Yang, J and Kim, HD and Barrila, J and Lee, SH and Nickerson, CA and Ott, CM and Israel, SA and Choukér, A and Yang, JY},
title = {Navigating mental health in space: gut-brain axis and microbiome dynamics.},
journal = {Experimental &amp; molecular medicine},
volume = {},
number = {},
pages = {},
pmid = {40588528},
issn = {2092-6413},
support = {RS-2023-00263702//National Research Foundation of Korea (NRF)/ ; NRF-2018R1A5A2023879//National Research Foundation of Korea (NRF)/ ; RS-2023-00301938//National Research Foundation of Korea (NRF)/ ; RS-2023-00301938//National Research Foundation of Korea (NRF)/ ; 80NSSC19K1597//National Aeronautics and Space Administration (NASA)/ ; PR230701//United States Department of Defense | United States Army | Army Medical Command | Congressionally Directed Medical Research Programs (CDMRP)/ ; },
abstract = {Long-term space travel presents significant mental health challenges, with documented psychological and neurological impacts observed during spaceflight and in simulated space environments. Terrestrial studies have highlighted the connection between the human gut microbiome and neuropsychological health, known as the gut-brain axis. Recent research has demonstrated alterations in astronauts' microbiomes during spaceflight. Here we explore interesting parallels between these microbiome changes in astronauts and those observed in terrestrial studies involving individuals experiencing psychological distress. Key areas of focus include how various space-related stressors impact the complex interplay between the gut microbiome, immune responses and mental health outcomes. This is illustrated by the effects of space radiation and circadian rhythm disruptions on the microbiome, as well as the roles of immune regulation and the integrity of gut and blood-brain barriers in shaping mental health outcomes through the gut-brain axis. Potential interventions and strategies for microbiome monitoring are suggested as critical to mitigating psychological risks during extended space missions. These findings underscore the need for further research to better understand how the microbiome responds to spaceflight environments and to develop targeted interventions that safeguard mental health during long-duration missions.},
}
@article {pmid40588232,
year = {2025},
author = {Ghribi, S and Degli Esposti, L and Steven, B and Zuverza-Mena, N and Yuan, J and LaReau, JC and White, JC and Jaisi, DP and Adamiano, A and Iafisco, M},
title = {Functionalization of Amorphous and Crystalline Calcium Phosphate Nanoparticles with Urea for Phosphorus and Nitrogen Fertilizer Applications.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c03970},
pmid = {40588232},
issn = {1520-5118},
abstract = {The development of nanofertilizers has gained significant attention for their potential to enhance nutrient delivery to plants while mitigating the environmental impact of intensive agriculture. In this study, we investigated the urea functionalization of two types of calcium phosphate nanoparticles, hydroxyapatite (HAP) and amorphous calcium phosphate (ACP), as nanofertilizers capable of simultaneously releasing phosphorus and nitrogen in a controlled manner. Leaching experiments using a vermiculite column revealed that ACP-urea significantly slowed urea release compared with free urea, whereas HAP-urea exhibited a release profile similar to that of free urea. Greenhouse experiments on corn (Zea mays) showed that ACP-urea treatment enhanced the dry biomass and relative chlorophyll content compared to treatments with free urea combined with either ACP or monocalcium phosphate. Microbiome analyses indicated that the improved plant performance with ACP-urea was primarily due to the material's physicochemical properties rather than significant shifts in the rhizosphere bacterial communities. These findings highlight the potential of ACP nanoparticles as effective nanofertilizers for controlled phosphorus and nitrogen release, contributing to more sustainable agricultural practices.},
}
@article {pmid40588202,
year = {2025},
author = {Zhang, Y and Liu, H and Liang, F and Liu, B and Jing, W and Wang, S and Lyu, B and Yu, H},
title = {High-purity soybean insoluble dietary fiber -microencapsulated Clostridium typhimurium: Intervention mechanisms in alleviating intestinal Dysbiosis.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {145636},
doi = {10.1016/j.ijbiomac.2025.145636},
pmid = {40588202},
issn = {1879-0003},
abstract = {The present study utilized high-purity soybean insoluble dietary fiber (HPIDF) as the primary wall material to encapsulate Clostridium typhimurium, thereby establishing a novel microcapsule system (HPIDF-MIC). A mouse model of intestinal microbiota dysbiosis was successfully established through cefuroxime induction. Multi-modal analysis revealed that the ingestion of HPIDF-MIC alleviated weight loss and colonic oedema, with a 53 % reduction in the colonic injury index when compared to the model group. In addition, inflammation and oxidative stress were inhibited, total SCFAs were restored to 1503.54 μg/g (approaching the control group's 1578.71 μg/g), and intestinal microbiota diversity was restored, thus achieving multidimensional intestinal protective effects. The efficacy of the intervention was found to significantly outperform that of single-component (HPIDF) and traditional probiotic interventions. The present study systematically investigated the intervention effects and mechanistic basis of HPIDF-MIC on intestinal homeostasis, providing an efficient and safe candidate solution for the treatment of intestinal diseases. This study not only demonstrates the potential of HPIDF as a functional food ingredient in maintaining gut health but also provides mechanistic insights for guiding the development of microbiome-targeted nutritional supplements.},
}
@article {pmid40588189,
year = {2025},
author = {Bishehsari, F and Post, Z and Swanson, GR and Keshavarzian, A},
title = {Circadian Rhythms in Gastroenterology: The Biological Clock's Impact on Gut Health.},
journal = {Gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1053/j.gastro.2025.06.017},
pmid = {40588189},
issn = {1528-0012},
abstract = {Chronic gastrointestinal (GI) diseases, including functional, inflammatory, and neoplastic conditions, are rising globally, partly due to modern lifestyles. The circadian rhythm, regulated by the central clock in the hypothalamus and synchronized with peripheral clocks in the gastrointestinal organs, orchestrates GI functions in response to environmental cycles. This clock is influenced by cues such as light, sleep, and eating times. The circadian machinery prepares the host to cope with environmental conditions to adjust cellular and organ function accordingly. Modern behaviors-like nighttime light exposure, travel across time zones, shift work, mistimed eating, and social jet lag-disrupt the circadian clock, affecting GI processes such as digestion, absorption, motility, intestinal barrier function, immune function, and the microbiome, promoting not only GI pathology, but also systemic inflammatory and metabolic disorders. This review summarizes the circadian rhythm's role in normal GI function, examines the consequences of circadian disruption in the GI tract, and discusses circadian-based therapeutic interventions. These interventions aim to realign the circadian clock with external cues or optimize medication timing according to biological rhythms. Understanding the role of the circadian clock in GI conditions can provide preventive and therapeutic opportunities to reduce the burden of GI diseases.},
}
@article {pmid40588151,
year = {2025},
author = {Graciano-España, MDC and Barnhart, K and Gonzalez-Monfort, M and Arenas-Barrero, M and Legro, RS and Thomas, TR and Rush, MA and Vilella, F and Fernández-Sánchez, M and Simon, C and Moreno, I},
title = {Fusobacterium nucleatum is not significantly present in eutopic endometrium from patients with minimal-mild and moderate-severe endometriosis.},
journal = {Fertility and sterility},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.fertnstert.2025.06.035},
pmid = {40588151},
issn = {1556-5653},
abstract = {OBJECTIVE: To evaluate the presence of Fusobacterium spp. and Fusobacterium nucleatum in eutopic endometrial samples from women with endometriosis compared to controls, and assess their association with the disease.<br><br>DESIGN: Retrospective case-control study.<br><br>SUBJECTS: Ninety-two women (55 endometriosis cases and 37 controls) aged 18-44 undergoing gynecologic endoscopy for endometriosis and/or benign conditions at University of Pennsylvania, Endomarker Study (PMID: 29524590).<br><br>EXPOSURE: DNA extraction from eutopic endometrial samples using QIAamp DNA Microbiome and IndiSpin&#xae; Pathogen Kits. Quantification of Fusobacterium spp. and F. nucleatum by quantitative PCR using genus- and species-specific primers.<br><br>MAIN OUTCOME MEASURE(S): Relative abundance of Fusobacterium spp. and F. nucleatum in cases versus controls, analyzed using the &#x394;Ct method.<br><br>RESULTS: No significant difference in Fusobacterium spp. or F. nucleatum abundance was observed between cases and controls (P = 0.258 for genus-specific primers, P = 0.738 for species-specific primers). Subgroup analysis by disease severity (minimal-mild: n=42; moderate-severe: n=13) also showed no significant differences (Fusobacterium spp.: P = 0.1465; F. nucleatum: P = 0.2936).<br><br>CONCLUSION: Fusobacterium spp. is not differentially present in eutopic endometrium of women with endometriosis, regardless of disease severity according to rASRM classification. This contrasts with prior findings in eutopic endometrium in patients with ovarian endometriosis, suggesting that Fusobacterium has limited diagnostic or prognostic value in endometriosis.},
}
@article {pmid40587824,
year = {2025},
author = {Lee, PC and Wu, CJ and Hung, YW and Lee, CJ and Mon, HC and Chi, CT and Lee, IC and Kuo, YL and Chou, SH and Luo, JC and Hou, MC and Huang, YH},
title = {Distinct gut microbiota but common metabolomic signatures between viral and MASLD HCC contribute to outcomes of combination immunotherapy.},
journal = {Hepatology (Baltimore, Md.)},
volume = {},
number = {},
pages = {},
doi = {10.1097/HEP.0000000000001446},
pmid = {40587824},
issn = {1527-3350},
abstract = {BACKGROUND AND AIMS: Gut microbiota could modulate outcome of cancer immunotherapy including hepatocellular carcinoma (HCC). Although metabolic dysfunction-associated liver disease-related HCC (MASLD-HCC) and viral hepatitis-related HCC (V-HCC) exhibit different tumor microenvironments and gut microbiome composition, both respond to combination immunotherapy. This study aimed to investigate whether distinct microbiota/metabolomic signatures are associated with outcomes of combination immunotherapy in MASLD-HCC and V-HCC, separately.<br><br>APPROACH AND RESULTS: Between January 2021 and April 2024, 77 V-HCC patients and 25 with MASLD-HCC initiating first-line combination immunotherapy were prospectively enrolled. Pre-treatment fecal microbiota/metabolites and serum cytokines/chemokines were analyzed in association with durable tumor response, overall survival (OS) and progression-free survival (PFS). MASLD-HCC patients showed predominant fecal Bacteroides ovatus, Kluyvera georgiana, Klebsiella oxytoca, and Enterococcus faecium, with lower levels of short-chain fatty acids (SCFAs) and ursodeoxycholic acid (UDCA) compared to V-HCC. Durable responders (DRs) of MASLD-HCC had enriched Mediterraneibacter gnavus ATCC_29149 and significantly higher SCFAs (acetate, propionate, butyrate, and isobutyrate) and UDCA. In contrast, V-HCC-DRs were characterized by predominant Bifidobacterium and similarly enriched SCFAs. In both MASLD-HCC and V-HCC, fecal acetate level was a common significant predictor of DR, PFS and OS. Patients with higher acetate levels had significantly longer OS (median: 25.2 vs. 11.3&#xa0;mos; p<0.001), and PFS (median: 15.3 vs. 4.2&#xa0;mos; p<0.001).<br><br>CONCLUSIONS: Distinct gut microbiota, but shared beneficial metabolites, particularly fecal acetate, are associated with durable response to combination immunotherapy and improved survival in both MASLD-HCC and V-HCC. Fecal acetate may serve as a potential biomarker and therapeutic target for optimizing HCC treatment.},
}
@article {pmid40587710,
year = {2025},
author = {Zhao, S and Zheng, X and Yang, C and Shen, W and Shen, Z},
title = {Gut microbiota causally affects ulcerative colitis by potential mediation of plasma metabolites: A Mendelian randomization study.},
journal = {Medicine},
volume = {104},
number = {26},
pages = {e42791},
doi = {10.1097/MD.0000000000042791},
pmid = {40587710},
issn = {1536-5964},
mesh = {*Gastrointestinal Microbiome/physiology/genetics ; Humans ; *Colitis, Ulcerative/microbiology/blood/genetics ; Mendelian Randomization Analysis ; Genome-Wide Association Study ; Mediation Analysis ; },
abstract = {Ulcerative colitis (UC) is a chronic inflammatory bowel disease with a multifactorial etiology, including genetic, immunological, and environmental factors, as well as alterations in the gut microbiome and plasma metabolites. The interplay between these factors is complex and not fully elucidated, particularly regarding the potential mediation of metabolites in the relationship between gut microbiota and UC. We performed a Mendelian randomization (MR) study to investigate the causal associations between gut microbiota, plasma metabolites, and UC. The study utilized a two-sample MR approach to discern causal relationships among these factors. Genetic variants from genome-wide association studies served as instrumental variables in the MR analyses, conducted using the "TwoSampleMR" package in R software. We adhered to the fundamental assumptions of MR analyses, ensuring the validity of our causal inferences. Additionally, we incorporated a mediation analysis to assess the potential mediating role of plasma metabolites in the relationship between gut microbiota and UC. Our current study found the substantial relationship between certain gut microbial taxa and the development of UC. Indeed, we have identified 6 microbial taxa, including Genus Dorea, Phylum Proteobacteria, Species Streptococcus parasanguinis, Species Ruminococcus obeum, Species Roseburia intestinalis, and Order Lactobacillales, which were found to be causally related to UC. Seventy-three metabolites and metabolite ratios of were also causally associated with UC, and a mediation analysis revealed that metabolites such as stearoylcarnitine, 3-hydroxyoctanoylcarnitine, 1-arachidonoyl-GPE (20:4n6), 3-(3-hydroxyphenyl)propionate sulfate, and thioproline mediated the effects of gut microbiota on UC and hence might play roles in disease pathogenesis. This microbiota-UC-specific MR study provides evidence for causal associations between specific gut microbiota and UC, potentially mediated through plasma metabolites. The findings give new perspectives on the causal nexus of the gut microbiota and plasma metabolites with UC, highlighting potential intervention targets for the disease. These findings call for confirmation in further research, together with investigation of the underlying mechanisms.},
}
@article {pmid40587382,
year = {2025},
author = {Muijsenberg, A and Canfora, EE and Blaak, EE},
title = {Metabolic Phenotypes, Genotypes, and Gut Microbiome Signatures in Obesity: Implications for Precision Nutrition Strategies in Type 2 Diabetes Prevention.},
journal = {Nutrition reviews},
volume = {},
number = {},
pages = {},
doi = {10.1093/nutrit/nuaf088},
pmid = {40587382},
issn = {1753-4887},
support = {//PRECINUT/ ; //Nestl&#xe9; Research and Development/ ; //BENEO GmbH/ ; //Barilla Group e R. Fratelli SpA/ ; //Clear.Bio/ ; //Humicon BV/ ; //Homed-IQ/ ; //Sudryso Group BV/ ; },
abstract = {The worldwide prevalence of overweight and obesity has increased rapidly in the last decades. This rise has led to a surge in comorbidities such as type 2 diabetes (T2D), cardiometabolic diseases, and mental health issues. While general population-based nutrition guidelines have proven effective in reducing T2D incidence by 50%, a significant 30% of participants do not respond to these interventions. Precision nutrition (PN), tailored towards the metabolic phenotype (metabotype), genotype, or microbial characteristics, has shown promise in improving blood glucose control and cardiometabolic health compared with standard nutritional guidelines. This scoping review aims to discuss advancements in PN over the past decade, focusing on heterogeneity in response to dietary interventions aiming to prevent T2D and related cardiometabolic disease in overweight and obese individuals. A semi-systematic PubMed search with defined criteria was conducted to identify precision nutrition (PN) randomized clinical trials and related post-hoc analyses reporting cardiometabolic health outcomes. Numerous studies have shown actionable diet-host interactions, with intervention stratification based on genotype, gut microbiome, metabolome, lipidome, fasting glucose and insulin, postprandial glycemic response, tissue-specific insulin resistance, or combinations thereof. Many of these metabotypes, genotypes, and microbial signatures allow for accurate cardiometabolic outcome predictions and are actionable targets for future PN research. More recently, machine-learning methodologies in the form of postprandial response prediction models have increasingly been used in PN research. However, prospective evidence on effective PN strategies that may prevent the onset of T2D is currently limited. A mechanistic understanding of response and nonresponse in cardiometabolic outcome improvement is crucial in the development of novel phenotyping methodologies and prediction models in PN. These advancements could lead to more inclusive and effective PN strategies to prevent T2D and related conditions.},
}
@article {pmid40587116,
year = {2025},
author = {Li, L and Li, R and Qiu, Z and Zhu, K and Li, R and Zhao, S and Che, J and Guo, T and Xu, K and Geng, T and Liao, Y and Pan, A and Liu, G},
title = {Prediction of Weight Loss and Regain Based on Multiomic and Phenotypic Features: Results From a Calorie-Restricted Feeding Trial.},
journal = {Diabetes care},
volume = {},
number = {},
pages = {},
doi = {10.2337/dc25-0728},
pmid = {40587116},
issn = {1935-5548},
support = {82073554//National Natural Science Foundation of China/ ; 82273623//National Natural Science Foundation of China/ ; 82325043//National Natural Science Foundation of China/ ; 2023YFC3606305//Key R&amp;D Program of China/ ; NNSRG2021-10//CNS/ ; 2021GCRC076//Fundamental Research Funds for the Central Universities/ ; },
abstract = {OBJECTIVE: To identify baseline multiomic and phenotypic predictors and develop prediction models for weight and body composition loss and regain in the Low-Carbohydrate Diet and Time-Restricted Eating (LEAN-TIME) trial.<br><br>RESEARCH DESIGN AND METHODS: A post hoc analysis was conducted of the LEAN-TIME feeding trial using data from 88 adults with overweight/obesity completing a 12-week calorie-restricted weight-loss phase and 79 completing a 28-week weight-regain phase. Baseline dietary, metabolic, fecal metabolome, and gut microbiome data were candidate predictors of changes in weight, body fat mass (BFM), and soft lean mass (SLM). Multivariable regression and the least absolute shrinkage and selection operator model were used to identify predictors and develop weighted-sum prediction models.<br><br>RESULTS: Multiomic and phenotypic models significantly outperformed phenotype-only models (P < 0.05), demonstrating strong predictive performance during both phases. During weight loss, the multiomic and phenotypic model yielded R2 values of 0.49, 0.61, and 0.54 for changes in weight, BFM, and SLM, respectively, with corresponding root mean square errors (RMSEs) of 1.59, 1.41, and 0.98 kg. For binary classification of clinically meaningful weight loss (&#x2265;5%), the model achieved an area under the curve of 0.95 (sensitivity 94.12%; specificity 86.79%). During weight regain, R2 values reached 0.72, 0.73, and 0.66 for weight, BFM, and SLM (RMSEs 1.40, 1.62, and 0.73 kg), respectively. Several key baseline predictors, primarily gut microbes and fecal metabolites, such as N-acetyl-l-aspartic acid, Ruminococcus callidus, and Bifidobacterium adolescentis, were shared for weight and body composition changes during both phases.<br><br>CONCLUSIONS: Baseline multiomic and phenotypic data effectively predict weight and body composition loss and regain, offering insights for personalized weight management.},
}
@article {pmid40587091,
year = {2025},
author = {},
title = {Correction to: Oral amoxicillin treatment disrupts the gut microbiome and metabolome without interfering with luminal redox potential in the intestine of Wistar Han rats.},
journal = {FEMS microbiology ecology},
volume = {101},
number = {7},
pages = {},
doi = {10.1093/femsec/fiaf070},
pmid = {40587091},
issn = {1574-6941},
}
@article {pmid40586878,
year = {2025},
author = {Talley, NJ and Duncanson, K and Williams, GM},
title = {Why are disorders of gut-brain interaction (DGBI) often food-related? Duodenal eosinophils and mast cells, small intestinal bacteria, food allergy and altered food intake in functional dyspepsia and the irritable bowel syndrome: a new paradigm.},
journal = {Journal of gastroenterology},
volume = {},
number = {},
pages = {},
pmid = {40586878},
issn = {1435-5922},
abstract = {The underlying causes of irritable bowel syndrome (IBS) and functional dyspepsia (FD) have remained largely elusive, but emerging data suggest immune activation and loss of small intestinal homeostasis may explain a major subgroup. FD and IBS symptoms often overlap and may occur early in the post-prandial period, suggesting the origin of symptoms may be much higher in gastrointestinal tract than colon. There is strong evidence low-grade duodenal inflammation, comprising eosinophils and/or mast cells associated with increased permeability, is present at least in a major subset with FD and IBS. This hypothesis is further supported by evidence of circulating increased small intestinal homing T cells and altered duodenal microbiota. We hypothesize a major etiologic pathway whereby interaction of food with intestinal bacteria switches on small intestinal immune activation in FD and IBS leading to presentation of antigens to the mucosa. While the low FODMAP diet provides symptom relief in both IBS and FD, this diet notably also reduces common food protein antigens (e.g., wheat, milk, soy) and urinary histamine levels. The obvious but often overlooked fact that food ingestion usually requires the act of eating adds nuance to determining whether food components or eating itself induces symptoms and that both need to be considered in DGBI in clinical practice. The exciting observations about subtle inflammation in DGBIs offer hope for new diagnostic biomarkers, and if considered in the context of altered dietary patterns and validated against symptom responses, will pave the way for novel DGBI treatment options.},
}
@article {pmid40586597,
year = {2025},
author = {Khatib, L and Song, SJ and Dilmore, AH and Sanders, JG and Brennan, C and Hernandez, AR and Myers, T and Oles, R and Farmer, S and Cowart, C and Birmingham, A and Diaz, EA and Nizet, O and Gilbert, K and Litwin, N and Das, P and Nowinski, B and Bryant, M and Tribelhorn, C and Sanders-Bodai, K and Chaumont, S and Knol, J and Roeselers, G and Laiola, M and Shetty, SA and Veiga, P and Tap, J and Derrien, M and Koutnikova, H and Cotillard, A and Lay, C and Tovar, AR and Torres, N and Arteaga, L and González, A and McDonald, D and Bartko, A and Knight, R},
title = {A three-country analysis of the gut microbiome indicates taxon associations with diet vary by taxon resolution and population.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0054425},
doi = {10.1128/msystems.00544-25},
pmid = {40586597},
issn = {2379-5077},
abstract = {UNLABELLED: Emerging research suggests that diet plays a vital role in shaping the composition and function of the gut microbiota. Although substantial efforts have been made to identify general patterns linking diet to the gut microbiome, much of this research has been concentrated on a small number of countries. Additionally, both diet and the gut microbiome have highly complex and individualized configurations, and there is growing evidence that tailoring diets to individual gut microbiota profiles may optimize the path toward improving or maintaining health and preventing disease. Using fecal metagenomic data from 1,177 individuals across three countries, we examine the relationship between diet and bacterial genera, focusing on Prevotella and Faecalibacterium, which have gained significant attention for their potential roles in human health and strong associations with dietary patterns. We find that these two genera in particular show significant associations with many aspects of diet but these associations vary in scale and direction, depending on the level of metagenomic resolution (i.e., genus level by reads and strain level by metagenome-assembled genomes) and the contextual population. These results highlight the growing importance of building metagenomic data sets that are standardized, comprehensive, and representative of diverse populations to increase our ability to tease apart the complex relationship between diet and the microbiome.<br><br>IMPORTANCE: An analysis of fecal microbiome data from individuals in the United States, United Kingdom, and Mexico shows that associations with dietary components vary both by country and by level of resolution (i.e., genus and strain). Our work sheds light on why there may be conflicting reports regarding microbial associations with diet, disease, and health.},
}
@article {pmid40586571,
year = {2025},
author = {Jiang, Y and An, Z and Li, W and Xia, S and Ding, Q and Zhong, J and Wang, H and Xu, Y and Chen, K and Shen, Y},
title = {Integrated multi-omics reveals the impact of ruminal keystone bacteria and microbial metabolites on average daily gain in Xuzhou cattle.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0076925},
doi = {10.1128/spectrum.00769-25},
pmid = {40586571},
issn = {2165-0497},
abstract = {UNLABELLED: The rumen microbiome plays a crucial role in determining the metabolic and digestive efficiency of livestock. Despite its crucial role, the impact of the rumen microbiome on average daily gain (ADG) in Xuzhou cattle remains underexplored. Xuzhou cattle is a well-known breed in China, renowned for rapid growth and superior meat quality. We selected 10 individuals from the Xuzhou cattle population and categorized Xuzhou cattle into High-ADG and Low-ADG groups and analyzed their rumen microbiota. Through comprehensive metagenomic and metabolomic analyses, we characterized the microbial diversity and functional composition of the rumen microbiome, uncovering distinct taxonomic and functional alterations associated with ADG. Thirteen kingdoms, 224 phyla, and over 16,000 species were identified, and principal coordinates analysis (PCoA) indicated significant microbial differentiation between the two groups on phylum, genus, and species levels (P < 0.05). Notably, Lentisphaerae, along with several other genera and species, presented a higher abundance in High, suggesting a potential connection with enhanced growth performance. Further functional annotation revealed that the High group displayed enriched carbohydrate and amino acid metabolism pathways, with a greater abundance of carbohydrate-active enzymes (CAZymes), particularly those involved in the degradation of complex carbohydrates. The Low-ADG group exhibited reduced metabolic activity in these pathways. Metabolomic analysis revealed 10 significantly altered metabolites, including gamma-glutamyltyrosine and N-acetylaspartic acid, which were upregulated in the High-ADG group, indicating their potential role in growth promotion. Spearman's rank correlation analysis further uncovered significant interactions between key microbiomes and metabolites, which correlated with ADG. Random forest analysis identified Victivallales and Lentisphaerae as key taxa, with gamma-glutamyltyrosine and Asp-Phe emerging as predictive biomarkers for ADG.<br><br>IMPORTANCE: This study identifies key microbiota (Victivallales and Lentisphaerae) and metabolites (gamma-glutamyltyrosine, Asp-Phe, N-acetylaspartic acid, Gly-Phe) that positively regulate average daily gain (ADG) in Xuzhou cattle through amino acid metabolism. This fundamental information is vital for the development of potential manipulation strategies to improve the daily gain level through precision feeding.},
}
@article {pmid40586568,
year = {2025},
author = {Macias, M and Irving, MR and Bandow, KM and Kim, K and Heredia, C and Hoskinson, CA and Duchild, NR and Nicholas, MT and Marian, LM and Sicangco, CK and Smith, KL and Davis, SD and Holmlund, HI and Stiemsma, LT},
title = {Effects of low wildfire burn severity due to pre-fire shrub thinning on the chaparral soil bacteriome in the Santa Monica Mountains of Southern California.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0018525},
doi = {10.1128/spectrum.00185-25},
pmid = {40586568},
issn = {2165-0497},
abstract = {Our objective was to study the longitudinal effect of decreased burn severity due to vegetation-type conversion (VTC) induced by chaparral shrub thinning prior to the Woolsey wildfire (November 2018) on soil chemistry and bacteriome composition and function. We compared soils from two study sites on the Malibu campus of Pepperdine University in the Santa Monica Mountains: one site had dense, unaltered chaparral shrubland and experienced a 4.5-fold increase in vegetation burn severity (high severity burn) compared to an adjacent altered site where the vegetative fuel load was 80% less prior to the fire (low severity burn). We analyzed soil nutrient concentrations and pH in 2019 and 2021 and soil respiration, measured by CO2 efflux, in 2019, 2020, and 2021. DNA was isolated from soil samples collected in 2019, 2020, 2021, and 2023 for Illumina Miseq paired-end 16S V3-V4 sequencing. We predicted the functional bacteriome from the 16S data using PICRUSt2. Relative to high severity soils, low severity soils showed decreased nutrient concentrations, pH, and % organic matter in 2019. The low severity burned site showed greater compositional stability over time, with increased pyrophilous taxa in 2021 and 2023 (Massilia, Conexibacter, etc.). High severity burned soils showed decreased metabolic capacity over time. We identified correlations between bacterial taxa and diversity and functional pathways, which remained only in the high severity soil samples after stratification. Our findings contribute to an improved understanding of bacterial succession in soil from sites that experienced VTC prior to wildfire, highlighting microbial ecological implications for fire management strategies.IMPORTANCEAlong with increased fire frequency, the wildfire-urban interface has been expanding, requiring the need for fire mitigation strategies, such as pre-fire vegetation thinning near urban structures. Pre-fire vegetation thinning contributes to vegetation-type conversion and decreases burn severity, but its effect on the soil microenvironment is largely unknown. Here, we compared soil sites that experienced burns of different severity due to pre-fire vegetation thinning and vegetation-type conversion at one site but not the other. We identified changes in soil chemistry and longitudinal shifts in soil bacterial abundance and metabolic capacity that are associated with decreased burn severity due to pre-fire vegetation-type conversion. Our work contributes to improved understanding of the effects of pre-fire vegetation thinning to manage wildfire impact on urban structures on the soil microenvironment. These findings demonstrate ecological implications for fire management strategies and recovery of the chaparral ecosystems following wildfire.},
}
@article {pmid40586555,
year = {2025},
author = {Yuan, X and Gao, J and Bajinka, O and Feng, X},
title = {Vaginal microbiome and recurrent pregnancy loss.},
journal = {Infection and immunity},
volume = {},
number = {},
pages = {e0005325},
doi = {10.1128/iai.00053-25},
pmid = {40586555},
issn = {1098-5522},
abstract = {The joy of every mother is to survive a healthy pregnancy and give birth to a healthy baby. However, until today, many couples are finding it difficult to welcome a baby. Among the factors that cause infertility and recurrent pregnancy loss (RPL) is the microbiome composition that inhabits the vaginal space. These microbiomes occupying the vaginal space play a role in balancing acids, pH, and metabolites to ensure a healthy vaginal environment that can prevent pregnancy loss. What is even more evident is that these microbiomes, when dominated by Lactobacillus spp., prevent the growth of vaginal pathogens and reduce the risk of developing drug resistance. Although there is compelling evidence centered on the vaginal microbiome in promoting a healthy vagina, RPL is attributed to their altered or reduced Lactobacillus spp. While there are discrepancies in the literature, this review aimed to summarize the recent findings on vaginal microbiome and RPL. In addition, this mini review further revealed vaginal microbiota as biomarkers that can predict a healthy vagina and the risk of vaginal microbiome causing RPL. In addition, the immune response and metabolite changes in vaginal microbiome-related RPL, as well as some limitations to this intervention and prospective studies, are summarized.},
}
@article {pmid40586543,
year = {2025},
author = {Begmatov, S and Beletsky, AV and Mardanov, AV and Lukina, AP and Glukhova, LB and Karnachuk, OV and Ravin, NV},
title = {Novel lineages of bacteria with reduced genomes from the gut of farm animals.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0029425},
doi = {10.1128/msphere.00294-25},
pmid = {40586543},
issn = {2379-5042},
abstract = {Genome reduction and associated metabolic deficiencies have been described in various lineages of parasitic and symbiotic microorganisms that obtain essential nutrients from their partners, and in some free-living microorganisms that inhabit stable environments. The animal gut is a relatively stable ecosystem, characterized by an abundance of organic substances and a high concentration of microorganisms, which provides favorable conditions for the survival of microorganisms with reduced genomes. Metagenomic analysis of 49 samples of feces of farm animals (cows, sheep, yaks, and horses) revealed uncultured lineages of bacteria with reduced genomes (<1 Mbp): family UBA1242 (Christensenellales, Firmicutes), order Rs-D84 (Alphaproteobacteria), and family UBA9783 (Opitutales, Verrucomicrobiota), defined in genome-taxonomy database. Analysis of the genomes showed that these bacteria lacked pathways for the biosynthesis of amino acids, nucleotides, lipids, and many other essential metabolites. The UBA9783 genomes encoded a near-complete Embden-Meyerhof glycolytic pathway and the non-oxidative phase of the pentose phosphate pathway, while in UBA1242 and Rs-D84, these pathways are incomplete. All bacteria are limited to fermentative metabolism and lack aerobic and anaerobic respiratory pathways. All UBA9783 and some Rs-D84 genomes encoded F0F1-type ATP synthase and pyrophosphate-energized proton pump; they also can import and utilize peptides and some amino acids. While UBA9783 bacteria could thrive as specialized free-living organisms in the organic-rich gut environment, the UBA1242 and Rs-D84 lineages appear to have adopted the lifestyle of an obligate symbiont/parasite, obtaining metabolites from other cells.IMPORTANCEThe microbiota of the animal gastrointestinal tracts is a complex community of microorganisms which interact in a synergistic or antagonistic relationship and play key nutritional and metabolic roles. However, despite its importance, the gut microbiota of farm animals, especially its uncultured majority, remains largely unexplored. We performed a metagenomic analysis of the gut microbiome of farm animals and characterized three uncultured lineages of bacteria with reduced genomes (<1 Mbp) from the phyla Firmicutes, Proteobacteria, and Verrucomicrobiota. These bacteria were predicted to possess key metabolic deficiencies such as the inability to synthesize essential cell metabolites, suggesting their adaptation to the lifestyle of a symbiont/parasite, or a scavenger obtaining nutrients from the organic-rich gut environment. This study shows that genome reduction with metabolic specialization and adaptation to a partner-dependent lifestyle occurred through convergent evolution in several phylogenetically distant lineages of gut microbiota.},
}
@article {pmid40586542,
year = {2025},
author = {Bruno, JS and Heidrich, V and Restini, FCF and Alves, TMMT and Miranda-Silva, W and Knebel, FH and Cóser, EM and Inoue, LT and Asprino, PF and Camargo, AA and Fregnani, ER},
title = {Dental biofilm serves as an ecological reservoir of acidogenic pathobionts in head and neck cancer patients with radiotherapy-related caries.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0025725},
doi = {10.1128/msphere.00257-25},
pmid = {40586542},
issn = {2379-5042},
abstract = {UNLABELLED: Radiotherapy-related caries (RRC) is an aggressive and debilitating oral toxicity that affects half of the patients who undergo radiotherapy for head and neck cancer. However, the etiology of RRC is not fully established, and there are no clinically validated methods for preventing it. To gain a better understanding of the risk factors and the microbiome's role in causing RRC, we compared clinicopathological characteristics, oncological treatment regimens, oral health condition, and the oral microbiota at three different oral sites of radiotherapy-treated patients with (RRC+) and without radiotherapy-related caries (RRC-). We observed no significant differences between these groups in the clinicopathological characteristics and treatment regimens. However, RRC+ patients were older and had poorer oral health conditions at the start of the radiotherapy treatment, with a lower number of teeth and a higher proportion of rehabilitated teeth. RRC+ patients had lower microbiota diversity and the dental biofilm of RRC+ patients displayed striking alterations in microbiome composition compared to RRC- patients, including enrichment of acidogenic species and altered metabolic potential, with a higher abundance of genes linked to energy-related pathways associated with the synthesis of amino acids and sugars. We also compared the microbiota of RRC+ tissue with conventional caries tissue, revealing lower bacterial diversity and enrichment of Lactobacillaceae members in RRC+. The insights into the irradiated oral microbiota enhance the understanding of RRC etiology and highlight the potential for microbial-targeted therapies in its prevention and treatment.<br><br>IMPORTANCE: This study focuses on a dedicated collection of diverse oral sites to comprehensively investigate microbial differences between patients who develop RRC and those who do not. RRC is a severe oral disease that profoundly impacts on the oral health and overall quality of life of cancer survivors. Leveraging shotgun metagenomics, we characterize the unique microbial variations in in vivo irradiated dental biofilms, unveiling novel insights into the microbial ecology of radiotherapy-treated patients. Furthermore, this research integrates extensive data on oral health and oncological profiles, providing a comprehensive understanding of the intricate relationship between oral microbial communities and the outcomes of radiotherapy-induced toxicity.},
}
@article {pmid40586419,
year = {2025},
author = {Dason, MS and Corà, D and Re, A},
title = {Sequence modeling tools to decode the biosynthetic diversity of the human microbiome.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0033325},
doi = {10.1128/msystems.00333-25},
pmid = {40586419},
issn = {2379-5077},
abstract = {Understanding the biosynthetic potential of the human microbiome remains a significant challenge with far-reaching scientific and translational implications. Analyses of human-associated (meta)genomic sequencing data undeniably show that the biosynthetic diversity encoded in these genomes is largely underexplored. A crucial step in studying specialized metabolites involves the sequence-based identification of genes encoding biosynthetic pathways, typically organized into biosynthetic gene clusters (BGCs). In this review, we provide a concise and updated overview of the widening range of computational approaches that have effectively addressed the sequence-based identification of BGCs across both isolated genomes and complex microbial communities. These advancements are set to deepen our understanding of the biosynthetic potential and diversity of microorganisms residing in different human body sites.},
}
@article {pmid40586417,
year = {2025},
author = {Nair, AP and Kaushik, D and Kumar, A and Singh, J and Oz, E and Sharma, A and Jebreen, A and Proestos, C and Oz, F and Kumar, M},
title = {Deciphering the Effect of Ginsenoside Rk3 on Gut Microbiota and Its Applications.},
journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology},
volume = {39},
number = {13},
pages = {e70784},
doi = {10.1096/fj.202501234RR},
pmid = {40586417},
issn = {1530-6860},
mesh = {*Ginsenosides/pharmacology ; *Gastrointestinal Microbiome/drug effects ; Humans ; Animals ; Panax/chemistry ; },
abstract = {Gut microbiota, a complex community of microorganisms residing in the gastrointestinal tract, has been implicated in the overall health and disease states of the host organism. Among various bioactive compounds, ginsenoside Rk3, a component of the medicinal plant Panax ginseng, has emerged as a potential modulator of gut microbial composition. This abstract aimed to highlight the impact of ginsenoside Rk3 on gut microbiota, uncovering its effects on microbial diversity, abundance, and functionality. By investigating the specific changes induced by ginsenoside Rk3 within the gut microbial ecosystem, the study illuminates its potential therapeutic roles, thereby expanding the understanding of host-microbiome interactions and their significance in health and disease.},
}
@article {pmid40586386,
year = {2025},
author = {Li, K and Arbab, S and Du, Q and Zhou, J and Chen, Y and Tian, Y and Qijie, L and Ullah, H and Zhang, B},
title = {Regulatory and Influencing Factors of Digestive Function in Elderly People: Roles of the Gut Microbiota and Nutritional Interventions.},
journal = {Aging and disease},
volume = {},
number = {},
pages = {},
doi = {10.14336/AD.2025.0565},
pmid = {40586386},
issn = {2152-5250},
abstract = {Aging is a natural and gradual biological process through which living organisms undergo physical, physiological, and sometimes psychological changes over time. Aging is commonly associated with a decline in gastrointestinal function, leading to various digestive disorders that impact the quality of life of older adults. The gut microbiota is a highly complex ecosystem that plays crucial roles in digestion, metabolic processes, immune functions, and overall health. However, emerging evidence indicates that many elderly individuals maintain relatively stable digestive health, suggesting the influence of modifiable regulatory factors. In this review, we describe the key physiological, microbial, and nutritional factors that regulate and influence digestive function in an aging population. Additionally, we explored the impact of age-associated alterations in the gut microbiota on digestive health challenges in older adults and emphasized the therapeutic potential of targeted nutritional intervention approaches, such as dietary modifications, prebiotics, probiotics, and symbiotic and fecal microbiota transplantation, which have shown promise in rebalancing the gut microbiome and reducing inflammation.},
}
@article {pmid40586319,
year = {2025},
author = {Gao, YD and Wang, ZJ and Ogulur, I and Li, SJ and Yazici, D and Li, XH and Pat, Y and Zheng, Y and Babayev, H and Zeyneloglu, C and Li, YC and Ardicli, S and Tian, WQ and Ardicli, O and Chen, SW and Bu, XT and Lu, G and Chang, LH and He, Y and Guttman-Yassky, E and Cabanillas, B and Ozdemir, C and Kiykim, A and Shamji, M and Nadeau, K and Torres, MJ and Akdis, M and Akdis, CA},
title = {Type 2 Immunity and Its Role in Allergic Disorders.},
journal = {Allergy},
volume = {},
number = {},
pages = {},
doi = {10.1111/all.16620},
pmid = {40586319},
issn = {1398-9995},
support = {72204214//National Natural Science Foundation of China/ ; BQD 2306//Start-up Research fund by The First Affiliated Hospital of Zhejiang University School of Medicine/ ; LTGY24H260001//Zhejiang Provincial Natural Science Foundation of China/ ; LQN25H030006//Zhejiang Provincial Natural Science Foundation of China/ ; LQN25H020010//Zhejiang Provincial Natural Science Foundation of China/ ; },
abstract = {The prevalence of allergic diseases, including allergic rhinitis, chronic rhinosinusitis, asthma, eosinophilic esophagitis, food and drug allergies, and atopic dermatitis, has been increasing globally over the past few decades. Allergic diseases are closely linked to type 2 immunity, which is characterized by the coordinated interplay between innate and adaptive immune responses. Significant advancements have been achieved in elucidating the cellular and molecular mechanisms that govern type 2 immunity, chiefly mediated by type 2 cytokines, including IL-4, IL-5, IL-9, and IL-13, which are primarily secreted by T helper 2 cells and group 2 innate lymphoid cells. In addition, a diverse array of effector cells, including mast cells, basophils, eosinophils, regulatory T cells, B lymphocytes, dendritic cells, and natural killer cells, are critically involved in orchestrating and modulating type 2 inflammatory responses. The activation of epithelial cells, secretion of alarmins and multiple chemokines, impairment of epithelial barrier integrity, and disruption of microbial dysbiosis serve as crucial mechanisms underlying not only the pathogenesis of allergic disorders but also the development of various systemic conditions. Biologic therapies targeting type 2 pathways-specifically effector functions of IL-4, IL-13, IL-5, thymic stromal lymphopoietin, and immunoglobulin E have-demonstrated promising efficacy. However, a subset of patients with severe allergic diseases remains unresponsive to these treatments, underscoring the need for deeper mechanistic insights and personalized therapeutic approaches. This review addresses the definition, evolution, cellular and molecular basis, and regulation of type 2 immunity. It then examines the common allergic diseases associated with type 2 responses and concludes by exploring the associations between inborn errors of immunity and type 2 responses.},
}
@article {pmid40586263,
year = {2025},
author = {Bonham, KS and Margolis, ET and Fahur Bottino, G and Sobrino, AC and Patel, F and McCann, S and Zieff, MR and Miles, M and Herr, D and Davel, L and Bosco, C and , and Huttenhower, C and Pini, N and Alexander, DC and Jones, DK and Williams, SCR and Amso, D and Gladstone, M and Fifer, WP and Donald, KA and Gabard-Durnam, LJ and Klepac-Ceraj, V},
title = {Codevelopment of gut microbial metabolism and visual neural circuitry over human infancy.},
journal = {mBio},
volume = {},
number = {},
pages = {e0083525},
doi = {10.1128/mbio.00835-25},
pmid = {40586263},
issn = {2150-7511},
abstract = {Infancy is a time of elevated neuroplasticity supporting rapid brain and sensory development. The gut microbiome, also undergoing extensive developmental changes in early life, may influence brain development through the metabolism of neuroactive compounds. Here, we leverage longitudinal data from 194 South African infants across the first 18 months of life to show that microbial genes encoding enzymes that metabolize molecules playing a key role in modulating early neuroplasticity are associated with visual cortical neurodevelopment, measured by the Visual-Evoked Potential (VEP). Neuroactive compounds included neurotransmitters GABA and glutamate, the amino acid tryptophan, and short-chain fatty acids involved in myelination, including acetate and butyrate. Microbial gene sets around 4 months of age were strongly associated with the VEP from around 9-14 months of age and showed more associations than concurrently measured gene sets, suggesting that microbial metabolism in early life may affect subsequent neural plasticity and development.IMPORTANCEOver the past decade, extensive research has revealed strong links between the gut microbiome and the brain, at least in adults or those with neuropsychiatric disorders. This study explores how these associations emerge in early development using a longitudinal sample of 194 infants with repeated microbiome metabolism and electroencephalography (EEG) measures during the critical early period of visual cortex neuroplasticity. We examined microbial genes encoding enzymes for neuroactive compounds (e.g., GABA, glutamate, tryptophan, and short-chain fatty acids) and their association with the visual-evoked potential (VEP). Genes from 4-month stool samples strongly correlated with VEP features between 9 and 14 months, suggesting that early microbial metabolism influences later visual neurodevelopment. These prospective associations were more numerous than the concurrent ones. Our findings suggest that early gut microbiome metabolic potential plays a crucial role in shaping neural plasticity and visual neurodevelopment.},
}
@article {pmid40586259,
year = {2025},
author = {Gross, M and Ramot, Y},
title = {Unraveling the Microbiome-Psoriasis Connection: Insights into Pathogenesis and Therapeutic Potential.},
journal = {The Israel Medical Association journal : IMAJ},
volume = {27},
number = {6},
pages = {382-387},
pmid = {40586259},
issn = {1565-1088},
}
@article {pmid40586245,
year = {2025},
author = {Kerr, EN and Hesse, RD and Carlson-Jones, JAP and Nalagampalli Papudeshi, B and Butcher, PA and Doane, MP and Dinsdale, EA},
title = {Draft genomes of five bacteria isolated from Carcharodon carcharias (white shark) and Carcharhinus brachyurus (bronze whaler shark).},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0022625},
doi = {10.1128/mra.00226-25},
pmid = {40586245},
issn = {2576-098X},
abstract = {Here, we isolated five bacterial species from the skin and cloaca of Carcharodon carcharias (white shark) and Carcharhinus brachyurus (bronze whaler or copper shark).},
}
@article {pmid40585855,
year = {2025},
author = {Burger, K and Michael Trauner, M and Bergheim, I},
title = {Pathogenic aspects of fructose consumption in metabolic dysfunction-associated steatotic liver disease (MASLD): A narrative review.},
journal = {Cell stress},
volume = {9},
number = {},
pages = {49-64},
pmid = {40585855},
issn = {2523-0204},
abstract = {Metabolic dysfunction-associated steatotic liver disease (MASLD), formerly referred to non-alcoholic fatty liver disease (NAFLD), has become a global health concern with a still increasing prevalence. One of the major contributing factors to its pathogenesis is overnutrition. In recent years, a discussion has been started that not only general overnutrition but also specific dietary patterns like the so-called 'Western diet' composed of foods rich in saturated fats, cholesterol, and sugar (especially fructose) but low in fiber and polyunsaturated fats, may contribute to the development of MASLD. Evidence from human (intervention) studies regarding the effects of sugar and especially fructose intake is limited and contradictory with respect to the development of MASLD. Still, some scientific liver societies have incorporated a reduction of sugar-sweetened beverages (SSBs) being rich in fructose in their life-style advice for the treatment of MASLD. Being metabolized independently of insulin, fructose has been proposed to be processed more rapidly than glucose, leading to increased lipogenesis and subsequently to hepatic lipid accumulation. Results of more recent experimental studies suggest that an elevated intake of fructose may also affect gut microbiota composition, alter small intestinal morphology and impair intestinal barrier function subsequently leading to an increased translocation of pathogen-associated molecular patterns (PAMPs) into the portal circulation. In this narrative review we summarize recent findings related to the relationship of fructose intake and MASLD, herein focusing on the gut-liver axis and the discrepancy between studies in humans and model organisms.},
}
@article {pmid40585846,
year = {2025},
author = {Singh, G and Chaudhry, Z and Boyadzhyan, A and Sasaninia, K and Rai, V},
title = {Dysbiosis and colorectal cancer: conducive factors, biological and molecular role, and therapeutic prospectives.},
journal = {Exploration of targeted anti-tumor therapy},
volume = {6},
number = {},
pages = {1002329},
pmid = {40585846},
issn = {2692-3114},
abstract = {Colorectal cancer (CRC) is the third leading cause of cancer-related death in the United States. Emerging evidence highlights the significant role of gut microbiota dysbiosis, characterized by a reduction in beneficial bacteria and an increase in pro-inflammatory and pro-carcinogenic bacteria, in CRC pathogenesis. Both genetic and environmental factors, including diet, antibiotic use, physical activity, aging, and obesity, contribute to this microbial imbalance. Dysbiosis promotes chronic inflammation and immune dysregulation, which facilitates tumor initiation and progression. This review examines the intricate interactions between gut microbiota, immune modulation, and CRC development. It explores current and emerging therapeutic strategies that target the microbiome to enhance treatment efficacy, discusses interventions aimed at restoring healthy microbiota in CRC patients, and outlines future directions for microbiome-based therapies to improve clinical outcomes.},
}
@article {pmid40585799,
year = {2025},
author = {Alty, JW and Barnes, CE and Nicoli, AM and Turner, BS and Beneman, EA and Dugan, AE and Brucks, SD and Kruger, AG and Schrock, RR and Ribbeck, K and Kiessling, LL},
title = {Synthetic Mucins as Glycan-Defined Prebiotics.},
journal = {ACS central science},
volume = {11},
number = {6},
pages = {918-926},
pmid = {40585799},
issn = {2374-7943},
abstract = {The human microbiome contains at least as many bacterial cells as human cells. Some bacteria offer benefits, like improving gut barrier function, suppressing pathobiont growth, and modulating immunity. These benefits have popularized probiotics, but probiotic retention is often hindered by low colonization efficiency in the mucosal layer that lines all epithelial cells. Mucins, the primary components of mucus, are essential for the organization and regulation of microbial populations. The molecular mechanisms of mucin-probiotic interactions remain understudied due, in part, to the inability to incisively manipulate native mucin sequences or their glycans. Here, we used synthetic mucins with defined glycan presentations to interrogate glycan-dependent interactions between mucus and three probiotic lactobacilli species. The nutrient conditions under which bacteria were cultured influenced glycan binding preferences, suggesting mucin-probiotic interactions change with nutrient availability. The addition of synthetic mucins to native mucin increased Limosilactobacillus fermentum adherence. Additionally, an increase in glycosidase activity indicated that native and synthetic mucins function as prebiotics, as probiotic bacteria can cleave the displayed O-glycans. Thus, synthetic mucins can cultivate target probiotic bacteria and increase adhesion as binding sites, highlighting their value as tools for elucidating native mucin functions and as promising agents for promoting human health.},
}
@article {pmid40585700,
year = {2025},
author = {Hamza Saeed, M and Qamar, S and Ishtiaq, A and Umaira Khan, Q and Atta, A and Atta, M and Ishtiaq, H and Khan, M and Saeed, MR and Iqbal, A},
title = {Fecal Microbiota Transplantation (FMT) in Clostridium difficile Infection: A Paradigm Shift in Gastrointestinal Microbiome Modulation.},
journal = {Cureus},
volume = {17},
number = {5},
pages = {e85054},
pmid = {40585700},
issn = {2168-8184},
abstract = {Clostridium difficile (C. difficile) infection (CDI) poses a tremendous clinical challenge, especially in patients with recurrent disease and antibiotic resistance. Fecal microbiota transplantation (FMT) has become a new therapeutic strategy for restoring gut microbiota and decreasing CDI recurrence. The study aims to assess the clinical effectiveness of FMT in adult subjects with recurrent or refractory CDI, determine its effect on gut microbiome diversity, and track safety outcomes and rates of recurrence post-treatment. FMT was compared against standard antibiotic treatments to establish its efficacy in decreasing infection persistence and improving patients' quality of life. This study examines the efficacy, safety, and modulation of microbiota by FMT in an ensemble of 250 patients diagnosed with CDI, with equal gender distribution and a mean age of 55.61. Among the study participants, 131 (52.4%) underwent FMT by various routes of administration, including 66 (25.2%) through colonoscopy, 73 (29.2%) via a nasogastric tube, 60 (24.0%) via enema, and 54 (21.6%) through oral capsule administration. The success rate for FMT was reported as 88 (35.2%), partial success at 74 (29.6%), and treatment failure at 88 (35.2%). CDI recurrence was reported in 130 (52.0%) of patients after FMT. The gut microbiome enhanced diversity, measured in terms of the Shannon Diversity Index, increased significantly from 3.96 before FMT to 5.88 after FMT, thus indicating a favorable impact on gut microbial composition. Furthermore, 132 (52.8%) converted from C. difficile polymerase chain reaction (PCR) toxin positive to negative, corroborating successful pathogen clearance. On secondary outcomes, the quality of life in patients improved in 90 (36%), antibiotic dependence was reduced in 88 (35.2%), and hospitalization was lessened in 72 (28.8%). Inflammatory markers, such as white blood cell (WBC) counts and C-reactive protein (CRP), went downward but did not reach statistical significance. Logistic regression analysis identified age, severity of CDI, and prior exposure to antibiotics as the main predictors for the efficacy of FMT (p < 0.05). It is concluded that FMT is a promising alternative treatment for recurrent CDI through modulation of gut microbiota and decreasing the severity of infection. Future work is, however, required to establish treatment protocols with optimized results for long-term effectiveness and minimized recurrence risks.},
}
@article {pmid40585508,
year = {2025},
author = {Zhu, B and Wu, H and Zhang, H and Song, Q and Xiao, Y and Yu, B},
title = {Gut microbiota from voluntary exercised mice protects the intestinal barrier by inhibiting neutrophil extracellular trap formation.},
journal = {iScience},
volume = {28},
number = {6},
pages = {112763},
pmid = {40585508},
issn = {2589-0042},
abstract = {Ulcerative colitis is an inflammatory bowel disease characterized by impaired intestinal barrier function, dysregulated immune responses, and alterations in the gut microbiota. Excessive formation of neutrophil extracellular traps (NETs), driven by peptidyl arginine deiminase 4 (PAD4) activity, contributes to inflammation modulated by the gut microbiota. In this study, we used a mouse model of dextran sulfate sodium-induced colitis to investigate the effects of voluntary exercise and its underlying mechanisms. Exercise preconditioning attenuated colitis severity, maintained intestinal barrier integrity, normalized gut microbiota composition, and suppressed NET formation. PAD4 inhibition further enhanced these effects. By contrast, the depletion of the gut microbiota by antibiotics largely abolished the benefits of exercise. Additionally, fecal microbiota transplantation from exercised mice recapitulated these protective effects. These findings elucidate the interplay among exercise, gut microbiota, and PAD4-mediated NET formation. Targeting these pathways may offer promising therapeutic strategies for colitis.},
}
@article {pmid40585396,
year = {2025},
author = {Maitre, A and Kratou, M and Cano-Argüelles, AL and Porcelli, S and Abuin-Denis, L and Piloto-Sardiñas, E and Mateos-Hernández, L and Obregon, D and Tonk-Rügen, M and Abdelali, SK and Moutailler, S and Cabezas-Cruz, A},
title = {Differential Impact of Simultaneous or Sequential Coinfections With Borrelia afzelii and Tick-Borne Encephalitis Virus on the Ixodes ricinus Microbiota.},
journal = {International journal of microbiology},
volume = {2025},
number = {},
pages = {7747795},
pmid = {40585396},
issn = {1687-918X},
abstract = {Ticks, particularly Ixodes ricinus, are significant vectors of pathogens such as Borrelia spp. and tick-borne encephalitis virus (TBEV), which cause Lyme borreliosis (LB) and tick-borne encephalitis (TBE), respectively. Understanding how these pathogens interact within the tick microbiome is essential for developing vector control strategies. This study investigates the impact of Borrelia afzelii and TBEV, as well as their coinfection, on the microbiota composition and structure of I. ricinus nymphs. Using a network-based approach, we analyzed the microbial communities of ticks exposed to infected or coinfected mice. DNA extracted from newly molted nymphs was sequenced for the bacterial 16S rRNA gene, and microbial diversity metrics (alpha and beta diversity) were calculated. Our results showed that TBEV infection increased microbiome diversity compared to the uninfected and Borrelia groups. Co-occurrence network analyses revealed that while microbial structures remained consistent across conditions, TBEV-infected networks exhibited higher robustness to perturbations, indicating a stabilizing effect on the tick microbiome. Furthermore, the hierarchical position and associations of Borrelia varied significantly depending on the infection scenario, highlighting its adaptive role within the tick microbiota. The study demonstrates that pathogen presence alters tick microbial dynamics, with TBEV enhancing stability, suggesting virus-mediated modifications of the microbiome. These findings advance our understanding of pathogen-tick-microbiome interactions and provide insights into the ecological mechanisms underlying pathogen coexistence within ticks. This research underscores the importance of microbial networks in ticks and offers new perspectives for targeted approaches in managing tick-borne diseases.},
}
@article {pmid40585352,
year = {2025},
author = {Klammsteiner, T and Heussler, CD and Insam, H and Schlick-Steiner, BC and Steiner, FM},
title = {Larval density drives thermogenesis and affects microbiota and substrate properties in black soldier fly trials.},
journal = {iScience},
volume = {28},
number = {7},
pages = {112794},
pmid = {40585352},
issn = {2589-0042},
abstract = {Industrial insect farming has potential for converting low-value organic waste into nutrient-rich insect biomass, producing valuable by-products like organic fertilizers. However, a better understanding of density-related thermogenesis and microbial dynamics is needed to enhance standardization and bridge gaps between laboratory and industry needs. This lab-scale study focuses on the black soldier fly (Hermetia illucens), which exhibits thermogenesis that intensifies with larval population size and its natural crowding behavior. Using high-resolution temperature monitoring and biomolecular methods, we found that doubling larval density (0, 1.25, 2.5, and 5 larvae/cm[2]) increased temperatures by 0.6°C-2.4°C, depending on the treatment. Adding potassium sorbate altered microbial profiles, increasing Enterobacter and decreasing Providencia, while promoting lactic acid bacteria. Density also impacted pH, water content, dry matter, volatile solids, and ash in the substrate. Our findings provide essential insights into managing microbial and thermal dynamics, offering valuable information for optimizing and standardizing conditions in rearing trials.},
}
@article {pmid40585204,
year = {2025},
author = {Langelier, C and Glascock, A and Maguire, C and Phan, HV and Lydon, E and Calfee, C and Network, I and Corry, D and Kheradmand, F and Baden, L and Sekaly, RP and McComsey, G and Haddad, E and Cairns, C and Pulendran, B and Fernandez-Sesma, A and Simon, V and Metcalf, J and Higuita, N and Messer, W and Davis, M and Nadeau, KC and Kraft, M and Bime, C and Schaenman, J and Erle, D and Atkinson, M and Ehrlich, LIR and Melamed, E and Montgomery, R and Shaw, A and Hough, C and Geng, L and Hoch, A and Hafler, D and Augustine, A and Becker, P and Peters, B and Ozonoff, A and Kim-Schulze, S and Krammer, F and Bosinger, S and Eckalbar, W and Altman, M and Wilson, M and Guan, L and Maecker, H and Steen, H and Diray-Arce, J and Rouphael, N and Kleinstein, S and Reed, E and Levy, O and Chu, V},
title = {Empiric Azithromycin in COVID-19 Impacts the Respiratory Microbiome and Antimicrobial Resistome without Anti-inflammatory Benefit.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-6875205/v1},
pmid = {40585204},
issn = {2693-5015},
abstract = {Azithromycin is often prescribed unnecessarily for respiratory infections, many of which are viral. During the COVID-19 pandemic, its use was widespread, in part due to alleged therapeutic benefits, which have since been disproven. Here, we sought to understand the impact of azithromycin exposure on the respiratory microbiome, antimicrobial resistome, and host immune response in a prospective multicenter cohort of 1164 patients hospitalized for SARS-CoV-2 infection. Using longitudinal nasal metatranscriptomics, we compared patients treated with azithromycin (n=366, 31.4%) to those who received no antibiotics (n=474, 40.7%) or antibiotics other than azithromycin (n=324, 27.8%). We found that azithromycin treatment altered the community composition of the nasal microbiome, reducing bacterial relative abundance, increasing fungal relative abundance, and increasing potentially pathogenic taxa such as Klebsiella and Staphylococcus. Azithromycin treatment was most notably associated with increases in the number of detectably expressed macrolide/lincosamide/streptogramin (MLS) antimicrobial resistance genes, as well as their relative proportion in the resistome, with changes observable after one day of exposure. Of the MLS resistance genes, the expression of ermC , msrA and ermX increased the most in patients receiving azithromycin. Correlation analyses demonstrated that MLS resistance gene expression was significantly associated with the abundance of several taxa, including both commensal (e.g., Dolosigranulum, Corynebacterium) and potentially pathogenic genera (e.g., Streptococcus, Staphylococcus). Assessment of the peripheral blood and upper airway host transcriptome demonstrated no differences in the expression of inflammatory genes. Taken together, our findings demonstrate that azithromycin treatment in COVID-19 leads to dysbiosis of the upper respiratory microbiome and changes in the expression of MLS resistance genes, without apparent anti-inflammatory benefit.},
}
@article {pmid40584618,
year = {2025},
author = {Yang, L and Ao, Y and Li, Y and Dai, B and Li, J and Duan, W and Dong, K and Han, Z and Guo, R},
title = {The anti-depressive role of the Pei Yuan Kai Yu formula in cerebral small vessel disease based on gut microbiota.},
journal = {Frontiers in pharmacology},
volume = {16},
number = {},
pages = {1510250},
pmid = {40584618},
issn = {1663-9812},
abstract = {BACKGROUND: Cerebral small vessel disease (CSVD), characterized by pathological changes in brain vessels, is a common cause of death in the elderly and often accompanied by depression, which significantly affects patients' quality of life and rehabilitation; understanding its pathogenesis and developing innovative therapies are urgently needed, especially considering the role of the blood - brain barrier impairment and the gut - microbiota - gut - brain axis in this complex condition.<br><br>METHODS: Dahl/SS rats were fed a diet containing 8% NaCl and were subjected to chronic unpredictable mild stress (CUMS) stimulation for 4&#xa0;weeks. PY (1.407&#xa0;g/kg/day) was administered intragastrically to evaluate its role in CSVD with depression. Pseudo germ-free rats were colonized with gut microbiota from high-salt-fed rats exposed to CUMS, followed by PY administration.<br><br>RESULTS: In rats with CSVD and depression, PY significantly increased body weight; alleviated depression-like behaviors; and decreased the levels of inflammatory cytokines such as TNF-&#x3b1;, IL-1&#x3b2;, and IL-6 in both serum and hippocampus. Additionally, PY reversed inflammation-induced nerve damage; reduced the overexpression of microglia in the hippocampus; decreased the levels of hippocampal VEGF and MMP-9, and increased the levels of hippocampal occludin, ZO-1, and claudin-5. Moreover, PY improved the composition of gut microbiota and enhanced microbial diversity. PY induced characteristic changes in the microbiome, which were associated with inflammation, endothelial dysfunction, and depressive-like behaviors. These significant metabolites were identified and were found closely related to inflammation, endothelial cell dysfunction, and depression-like behaviors.<br><br>CONCLUSION: In conclusion, PY acts as an antidepressant to slow down the progression of CSVD by inhibiting microglial activation, reducing inflammation and ameliorating endothelial dysfunction. It exerts its effect, at least in part, by enhancing microbiota-mediated metabolism in vivo.},
}
@article {pmid40584555,
year = {2025},
author = {Li, W and Fan, Q and Yang, Y and Xiao, X and Li, J and Zhang, Y},
title = {Benchmarking and optimizing qualitative and quantitative pipelines in environmental metatranscriptomics using mixture controlling experiments.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf090},
pmid = {40584555},
issn = {2730-6151},
abstract = {Metatranscriptomic analysis is increasingly performed in environments to provide dynamic gene expression information on ecosystems, responding to their changing conditions. Many computational methods have undergone remarkable development in the past years, but a comprehensive benchmark study is still lacking. There are concerns regarding the accuracies of the qualitative and quantitative profilers obtained from metatranscriptomic analysis, especially for the microbiota in extreme environments, most of them are unculturable and lack well-annotated reference genomes. Here, we presented a benchmark experiment that included 10 single-species and their cell or RNA-admixtures with the predefined species compositions and varying evenness, simulating the low annotation rate and high heterogeneity. In total, 1 metagenome sample and 24 metatranscriptome were sequenced for the comparisons of 36 combination of analysis methods for tasks ranging from sample preparation, quality control, rRNA removal, alignment strategies, taxonomic profiling, and transcript quantification. For each part of the workflow mentioned above, corresponding metrics have been established to serve as standards for assessment and comparison. Evaluation revealed the performances and proposed an optimized pipeline named MT-Enviro (MetaTranscriptomic analysis for ENVIROnmental microbiome). Our data and analysis provide a comprehensive framework for benchmarking computational methods with metatranscriptomic analysis. MT-Enviro is implemented in Nextflow and is freely available from https://github.com/Li-Lab-SJTU/MT-Enviro.},
}
@article {pmid40584458,
year = {2025},
author = {Newton, JM and Edwards, WJS and Thompson, GS and Gentekaki, E and Tsaousis, AD},
title = {Effect of antibiotic administration on Blastocystis persistence and gut microbiome-metabolome dynamics in an irritable bowel syndrome longitudinal case study.},
journal = {Access microbiology},
volume = {7},
number = {6},
pages = {},
pmid = {40584458},
issn = {2516-8290},
abstract = {Background. Blastocystis, the most prevalent microbial eukaryote in humans, has a global distribution. Studies have linked its presence with distinct gut microbiome and metabolome profiles compared to those where the organism is absent. However, the interplay of antibiotic administration, Blastocystis and the surrounding gut microbiome remains understudied. This case study aimed to explore antibiotic consumption and the presence of Blastocystis with subsequent changes in the gut microbiome and metabolome of an individual diagnosed with irritable bowel syndrome (IBS). Methods. Stool samples from an IBS patient, collected at 12 time points, were tested for the presence of Blastocystis using real-time PCR targeting the SSUrRNA gene, followed by sequencing of positive samples. Illumina sequencing determined the gut microbiome composition, while one-dimensional proton NMR spectroscopy was used to analyse the metabolome composition. Statistical analyses were conducted to identify relationships between antibiotic consumption, bacterial diversity, metabolome composition and Blastocystis presence. Results. Antibiotics significantly impacted the gut microbiome, with diversity declining early in the antibiotic course, then recovering later and post-course. Blastocystis was detected early, late and post-course but was not detectable mid-course, coinciding with the decline in bacterial diversity. Significant differences were observed between Blastocystis-positive and Blastocystis-negative samples, with bacterial composition significantly changing between samples collected before, early and after the antibiotic course compared to those collected mid-course. Metabolite groups, including short-chain fatty acids, amino acids and succinate, exhibited changes throughout the antibiotic course, indicating that gut metabolite composition is affected by antibiotic consumption. Discussion/Conclusion. While antibiotics did not significantly impact Blastocystis colonization, they did cause a mid-course decline in microbial diversity and Blastocystis presence. The study also revealed significant alterations in important metabolites such as short-chain fatty acids and amino acids throughout the antibiotic course, with an altered metabolome observed post-course. This case study underscores the complex interactions between antibiotics, gut microbiota and metabolites, highlighting the resilience of Blastocystis in the gut ecosystem.},
}
@article {pmid40584174,
year = {2025},
author = {Lili, L and Kunces, LJ and Meydan, C and Pesce, S and Afshin, EE and Rickard, N and Stujenske, TM and D'Adamo, CR and Dudley, JT and Zhang, B and Mason, CE},
title = {A multi-omic study profiles women with PCOS to reveal unique gut microbiome compositions.},
journal = {Precision clinical medicine},
volume = {8},
number = {3},
pages = {pbaf012},
pmid = {40584174},
issn = {2516-1571},
}
@article {pmid40584040,
year = {2025},
author = {Pan, H and Liu, H and Liu, F and Xie, J and Zhou, Y and Zheng, Q and Guo, M},
title = {Gut microbiota: a new frontier in understanding and protecting endangered plateau schizothorax fish.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1592312},
pmid = {40584040},
issn = {1664-302X},
abstract = {INTRODUCTION: Against the backdrop of global biodiversity decline, the role of gut microbiota in endangered species conservation remains underexplored. Endemic fish species in Xizang are critical to plateau ecosystems, yet many face severe survival threats. This study investigates the association between gut microbiota composition and conservation status in five endemic fish species, including the nationally protected Oxygymnocypris stewarti, Schizothorax waltoni, and Schizothorax macropogon.<br><br>METHODS: Using 16S rRNA sequencing, we systematically analyzed gut microbiota community structures across the five fish species. We compared microbial diversity, dominant bacterial phyla, and the influence of dietary habits on microbiota composition.<br><br>RESULTS: Dominant Bacterial Phyla: Fusobacteria, Proteobacteria, and Verrucomicrobia were common across species, while Tenericutes was uniquely dominant in endangered fish. Diversity Trends: Gut microbiota diversity followed the order: Ptychobarbus dipogon > S. waltoni > Schizothorax o-connori > S. macropogon > O. stewarti. Conservation Status Correlation: Species with higher endangerment levels exhibited significantly lower diversity: Least Concern (LC) > Near Threatened (NT) > Vulnerable (VU) > Endangered (EN). Dietary Influence: Phytophagous (PHY) fish had higher microbial diversity than omnivorous (OMN) and sarcophagous (SAR) fish, confirming diet as a key factor shaping gut microbiota.<br><br>DISCUSSION: This study provides the first evidence linking gut microbiota composition to the conservation status of endemic Tibetan fish. The reduced microbial diversity in endangered species suggests potential microbiome-related health vulnerabilities. Additionally, dietary differences significantly influence microbiota structure, highlighting the need for habitat and dietary conservation strategies. These findings open new avenues for microbiome-based conservation approaches in endangered species management.},
}
@article {pmid40584033,
year = {2025},
author = {Jin, X and Zhang, L and Ying, C and Pan, K and Zhu, D},
title = {Pulmonary microbiome and metabolome signatures associate with chemotherapy response in lung cancer patients.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1604999},
pmid = {40584033},
issn = {1664-302X},
abstract = {BACKGROUND: Lung cancer is a leading cause of cancer-related mortality worldwide, with chemotherapy response varying significantly among patients. Emerging evidence suggests that the pulmonary microbiota and metabolome may influence treatment outcomes, but their roles remain unclear.<br><br>METHODS: This study enrolled 25 lung cancer patients undergoing chemotherapy, categorized into chemotherapy-sensitive (n&#x202f;=&#x202f;15) and chemotherapy-insensitive (n&#x202f;=&#x202f;10) groups. Bronchoalveolar lavage fluid (BALF) was collected for 16S rDNA sequencing and untargeted metabolomics (LC-MS). Serum bile acids were also analyzed.<br><br>RESULTS: The study identified 92 significantly altered metabolites in BALF between the two groups. Trans-urocanate showed the highest increase, while phenylalanylphenylalanine exhibited the greatest decrease in sensitive patients. Key metabolic pathways, including ABC transporters, glutathione metabolism, and bile acid biosynthesis, were enriched. Microbiome analysis revealed differential abundances of specific bacterial genera, particularly increased Caulobacter and decreased Acinetobacter in sensitive patients. Notably, serum levels of four bile acids (chenodeoxycholic acid, cholic acid, deoxycholic acid, and ursodeoxycholic acid) were significantly elevated in chemotherapy-sensitive patients, demonstrating good predictive value with AUCs ranging from 0.633 to 0.830.<br><br>CONCLUSION: The study highlights distinct microbial and metabolic signatures associated with chemotherapy response, suggesting potential biomarkers for personalized therapy.},
}
@article {pmid40583967,
year = {2025},
author = {Wang, H and Tian, J and Mi, J},
title = {Clinical effectiveness of fecal microbial transplantation for metabolic syndrome: Advances in clinical efficacy and multi-omics research.},
journal = {Current research in microbial sciences},
volume = {9},
number = {},
pages = {100415},
pmid = {40583967},
issn = {2666-5174},
abstract = {Even though metabolic syndrome (MetS) poses a serious risk to human health and life, existing treatment approaches are not very effective. The impact of gut bacteria on host metabolism has been the subject of numerous research, and fecal microbial transplantation (FMT) has demonstrated great promise in reducing insulin resistance and abdominal obesity in individuals with metabolic syndrome. These FMT investigations have connected alterations in the gut microbiota to clinical indicators of insulin resistance and obesity, in addition to using high-throughput methods to analyze the gut microbiome, metabolome, and epigenome of peripheral blood mononuclear cells in patients with MetS. It is still necessary to clarify and assess the clinical effectiveness and mode of action of FMT in the management of MetS. This review examines the connection between gut bacteria and MetS, the effectiveness of FMT as a treatment, and the changes in the gut microbiome, metabolome, epigenome, and other histones following the intervention. We also discuss the safety of FMT and suggest areas for further investigation.},
}
@article {pmid40583731,
year = {2025},
author = {Mei, JL and Chai, LJ and Lu, ZM and Zhang, XJ and Lu, YH and Chi, YL and Wang, ST and Shen, CH and Shi, JS and Xu, ZH},
title = {Strong-Flavor Baijiu Pit Mud Microbiome in the Context of Modern Industry: From a Black Box Under Empiricism to the Gradual Revelation of Microbial Ecosystems.},
journal = {Comprehensive reviews in food science and food safety},
volume = {24},
number = {4},
pages = {e70224},
doi = {10.1111/1541-4337.70224},
pmid = {40583731},
issn = {1541-4337},
support = {32370142//National Natural Science Foundation of China/ ; 2025ZNSFSC0199//Sichuan Science and Technology Program/ ; 2024T170375//China Postdoctoral Science Foundation/ ; 2023M741512//China Postdoctoral Science Foundation/ ; },
mesh = {*Microbiota ; Fermentation ; *Alcoholic Beverages/microbiology/analysis ; Flavoring Agents ; },
abstract = {Chinese strong-flavor Baijiu (CSFB), one of the most popular categories in the alcoholic beverage market, is supposed to comply with the current industry development trend and achieve mechanization, modernization, and unification of production. Solid-state fermentation in the mud cellar is the fundamental characteristic of CSFB. Pit mud, which provides the necessary conditions for producing the precursors of crucial flavor substances, plays a decisive role in CSFB's characteristics and quality. How to intervene and regulate the microbiome of pit mud, either using top-down or bottom-up approaches, to ultimately obtain an ecosystem that consistently provides the characteristic flavor substances in unified, standard, and mechanized production has become an urgent problem to be solved. This review summarizes the current knowledge of the pit mud microbiome in Baijiu fermentation, focusing on evolution and assembly patterns, functional roles, and ecological succession over batch-to-batch fermentation for decades or even centuries. Key challenges are identified, including controlling microbial interactions and enabling standardized, large-scale production of microbiome adaptations. This review also explores the application of advanced techniques such as omics tools and synthetic community design to improve microbiome regulation. We hold the view that the understanding of pit mud microbial ecosystems combined with technological advances provides an opportunity for intelligent microbiome management. By utilizing these tools, the production of CSFB can move in the direction of more consistent flavor and better quality control, with the potential for significant improvements in microbial engineering and industrial practices.},
}
@article {pmid40583481,
year = {2025},
author = {Hellinga, AH and Cajic, S and Linde, HF and van Stigt, AH and de Vries, JHM and Brouwer-Brolsma, EM and Hennig, R and Rapp, E and Mank, M and Stahl, B and Kraneveld, AD and Leusen, JHM and Bont, L and Van't Land, B and , },
title = {Maternal Dietary Fiber Intake During Lactation and Human Milk Oligosaccharide Fucosylation: a PRIMA Birth Cohort Study.},
journal = {Molecular nutrition &amp; food research},
volume = {},
number = {},
pages = {e70165},
doi = {10.1002/mnfr.70165},
pmid = {40583481},
issn = {1613-4133},
support = {//Regio Deal food valley (grant nr 162135, Dutch ministery of Health, Welfare and Sport)./ ; //Danone Research &amp; Innovation, as part of the UMC Utrecht collaboration grant 'Early Life Nutrition and Immune Development'./ ; //WKZ research fund-Nutricia call 2020 "Breast milk T cells: frontline protection for infants and mothers?"/ ; },
abstract = {Human milk oligosaccharides (HMOs) have an important role in the microbiome and immune system development of breastfed infants. Previous explorative studies indicated an association between maternal carbohydrate intake, including dietary fibers, and specific fucosylated HMOs in human milk (HM). Here, we aim to test whether the intake of dietary fibers by breastfeeding mothers is associated with the level of HMO-bound fucose in HM samples within a prospective birth cohort study. We assessed dietary fiber intake of healthy mothers (n = 164). HMO levels were semi-quantified in HM samples collected at 1 month postpartum. We found no correlation between fiber intake and HMO-bound fucose levels. However, secretor mothers (β = 2.22, p < 0.001) and mothers with a baby girl showed a positive correlation (β = 0.41, p = 0.016) with the level of HMO-bound fucose. In contrast, vaginal delivery negatively correlated with the level of HMO-bound fucose (β = -4.93, p = 0.008). Overall, there was no association between maternal fiber intake and HMO-bound fucose levels. Delivery mode, secretor status, and infant sex emerged as the dominant factors associated with HMO fucosylation in HM. Future research should investigate mechanisms underlying HMO fucosylation and its relevance for infant's health.},
}
@article {pmid40583454,
year = {2025},
author = {Aldrian, D and Pollio, A and Mayerhofer, C and Diederen, K and Jacobs, JP and Pai, N and Szamosi, JC and Hart, L and Turner, D and Del Chierico, F and Cardile, S and Grigoryan, Z and Chen, LA and Hurych, J and Cinek, O and Taddei, CR and Schwerd, T and Wine, E and Griffiths, AM and Müller, T and Vogel, GF},
title = {Fecal Microbial Community Profiling Allows Discrimination of Phenweotype and Treatment Response in Pediatric Crohn's Disease and Ulcerative Colitis-An International Meta-Analysis.},
journal = {Inflammatory bowel diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/ibd/izaf135},
pmid = {40583454},
issn = {1536-4844},
abstract = {BACKGROUND AND AIMS: The pathophysiology of pediatric inflammatory bowel disease (PIBD), encompassing Crohn's disease (CD) and ulcerative colitis (UC), is not entirely understood. Dysregulation of the intestinal microbiome is recognized as both a disease-driving and a potential therapeutic target. This study aimed to systematically analyze gut microbiome compositions and its applicability as a biomarker for disease progress and treatment response.<br><br>METHODS: Bibliographic and nucleotide databases were searched. Raw 16S-rRNA sequencing reads were subjected to a uniform downstream dada2/phyloseq pipeline to extract taxonomy, community structure, and abundance information. Patient metadata were extracted from publications, and study authors were contacted for further details if required.<br><br>RESULTS: Twenty-six studies comprising 3956 stool samples (CD 41%, UC 36%, 23% healthy) were included in the analyses. Median age of individuals was 12 (interquartile range 4). Sex distribution was comparable. Alpha diversity was reduced between the healthy and both UC and CD treatment-na&#xef;ve groups (P&#x2005;<&#x2005;.001) and further reduced with increasing clinical disease activity. Beta diversity revealed altered community structure in treatment-na&#xef;ve children with PIBD (P&#x2005;<&#x2005;.001). This alteration remained in patients in clinical remission (P&#x2005;<&#x2005;.001). Machine learning models discriminated between treatment-na&#xef;ve patients with CD or UC with an area under the receiver operating characteristics curve (AUROC) of 98%. Microbial communities differed between patient responders versus nonresponders to treatment (P&#x2005;<&#x2005;.001). Further, microbial community profiling distinguished treatment response (eg, steroid, nutrition, or TNF&#x3b1;) with AUROCs of 82%-90%.<br><br>CONCLUSIONS: Gut microbial community structure is substantially altered in active and inactive PIBD and may be utilized as a biomarker for differentiating PIBD subtype and predicting treatment response.},
}
@article {pmid40583417,
year = {2025},
author = {Klümpen, L and Donkers, A and Seel, W and Dicks, L and Holst, JJ and Stehle, P and Simon, MC and Ellinger, S},
title = {GLP-1 Responses to a Single Meal Fortified With Oyster Mushroom Powder in Adults With Impaired Glucose Tolerance Depend on the Gut Microbiota Composition Before the Meal.},
journal = {Molecular nutrition &amp; food research},
volume = {},
number = {},
pages = {e70159},
doi = {10.1002/mnfr.70159},
pmid = {40583417},
issn = {1613-4133},
support = {01EA1707//German Federal Ministry of Education (BMBF)/ ; //German Research Foundation (DFG)/ ; FHSTRUKTUR 2016(RF//Ministerium f&#xfc;r Innovation, Wissenschaft und Forschung des Landes Nordrhein-Westfalen/ ; 322-8.03.04.02-FH-STRUKTUR)//Ministerium f&#xfc;r Innovation, Wissenschaft und Forschung des Landes Nordrhein-Westfalen/ ; Germany's Excellence Strategy - EXC2151 - 39//Deutsche Forschungsgemeinschaft/ ; 01EA1707//Bundesministerium f&#xfc;r Bildung und Forschung/ ; },
abstract = {Fortification of a single meal with β-glucan-rich oyster mushroom (Pleurotus ostreatus) powder has been shown to increase the response of glucagon-like peptide 1 (GLP-1) and reduce concentrations of non-esterified fatty acids (NEFAs) in adults with impaired glucose tolerance (IGT). This secondary analysis of a randomized controlled crossover study (DRKS00015244) aimed to determine whether these effects are modulated by baseline gut microbiota composition. A fecal sample was collected once at baseline before consumption of either a P. ostreatus-enriched meal (EN) or a non-enriched meal (CON). The microbiota was analyzed using 16S rRNA V3-V4 sequencing. An inverse association was observed between alpha diversity and differences in the meal-induced GLP-1 response (p < 0.05), whereas NEFA responses appeared unaffected. Notably, only participants with lower microbial evenness showed a greater GLP-1 response after EN versus CON (p = 0.012). Additionally, the presence of Eubacterium ventriosum group and Clostridium methylpentosum group was associated with increased GLP-1 concentrations following EN (p < 0.05). Baseline gut microbiota composition modulates the GLP-1 response to a single meal fortified with β-glucan-rich oyster mushroom powder, with differences in GLP-1 response being more pronounced in individuals whose microbiome is more specialized in fermenting fiber into SCFAs.},
}
@article {pmid40583322,
year = {2025},
author = {Haarhuis, JE and Day-Walsh, P and Shehata, E and Savva, GM and Peck, B and Philo, M and Kroon, PA},
title = {A Pomegranate Polyphenol Extract Suppresses the Microbial Production of Proatherogenic Trimethylamine (TMA) in an In Vitro Human Colon Model.},
journal = {Molecular nutrition &amp; food research},
volume = {},
number = {},
pages = {e70166},
doi = {10.1002/mnfr.70166},
pmid = {40583322},
issn = {1613-4133},
support = {//Wellcome Trust [218467/Z/19/Z]/ ; BB/R012512/1//BBSRC Institute Strategic Programmes "Food Innovation and Health"/ ; BBS/E/F/000PR10343//BBSRC Institute Strategic Programmes "Food Innovation and Health"/ ; BBS/E/F/000PR10346//BBSRC Institute Strategic Programmes "Food Innovation and Health"/ ; BB/X011054/1//"Food Microbiome and Health"/ ; BBS/E/QU/230001B//"Food Microbiome and Health"/ ; BBS/E/QU/230001D//"Food Microbiome and Health"/ ; },
abstract = {High circulating levels of trimethylamine N-oxide (TMAO) are linked to metabolic diseases, adverse outcomes after heart failure, and atherogenic effects in animal models and in human subjects. l-Carnitine and choline are major dietary precursors of TMAO. These are first converted to trimethylamine (TMA) by gut microbiota, which is absorbed by the host and converted into TMAO by hepatic flavin-containing monooxygenases (FMOs). The minimal absorption of pomegranate polyphenols by the host suggests that they may reach the colon for further metabolism by the gut microbiome. This study investigates the ability of a polyphenol-rich pomegranate extract to inhibit TMA production by human fecal microbiota. Batch fermentations were conducted with 1% human fecal inoculum, l-carnitine, or choline, and a pomegranate extract (anaerobic, pH 6.6-7.1, 37°C) for 24 or 48 h. Methylamines were quantified using LC-MS/MS with isotopically labeled internal standards. The pomegranate extract significantly delayed and reduced the rate of TMA production from both choline and l-carnitine. The effect was dose-dependent for l-carnitine, with the highest dose delaying the average midpoint of l-carnitine metabolism by 16 h (95% CI = 8.4-24; p = 0.001). The pomegranate extract significantly reduced TMA production from choline and l-carnitine in vitro.},
}
@article {pmid40583013,
year = {2025},
author = {Liu, C and Yue, S and Niu, D and Zhang, L and Chen, J and Chen, Y and Guan, Y and Hua, X and Chen, X and Zhang, L and Du, H and Liang, C},
title = {Alcohol Intake-Induced Aggravation of Chronic Prostatitis/Chronic Pelvic Pain Syndrome is Associated with Reduced Gut Microbiota-Driven Short-Chain Fatty Acid Propionate and Butyrate.},
journal = {The world journal of men's health},
volume = {},
number = {},
pages = {},
doi = {10.5534/wjmh.240223},
pmid = {40583013},
issn = {2287-4208},
support = {82100815/NNSFC/National Natural Science Foundation of China/China ; 82170787/NNSFC/National Natural Science Foundation of China/China ; 81870519/NNSFC/National Natural Science Foundation of China/China ; 2108085QH315//Anhui Natural Science Foundation/China ; 2023xkj132//Anhui Medical University Funded Project/China ; },
abstract = {PURPOSE: Chronic prostatitis (CP) is a common urological disease and about 8.4% to 13.5% of men suffer from prostatitis symptoms in China. This study was conducted to evaluate the effect of alcohol usage on patients with chronic prostatitis/chronic pelvic pain syndrome (CP/CPPS) and the role of the gut microbiome in this course.<br><br>MATERIALS AND METHODS: A total of 151 individuals were recruited when they were diagnosed with CP/CPPS. Eventually, 38 patients were enrolled and grouped into three groups: the CP/CPPS group, alcohol group, and quitter group. 16S ribosomal ribonucleic acid sequencing was used to investigate the fecal samples, and a liquid chromatograph-mass spectrometer was used to analyze untargeted metabolomics. Next, targeted identification of short-chain fatty acids was carried out. T helper 17 (Th17) cells and cytokines were measured by flow cytometry and enzyme-linked immunosorbent assay, respectively. Furthermore, the associations among intestinal microbiota, short-chain fatty acids, and clinical symptoms were evaluated through correlation analysis.<br><br>RESULTS: Alcohol consumption results in different microbial composition in patients with CP. Higher symptom scores, Th17 cell percentages and interleukin-17 concentrations were observed in the alcohol group. Notably, correlation analysis revealed that several gut microbes were correlated with propionate and butyrate contents and patient's symptoms. Contrarily, lower symptom scores, Th17 cell percentages and interleukin-17 concentrations were observed in the quitter group.<br><br>CONCLUSIONS: This study preliminarily explores the potential association between alcohol and CP/CPPS, in which short-chain fatty acid-producing gut flora may play a key role. This study may enhance the understanding of the effect of alcohol on CP/CPPS and provide a preliminary foundation for formulating prevention strategies. The main limitation of this study is the small sample size, and further large-scale plus in-depth research ought to be carried out in the future.},
}
@article {pmid40582875,
year = {2025},
author = {Takahashi, H and Fujii, T and Yamada, C and Fujiki, K and Kondo, N and Kuramitsu, K and Funasaka, K and Ohno, E and Hirooka, Y and Tochio, T},
title = {Synergistic Effects of Short- and Long-Chain Fructans: A Novel Strategy for Mitigating Ovalbumin Allergy via Microbiome-Driven Acetate Production.},
journal = {Journal of nutritional science and vitaminology},
volume = {71},
number = {3},
pages = {238-247},
doi = {10.3177/jnsv.71.238},
pmid = {40582875},
issn = {1881-7742},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Ovalbumin/immunology ; *Fructans/pharmacology/administration &amp; dosage ; *Food Hypersensitivity/drug therapy/prevention &amp; control/microbiology ; Mice ; *Acetates/metabolism ; Inulin/pharmacology/administration &amp; dosage ; Immunoglobulin E/blood ; Mice, Inbred BALB C ; Disease Models, Animal ; Female ; *Trisaccharides/pharmacology/administration &amp; dosage ; Drug Synergism ; },
abstract = {The gut microbiota has been implicated in the modulation of food allergies. Building on previous studies on the preventive effects of combining short-chain fructan 1-kestose (Kes) and long-chain fructan inulin (Inu) in food allergies, we investigated their therapeutic effects in an ovalbumin (OVA)-induced food allergy mouse model. Following OVA sensitization, the mice received 5% Kes and Inu, either individually or a combined 2.5% dose of each, for 4 wk. We assessed allergy-related markers, such as OVA-specific serum IgE (OVA-sIgE) levels, in the blood and monitored changes in the gut microbiome. The intake of fructans ameliorated allergic symptoms and stabilized rectal temperatures, with a significant reduction in OVA-sIgE levels only in the combined Kes and Inu group (Kes+Inu), p<0.05. Gut microbiota diversity analysis revealed significant differences in beta diversity between the groups not receiving fructans and those receiving Kes, Inu, or Kes+Inu (p<0.01 each). Specifically, in the Kes+Inu group, the abundance of the genus UBA7173 belonging to the family Muribaculaceae significantly increased. Additionally, acetate levels were significantly elevated only in the Kes+Inu group and correlated positively with the presence of the genus UBA7173. These findings indicated that the combined intake of Kes and Inu improves allergic outcomes, positively affects the gut microbiome, and enhances the production of acetate.},
}
@article {pmid40582869,
year = {2025},
author = {Kang, HS and Yamade, I and Inoue, T and Otsubo, M and Hamada, H and Sudo, S and Ogiso, N and Hamakita, S and Sawada, M and Hatayama, H},
title = {Relationship between Circulating Vitamin D Concentration and the Maternal Gut Microbiota during Early Pregnancy in Japanese Women: Results of a Pilot Study of Antenatal Vitamin D3 Supplementation.},
journal = {Journal of nutritional science and vitaminology},
volume = {71},
number = {3},
pages = {185-191},
doi = {10.3177/jnsv.71.185},
pmid = {40582869},
issn = {1881-7742},
mesh = {Humans ; Female ; Pregnancy ; *Gastrointestinal Microbiome/drug effects ; *Cholecalciferol/administration &amp; dosage/blood ; Pilot Projects ; *Dietary Supplements ; Adult ; *Vitamin D/blood/analogs &amp; derivatives ; Japan ; Vitamin D Deficiency/blood ; Pregnancy Trimester, First ; Pregnancy Complications/microbiology ; Young Adult ; East Asian People ; },
abstract = {Recent studies have demonstrated a significant role for gut microbiota dysbiosis in the pathogenesis of various diseases, pregnancy outcomes, and fetal growth. Vitamin D modulates innate immunity and promotes immune tolerance, suggesting involvement in shaping the gut microbiota. However, the relationship between vitamin D and the gut microbiota during pregnancy has not been evaluated in detail. In this study, we administered a vitamin D3 supplement (VD) to pregnant Japanese women, starting during the first trimester of pregnancy, and characterized changes in the circulating concentration of vitamin D and the gut microbiome. Sixty-two pregnant women were randomly allocated to three groups. VD was administered at low (200 IU/d), medium (400 IU/d), or high (1,000 IU/d) doses for 8 wk from 12 to 15 wk of pregnancy, and changes in the serum 25-hydroxyvitamin D (25(OH)D) concentration and the gut microbiome were evaluated. Changes in gut microbial taxa abundance were analyzed by Wilcoxon matched-pairs signed-rank test. Before VD administration, 96.8% of the participants were VD-deficient, and none had a sufficient VD concentration. The serum 25(OH)D concentration increased in a dose-dependent manner in all the dose groups. Additionally, the abundance of Fusicatenibacter in the gut microbiota increased in a VD dosedependent manner, with a significant increase observed in the high-dose group. From these results, in pregnant Japanese women, the administration of high-dose VD increases the prevalence of VD sufficiency and alters the gut microbial composition, suggesting that this has benefits for the maternal and neonatal immune systems.},
}
@article {pmid40582768,
year = {2025},
author = {Lu, Y and Zhang, W and Yu, M and Chen, X and Liu, C and Gao, X},
title = {Association between Serum Uric Acid Levels and Salivary Microbiota in Patients with Obstructive Sleep Apnea.},
journal = {Journal of microbiology and biotechnology},
volume = {35},
number = {},
pages = {e2503042},
doi = {10.4014/jmb.2503.03042},
pmid = {40582768},
issn = {1738-8872},
mesh = {Humans ; *Uric Acid/blood ; *Sleep Apnea, Obstructive/microbiology/blood ; Adult ; Male ; *Saliva/microbiology ; RNA, Ribosomal, 16S/genetics ; Middle Aged ; *Microbiota/genetics ; *Hyperuricemia/microbiology/blood/complications ; Female ; Bacteria/classification/genetics/isolation &amp; purification ; Proteomics ; },
abstract = {The microbiota is associated with obstructive sleep apnea (OSA) and hyperuricemia (HUA), but the relationship between oral microbiota and OSA-related HUA remains unclear. Our study investigated salivary microbiota differences between individuals with OSA and those with both OSA and HUA, and explored the link between oral microbiome alterations and uric acid fluctuations in OSA patients. Seventy-two adults were divided into four groups: controls (n = 20, 33.75 ± 9.46 years), OSA (n = 23, 44.08 ± 13.70 years), OSA with comorbid HUA (OSA+HUA, n = 22, 40.18 ± 9.58 years), and OSA with medication-controlled HUA (n = 7, 44.56 ± 15.14 years). Salivary microbiota and proteomic profiles were analyzed using 16S rRNA sequencing and Astral DIA. OSA and OSA+HUA showed reduced alpha-diversity compared to controls. The OSA+HUA group had increased Oribacterium abundance relative to the OSA group, which decreased after uric acid treatment, whereas Rothia, Capnocytophaga, and Aggregatibacter showed the opposite trend. 104 differentiated proteins were identified between the OSA and OSA+HUA groups. Oribacterium was positively correlated with several antioxidant proteins, while the other three genera were negatively correlated. This study identifies non-invasive biomarkers in the OSA+HUA group, as the first of its kind, highlighting the role of oral microbiota in future research and therapies.},
}
@article {pmid40582671,
year = {2025},
author = {Bi, R and Abbas, W and Li, J and Huang, J and Hu, J and Guo, F and Wang, Z},
title = {Yeast β-glucan ameliorated Salmonella-induced gut impairment in broiler chickens by modulating gut microbiome.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {145630},
doi = {10.1016/j.ijbiomac.2025.145630},
pmid = {40582671},
issn = {1879-0003},
abstract = {Yeast β-glucan (YG) was reported to control Salmonella infection in poultry. Gut microbiota plays an important role in regulating immune functions and intestinal health. However, it is still unclear whether YG protects chickens from Salmonella infection by regulating gut microbiota. The impacts of YG on gut health of chickens infected with Salmonella enteritidis (SE) was investigated through histochemical and immunological methods, along with microbiomics. The role of gut microbiome induced by YG treatment in combating Salmonella infection was explored through FMT. Our findings showed that YG administration significantly ameliorated SE-induced gut impairment by decreasing gut permeability, enhancing intestinal barrier function, inhibiting intestinal inflammation, reducing Salmonella colonization, lowering g_Streptococcus and g_Ligilactobacillus but increasing g_Blautia, g_Bacillus and g_Faecalibacterium relative abundance. Transplantation fecal microbiota from YG-treated healthy donor chickens to antibiotic-treated recipient chicks significantly attenuated gut injury caused by SE infection through decreasing Salmonella colonization and invasion along with intestinal permeability, improving gut morphology, upregulating intestinal tight junction genes and proteins expression, downregulating pro-inflammatory cytokines expression. Additionally, FMT remarkably increased g_Bacteroides and g_Faecalibacterium relative abundances and butyric acid level, decreased g_Ruminococcus-torque-group relative abundance in the cecum.Collectively, we assume that yeast β-glucan alleviated Salmonella-induced gut impairment, a mechanism that is dependent on the gut commensal Bacteroides and Faecalibacterium.},
}
@article {pmid40582570,
year = {2025},
author = {Alghamdi, B and Liu, M and Huang, X and Debnath, R and Afzali, H and Troka, M and Hasuike, A and Easter, Q and Zhou, M and Byrd, K and Gonzalez, M and Ko, KI and Graves, DT},
title = {Single-cell RNA profiling identifies immune cell population shifts in diabetes associated mucosal inflammation.},
journal = {Mucosal immunology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.mucimm.2025.06.008},
pmid = {40582570},
issn = {1935-3456},
abstract = {Poorly controlled diabetes significantly transforms periodontal disease from manageable to advanced, affecting millions worldwide, yet the mechanisms driving this destructive synergy remain unclear. To investigate these pathological interactions, we generated single-cell RNA sequencing profiles of diabetic periodontal tissue, revealing γ[δ] T-cells as previously unrecognized central mediators of diabetes-enhanced periodontal destruction. Flow cytometry validation confirmed significant expansion of IL-17A-producing γ[δ] T-cells in diabetic versus normoglycemic mice, with parallel findings of elevated IL-17A + cells in human diabetic periodontal specimens. Selective γ[δ] T-cell inhibition substantially reversed diabetes-enhanced periodontal destruction while minimally affecting normoglycemic controls and returned neutrophil infiltration to normoglycemic levels. scRNAseq identified other factors, including greater neutrophil polarization toward a pro-inflammatory phenotype and loss of Tregs. These findings point to unique aspects of diabetes-induced dysregulation and implicate γ[δ] T-cells as a driving factor in this process. The results also point γ[δ] to T-cells as a therapeutic target in periodontitis and other diabetic complications.},
}
@article {pmid40582565,
year = {2025},
author = {Gao, T and Jiang, Y and Han, Y and Wāng, Y},
title = {Intestinal microplastic debris, flora dysbiosis, and insidious combined hazards across diverse aquatic and terrestrial organisms.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2025.06.074},
pmid = {40582565},
issn = {2090-1224},
abstract = {BACKGROUND: Microplastics and nanoplastics, ubiquitous in ecosystems, pose significant ecological and health risks. At the biological level, plastics impact multiple trophic levels. While numerous studies have confirmed this phenomenon, conflicting conclusions may arise due to variations in particle types or target organisms, underscoring the necessity for additional exploration.<br><br>AIM OF REVIEW: This review explores their sources, environmental pathways, and interactions with other pollutants, emphasizing the multifaceted threats they present to biodiversity and ecosystem stability. This paper delves deeply into bridging knowledge gaps by presenting emerging evidence of differential effects across trophic levels and organism groups, and highlighting the role of vectors for other environmental pollutants and modifying factors of photodegradation and weathering, offering a nuanced analysis of their synergistic effects on gut microbiota and intestinal health.<br><br>Emerging insights into photodegraded plastics, synergistic toxicities, and their role as pollutant vectors call for immediate action. Ultraviolet radiation accelerates the aging of plastics, enhancing their adsorption capacity for pollutants like heavy metals and persistent organic pollutants, thereby amplifying their toxicity. For instance, aged plastic particles in zebrafish have been shown to induce severe intestinal damage and disrupt microbial balance. Similarly, combined exposures of plastics and antibiotics alter the gut microbiota in organisms, affecting phyla such as Firmicutes and Bacteroidetes. In soil ecosystems, aged plastics elevate heavy metal accumulation in earthworms, intensifying intestinal injury. Our analysis reveals a remarkable ability of the gut microbiota in certain terrestrial organisms to break down microplastics, while specific chemicals help alleviate the intestinal toxicity caused by microplastics and nanoplastics. These findings provide fresh perspectives for future mitigation tactics, underscoring the need for sustainable plastic alternatives, improved waste management strategies, and further research to mitigate the long-term impacts of microplastics and nanoplastics on ecosystem health and functionality.},
}
@article {pmid40582554,
year = {2025},
author = {Zhang, W and Xie, QY and Huang, S and Chu, CH and Lo, ECM},
title = {Changes in oral microbiome in preschool children after using toothpaste with different fluoride concentrations.},
journal = {Journal of dentistry},
volume = {},
number = {},
pages = {105941},
doi = {10.1016/j.jdent.2025.105941},
pmid = {40582554},
issn = {1879-176X},
abstract = {OBJECTIVES: Dental caries is a multifactorial disease primarily driven by an imbalanced oral microbiome, with cariogenic bacteria in dental plaque playing a central role. Fluoride-containing toothpaste is commonly used for caries prevention, but its effects on the oral microbiome, particularly at different fluoride concentrations, remain unclear. This study aimed to assess the short-term impact of fluoride toothpaste with different fluoride concentrations (standard fluoride 1000 ppm, low fluoride 500 ppm, and non-fluoride) on the oral microbial community in preschool children.<br><br>METHODS: A total of 48 children participated, with dental plaque samples collected at baseline, and at 1-week and 4-week follow-up after using the assigned toothpaste. The microbial community was analyzed using 16S rDNA sequencing to evaluate diversity, composition and shifts in bacterial populations.<br><br>RESULTS: The results showed no significant differences in alpha diversity indices (Chao1, Shannon, Simpson, etc.) between pre- and post-intervention samples in all groups, indicating overall microbial stability. However, beta diversity analysis revealed significant differences in microbial composition between the fluoride and non-fluoride groups. Notably, the standard fluoride group exhibited a more substantial shift in bacterial structure, with an increase in the abundance of beneficial species such as Streptococcus parasanguinis and Veillonella, and a reduction in genus, such as Haemophilus and Neisseria, which are associated with biofilm formation and may affect the colonization of cariogenic bacteria.<br><br>CONCLUSION: These findings suggest that fluoride-containing toothpaste, especially standard fluoride (1000 ppm) toothpaste, can modulate the oral microbiome by decreasing harmful bacteria and promoting a more balanced microbial environment, potentially reducing the risk of dental caries in preschool children.<br><br>CLINICAL SIGNIFICANCE: This study demonstrates that standard fluoride (1000 ppm) toothpaste effectively shifts the oral microbiome in preschool children by reducing harmful bacteria (e.g., Haemophilus) while enriching beneficial species (e.g., Streptococcus parasanguinis). These findings suggest a potential role for fluoride toothpaste in caries prevention by promoting a healthier microbial balance, offering supportive evidence for its use in evidence-based pediatric dental care.},
}
@article {pmid40582100,
year = {2025},
author = {Yu, J and Sanjay, and Jaiswal, V and Jang, Y and Park, M and Lee, HJ},
title = {Salvia miltiorrhiza activates Nrf2/HO-1 signaling and restores steroidogenesis in Leydig TM3 cells and an aging rat model.},
journal = {Biomedicine &amp; pharmacotherapy = Biomedecine &amp; pharmacotherapie},
volume = {189},
number = {},
pages = {118297},
doi = {10.1016/j.biopha.2025.118297},
pmid = {40582100},
issn = {1950-6007},
abstract = {Male aging is often accompanied by a gradual decline in testosterone production, referred to as andropause, which is associated with fatigue, reduced libido, hormonal imbalances, and metabolic disturbances. Testosterone replacement therapy poses risks such as prostate and cardiovascular complications, prompting interest in natural alternatives. This study explored the therapeutic effects of Salvia miltiorrhiza extract (SME) in an in vitro H2O2-induced Leydig TM3 cell model and an in vivo aged rat model. HPLC/MS analysis confirmed the presence of tanshinone IIA (10.629 mg/g) in SME. SME (1-2 μg/mL) attenuated oxidative stress, restored antioxidant gene and protein expression (Nrf2, HO-1, SOD, CAT, and GPx), and enhanced the steroidogenic pathway by upregulating STAR, CYP11A1, CYP17A1, 3β-HSD, and 17β-HSD while downregulating 5α-reductase. In aged rats, oral administration of SME (particularly 50 mg/kg) restored testosterone, LH, FSH, and progesterone levels, while reducing SHBG and DHT levels. SME also improved liver function markers (ALT and AST) and lipid profiles (TG, TC, LDL, and HDL), and reduced MDA and serum PSA levels. Also, HPLC/MS analysis detected the presence of tanshinone IIA in the serum of SME-administered animals. Furthermore, fecal microbiome analysis revealed an abundance of the propionate-producing microbe Succinispira mobilis, indicating a possible role of SME in improving gut health and hormone levels. These findings suggest that SME may serve as a promising natural intervention against andropause by regulating oxidative stress, steroidogenesis, and gut dysbiosis.},
}
@article {pmid40581894,
year = {2025},
author = {Mudasir, M and Shahzad, A},
title = {Decoding plant responses to waterlogging: from stress signals to molecular mechanisms and their future implications.},
journal = {Plant molecular biology},
volume = {115},
number = {4},
pages = {78},
pmid = {40581894},
issn = {1573-5028},
mesh = {*Signal Transduction ; *Stress, Physiological ; Plant Growth Regulators/metabolism ; *Plant Physiological Phenomena ; *Plants/metabolism/genetics ; Gene Expression Regulation, Plant ; Floods ; Ethylenes/metabolism ; Climate Change ; Water/metabolism ; },
abstract = {Climate change and global warming drastically alter ecosystems, intensifying extreme weather events such as heavy rainfall and glacier melting, leading to increased soil flooding and threatening agriculture. Waterlogging, a direct consequence of prolonged soil saturation, severely affects plant growth by causing hypoxia, impaired nutrient uptake, photosynthesis inhibition, energy depletion, and microbiome disturbances, ultimately leading to plant mortality. Despite research progress in mitigating waterlogging stress, the molecular mechanisms underlying plant perception and their subsequent adaptive responses remain largely unclear. Recent advancements in molecular, biochemical, and multi-omics technologies have enabled significant progress in understanding the molecular mechanisms of plant responses to stress conditions. In this review, we highlight the metabolic pathways and key genes that could be targeted to enhance waterlogging tolerance and discuss how advanced techniques can be implemented to understand waterlogging responses and develop resistant cultivars. We review molecular insights into how ethylene and hypoxia signaling pathways trigger waterlogging responses and highlight key factors involved in energy metabolism and phytohormone signaling pathways, along with possible directions for further study.},
}
@article {pmid40581777,
year = {2025},
author = {Weklar, O and Bishop, T and Alaasam, VJ and Winchell, KM and Hazlehurst, JA},
title = {Urbanization and the Gut Microbiome: Insights from the Anna's Hummingbird (Calypte anna) in California.},
journal = {Integrative and comparative biology},
volume = {},
number = {},
pages = {},
doi = {10.1093/icb/icaf116},
pmid = {40581777},
issn = {1557-7023},
abstract = {Complex environmental characteristics shape the gut microbiome of wildlife with critical implications for host health, pathogen resistance, digestion, and overall fitness. While foundational avian microbiome research has focused mainly on domestic birds and poultry due to their proximity to humans and the associated zoonotic risks from imbalanced microbiomes, studying the gut microbiome of wild birds is also essential. Wild birds fill important roles in their habitats-serving as critical pollinators and bioindicators of ecosystem health. Despite this, their gut microbiomes remain less explored, particularly concerning how urbanization affects microbiome composition and diversity, which may provide insight into the health of birds in urban habitats. This study investigates the gut microbiome of the Anna's Hummingbird (Calypte anna), a species that thrives in urban and rural environments across the West Coast. We amplified the V1-V3 region of bacterial 16S rRNA extracted from fecal samples and used the QIIME2 platform to characterize bacterial communities. By analyzing bacterial communities from birds sampled across a range of anthropogenically altered locations, we explore correlations between microbiome composition and habitat characteristics (artificial light at night, human density, air pollution, and percent imperviousness). We show that air quality is an important driver of microbial diversity and offer insights into how the heterogeneity of urban landscapes impacts the microbiome composition of wild birds.},
}
@article {pmid40581743,
year = {2025},
author = {Mordant, A and Blakeley-Ruiz, JA and Kleiner, M},
title = {Metaproteomics-based stable isotope fingerprinting links intestinal bacteria to their carbon source and captures diet-induced substrate switching.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf127},
pmid = {40581743},
issn = {1751-7370},
abstract = {Diet has strong impacts on the composition and function of the gut microbiota with implications for host health. Therefore, it is critical to identify the dietary components that support growth of specific microorganisms in vivo. We used protein-based stable isotope fingerprinting (Protein-SIF) to link microbial species in gut microbiota to their carbon sources by measuring each microorganism's natural 13C content (δ13C) and matching it to the 13C content of available substrates. We fed gnotobiotic mice, inoculated with a 13 member microbiota, diets in which the 13C content of all components was known. We varied the source of protein, fiber or fat to observe 13C signature changes in microbial consumers of these substrates. We observed significant changes in the δ13C values and abundances of specific microbiota species, as well as host proteins, in response to changes in 13C signature or type of protein, fiber, and fat sources. Using this approach we were able to show that upon switching dietary source of protein, fiber, or fat (1) some microbial species continued to obtain their carbon from the same dietary component (e.g., protein); (2) some species switched their main substrate type (e.g., from protein to carbohydrates); and (3) some species might derive their carbon through foraging on host compounds. Our results demonstrate that Protein-SIF can be used to identify the dietary-derived substrates assimilated into proteins by microorganisms in the intestinal tract; this approach holds promise for the analysis of microbiome substrate usage in humans without the need of substrate labeling.},
}
@article {pmid40581654,
year = {2025},
author = {Döding, A and Wurschi, L and Zubiria-Barrera, C and Klassert, TE and Bereuter, L and Rao, Z and Bär, AK and Domuncu, A and Koeberle, A and Noels, H and Slevogt, H and Sigusch, B and Schulze-Späte, U},
title = {Mediterranean diet component oleic acid decreases systemic impact of periodontal Porphyromonas gingivalis-infection in age: addressing role of stress resistance and microbiome.},
journal = {npj aging},
volume = {11},
number = {1},
pages = {54},
pmid = {40581654},
issn = {2731-6068},
support = {Doctoral Program//Interdisciplinary Center of Clinical Research of the Medical Faculty Jena/ ; Doctoral Program//Interdisciplinary Center of Clinical Research of the Medical Faculty Jena/ ; 10.55776/P36299//Austrian Science Fund/ ; UKJ FF02//Interdisciplinary Center of Clinical Research of the Medical Faculty Jena (IZKF)/ ; 01EC1901B, Project 2//German Federal Ministry of Education and Research (BMBF)/ ; Else Kr&#xf6;ner Promotionskolleg JSAM//Else Kr&#xf6;ner-Fresenius-Stiftung/ ; },
abstract = {Periodontitis (PD) is an age-associated infectious periodontal disease driven by dysbiosis and hyperinflammatory host response, resulting in bone and tissue loss. Often linked to systemic inflammatory comorbidities, modulating host response emerged as promising clinical target. This study investigates whether nutritional intervention mitigates age-associated systemic impact of oral infection with PD key pathogen Porphyromonas gingivalis. Young (5 weeks) and aged (≥73 weeks) mice received palmitic acid-enriched Western-diet (PA-ED) or Mediterranean-diet enriched with oleic acid (OA-ED), both known for immunomodulatory properties. PA-ED exacerbated oral bone loss and systemic effects, particularly in aged mice, correlated with gut microbiota destabilization and impaired stress responses. Further, PA-ED enhanced osteoclast differentiation and primed bone marrow cells towards inflammation. Contrarily, OA-ED mitigated these effects. Osteoblasts showed baseline inflammation and reduced responsiveness in aged mice, thereby promoting a pro-inflammatory micro-environment. Findings suggest OA-ED as protective, especially for the elderly, by limiting local and systemic tissue damage associated with PD.},
}
@article {pmid40581627,
year = {2025},
author = {Nørgaard, JC and Marandi, RZ and Ilett, EE and Gulay, A and Paredes, R and Lundgren, JD and Jørgensen, M and Sengeløv, H},
title = {The gut microbiome and its resistome as predictors of clinical infections and phenotypic antibiotic resistance in hematopoietic stem cell transplant recipients.},
journal = {The Journal of infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/infdis/jiaf330},
pmid = {40581627},
issn = {1537-6613},
abstract = {A relationship between the gut microbiome composition, its resistome, and risk of clinical infections may exist and was explored here using 663 shotgun-sequenced fecal samples from 276 stem cell transplant patients. E. faecium, E. coli, and E. faecalis were the three most prevalent causes of clinical infection, with vancomycin resistance in E. faecium as the most common antibiotic resistance feature. Associations between the gut microbiome, resistome, and clinical infections were tested, with significant findings (FDR<0.05) evaluated in multivariable analysis. A 10% increase in gut abundance of E. faecium was positively associated with subsequent clinical infection with E. faecium (OR=1.14, p=0.02). Additionally, a 1% increase in vanA gene abundance was positively associated with vancomycin-resistant E. faecium infection (OR=1.27, p<0.01). Here we used metagenomics to enhance the understanding of infectious sources and to identify patients at risk of clinical infection with antibiotic-resistant bacterial strains.},
}
@article {pmid40581554,
year = {2025},
author = {Wang, Z and Yuan, C and Huang, T and Lu, B},
title = {Early nutritional interventions for chronic low-grade inflammation.},
journal = {Trends in endocrinology and metabolism: TEM},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tem.2025.06.001},
pmid = {40581554},
issn = {1879-3061},
abstract = {Current research on inflammatory disorders tends to focus on the advanced stages of disease; however, acting against chronic low-grade inflammation (a stage before overt disease) through early nutritional interventions may be an alternative, beneficial approach. We systematically evaluate how diet modulates chronic low-grade inflammation through several physiological processes. Furthermore, we suggest three intervention strategies tailored to specific stages of disease: (i) promoting anti-inflammatory dietary patterns in the general population, (ii) implementing precision nutrition targeting inflammatory biomarkers in individuals at risk, and (iii) utilizing adjuvant dietary therapies for existing inflammation. Overall, we argue that early nutritional interventions could address the unmet clinical need to alter inflammatory trajectories before clinical manifestation.},
}
@article {pmid40580932,
year = {2025},
author = {Haykal, D and Haddad, A and Cartier, H and Avelar, L},
title = {Poly-L-Lactic Acid in Aesthetic Dermatology: A Decade Beyond Volume Restoration Toward Regenerative Biostimulation.},
journal = {Aesthetic surgery journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/asj/sjaf121},
pmid = {40580932},
issn = {1527-330X},
abstract = {Over the past decade, Poly-L-lactic acid (PLLA), a synthetic, biodegradable, and biocompatible polymer, has evolved from a volumizing solution for HIV-associated lipoatrophy into a foundational tool in regenerative aesthetic dermatology. This systematic review explores PLLA's transformation across clinical generations, emphasizing its role as a biostimulatory scaffold rather than a conventional filler. Through an extensive literature review, we identify and analyze 67 studies published between January 2013 and March 2025. Findings confirm that PLLA induces a regenerative cascade marked by M2 macrophage polarization, TGF-β1-mediated fibroblast activation, and sustained neocollagenesis, thereby promoting long-term remodeling of the extracellular matrix (ECM), improved dermal density, and enhanced skin quality. The applications of PLLA have extended beyond facial volumization to full-body rejuvenation, with significant roles in post-GLP-1 therapy restoration and preventive ("prejuvenation") strategies. Protocol refinements, including optimized dilutions and cannula techniques, have enhanced safety and efficacy. This review also highlights emerging areas such as PLLA's integration with energy-based devices, digital imaging, AI diagnostics, and microbiome-focused care. Collectively, the evidence supports PLLA's utility as a versatile biostimulatory agent that bridges aesthetic innovation and regenerative dermatology.},
}
@article {pmid40580838,
year = {2025},
author = {Mirzaei, S and Gorczyca, B and Uyaguari-Diaz, M and Sparling, R and Maksimova, E},
title = {Microbial consortia in full-scale pre-ozonated biologically active filters treating a high-DOC water: Effects of seasonal and operational variations.},
journal = {Water research},
volume = {285},
number = {},
pages = {124065},
doi = {10.1016/j.watres.2025.124065},
pmid = {40580838},
issn = {1879-2448},
abstract = {This study investigated the microbial dynamics in full-scale biologically active anthracite/silica sand (BAS) and granular activated carbon (BAC) filters used to treat high-DOC coagulated softened water. By analyzing these filter types across two seasons (winter and summer), we examined the impact of operational conditions-including temperature (1 °C vs. 25 °C), backwashing cycle (72 h vs. two weeks), and empty bed contact time (10 vs. 24 min in BAC and 4 vs. 10 min in BAS)-on organic matter removal, biological activity, and bacterial taxonomy and functionality. The highest DOC (19.1 %) and BDOC (34.8 %) removal rates were observed in BAC during summer and post-backwashing, whereas BAS in both seasons and BAC in the winter showed minimal effects on the organic matter concentration. No direct correlation was found between ATP levels, bacterial 16S rRNA bacterial gene copy numbers, and DOC/BDOC removal in BAC. However, an optimal condition of 13 × 10[-6] ATP per bacterial gene copy number in BAC during summer post-backwashing coincided with the highest DOC and BDOC removal. Bacterial taxa with established associations to DOC degradation accounted for over 60 % of the total bacterial orders identified in both BAS and BAC across seasons. The BAC environment appeared to selectively enrich consortia capable of transforming complex DOC fractions, likely facilitated by its greater surface area, extended EBCT, and less frequent backwashing. These conditions supported the persistence and activity of specific bacterial orders, including Actinomycetales, Myxococcales, Planctomycetales, and Rhizobiales. Subsystem-level metagenomic analysis indicated a significant enrichment of genes associated with metabolic functions linked to enzymes such as decarboxylase, N-methylhydantoinase A, cyclic beta-1,2-glucan synthase, carbon monoxide dehydrogenase, cell division protein FtsH, N-methylhydantoinase B, and UDP-glucose 4-epimerase in BAC samples. This study deepens our understanding of the BAF microbiome's role in natural organic matter removal and its relationship with operational parameters, addressing critical gaps in drinking water biological treatment.},
}
@article {pmid40580576,
year = {2025},
author = {Paterson, C and Nikolic, A and Glyn, T and Eglinton, T and Singh, P and Hill, A},
title = {Do Perioperative Probiotics/Synbiotics Reduce Postoperative Infection Rates Following Elective Colorectal Surgery? A Systematic Review and Meta-Analysis.},
journal = {The Journal of surgical research},
volume = {312},
number = {},
pages = {163-176},
doi = {10.1016/j.jss.2025.05.026},
pmid = {40580576},
issn = {1095-8673},
abstract = {INTRODUCTION: Postoperative infections remain common in elective colorectal surgery (CRS). Perioperative probiotics/synbiotics have been investigated as a strategy to optimize the intestinal microbiota and reduce postoperative infections. The aim of this study was to conduct an updated systematic review and meta-analysis on the efficacy of perioperative probiotics/synbiotics on postoperative infection rates following elective CRS.<br><br>METHODS: Six databases were searched on February 7, 2023, in accordance with the Preferred Reporting Items for Systematic reviews and Meta-Analyses 2020 guidelines (International Prospective Register of Systematic Reviews: CRD420233392754).<br><br>INCLUSION CRITERIA: randomized controlled trials comparing perioperative probiotics or synbiotics in colorectal resection for malignant or benign disease in patients > 18 y, reporting data on infectious complications within 30 d of surgery.<br><br>EXCLUSION CRITERIA: patients undergoing acute colorectal resection, nonrandomized controlled trials, prebiotics alone used as the intervention or control. The primary outcome measure was total postoperative infection rates within 30 d of elective CRS.<br><br>RESULTS: Twenty-eight randomized controlled trials involving 2686 participants demonstrated an association between probiotics/synbiotics and reduced rates of total postoperative infections within 30 d of elective CRS (relative risk 0.55, 95% confidence interval 0.41-0.74, P < 0.001).<br><br>CONCLUSIONS: Perioperative probiotics/synbiotics are associated with almost halved total postoperative infection rates within 30 d of elective CRS. Further investigation into optimal regimens and the confounding effect of modern colorectal surgical practice is essential prior to implementation into clinical practice.},
}
@article {pmid40580532,
year = {2025},
author = {Urbonas, T and Petrauskas, D and Kiudelis, V and Jonaitis, L and Skieceviciene, J and Gedgaudas, R and Kiudeliene, E and Valantiene, I and Zykus, R and Varkalaite, G and Inciuraite, R and Trapenske, E and Kulokiene, U and Jonaitis, P and Ramonaite, R and Velickiene, J and Zvirbliene, A and Morkunas, E and Kuliaviene, I and Sumskiene, J and Adamonis, K and Macas, A and Kupcinskiene, K and Lukosiene, L and Janciauskas, D and Poskiene, L and Vitkauskiene, A and Ianiro, G and Gasbarrini, A and Kiudelis, G and Kupcinskas, J},
title = {Fecal Microbiome Transplantation for Recurrent CDI: Treatment Efficacy and Safety with Oral Capsules.},
journal = {Journal of gastrointestinal and liver diseases : JGLD},
volume = {34},
number = {2},
pages = {199-204},
doi = {10.15403/jgld-5990},
pmid = {40580532},
issn = {1842-1121},
mesh = {Humans ; *Fecal Microbiota Transplantation/methods/adverse effects ; Male ; Female ; Retrospective Studies ; Middle Aged ; Treatment Outcome ; Administration, Oral ; *Clostridium Infections/therapy/microbiology/diagnosis ; Aged ; Capsules ; Recurrence ; *Clostridioides difficile ; Adult ; Anti-Bacterial Agents/administration &amp; dosage ; Time Factors ; Feces/microbiology ; },
abstract = {BACKGROUND AND AIMS: Fecal microbiota transplantation is an effective treatment method for recurrent Clostridioides difficile infection. Widely used enteric tube and colonoscopy methods demonstrate excellent efficacy and safety results. Recent data suggest that new fecal microbiota transplantation methods using oral capsules may provide a less invasive approach. In this study, we aimed to compare primary fecal microbiota transplantation efficacy as well as short- and long-term safety of two different administration routes: oral capsules and enteric tube.<br><br>METHODS: This retrospective study included 60 consecutive patients who underwent fecal microbiota transplantation for recurrent Clostridioides difficile infection. Thirty participants received 50 oral capsules containing frozen material for a single day and 30 patients received fecal microbiota transplantation via nasoenteric tube. All patients received standard treatment with oral vancomycin 500 mg q.i.d. for at least five days before the procedure. After intervention, patients were followed up for at least six months. Data on Clostridioides difficile infection recurrences and health status were collected and analyzed.<br><br>RESULTS: The oral capsules group consisted of 30 patients. Among them, 22 (73.3%) participants experienced resolution of symptoms after a single fecal microbiota transplantation, while eight (26.7%) patients developed recurrent diarrhea within eight weeks. The other 30 patients received treatment via nasoenteric tube. Among them, 24 (80%) patients were cured after a single fecal microbiota transplantation, while six (20%) experienced recurrent disease within eight weeks. The primary efficacy did not show significant differences between the two groups (p=0.85). Throughout the follow-up period, no serious adverse events or fecal microbiota transplantation related deaths were reported in both groups.<br><br>CONCLUSIONS: Fecal microbiota transplantation with frozen oral capsules is a safe, less invasive method with comparable efficacy to nasoenteric administration route.},
}
@article {pmid40580347,
year = {2025},
author = {Leonov, G and Livantsova, E and Varaeva, Y and Starodubova, A},
title = {Probiotics and Prebiotics in Post-Myocardial Infarction Rehabilitation: Mechanisms, Benefits, and Future Directions.},
journal = {Current nutrition reports},
volume = {14},
number = {1},
pages = {88},
pmid = {40580347},
issn = {2161-3311},
support = {FGMF-2025-0003//The research was carried out at the expense of the subsidy for the implementation of the state task/ ; FGMF-2025-0003//The research was carried out at the expense of the subsidy for the implementation of the state task/ ; FGMF-2025-0003//The research was carried out at the expense of the subsidy for the implementation of the state task/ ; FGMF-2025-0003//The research was carried out at the expense of the subsidy for the implementation of the state task/ ; },
mesh = {*Probiotics/therapeutic use/administration &amp; dosage ; Humans ; *Prebiotics/administration &amp; dosage ; *Myocardial Infarction/rehabilitation ; Gastrointestinal Microbiome ; *Cardiac Rehabilitation/methods ; Dysbiosis ; },
abstract = {PURPOSE OF REVIEW: Myocardial infarction (MI) remains a leading cause of morbidity and mortality worldwide, and rehabilitation is essential to improve patient outcomes and reduce the risk of recurrent cardiovascular events. This review aims to summarize research on the gut-heart axis and the therapeutic potential of probiotics and prebiotics in MI rehabilitation, highlighting their ability to modulate gut microbiota composition and activity to benefit cardiovascular health.<br><br>RECENT FINDINGS: Recent studies have identified the gut microbiome as a critical modulator of myocardial health, with dysbiosis-an imbalance in microbial populations-associated with increased production of proinflammatory metabolites such as trimethylamine-N-oxide (TMAO), which exacerbate endothelial dysfunction and thrombosis in MI patients. Studies show that probiotic strains and prebiotics can improve blood lipid profiles, regulate blood pressure, inhibit the progression of endothelial dysfunction, promote the growth of beneficial bacteria, and increase cardioprotective short-chain fatty acids. The use of probiotics and prebiotics in MI patients may be of advantage in cardiac rehabilitation. Probiotics and prebiotics have been shown to offer potential benefits in mitigating inflammation, improving endothelial function, and optimizing metabolic health. These microbiome-targeted strategies may complement existing rehabilitation approaches, potentially reducing the risk of recurrent cardiovascular events and improving long-term outcomes for patients with MI. However, further research is necessary to elucidate the underlying mechanisms and substantiate the clinical efficacy of these therapeutic interventions.},
}
@article {pmid40580166,
year = {2025},
author = {Mark Welch, JL and Borisy, GG},
title = {Dental plaque: Who is in the neighborhood and why it matters.},
journal = {Journal of the American Dental Association (1939)},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.adaj.2025.05.005},
pmid = {40580166},
issn = {1943-4723},
}
@article {pmid40580119,
year = {2025},
author = {Warne, RW and Kirschman, L},
title = {Microbiomes in animal ecology: Advances, assumptions, and opportunities.},
journal = {Integrative and comparative biology},
volume = {},
number = {},
pages = {},
doi = {10.1093/icb/icaf112},
pmid = {40580119},
issn = {1557-7023},
abstract = {The study of animal microbiomes has revolutionized our understanding of host physiology, behavior, and ecology. However, many studies focus on correlations rather than causal functional interaction and critical caps persist in linking microbial dynamics to ecological and fitness-relevant outcomes. Advances in multi-omics approaches, combined with stable isotope microbiomics, offer promising tools for linking microbial community dynamics to host function in ecologically relevant conditions. Here, we highlight the importance of longitudinal studies, controlled physiological comparisons, and integrative methodological approaches for microbe-host interactions beyond laboratory models. We emphasize the integration of multi-omics approaches and stable isotope probing to track microbial metabolites and their effects on hosts. Examples from African herbivores, geladas, and amphibians illustrate how longitudinal sampling and isotopic labeling can reveal microbiome plasticity in response to environmental variability. Furthermore, experimental systems such as larval amphibians, fish models, and dietary specialists like koalas demonstrate the potential of combining microbiome manipulations with multi-omics to disentangle host-microbe interactions in ecologically relevant contexts. We argue that advancing this field requires moving beyond disease-focused study of model organisms to explore microbiome contributions to life-history traits, nutrient provisioning, and resilience in wild populations. Coupling stable isotope probing with multi-omics in field experiments that compare dichotomous physiological and/or ecological states can be a powerful approach for providing insight into microbiome functional effects on hosts in fitness relevant contexts.},
}
@article {pmid40580061,
year = {2025},
author = {Rathour, R and Ma, Y and Xiong, J and Wang, XW and Petersen, J and Zhang, X},
title = {Hemolymph microbiota and host immunity of crustaceans and mollusks.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf133},
pmid = {40580061},
issn = {1751-7370},
abstract = {None declared.Conflicts of interestCrustaceans and mollusks have major economic importance and are also key players in aquatic biogeochemical cycles. However, disease outbreaks, temperature fluctuations, pollutants, and other stressors have severely threatened their global production. Invertebrates generally rely on their innate immune system as the primary defence mechanism, operating at cellular and humoral levels to protect against pathogens. The hemolymph plays a vital role in immune responses, containing microbial communities that interact with the host's immune processes. Significant advances in molecular methods such as metagenomics, metatranscriptomics, metaproteomics, and metabolomics have revealed the presence of a resident hemolymph microbiome and delineated its potentially vital role in immune homeostasis and overall host health. Accordingly, understanding the composition and role of the hemolymph microbiota, alongside innate immune responses, has become a key focus in recent research aimed at unravelling disease resistance mechanisms and supporting sustainable aquaculture practices. Here, we summarize the latest advancements in understanding the host and environmental factors that shape hemolymph microbiota diversity in various crustaceans and mollusks species. We also consider the innate immune responses of the hosts, as these modulate interactions between hosts, microbes, and environments. Interactions within the hemolymph microbiome significantly affect host health, providing critical insights for advancing sustainable aquaculture.},
}
@article {pmid40580037,
year = {2025},
author = {},
title = {Correction to 'GutMetaNet: an integrated database for exploring horizontal gene transfer and functional redundancy in the human gut microbiome'.},
journal = {Nucleic acids research},
volume = {53},
number = {12},
pages = {},
doi = {10.1093/nar/gkaf654},
pmid = {40580037},
issn = {1362-4962},
}
@article {pmid40580016,
year = {2025},
author = {Hwang, DY and An, MH and Lee, PH and Baek, AR and Park, S and Nam, Y and Lee, JH and Park, SW and Kim, DJ and Jang, AS},
title = {The impact of a bacterial lysate on composition of the lung microbiota in a mouse model of asthma exposed to titanium dioxide as one of air pollutants.},
journal = {Letters in applied microbiology},
volume = {78},
number = {6},
pages = {},
doi = {10.1093/lambio/ovaf089},
pmid = {40580016},
issn = {1472-765X},
support = {2022R1G1A1009464//National Research Foundation of Korea/ ; //Soonchunhyang University/ ; },
mesh = {Animals ; *Titanium/toxicity/adverse effects ; *Lung/microbiology/drug effects ; *Microbiota/drug effects ; *Asthma/microbiology/chemically induced ; Mice ; Disease Models, Animal ; *Air Pollutants/toxicity/adverse effects ; Bronchoalveolar Lavage Fluid/microbiology ; *Bacteria/genetics/classification/isolation &amp; purification/drug effects ; Female ; RNA, Ribosomal, 16S/genetics ; Mice, Inbred BALB C ; DNA, Bacterial/genetics/chemistry ; Bacterial Lysates ; },
abstract = {Environmental microbes have been linked to both beneficial and harmful effects on the lungs in relation to asthma. The aim of our study was to characterize the bacterial microbiome in lung samples from a mouse model of asthma exposed to titanium dioxide (TiO2) particles, and the effect of OM-85 Broncho-Vaxom®, a bacterial lysate on lung microbiome in mice. The mice were divided randomly into four groups of 6-8 mice per group. To identify the microbial communities in lung samples the upper right lung of all groups, we amplified and sequenced the rRNA gene regions from bacterial DNA (16S). The amplified 16S region was sequenced using the Roche-454 Life Sciences Titanium pyrosequencing platform. In the OVA + TiO2 + OM-85 group, airway hyperresponsiveness and inflammatory cells in bronchoalveolar lavage fluid (BALF) decreased compared to the OVA + TiO2 group. Inflammatory cytokine levels were lower in the OVA + TiO2 + OM-85 group. Certain bacteria, and Collinsella aerofaciens, decreased in the OVA + TiO2 + OM-85 group, while Neisseria perflava and Fusobacterium periodonticum increased. Lactic acid bacteria groups decreased in the OVA + TiO2 + OM-85 group. TiO2 particles exposure changed lung microbial taxa, and modified by a bacterial lysate, suggesting that a probiotic can be helpful in reducing exacerbation of airway disease exposed to air pollutants.},
}
@article {pmid40579603,
year = {2025},
author = {Caviness, P and Mulakala, BK and Lorenzo, OP and Yao, T and Lindemann, SR and Rosa, F and Yeruva, L and Chen, JR},
title = {Microbes Matter: Exploring the Connection Between Infant Gut Microbiota and Bone Development.},
journal = {Calcified tissue international},
volume = {116},
number = {1},
pages = {90},
pmid = {40579603},
issn = {1432-0827},
support = {6026-10700-001-000D//USDA-ARS/ ; },
mesh = {*Gastrointestinal Microbiome/physiology ; Animals ; *Milk, Human/microbiology ; Humans ; *Bone Development/physiology ; Mice ; Infant Formula ; Female ; Infant ; Feces/microbiology ; Male ; },
abstract = {Human milk, compared to milk formula, is considered the optimal source of nutrition for infants as it can shape offspring microbiome composition, which is necessary for the production of key biomolecules that aid in development of infant physiological systems. A variety of factors in human milk can influence infant microbiome composition. One such factor is the type of oligosaccharides present, which is determined in part by maternal secretor status and itself determined by expression of fucosyltransferase-2 (FUT2). The aim of this study was to investigate the effects of secretor or non-secretor human milk as well as infant milk formula on infant gut microbiome composition and whether these changes in microbiota impact bone development. Fecal microbiota transfer from infants fed human milk from secretor mothers (SMM) or non-secretor mothers (NSM) as well as those fed infant milk formula (MFM) into 21-day-old germ-free mice were performed. After 35 days, gut microbiome composition and bone development were analyzed using 16S rRNA sequencing and µCT analysis. At the genus level, Phocaeicola and Akkermansia are upregulated for SMM and NSM mice respectively, while family Ruminococcaceae is increased for MFM mice. Percent bone volume (BV/TV) and trabecular number (Tb N) were significantly decreased for MFM mice but unaltered for SMM and NSM mice compared to germ-free controls (GF CTRL). Measurement of bone marrow plasma inflammatory factor levels shows a significant increase in TNF-α and IL-1β for SMM and NSM mice, both potential promoters of osteoclastogenesis under certain conditions, compared to MFM and GF CTRL mice. Data suggests that milk formula feeding may suppress infant bone growth and development by altering gut microbiome composition.},
}
@article {pmid40579598,
year = {2025},
author = {Zahid, K and Rehman, A},
title = {Letter to the Editors re: The gut microbiome and metabolome in children with a first febrile urinary tract infection: a pilot study.},
journal = {Pediatric nephrology (Berlin, Germany)},
volume = {},
number = {},
pages = {},
pmid = {40579598},
issn = {1432-198X},
}
@article {pmid40579430,
year = {2025},
author = {Xavier, JB},
title = {Ecological management of the microbiota in patients with cancer.},
journal = {Nature reviews. Clinical oncology},
volume = {},
number = {},
pages = {},
pmid = {40579430},
issn = {1759-4782},
abstract = {The composition of the intestinal microbiota influences the outcomes of patients receiving cancer treatment, although the best way to use this knowledge to improve cancer care remains unclear. In this Review, I synthesize the current understanding of host-microbiota dynamics in patients with cancer, and propose the integration of microbiota management guided by ecological principles in cancer care. Ecological management of the microbiota emphasizes the preservation of microbial populations - and the benefits they provide to the host - from the disruption caused by treatments such as chemotherapy and prophylactic antibiotics. The microbiota can be routinely and longitudinally monitored in patients using proven non-invasive methods, such as 16S ribosomal RNA amplicon sequencing. Longitudinal microbiome data can be processed with innovative computational tools based on principles of mathematical ecology to predict the risk of microbiota-related complications, guide treatment choices that minimize disturbance to the microbiota and restore microbial populations damaged by cancer treatment. Routine microbiome monitoring could also generate extensive datasets for human-based research, which could inform new microbiota-targeted interventions that improve responses to cancer treatments, including immune-checkpoint inhibitors. Applying ecological approaches to manage microbiota could enhance cancer care and improve patient outcomes.},
}
@article {pmid40579314,
year = {2025},
author = {Caton, JS and Crouse, MS and Dahlen, CR and Ward, AK and Diniz, WJS and Hammer, CJ and Swanson, RM and Hauxwell, KM and Reynolds, LP},
title = {Review: Micronutrient supply, developmental programming, and strategic supplementation in ruminant livestock.},
journal = {Animal : an international journal of animal bioscience},
volume = {},
number = {},
pages = {101563},
doi = {10.1016/j.animal.2025.101563},
pmid = {40579314},
issn = {1751-732X},
abstract = {Developmental programming, also known as fetal programming, is the idea that changes in offspring development with both immediate and longer-term consequences can arise from in utero stress, including compromised maternal nutrition. Large animal models demonstrate that perturbed maternal nutrition, including macro- and micronutrient supply, (amino acids, vitamins, and trace elements) can alter development during gestational and postnatal offspring outcomes. Strategic supplementation of micronutrients (methionine, arginine, selenium, folate, vitamin B12, choline, cobalt, sulfur and others) also alters placental function and therefore, fetal nutrient supply. Specifically, in the offspring, multiple visceral tissues, metabolism, growth, and reproduction are impacted by compromised nutrition and these effects are potentially mitigated by strategic supplementation. Furthermore, compromised maternal nutrition and strategic supplementation alter gene expression, metabolomic patterns, and biochemical pathways in the offspring. Developmental programming is mechanistically driven, at least in part, by epigenetic mechanism and one carbon-metabolism and associated specific micronutrients. The concept of developmental programming is strongly supported by data from ruminant animal models, wherein compromised maternal nutrition is a stressor driving programming events. Changes in the offspring's transcriptome and metabolome can be influenced by changes in maternal nutrition during development. Evidence suggests that strategic supplementation of micronutrients potentially mitigates the compromised development. Future research needs include efforts focused on: mechanistic investigations, livestock production outcomes, animal health implications, and host-microbiome interrelationships associated with maternal nutrition, developmental programming and strategic supplementation.},
}
@article {pmid40579258,
year = {2025},
author = {Weckwerth, W and Chaturvedi, P and Ghatak, A and Kerou, M and Garg, V and Bohra, A and Subbarao, GV and Stein, L and Schleper, C and Varshney, RK and Snapp, S},
title = {Natural variation of the holobiont for sustainable agroecosystems.},
journal = {Trends in plant science},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tplants.2025.05.006},
pmid = {40579258},
issn = {1878-4372},
abstract = {Plant evolution is largely driven by plant-microbe interactions, yet the ecology of the plant holobiont is not well understood at a molecular level. However, these relationships hold diverse benefits for sustainable agriculture as nature-based solutions (NbS). We propose a workflow to enhance understanding of natural variation in the plant-soil microbiome holobiont, addressing key challenges like growth promotion, stress resilience, nitrogen use efficiency (NUE), biological nitrification inhibition (BNI), healthy soils, and improving fertilization practices towards a more natural agroecosystem. We discuss a panome-wide association study (PWAS) approach to discover and incorporate novel genetic diversity from exotic germplasm into breeding populations. Ultimately, understanding natural variation of the holobiont in agroecosystems will contribute to the development of novel climate-resilient crop varieties for food security.},
}
@article {pmid40579233,
year = {2025},
author = {Safarzadeh, H and Aliramezani, A and Rahimi, A and Yousefi, B and Heidarzadeh, S},
title = {The advantages of Faecalibacterium prasnitzii in gestational diabetes mellitus.},
journal = {Future microbiology},
volume = {},
number = {},
pages = {1-12},
doi = {10.1080/17460913.2025.2520699},
pmid = {40579233},
issn = {1746-0921},
abstract = {In recent years, the incidence of metabolic disorders has exponentially increased worldwide mainly due to the misfunctioning of chemical reactions. Gestational diabetes mellitus (GDM) occurred during pregnancy when placenta prevent absorption of sufficient insulin in mother's body. Although this disorder usually disappears after delivery, it could raise the probability of developing complications in the future. GDM is associated with adverse effects on women and their children, such as obesity, cardiovascular disease, and type 2 diabetes. On the other hand, administration of probiotics as a live microorganism with the wide array of health values could contribute to restore and stabilize gut microbiota and subsequently regulate essential internal functions such as development of immunity. In this review, we focus primarily on some causes and effects of GDM in pregnant women and then Faecalibacterium prasnitzii, the most abundant butyrate-producing bacterium in gut, which have been using as a prominent biomarker in health and disease and also potential anti-inflammatory treatment owing to the production of active molecules.},
}
@article {pmid40579185,
year = {2025},
author = {Young, JD and Schneid, KN and Pinell, LJ and Wolfe, CA and Lawrence, TE and Samuelson, KL and Richeson, JT and Morley, PS},
title = {Evaluation of gastrointestinal and fecal microbial communities as markers of liver abscess risk in beef feedlot cattle.},
journal = {Journal of animal science},
volume = {},
number = {},
pages = {},
doi = {10.1093/jas/skaf210},
pmid = {40579185},
issn = {1525-3163},
abstract = {Liver abscesses (LAs) are a prevalent and costly issue in the beef industry. Microbial translocation from the gastrointestinal tract is believed to be the underlying cause of LAs. However, little is understood about the factors that permit passage of bacteria into the portal bloodstream, or where this translocation is likely to occur. This study used 16S rRNA gene sequencing to characterize the microbial community composition of the rumen, small intestine, large intestine, and feces of steers with edible and abscessed livers of varying severity. The small intestine of steers with severe LAs had increased (P = 0.02) richness and evenness compared to cattle with edible livers. However, there were no differences in the alpha diversity among samples collected at other locations (P ≥ 0.08). Small intestine samples also had a reduced (P < 0.01) Firmicutes to Bacteroidota ratio for cattle with LAs compared to those with edible livers. Prevotellaceae and Synergistaceae family abundance differed in the small intestine of cattle with LAs. Differences in community composition were not identified in fecal, colon, or rumen samples in association with LA occurrence, and there were no differences related to bacteria that have been traditionally considered LA pathogens (e.g., Fusobacteria or Trueperella spp.). These findings suggest that the microbial communities of the small intestine may have an important influence on LA occurrence. However, differences in microbial communities were not identified in rumen and fecal samples that might be used in predicting LA occurrence. Although sampling techniques during the feeding period are still limited and advances in this area would greatly benefit LA research.},
}
@article {pmid40578793,
year = {2025},
author = {Maneira, C and Becker, S and Chamas, A and Lackner, G},
title = {A Multilayered Biocontainment System for Laboratory and Probiotic Yeast.},
journal = {Metabolic engineering},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ymben.2025.06.009},
pmid = {40578793},
issn = {1096-7184},
abstract = {The containment of genetically engineered microorganisms to designated environments of action is a paramount step in preventing their spread to nature. Physical barriers were traditionally employed to solve this issue, nevertheless, the growing number of biotechnological operations in open dynamic environments calls for intrinsic biocontainment. Here we describe the development of genetically embedded safeguard systems for both a laboratory strain of Saccharomyces cerevisiae and the commercial probiotic Saccharomyces cerevisiae var. boulardii. In a stepwise approach, single-input metabolic circuits based either on a synthetic auxotrophy or a CRISPR-based kill switch were developed before their combination into an orthogonal two-input system. All circuits are based on gut-active molecules or environmental cues, making them amenable to microbiome therapy applications. The final two-input system is stable for more than a hundred generations while achieving less than one escapee in 10[9] CFUs after incubation under restrictive conditions for at least six days. Biocontained strains can robustly produce heterologous proteins under permissive conditions, supporting their future use in the most varied applications, like in-situ production and delivery of pharmaceutically active metabolites.},
}
@article {pmid40578434,
year = {2025},
author = {Kelley, M and Limbach, PA and Benoit, JB},
title = {tRNA expression and modifications as critical components in the biology of blood feeding arthropods.},
journal = {Current opinion in insect science},
volume = {},
number = {},
pages = {101404},
doi = {10.1016/j.cois.2025.101404},
pmid = {40578434},
issn = {2214-5753},
abstract = {Alterations to the proteome are necessary for physiological processes in blood feeding arthropods. To account for this, transfer RNA (tRNA) levels and chemical modifications are utilized for protein synthesis. Here, we discuss an overview of tRNA regulation in blood feeding systems. This topic expands to host-microbial interactions as modifications require micronutrients acquired from symbionts and diet. Lastly, modifications are likely involved in the molecular dynamics between vectors and pathogens, which may impact transmission to vertebrate hosts. The tRNA levels and their modifications likely play crucial roles in the tripartite interaction between mosquito-microbiome-pathogens, providing a novel target to suppress pathogen transmission.},
}
@article {pmid40578342,
year = {2025},
author = {Wong, KK and Wu, BG and Chung, M and Li, Q and Darawshy, F and Tsay, JJ and Holub, M and Barnett, CR and Kwok, B and Kugler, MC and Chung, C and Natalini, JG and Singh, S and Li, Y and Schluger, R and Ficaro, L and Carpenito, J and Collazo, D and Perez, L and Kyeremateng, Y and Chang, M and Czachor, A and Singh, R and Mccormick, C and Campbell, CD and Keane, R and Askenazi, M and Hansbro, PM and Weiden, MD and Huang, YJ and Stringer, KA and Clemente, JC and Li, H and Jones, D and Ghedin, E and Segal, LN and Sulaiman, I},
title = {Microbial contribution to metabolic niche formation varies across the respiratory tract.},
journal = {Cell host &amp; microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2025.06.002},
pmid = {40578342},
issn = {1934-6069},
abstract = {Variations in the airway microbiome are associated with inflammatory responses in the lung and pulmonary disease outcomes. Regional changes in microbiome composition could have spatial effects on the metabolic environment, contributing to differences in the host response. Here, we profiled the respiratory microbiome (metagenome/metatranscriptome) and metabolome of a patient cohort, uncovering topographical differences in microbial function, which were further delineated using isotope probing in mice. In humans, the functional activity of taxa varied across the respiratory tract and correlated with immunomodulatory metabolites such as glutamic acid/glutamate and methionine. Common oral commensals, such as Prevotella, Streptococcus, and Veillonella, were more functionally active in the lower airways. Inoculating mice with these commensals led to regional increases in several metabolites, notably methionine and tyrosine. Isotope labeling validated the contribution of Prevotella melaninogenica in generating specific metabolites. This functional characterization of microbial communities reveals topographical changes in the lung metabolome and potential impacts on host responses.},
}
@article {pmid40578285,
year = {2025},
author = {Ashwini, K and Acharya, R and Roopashree, PG and Raghotham, A and Baud, S and Rao, RM and Suchetha Kumari, N},
title = {Molecular basis of the therapeutic effect of butyrate in glioblastoma revealed by in vitro and in silico approach.},
journal = {Biochemical and biophysical research communications},
volume = {777},
number = {},
pages = {152216},
doi = {10.1016/j.bbrc.2025.152216},
pmid = {40578285},
issn = {1090-2104},
abstract = {Glioblastoma (GBM) remains among the most difficult to treat cancers globally. Complexity of this disease and the existing inadequacies of modern therapy put forward the need for ongoing research into new therapies. Short Chain Fatty Acids (SCFAs) are among the major metabolites secreted by the gut microbiome, and are thought to play an important role in gut microbiome-brain interactions. While earlier experimental studies have hinted towards a therapeutic potential of butyrate in glioblastoma, we demonstrate here the molecular mechanism behind this effect through a combination of in vitro and in silico approaches. LN229 and U87 GBM cells were treated with butyrate, and anti-proliferative potential was evaluated through colony formation assay, flow cytometry and qRT-PCR experiments. Molecular mechanism was mapped through butyrate target prediction, molecular docking, molecular dynamics simulations and analyses of binding free energy calculations. Butyrate inhibited the proliferation, and colony formation in U87 and LN229 GBM cell lines. We also found that it arrested the cell cycle progression at the G0/G1 phase in U87 cells and the G2/M Phase in LN229 cell lines, along with initiation of apoptosis in both the cells. Similarly, butyrate treatment also reduced the expression of Epidermal Growth Factor Receptor (EGFR) in a dose-dependent manner. The molecular mechanism behind the anti-cancer effect of butyrate was demonstrated through molecular docking and simulation studies. Butyrate bound to Histone Deacetylase-3 (HDAC3)-Nuclear CoRepressor2 complex, and induced allosteric dynamics that further blocked HDAC3 activation. The observations in this study demonstrate the potential of butyrate as a viable therapeutic agent for glioblastoma.},
}
@article {pmid40578104,
year = {2025},
author = {Li, X and Wang, H and Abdelrahman, HA and Kelly, AM and Roy, LA and Soto, E and Wang, L},
title = {Resistome and microbiome shifts in catfish rearing water: the influence of temperature and antibiotic treatments.},
journal = {Water research},
volume = {285},
number = {},
pages = {124074},
doi = {10.1016/j.watres.2025.124074},
pmid = {40578104},
issn = {1879-2448},
abstract = {The increasing reliance on aquaculture for sustainable protein production highlights the need for responsible antibiotic use to manage bacterial infections, particularly in intensive farming systems. This study investigated the effects of three FDA-approved antibiotics (Aquaflor®, Romet®, Terramycin®) at common fish bacterial disease outbreak temperatures (20 °C, 25 °C, and 30 °C) on the microbiome and resistome of aquaculture water using a catfish model system. Metagenomic analyses evaluated the abundance, diversity, and mobility of antimicrobial resistance genes (ARGs) and antibiotic-resistant bacteria (ARB). The impact of temperature on Aquaflor- and Romet-induced changes in ARG abundance, richness, and resistome composition followed a U-shaped trend, with the least effect observed at 25 °C. Of the three antibiotics tested, Terramycin exerted the most significant influence on the water microbiome and resistome, enriching tetracycline resistance genes and co-selecting for floR, sul, and dfrA genes. Temperature also induced notable shifts in the ARB population, with Mantel tests revealing strong correlations between ARG profiles and changes in the overall bacterial community and ARB populations. While certain ARG classes consistently remained associated with specific host phyla, others shifted, highlighting the potential for horizontal gene transfer (HGT) as a critical mechanism for disseminating resistance genes like tet(C), particularly after antibiotic treatment. This is further supported by the observed reduction in plasmid numbers following treatment, which coincided with increased HGT events. Our findings highlight the pivotal role of temperature in influencing resistome dynamics, emphasizing the importance of accounting for environmental factors when applying antibiotics to effectively mitigate antimicrobial resistance in aquaculture systems.},
}
@article {pmid40577950,
year = {2025},
author = {Yaxiao, H and Ran, Z and Rongyan, Z and Zhenhong, Z and Yinliang, Z and Shulong, Y and Lanhui, L},
title = {Identification of biomarkers associated with sexual maturity in laying hens based on metabolomics and gut microbiology.},
journal = {Poultry science},
volume = {104},
number = {9},
pages = {105469},
doi = {10.1016/j.psj.2025.105469},
pmid = {40577950},
issn = {1525-3171},
abstract = {Sexual maturation is an important trait in poultry production. The initiation mechanism of sexual maturity is significant for breeding high-yield laying hens. Plasma metabolomics and gut microbiology were used to identify biomarkers of sexual maturity in laying hens. Cecal contents and plasma samples were collected from laying hens at 15 w, 17 w, and 22 w during the sexual maturity transition period. A total of 208 differential metabolites are significantly enriched pathways of sphingolipid metabolism, glycine, serine, and threonine metabolism between 15 w and 17 w. A total of 183 differential metabolites were significantly enriched pathways of valine, leucine, isoleucine biosynthesis and glycerophospholipid metabolism between 17 w and 22 w. A total of 56 potential biomarkers, mainly consisting of carnitine and choline metabolites, was identified for the transition from 15 w to 22 w with the receiver operating characteristic (ROC) curve analysis. A positive correlation between metabolites and estrogen was identified through Weighted Gene Co-expression Network Analysis (WGCNA). The bacterial taxa associated with sexual maturity were identified in hens at three week-of-age by 16S rDNA Amplicon Sequencing. The bacterial compositions of 15 w, 17 w, and 22 w are distinct, with their main bacterial genera being Bacteroidetes, Desulfovibrio, and Lactobacillus, respectively. The bacterial species enriched in the three groups were key biomarkers distinguishing sexual maturity and significantly correlated with the shifts in the functional capacities of the gut microbiome. The choline, betaine, and methionine in metabolites are correlated with different bacteria using joint analysis, indicating that microbial communities can affect host metabolism. These results provide important insights into the dynamic change of plasma metabolism and gut microbiome in laying hens.},
}
@article {pmid40577939,
year = {2025},
author = {White, ML and Crook, JM and Hansford, KM and Carter, DP and Elmore, MJ and Johnston, C and Gandy, S and Lewandowski, K and Vaux, A and Osman, KL and Vipond, R and Medlock, JM and Feil, EJ and Pullan, ST},
title = {A full-length 16S survey using Nanopore sequencing to uncover the bacterial microbiome in Ixodes ricinus ticks from a single UK woodland, collected across three springs (2019-2021).},
journal = {Ticks and tick-borne diseases},
volume = {16},
number = {4},
pages = {102506},
doi = {10.1016/j.ttbdis.2025.102506},
pmid = {40577939},
issn = {1877-9603},
abstract = {Ixodes ricinus is a key vector of several bacterial pathogens, including Borrelia and Rickettsia species. To assess bacterial prevalence and diversity, we characterised the microbiome of ticks collected from a single UK woodland, comparing different woodland types, life stages (adult male, female, and nymph), and sampling years (spring 2019-2021). Unlike previous studies that target short regions of the 16S rRNA gene, we used Nanopore sequencing to generate full-length 16S reads, allowing for higher taxonomic resolution. Our results showed significant microbiome differences across life stages, but not by woodland type or year. Rickettsia was the most abundant taxon, with prevalence varying by life stage and year. Borrelia was present in all life stages but absent in 2021 samples. Anaplasma abundance varied significantly by year and life stage, peaking in nymphs from Pine woodland. Bartonella was found across all woodland types, with the highest abundance in nymphs from Oak-dominated areas.},
}
@article {pmid40577816,
year = {2025},
author = {Herrera, MJ and Heras, J and Catabay, C and Booth, M and Connor, KM and German, DP},
title = {Diet-Induced Shifts in the Hindgut Microbiome Leads to Subtle Changes in Gut and Liver Function of a Marine Herbivorous Fish.},
journal = {Ecological and evolutionary physiology},
volume = {98},
number = {2},
pages = {111-131},
doi = {10.1086/736035},
pmid = {40577816},
issn = {2993-7973},
mesh = {Animals ; *Liver/physiology/metabolism ; *Diet/veterinary ; *Gastrointestinal Microbiome ; Herbivory ; *Gastrointestinal Tract/microbiology/physiology ; Fishes/physiology/microbiology ; Transcriptome ; },
abstract = {AbstractThe diet of an organism can influence various biological processes, including digestion. By examining how dietary changes can shift gut physiology in an herbivorous fish, we can gain insight into what that species can tolerate in terms of dietary shifts. Thus, we investigated how gut mass, digestive enzyme activity, hindgut microbial diversity, levels of gastrointestinal fermentation, and hindgut and liver transcriptomics respond to dietary perturbations in the marine herbivorous fish Cebidichthys violaceus. Contrary to our expectations, fish fed an omnivore diet (45% protein) in the laboratory exhibited the most similarity to wild-caught herbivorous fish, sharing a high abundance of taxa in the Bacteroidota and Bacillota phyla (families Ruminococcaceae and Rikenellaceae) and the highest concentrations of short-chain fatty acids. Fish in these groups shared similarities in gene expression patterns too. Fish fed herbivore (~23% protein) or carnivore (~69% protein) diets in the laboratory had a high abundance of taxa from the Pseudomonadota phylum (families Burkholderiaceae and Oxalobacteraceae) and lower short-chain fatty acid concentrations. The hindgut had 519 differentially expressed genes, with wild-caught fish exhibiting a high expression of genes associated with ion transport, lipid metabolism, and glucose metabolism. The liver had 4,650 differentially expressed genes, and wild-caught fish had a high expression of genes related to fatty acid synthesis and proteolysis. Hindgut digestive enzyme activities also varied with diet and microbial diversity. Our integrative study furthers our understanding of the physiology of an herbivorous fish and how it responds to shifting dietary resources, particularly with an eye toward herbivorous fish aquaculture.},
}
@article {pmid40577810,
year = {2025},
author = {McMurtrie, J and Bell, AG and Cable, J and Temperton, B and Tyler, CR},
title = {The ecology and plasticity of fish skin and gill microbiomes: Seeking what matters in health and disease.},
journal = {FEMS microbiology reviews},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsre/fuaf027},
pmid = {40577810},
issn = {1574-6976},
abstract = {The microbiomes of skin and gill mucosal surfaces are critical components in fish health and homeostasis by competitively excluding pathogens, secreting beneficial compounds, and priming the immune system. Disruption of these microbiomes can compromise their capacity for disease resilience and maintaining host homeostasis. However, the extent and nature of microbiome disruption required to impact fish health negatively remains poorly understood. This review examines how various stressors influence the community composition and functionality of fish skin and gill microbiomes, and the subsequent effects on fish health. Our findings highlight that the impact of stressors on skin and gill microbiomes may differ for different body sites and are highly context-dependent, influenced by a complex interplay of host-specific factors, stressor characteristics, and environmental conditions. By evaluating current knowledge on the genesis and homeostasis of these microbiomes, we highlight a strong influence of environmental factors especially on skin and gill microbiomes compared with fish gut microbiomes, which appear to be more closely regulated by the host's homeostatic and immunological systems. This review emphasises the importance of understanding the ecology and plasticity of fish skin and gill microbiomes to identify critical thresholds for microbiome shifts that impact fish health and disease resilience.},
}
@article {pmid40577689,
year = {2025},
author = {Li, TP and Wang, CH and Wang, ZH and Hao, BR and Xie, JC and Li, HX and Cai, DJ and Ye, SC and Zhao, LQ},
title = {Tetracycline changes the microbial assembly of Hyphantria cunea and reduces its fitness.},
journal = {Environmental entomology},
volume = {},
number = {},
pages = {},
doi = {10.1093/ee/nvaf063},
pmid = {40577689},
issn = {1938-2936},
support = {32301594//National Natural Science Foundation of China/ ; KYCX24_1265//Nanjing Forestry University/ ; },
abstract = {The strong environmental adaptability of the fall webworm Hyphantria cunea is closely linked to its internal microbiota. However, with the widespread usage and environmental residuals of antibiotics, their effects on the microbiome and fitness of H. cunea remain unknown. In this study, we found that tetracycline significantly decreased bacterial diversity in H. cunea, evident in a notable reduction in both the number of bacterial species and their relative abundance. Furthermore, the bacterial community structure was influenced by tetracycline, resulting in an increase in the relative abundance of Firmicutes and a decrease in the relative abundances of Proteobacteria, Bacteroidota, and others. Additionally, the potentially tetracycline-resistant bacterial genus ZOR0006 became dominant after tetracycline ingestion. The tetracycline also led to significant alterations in the function of the bacterial community, particularly in defense mechanisms, cell motility, energy production, and conversion. Corresponding to the changes in the microbiota, tetracycline significantly reduced the fitness of H. cunea, mainly manifested as an extension of the developmental duration and a decrease in the survival rate. These findings elucidate the effects of tetracycline on the microbial assembly and fitness of H. cunea, providing an important reference for a deeper understanding of the complex roles of antibiotics in ecological environments.},
}
@article {pmid40577613,
year = {2025},
author = {Morris, A and Vander Meer, RK and Pereira, R and Baldwin, R and Chinta, S},
title = {The effect of fire ant (Hymenoptera: Formicidae) venom on ecologically relevant bacteria.},
journal = {Journal of economic entomology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jee/toaf127},
pmid = {40577613},
issn = {1938-291X},
support = {58-6036-0-010//USDA-ARS Non-Assistance Cooperative Agreement/ ; },
abstract = {Fire ants, Solenopsis invicta Buren (Hymenoptera: Formicidae) and Solenopsis geminata (Fabricius), have evolved a variety of physiological and chemical defenses against microbe introduction and infection in their colonies. Compounds of most interest are the piperidine alkaloids found in S. invicta and S. geminata. Alkaloids are produced by the poison gland, stored in the venom sac, and released through the sting. These compounds have antibiotic, antifungal, antiparasitic, antiviral, and hemolytic properties. We hypothesize that fire ants alter the microbiome of their environment through the consistent use of these chemicals in and around their nests, affecting plant-microbe interactions and the rhizobia-legume nodulation process. In this study, S. invicta and S. geminata worker ant venom extracts were evaluated in disc-diffusion bioassays against the nitrogen-fixing soybean (Glycine max L.) (Fabales: Fabaceae) symbionts Bradyrhizobium japonicum (Kirchner) (Hyphomicrobiales: Nitrobacteraceae) and Bradyrhizobium elkanii Kuykendall and the microbial insecticide Bacillus thuringiensis Berliner (Bacillales: Bacillaceae). Venom extracts inhibited the growth of all tested microbes, with S. geminata extracts having a greater inhibitory effect than those from S. invicta.},
}
@article {pmid40577235,
year = {2025},
author = {Mazinani, S and Aghazadeh, M and Poortahmasebi, V and Arafi, V and Hasani, A},
title = {Cervical cancer pathology and vaginal and gut microbiota: conception of the association.},
journal = {Letters in applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/lambio/ovaf088},
pmid = {40577235},
issn = {1472-765X},
abstract = {The role of gut and vaginal microbiota has been examined as potential markers in the progression of cervical cancer and inspired heightened attention. We attempted to identify the current status, the influence of changing trends in the gut and vaginal microbiota, and their impact on cervical cancer. All publications were searched in online databases such as PubMed, Scopus, Medline, and Google Scholar using the keywords "cervical cancer," "vaginal microbiota," "gut microbiota," "dysbiosis," "cervical intraepithelial neoplasia," and "HPV." Growing evidence that gut microbiota dysbiosis is involved in many diseases has attracted many researchers. The vaginal microbiome is a micro-ecosystem complex that undergoes continuous fluctuations throughout a woman's life. Decrease in Lactobacilli spp. Levels can lead to an overgrowth of anaerobic bacteria, resulting in bacterial vaginosis that accounts for adverse health outcomes, including increased susceptibility to sexually transmitted infections, including human papillomavirus, and cervical intraepithelial neoplasia, leading to cervical cancer. Thus, dysbiosis, characterized by an imbalance of beneficial and harmful bacteria, can negatively affect health. Understanding the intricate interactions between the microbiota and cervical cancer can provide valuable insights into potential therapeutic strategies and the development of preventive measures.},
}
@article {pmid40577168,
year = {2025},
author = {Bergmann, KC and Zuberbier, T},
title = {Effect of the Multi-Strain Probiotic SYN-53 in the Management of Allergic Rhinoconjunctivitis.},
journal = {Allergy},
volume = {},
number = {},
pages = {},
doi = {10.1111/all.16634},
pmid = {40577168},
issn = {1398-9995},
support = {//Synformulas/ ; },
abstract = {Dysbiosis is increasingly linked to allergy development. This study evaluates the efficacy of the multi-strain probiotic SYN-53 in the management of allergic rhinoconjunctivitis (ARC). Eighty-four subjects with confirmed grass pollen allergy underwent up to three bi-weekly 3-day intake cycles with SYN-53 or placebo. After each cycle, subjects were exposed to grass pollen in an allergen exposure chamber. ARC symptoms were assessed using the Total Symptom Score (TSS) before and after each use of SYN-53. After one intake cycle, SYN-53 already showed a trend towards greater efficacy over placebo, which became significant after two cycles (ΔTSSMAX: -3.44 ± 0.42 vs. -1.87 ± 0.37; p = 0.0067), with 38% vs. 24% symptom relief. In subjects with moderate to severe symptoms, SYN-53 was already significantly superior after one single intake cycle and improved further after two cycles (ΔTSSMAX: -4.78 ± 0.51 vs. -2.43 ± 0.47; p = 0.0014), with 45% vs. 26% symptom relief. SYN-53 is effective in the management of ARC, highlighting the role of bacterial diversity and dosage in probiotic nutritional supplements.},
}
@article {pmid40576768,
year = {2025},
author = {Sima, S and Jeffries, T and Sial, A and Sharma, S and De La Lande, R and Chopra, N and Kohan, S and Khong, P and Diwan, A},
title = {Microbiome impacts surgical outcomes- comparison of gut microbiome dysbiosis in patients undergoing lumbar microdiscectomy: results from the MISO pilot study.},
journal = {European spine journal : official publication of the European Spine Society, the European Spinal Deformity Society, and the European Section of the Cervical Spine Research Society},
volume = {},
number = {},
pages = {},
pmid = {40576768},
issn = {1432-0932},
}
@article {pmid40576748,
year = {2025},
author = {Gupta, MK and Chauhan, K and Bhardwaj, S and Srivastava, R},
title = {Innovative Interventions: Postbiotics and Psychobiotics in Neurodegenerative Disease Treatment.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {40576748},
issn = {1867-1314},
abstract = {Neurodegenerative disorders, including Huntington's disease, Amyotrophic lateral sclerosis, Alzheimer's disease, and Parkinson's disease, create more challenges as the population gets older and there are no curative therapies available. Recent advances in gut microbiome research have spotlighted postbiotics and psychobiotics as innovative therapeutic strategies targeting the gut-brain axis to alleviate neurodegenerative symptoms and slow disease progression. Postbiotics, which are metabolites and cellular components released by probiotic bacteria, and psychobiotics, a class of probiotics with potential mental health benefits, offer novel approaches to neuroprotection. This chapter examines the ways in which postbiotics and psychobiotics modulate inflammation, oxidative stress, neurotrophic factors, and gut barrier integrity to provide neuroprotective effects. We review scientific research that highlights the efficacy of specific microbial strains and their metabolites in enhancing cognitive function and reducing neurodegeneration. In addition, we explore the consequences of diet and specific nutrition on strengthening the therapeutic results of these medications. The purpose of this chapter is to provide a detailed analysis of the existing data supporting the use of postbiotics and psychobiotics in both the prevention and management of neurological diseases. By integrating perspectives from microbiology, neurology, and clinical nutrition, we highlight the potential of these interventions to enhance patient outcomes and quality of life. In addition, we discuss the translational limitations and future research approaches required to successfully transition these microbiome-based treatments from the laboratory to clinical practice, emphasizing the importance of a holistic and personalized approach in combating neurodegenerative diseases.},
}
@article {pmid40576702,
year = {2025},
author = {Shtrozberg, S and Bazzichi, L and Sarzi-Puttini, P and Aloush, V and Ablin, JN},
title = {Is the gut microbiome of importance in fibromyalgia? A critical review of emerging evidence.},
journal = {Clinical and experimental rheumatology},
volume = {43},
number = {6},
pages = {990-998},
doi = {10.55563/clinexprheumatol/pmajsv},
pmid = {40576702},
issn = {0392-856X},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Fibromyalgia/microbiology/physiopathology/therapy/diagnosis ; Animals ; Probiotics/therapeutic use ; Nutritional Status ; Dysbiosis ; Prebiotics ; Fecal Microbiota Transplantation ; },
abstract = {Fibromyalgia (FM) is a multifaceted chronic pain syndrome, predominantly affecting women, and characterised by a constellation of symptoms including diffuse musculoskeletal pain, fatigue, cognitive impairment and poor sleep quality. Its complex pathophysiology likely involves genetic, environmental and psychosocial factors. Recent studies have raised the possibility that the gut microbiome may influence FM symptoms via the gut-brain axis, although this hypothesis remains unconfirmed. This review aims to explore potential associations between gut microbiome alterations, nutrition, and FM, with particular attention to the limitations of current evidence. While certain studies have reported differences in the gut microbiota composition of patients with FM, these findings are preliminary and often derive from small, heterogeneous cohorts. Likewise, faecal microbiota transplantation studies in animals and limited human trials suggest a possible link to pain sensitivity, but further validation is needed.Nutritional interventions, including prebiotics, probiotics and specific dietary strategies, have shown early promise in modulating gut microbiota and alleviating FM symptoms. Nutrients such as magnesium, selenium and omega-3 fatty acids, as well as antioxidant compounds, may influence pain and inflammation pathways, but definitive clinical recommendations are lacking. Given the emerging nature of this field, larger and better-controlled studies are required to clarify the role of the gut microbiome and nutrition in FM. A multidisciplinary management strategy, integrating nutritional approaches cautiously and based on individual profiles, may offer benefits, although no standard therapeutic guidelines currently exist.},
}
@article {pmid40576634,
year = {2025},
author = {Figueiredo, JC and Redwood, D and Li, L and Donato, E and Fort, D and Fox, EE and Grady, WM and Green, H and Harrison, TA and Haupt, C and Hsu, L and Hullar, MAJ and Huyghe, JR and Johnson, W and Koehne, AL and LaBrie, SD and Lakey, MA and Lin, M and Loroña, NC and Maresh, GA and Matrana, M and Mizrahi, JD and Nash, SH and Nguyen, NT and Paruch, JL and Phipps, AI and Qu, C and Randolph, TW and Romo, S and Thomas, CE and Thomas, S and Tiesinga, J and Whitlow, C and Yeung, CCS and Yin, H and Zibilich, CM and Li, CI and Thomas, TK and Peters, U},
title = {The Translational Research Program in Cancer Differences across Populations.},
journal = {Cancer epidemiology, biomarkers &amp; prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology},
volume = {},
number = {},
pages = {},
doi = {10.1158/1055-9965.EPI-24-1711},
pmid = {40576634},
issn = {1538-7755},
abstract = {BACKGROUND: Colorectal cancer (CRC) incidence and mortality vary substantially across populations. The Translational Research Program in Cancer Differences across Populations (TRPCDP) was established in 2020 to address differences in CRC incidence and mortality rates within the United States.<br><br>METHODS: TRPCDP centralized data acquisition and harmonization across three sites in the U.S. to create a well-annotated resource of CRC tumors across four populations: African American/Black, Alaska Native, Hispanic/Latino/a, and non-Hispanic White. Using a case-control framework, patients with lethal CRC were matched to two controls with non-lethal CRC. Formalin-fixed paraffin-embedded tumor and normal tissue were retrieved and sent for centralized pathology review, followed by DNA and RNA extraction and tissue microarray development. Multi-omics and spatial profiling are underway to evaluate the transcriptome, proteome, and microbiome. Patient demographic and clinical data were obtained by medical record review, patient self-report, or linkage to cancer registries. Additional health-related factors were assessed using geospatial linkage.<br><br>RESULTS: The virtual biorepository includes 7,181 patients [African American (n=1,345), Alaska Native (n=1,640), Hispanic (n=1,659), and non-Hispanic White (n=2,537)]. Tissue blocks (1,594 tumor, 728 normal colon) were selected for 938 patients. To date, DNA and RNA have been extracted (n=831) and tissue microarrays have been constructed (n=414). Transcriptomic, spatial tumor profiling (multiplex immunofluorescence, PhenoCycler, GeoMx) and microbiome data (16S rRNAseq, ddPCR) are available.<br><br>CONCLUSION: The TRPCDP has developed a clinically annotated biorepository for future molecular epidemiology studies.<br><br>IMPACT: TRPCDP is a unique program that supports collaborative research, community engagement, and pipeline development for the next generation of scientists.},
}
@article {pmid40576627,
year = {2025},
author = {Marlicz, W and Skonieczna-Żydecka, K and Łoniewski, I and Koulaouzidis, A},
title = {Rethinking iron therapy in IBD: integrating the microbiota perspective.},
journal = {Scandinavian journal of gastroenterology},
volume = {},
number = {},
pages = {1-3},
doi = {10.1080/00365521.2025.2525909},
pmid = {40576627},
issn = {1502-7708},
abstract = {Iron deficiency and anemia are common in patients with inflammatory bowel disease (IBD), requiring effective and well-tolerated iron replacement strategies. While oral iron is widely used, growing evidence suggests it can disrupt the gut microbiota by reducing beneficial commensal bacteria and promoting pro-inflammatory shifts in the intestinal environment. These changes may exacerbate mucosal inflammation and contribute to gastrointestinal side effects, often resulting in poor adherence. Intravenous iron, by bypassing the gastrointestinal tract, appears to have a less disruptive effect on the microbiota and may more reliably restore iron stores, particularly in patients with active disease or intolerance to oral formulations. Current expert recommendations support intravenous iron as the first-line option in such cases, though oral iron remains a practical choice for selected patients with mild anemia and inactive disease. Emerging research also raises concerns about the safety of oral iron in vulnerable populations, as it may promote dysbiosis and expansion of potentially pathogenic bacteria. In response, adjunctive strategies are being explored to support the microbiota and improve the tolerability and efficacy of oral iron. Incorporating microbiota-related considerations into treatment decisions may enhance outcomes and reduce side effects. Future clinical guidelines should reflect the evolving understanding of the gut microbiome's role in iron metabolism and inflammation, promoting more personalized, microbiota-conscious approaches to iron therapy in IBD.},
}
@article {pmid40576466,
year = {2025},
author = {Bacińska, Z and Strub, DJ and Balcerzak, L},
title = {Antibacterial potential of essential oils against oral pathogenic bacteria: A literature and clinical review.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxaf161},
pmid = {40576466},
issn = {1365-2672},
abstract = {The human oral microbiome is a complex ecosystem, comprising diverse microbial species in symbiotic relationships. Environmental factors such as diet, immune response, and inflammation can disrupt the balance of the oral microbiome, leading to increased activity and proliferation of pathogenic species associated with oral diseases. In response to global dental problems, there is a burgeoning interest in exploiting the antibacterial properties of essential oils (EOs) for clinical applications, being promising alternative to traditional antiseptics. This review synthesizes literature on the Minimum Inhibitory Concentration (MIC) of plant-derived EOs and their effectiveness against key oral pathogenic bacteria, which belong to the so-called 'red', 'orange', 'purple', 'yellow', and 'green' complexes, and includes newly discovered oral bacteria. Furthermore, it examines clinical investigations into oral hygiene products infused with EOs, evaluating their antiplaque, antigingivitis properties, and effectiveness in reducing tartar formation and gingival bleeding. Overall, this review highlights the high antibacterial efficacy of EOs against oral bacteria and their potential therapeutic abilities. It is expected that they will be used as a potential alternative for chemical preservatives in oral care products in the future. Based on the searched clinical studies, EO-based oral care products seem to be effective in the treatment of dental problems, such as e.g. dental plaque, gingivitis, and caries.},
}
@article {pmid40576342,
year = {2025},
author = {Napier, EG and Cinco, IR and Wagner, SB and Stuart, EV and Qiao, Q and Taylor, J and Stevenson, B and Messaoudi, I},
title = {Borreliosis and doxycycline treatment disrupt gut microbiota and immune responses in nonhuman primates.},
journal = {mBio},
volume = {},
number = {},
pages = {e0143725},
doi = {10.1128/mbio.01437-25},
pmid = {40576342},
issn = {2150-7511},
abstract = {Borrelia burgdorferi (Bb) is the spirochete that causes Lyme disease (LD). Transmission to humans occurs via bites of infected Ixodes spp. ticks. Doxycycline is often used to treat LD patients, which is sometimes delayed due to current diagnostic challenges. Recently, several lines of evidence show dysbiosis of the gut microbiome in LD patients, which may be a host factor contributing to pathogenesis and symptomology but is still an understudied area in the field. To address this knowledge gap, we longitudinally compared the immune response and gut microbial composition of Japanese macaques after intradermal infection with Bb strain 297 with or without doxycycline treatment. Immunological and microbial changes were monitored longitudinally using enzyme-linked immunosorbent assay, flow cytometry, single-cell genomics, and 16S amplicon sequencing assays. All Bb-inoculated animals seroconverted to produce Bb-specific antibodies. Borrelial DNA was undetected by real-time quantitative PCR in the skin, blood, and cerebrospinal fluid. Levels of CXCL13, a B cell chemoattractant, increased following infection but reached a nadir after treatment. The frequency of circulating immune cells remained constant over the course of the study, but gene expression analysis showed downregulation of antimicrobial genes in monocytes, dendritic cells, and B cells until late in infection, regardless of treatment. Infection and antibiotic treatment led to a loss of gut commensals important for maintaining gut integrity. Finally, untreated infected animals showed mononuclear myocarditis along with sporadic detection of borrelial DNA. Data from this study suggest aberrant B cell activity, myocarditis, and loss of important commensal microbes as factors contributing to symptoms of untreated Lyme disease.IMPORTANCELyme disease (LD) is caused by Borrelia burgdorferi (Bb) transmitted via tick bite. The incidence of LD is expanding in North America and Southeast Asia. LD patients are frequently misdiagnosed or receive delayed treatment due to the lack of sensitive diagnostic strategies. The pathophysiology of LD remains poorly understood because of challenges with clear infection timelines in clinical studies. Here, we utilize Japanese macaques to provide an in-depth longitudinal investigation into the host immunological and gut microbial changes in response to Bb infection. This work highlights CXCL13 as a potential Bb diagnostic marker, as well as host factors such as aberrant B cell activity, mononuclear myocarditis, and gut dysbiosis as potential therapeutic targets.},
}
@article {pmid40576334,
year = {2025},
author = {Lee, EM and Srinivasan, S and Purvine, SO and Fiedler, TL and Leiser, OP and Proll, SC and Minot, SS and Djukovic, D and Raftery, D and Johnston, C and Fredricks, DN and Deatherage Kaiser, BL},
title = {Syntrophic bacterial and host-microbe interactions in bacterial vaginosis.},
journal = {The ISME journal},
volume = {19},
number = {1},
pages = {},
pmid = {40576334},
issn = {1751-7370},
support = {S10OD021562/RI/ORIP NIH HHS/United States ; GM103493/GM/NIGMS NIH HHS/United States ; U19 AI113173/NH/NIH HHS/United States ; R01AI061628/NH/NIH HHS/United States ; },
mesh = {Female ; *Vaginosis, Bacterial/microbiology ; Humans ; Vagina/microbiology ; *Host Microbial Interactions ; *Bacteria/metabolism/classification/genetics/isolation &amp; purification ; Formates/metabolism ; Adult ; Putrescine/metabolism ; Proteomics ; Microbiota ; Bacterial Proteins/metabolism ; },
abstract = {Bacterial vaginosis (BV) is a common, polymicrobial condition of the vaginal microbiota that is associated with symptoms such as malodor and excessive discharge, along with increased risk of various adverse sequelae. Host-bacteria and bacteria-bacteria interactions are thought to contribute to the condition, but many of these functions have yet to be elucidated. Using untargeted metaproteomics, we identified 1068 host and 1418 bacterial proteins in a set of cervicovaginal lavage samples collected from 20 participants with BV and 9 who were negative for the condition. We identified Dialister micraerophilus as a major producer of malodorous polyamines and identified a syntrophic interaction between this organism and Fannyhessea vaginae that leads to increased production of putrescine, a metabolite characteristic of BV. Although formate synthesis has not previously been noted in BV, we discovered diverse bacteria associated with the condition express pyruvate formate-lyase enzymes in vivo and confirm these organisms secrete formic acid in vitro. Sodium hypophosphite efficiently inhibited this function in multiple taxa. We also found that the fastidious organism Coriobacteriales bacterium DNF00809 can metabolize formic acid secreted by Gardnerella vaginalis, representing another syntrophic interaction. We noted an increased abundance of the host epithelial repair protein transglutaminase 3 in the metaproteomic data, which we confirmed by enzyme-linked immunosorbent assay. Other proteins identified in our samples implicate Finegoldia magna and Parvimonas micra in the production of malodorous trimethylamine. Some bacterial proteins identified represent novel targets for future therapeutics to disrupt BV communities and promote vaginal colonization by commensal lactobacilli.},
}
@article {pmid40576243,
year = {2025},
author = {Omeir, K and Ancira, J and Gabrilska, R and Tipton, C and Miller, C and Noe, A and Subasinghe, K and Rowe, M and Phillips, N and Wolcott, J and Philips, CD},
title = {Heritable Tissue-Specific Gene Expression Associates With Chronic Wound Microbial Species.},
journal = {Wound repair and regeneration : official publication of the Wound Healing Society [and] the European Tissue Repair Society},
volume = {33},
number = {4},
pages = {e70055},
pmid = {40576243},
issn = {1524-475X},
support = {R15GM141973-01/NH/NIH HHS/United States ; },
mesh = {Humans ; *Microbiota/genetics ; Female ; Male ; *Wound Healing/genetics ; Middle Aged ; Chronic Disease ; *Wound Infection/microbiology/genetics ; *Wounds and Injuries/microbiology/genetics ; Aged ; Gene Expression Profiling ; Adult ; Transcriptome ; Genome-Wide Association Study ; },
abstract = {The reasons for interpatient variability in chronic wound microbiome composition are thought to be complex but are poorly known. To investigate how patients' genetically regulated tissue expression may influence chronic wound bacterial composition, we performed a microbiome-transcriptome-wide association study. This approach involved estimating for 509 patients their tissue-specific gene expression from DNA genotypes, followed by associating gene expression to the relative abundances of species detected in their wounds as provided on clinical reports to the physician. Comparisons to artery, blood, fibroblast, skeletal muscle, skin, subcutaneous fat, and nerve tissue resulted in 251 transcriptional differences at 109 genes significantly explaining abundances of 39 different species. Overall, these species were detected in ~63% of wounds. A similar number of associations per tissue was observed (range 31-39), and many genes were associated at multiple tissues in distinct ways. The cumulative variance across loci for species relative abundance explained ranged from ~5%-36%, depending on species. Although the same gene was almost never associated with more than one species, ~14% of enriched pathways were independently enriched for multiple species, which may reflect the diversity of ways microbes interact with partially overlapping attributes of the wound bed. Commonly enriched pathways pertained to collagen formation and modification, cell signalling, cytoskeletal dynamics, interactions with extracellular matrix, transmembrane proteins, amongst others. This work expands the new perspective that individual genetics may partially determine microbial colonisation and infection.},
}
@article {pmid40575713,
year = {2025},
author = {Masri, MTA and Al-Deeb, MA},
title = {A systematic review of the microbiome of Hyalomma Koch, 1844 ticks using next-generation sequencing of the 16S ribosomal RNA gene.},
journal = {Veterinary world},
volume = {18},
number = {5},
pages = {1090-1100},
pmid = {40575713},
issn = {0972-8988},
abstract = {BACKGROUND AND AIM: Ticks are critical vectors of pathogens affecting humans and livestock globally. The microbiome of ticks, comprising diverse bacterial communities, plays a crucial role in tick biology and vector competence. Hyalomma ticks are prominent in the Middle East and North Africa (MENA) region and are known carriers of significant pathogens. This study aimed to systematically evaluate existing literature regarding the microbiome composition of Hyalomma ticks in the MENA region, identify predominant bacterial genera, and highlight knowledge gaps.<br><br>MATERIALS AND METHODS: A systematic literature search was conducted using four databases: ScienceDirect, PubMed, Google Scholar, and Scopus. The search covered studies published between 2014 and 2024 employing 16S ribosomal RNA gene sequencing to analyze microbiomes of Hyalomma ticks within the MENA region. Studies not fulfilling these criteria were excluded through independent assessment by two authors.<br><br>RESULTS: Out of 1,220 screened articles, seven studies met inclusion criteria, involving five Hyalomma species: Hyalomma dromedarii, Hyalomma anatolicum, Hyalomma excavatum, Hyalomma marginatum, and Hyalomma scupense. Most studies (57.14%) focused on H. dromedarii, primarily collected from camels. The geographical distribution of studies included the United Arab Emirates (42.86%), Saudi Arabia (28.57%), Iran (14.29%), and Tunisia (14.29%). Common bacterial genera identified across multiple studies included Acinetobacter, Bacillus, Flavobacterium, Francisella, Rickettsia, Staphylococcus, Pseudomonas, and Corynebacterium. However, substantial gaps were noted, particularly concerning variations related to tick lifecycle stages, host interactions, temporal dynamics, and extensive geographic coverage within the MENA region.<br><br>CONCLUSION: This systematic review underscores the presence of key bacterial genera within Hyalomma ticks across the MENA region, revealing their potential roles in tick biology and pathogen transmission. Major research gaps identified include limited geographical scope, insufficient exploration of microbiome variation across tick life stages, host-specific interactions, and the environmental factors influencing microbial communities. Addressing these gaps through comprehensive, longitudinal, and multi-regional studies is imperative for improving public health strategies and developing targeted tick-control methods.},
}
@article {pmid40490139,
year = {2025},
author = {Alvarez, B and Canil, OF and Low, KE and Hettle, AG and Abbott, DW and Boraston, AB},
title = {Analysis of chondroitin degradation by components of a Bacteroides caccae polysaccharide utilization locus.},
journal = {The Journal of biological chemistry},
volume = {301},
number = {7},
pages = {110354},
doi = {10.1016/j.jbc.2025.110354},
pmid = {40490139},
issn = {1083-351X},
abstract = {The human gut microbiota (HGM) possesses an enormously diverse capacity to metabolize both host and dietary glycans. Glycosaminoglycans (GAG) are complex polysaccharides that may be in the diet (e.g., from animal products) or may be presented by host tissues. These polysaccharides are known to be prioritized as a nutrient source by some members of the HGM. While significant advances in understanding how GAGs are metabolized by the HGM have been made, the varied architectures of the numerous polysaccharide utilization loci (PULs) targeting varied polysaccharides suggest that all the mechanisms of GAG degradation may not have been uncovered. Here we show that components of a (PUL) from Bacteroides caccae have activities consistent with comprising a unique pathway for depolymerization of chondroitin sulfate, a common GAG. After prior desulfation by an endo-sulfatase, BcSulf, to produce unsulfated chondroitin from chondroitin sulfate, the depolymerization pathway begins with the activity of a polysaccharide lyase from family 35, BcPL35. BcPL35 activity is coupled with BcGH88, an exo-β-uronyl hydrolase, and presumably BcGH109, a confirmed α/β-N-acetylgalactosaminidase. The most unique feature of the pathway is a β-D-glucuronate dehydratase, BcGDH, which we show through structural and functional analyses primes saturated non-reducing end β-D-glucuronate residues for hydrolysis by BcGH88. BcGDH is a member of a large family previously classified as glycoside hydrolase family 154. The potential reclassification of GH154 enzymes as uronate sugar dehydratases not only improves our understanding of chondroitin metabolism by B. caccae but will be broadly applicable to predicting the function of other pathways relevant to uronate sugar metabolism.},
}
@article {pmid40575647,
year = {2025},
author = {Tüsüz Önata, E and Özdemir, &#xd6;},
title = {Microbiome, dysbiosis and use of probiotics in various diseases.},
journal = {World journal of virology},
volume = {14},
number = {2},
pages = {99574},
pmid = {40575647},
issn = {2220-3249},
abstract = {The community of microorganisms that colonize certain areas of the human body is called microbiota. Microorganisms such as bacteria, fungi and viruses make up the microbiota. The sum of the genomes of these microorganisms and microorganisms refers to the microbiome. It has been shown that microbiota has important effects such as protecting the organ from pathogens, contributing to metabolic functions (such as vitamin synthesis, carbohydrate digestion) and providing immunoregulation. Dysbiosis refers to compositional and functional changes in the microbiota. At the beginning of the 21[st] century, numerous studies have investigated the human microbiota and its imbalance in relation to various diseases and found that dysbiosis is associated with many diseases. The aim of this mini-review article is to provide brief information about dysbiosis and its care and to raise awareness.},
}
@article {pmid40575486,
year = {2025},
author = {Nieves, L and Roach, A and Hunter, J and Smeh, S and Islas, A and Islas, A and Blattman, J and Di Palma, M},
title = {Harnessing the microbiome to improve clinical outcomes for cancer, transplant, and immunocompromised patients in the intensive care unit (ICU).},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1577108},
pmid = {40575486},
issn = {2235-2988},
mesh = {Humans ; *Intensive Care Units ; *Neoplasms/microbiology/therapy/immunology ; *Immunocompromised Host ; *Microbiota ; Dysbiosis/microbiology ; *Transplant Recipients ; Treatment Outcome ; },
abstract = {In recent decades, there has been a growing emphasis on understanding how the architecture of the human microbiome can impact typical biological processes and patient clinical outcomes. In fact, microbiome modifications and modulations have not only been associated with impacts on general health and well-being but have also been shown to yield differences in patient responsiveness to vaccines, medications, and chemotherapeutic regimens. Much of this influence likely stems from how changes in the microbiome result in differences in microbial communities and the subsequent release of microbial-derived metabolites that can alter typical immunological processes. Understanding how microbial composition can impact patient responsiveness can be particularly important in the intensive care unit (ICU), where the efficacy of medications and treatments can result in negative patient outcomes if unsuccessful. Clinical scientists have further developed the concept of the pathobiome, a disease-promoting microbiome whose development can be associated with dysbiosis. Understanding how the microbiome and its associated components can impact patient responsiveness, especially in the ICU, must be further researched and understood. Here, we analyze what causes variances in the microbiome and pathobiome in significant immunocompromised populations, including cancer patients and transplant recipients, and how variances in the microbiome can impact patient outcomes in the ICU. Further, we detail potential future applications of how our understanding of what impacts the human microbiome during the treatment of these populations may be exploited to improve patient prognosis.},
}
@article {pmid40575430,
year = {2025},
author = {Brar, AS and Vemula, SL and Yanamaladoddi, V and Sodhi, S and Hatwal, J and Sohal, A and Batta, A},
title = {Impact of gut microbiome on atrial fibrillation: Mechanistic insights and future directions in individualized medicine.},
journal = {World journal of cardiology},
volume = {17},
number = {6},
pages = {107386},
pmid = {40575430},
issn = {1949-8462},
abstract = {Atrial fibrillation (AF) is a growing global health burden, with a prevalence of over 52.55 million cases. Rising disability-adjusted life-years, increasing age, and disparities in care have contributed to the worsening severity and mortality of AF. Modifiable risk factors, such as hypertension, obesity, and diabetes mellitus, are associated with alterations in gut microbiota, making the gut-heart axis a potential therapeutic target. Gut dysbiosis influences AF pathogenesis through inflammation, metabolic disruption, and autonomic dysfunction. Key mechanisms include gut barrier dysfunction, short-chain fatty acid (SCFA) depletion, lipopolysaccharides (LPS)-induced inflammation, and ferroptosis-mediated atrial remodeling. Trimethylamine N-oxide, bile acids, and tryptophan metabolites contribute to arrhythmogenic remodeling. Emerging evidence suggests that dietary interventions, including prebiotics and probiotics, as well as gut surveillance, may help mitigate AF progression. Clinical implications of gut modulation in AF include personalized dietary strategies, microbiome assessment through metagenomic sequencing, and targeted interventions such as SCFA-based therapies and ferroptosis inhibition. Metabolite surveillance, including LPS and indoxyl sulfate monitoring, may influence the effectiveness of anticoagulant and antiarrhythmic therapy. Despite growing mechanistic evidence linking gut dysbiosis to AF, clinical applications remain unexplored. This review summarizes the current understanding of the gut microbiome's role in AF.},
}
@article {pmid40575364,
year = {2025},
author = {Bangolo, A and Amoozgar, B and Habibi, M and Simms, E and Nagesh, VK and Wadhwani, S and Wadhwani, N and Auda, A and Elias, D and Mansour, C and Abbott, R and Jebara, N and Zhang, L and Gill, S and Ahmed, K and Ip, A and Goy, A and Cho, C},
title = {Exploring the gut microbiome's influence on cancer-associated anemia: Mechanisms, clinical challenges, and innovative therapies.},
journal = {World journal of gastrointestinal pharmacology and therapeutics},
volume = {16},
number = {2},
pages = {105375},
pmid = {40575364},
issn = {2150-5349},
abstract = {BACKGROUND: Anemia is a prevalent and challenging complication in patients with hematologic and solid malignancies, which stems from the direct effects of malignancy, treatment-induced toxicities, and systemic inflammation. It affects patients' survival, functional status, and quality of life profoundly. Recent literature has highlighted the emerging role of the gut microbiome in the pathogenesis of cancer-associated anemia. The gut microbiota, through its intricate interplay with iron metabolism, inflammatory pathways, and immune modulation, may either exacerbate or ameliorate anemia depending on its composition, and functional integrity. Dysbiosis, characterized by disruption in the gut microbial ecosystem, is very common in cancer patients. This microbial imbalance is implicated in anemia causation through diminished iron absorption, persistent low-grade inflammation, and suppression of erythropoiesis.<br><br>AIM: To consolidate current evidence regarding the interplay between gut microbiome and anemia in the setting of malignancies. It aims to provide a detailed exploration of the mechanistic links between dysbiosis and anemia, identifies unique challenges associated with various cancer types, and evaluates the efficacy of microbiome-focused therapies. Through this integrative approach, the review seeks to establish a foundation for innovative clinical strategies aimed at mitigating anemia and improving patient outcomes in oncology.<br><br>METHODS: A literature search was performed using multiple databases, including Google Scholar, PubMed, Scopus, and Web of Science, using a combination of keywords and Boolean operators to refine results. Keywords included "cancer-associated anemia", "gut microbiome", "intestinal microbiota", "iron metabolism", "gut dysbiosis", "short-chain fatty acids", "hematopoiesis", "probiotics", "prebiotics", and "fecal microbiota transplantation". Articles published in English between 2000 and December 2024 were included, with a focus on contemporary and relevant findings.<br><br>RESULTS: Therapeutic strategies aimed at restoration of gut microbial homeostasis, such as probiotics, prebiotics, dietary interventions, and fecal microbiota transplantation (FMT), can inhibit anemia-causing pathways by enhancing microbial diversity, suppressing detrimental flora, reducing systemic inflammation and optimizing nutrient absorption.<br><br>CONCLUSION: Gut dysbiosis causes anemia and impairs response to chemotherapy in cancer patients. Microbiome-centered interventions, such as probiotics, prebiotics, dietary modifications, and FMT, have shown efficacy in restoring microbial balance, reducing inflammation, and enhancing nutrient bioavailability. Emerging approaches, including engineered probiotics and bacteriophage therapies, are promising precision-based, customizable solutions for various microbiome compositions and imbalances. Future research should focus on integrating microbiome-targeted strategies with established anemia therapies.},
}
@article {pmid40575334,
year = {2025},
author = {Bhagavathula, AS and Al Qady, AM and Aldhaleei, WA},
title = {Diagnostic accuracy and quality of artificial intelligence models in irritable bowel syndrome: A systematic review.},
journal = {World journal of gastroenterology},
volume = {31},
number = {23},
pages = {106836},
pmid = {40575334},
issn = {2219-2840},
mesh = {Humans ; *Irritable Bowel Syndrome/diagnosis/microbiology ; *Artificial Intelligence/standards ; Biomarkers/analysis ; Sensitivity and Specificity ; Gastrointestinal Microbiome ; Feces/microbiology ; Observational Studies as Topic ; },
abstract = {BACKGROUND: Irritable bowel syndrome (IBS) affects approximately 9%-12% of the global population, presenting substantial diagnostic challenges due to symptom subjectivity and lack of definitive biomarkers.<br><br>AIM: To systematically examine the diagnostic accuracy of artificial intelligence (AI) models applied to various biomarkers in IBS diagnosis.<br><br>METHODS: A comprehensive search of six databases identified 18053 articles published up to May 31, 2024. Following screening and eligibility criteria, six observational studies involving 1366 participants from the United Kingdom, China, and Japan were included. Risk of bias and reporting quality were assessed using quality assessment of diagnostic accuracy studies-2, prediction model risk of bias assessment tool-AI, and transparent reporting of a multivariable prediction model for individual prognosis or diagnosis-AI tools. Key metrics included sensitivity, specificity, accuracy, and area under the curve (AUC).<br><br>RESULTS: The included studies applied AI models such as random forests, support vector machines, and neural networks to biomarkers like fecal microbiome composition, gas chromatography data, neuroimaging features, and protease activity. Diagnostic accuracy ranged from 54% to 98% (AUC: 0.61-0.99). Models using fecal microbiome data achieved the highest performance, with one study reporting 98% sensitivity and specificity (AUC = 0.99). While most studies demonstrated high methodological quality, significant variability in datasets, biomarkers, and validation methods limited meta-analysis feasibility and generalizability.<br><br>CONCLUSION: AI models show potential to improve IBS diagnostic accuracy by integrating complex biomarkers which will aid the development of algorithms to direct treatment strategies. However, methodological inconsistencies and limited population diversity underscore the need for standardized protocols and external validation to ensure clinical applicability.},
}
@article {pmid40575111,
year = {2025},
author = {Cheng, P and Jia, R and Jin, B and Zhou, F and Xu, H and Wang, B},
title = {IBS May Have a Causal Effect on Increased Tryptophan Metabolites Levels: Insights from a Bidirectional Two-Sample Mendelian Randomization Study.},
journal = {International journal of tryptophan research : IJTR},
volume = {18},
number = {},
pages = {11786469251327399},
pmid = {40575111},
issn = {1178-6469},
abstract = {BACKGROUND: Irritable Bowel Syndrome (IBS) is a chronic functional gastrointestinal disorder characterized by abdominal pain and altered bowel habits. Tryptophan, an essential amino acid derived from dietary proteins, can be metabolized into various compounds by the gut microbiome. Emerging evidence suggests that tryptophan metabolites play a role in functional gastrointestinal disorders. However, the causal relationship between tryptophan metabolites and IBS remains to be fully elucidated.<br><br>OBJECTIVE: This study aims to evaluate the potential causal relationship between tryptophan metabolites and IBS using Mendelian randomization (MR).<br><br>METHODS: Instrumental variables (IVs) were selected from summary data of genome-wide association studies (GWAS) for tryptophan and IBS. SNPs potentially influencing MR results were excluded through outlier detection using MR-PRESSO. Bidirectional two-sample MR analyses were conducted using the inverse-variance weighted (IVW), MR-Egger regression, weighted median, weighted mode, and simple mode methods. The MR-Egger intercept test was employed to assess pleiotropy and heterogeneity among IVs, with visualization of the MR results through scatter plots, funnel plots, and forest plots.<br><br>RESULTS: Genetically predicted tryptophan metabolites were not associated with the risk of IBS. In the reverse direction, genetically predicted IBS was associated with increased levels of tryptophan, serotonin, and kynurenine in the IVW analysis. Sensitivity and replication analyses confirmed these findings.<br><br>CONCLUSION: The findings of this Mendelian randomization study suggest that IBS may lead to elevated levels of tryptophan, serotonin, and kynurenine. These results have important implications for understanding the interplay between tryptophan metabolism and IBS in clinical settings. Further research is warranted to explore the underlying mechanisms.},
}
@article {pmid40575011,
year = {2025},
author = {Pilmer, L and Woolley, L and Lymbery, A and Salini, M and Dam, C and Foysal, MJ and Partridge, G},
title = {Sustainable Fishmeal Alternatives: Impact of Partially Defatted Black Soldier Fly (Hermetia illucens) Meal on Growth and Health of Yellowtail Kingfish (Seriola lalandi).},
journal = {Aquaculture nutrition},
volume = {2025},
number = {},
pages = {1804215},
pmid = {40575011},
issn = {1365-2095},
abstract = {Reducing fishmeal (FM) in aquaculture diets is essential for improving sustainability and reducing reliance on marine resources. Black soldier fly (BSF; Hermetia illucens) larvae meal is a promising alternative protein source. This study evaluated the effects of replacing FM with BSF meal on the growth and health of juvenile yellowtail kingfish (YTK) (Seriola lalandi, initial weight ~22 g). Fish were reared in 24 tanks (three replicates per treatment) and fed for 33 days under controlled conditions. Eight diets were tested: a control (40% FM) and seven diets with BSF meal replacing FM at 25%, 50%, or 75%, with or without garlic and tuna hydrolysate additives. Fish fed 25% and 50% BSF diets showed growth and feed conversion comparable to the control, while 75% BSF significantly reduced growth due to decreased feed intake. Additives did not improve feed intake. Histological analysis indicated good gut health and nutrient absorption. Serum cholesterol decreased with BSF inclusion, and urea levels varied. No significant changes in gene expression were observed in the gut, liver, or brain. Microbiome analysis showed increased diversity and compositional shifts at higher BSF levels. These results support the use of BSF meal as a sustainable FM replacement at moderate inclusion levels, with further research needed to address palatability at higher levels.},
}
@article {pmid40574876,
year = {2025},
author = {Odenwald, MA and Ramaswamy, R and Lin, H and Lehmann, C and Moran, A and Mullowney, MW and Sidebottom, AM and Hernandez, A and McMillin, M and Rose, A and Moran, D and Little, J and Sulakhe, D and D'Souza, M and Woodson, C and Tanveer, T and de Porto, A and Dylla, N and Sundararajan, A and Burgo, V and Cantoral, J and Jadczak, C and Adler, E and Aronsohn, A and Pamer, EG and Rinella, ME},
title = {Fecal Butyrate and Deoxycholic Acid Concentrations Correlate With Mortality in Patients With Liver Disease.},
journal = {Gastro hep advances},
volume = {4},
number = {8},
pages = {100695},
pmid = {40574876},
issn = {2772-5723},
abstract = {BACKGROUND AND AIMS: The intestinal microbiome produces metabolites, including short chain fatty acids (SCFAs) and secondary bile acids (BAs), that impact host physiology. Loss of intestinal microbiome diversity is associated with cirrhosis progression, but the impact of microbiome-associated metabolites on liver disease remains largely undefined. We aimed to correlate fecal metabolite concentrations with the severity and progression of liver disease.<br><br>METHODS: In this cross-sectional study, fecal samples from patients hospitalized with liver disease were analyzed by shotgun metagenomic sequencing to determine microbiome compositions and targeted mass spectrometry to quantify SCFAs and BAs. Random survival forest and logistic regression models identified clinical, metagenomic, and metabolomic features associated with rehospitalization and survival.<br><br>RESULTS: This cross-sectional study included 24 chronic liver disease, 18 compensated cirrhosis, 225 decompensated cirrhosis and 40 acute-on-chronic liver failure patients and 27 control fecal donors. Microbiome sequencing and metabolite profiling correlated microbial diversity and SCFA and BA concentrations with liver disease severity. Butyrate and deoxycholic acid (DCA) were more important features than individual microbial species in random survival forest models predicting 30-day transplant-free survival, and low butyrate and DCA were associated with 30-day mortality (P < .0001). After controlling for model for end stage liver disease (MELD)-sodium score, disease stage, age and gender, low fecal concentrations of butyrate and DCA remained significant risk factors for death (Cox 1.38, P = .027). Bacterial species associated with butyrate and DCA concentrations included Bifidobacterium spp. and F. prausnitzii.<br><br>CONCLUSION: Mass spectrometry rapidly identifies patients with low fecal butyrate and DCA concentrations who are at increased risk of 30-day mortality. These findings set the stage for clinical trials of microbiome reconstitution with butyrate and DCA-producing bacterial species.},
}
@article {pmid40574855,
year = {2025},
author = {Mo, Y and He, X and Shi, P and Ning, Y and Zhou, M and Cui, H and Zhang, T},
title = {Hematopoietic effects of Fufang E'jiao Jiang revealed by microbiome, metabolome and transcriptome analyses: a multi-omics strategy.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1561477},
pmid = {40574855},
issn = {1664-3224},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Metabolome/drug effects ; Mice ; *Anemia/chemically induced/drug therapy/metabolism/microbiology ; *Transcriptome/drug effects ; Gene Expression Profiling ; Metabolomics/methods ; Male ; *Hematopoiesis/drug effects ; Cyclophosphamide ; Feces/microbiology ; Multiomics ; },
abstract = {INTRODUCTION: Fufang E'jiao Jiang has been extensively utilized to replenish qi and nourish blood as the homology of medicine and food.<br><br>METHODS: We analyzed the effects of FEJ on cyclophosphamide and acetylphenylhydrazine-induced anemia mice through gut microbiome analysis, fecal metabolomics, and transcriptome sequencing.<br><br>RESULTS: FEJ markedly alleviated the anemia symptoms in the mice. FEJ markedly alleviated the anemia symptoms caused by cyclophosphamide and acetylphenylhydrazine induction. FEJ improved the gut microbiome imbalance by inhibiting the proliferation of harmful bacteria Turicibacter, Akkermansia and Tuzzerella. Fecal metabolomic data showed that FEJ regulated metabolic disorders in anemia mice and was probably associated with L-leucine, L-proline, glycine, phenylalanine, propanoic acid and butanoic acid. Transcriptome analysis indicated the amelioration of anemia was predominantly associated with the hematopoietic cell lineage, osteoclast formation and B cell receptor signaling pathway. According to Spearman's correlation analysis, there was a strong link between gut microbiota and hematopoietic index, metabolites and genes.<br><br>DISCUSSION: Our study supports the application of FEJ in anemia treatment.},
}
@article {pmid40574831,
year = {2025},
author = {Guo, X and Wang, K and Liu, Q and Baran, N and Ma, W},
title = {The gut-immune axis in primary immune thrombocytopenia (ITP): a paradigm shifts in treatment approaches.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1595977},
pmid = {40574831},
issn = {1664-3224},
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; *Purpura, Thrombocytopenic, Idiopathic/therapy/immunology/microbiology ; Dysbiosis/immunology ; Fecal Microbiota Transplantation ; Animals ; Blood Platelets/immunology ; Probiotics/therapeutic use ; },
abstract = {Primary immune thrombocytopenia (ITP) is an autoimmune disorder characterized by platelet destruction and impaired production, leading to bleeding risk. While immunosuppressive therapies are standard, many patients experience relapses or refractory disease, highlighting the need for novel approaches. Emerging evidence suggests the gut microbiota plays a role in immune regulation, yet its impact on ITP remains unclear. Dysbiosis has been linked to immune dysfunction in other autoimmune diseases, but whether it drives or results from immune dysregulation in ITP is debated. This review explores the gut-immune axis in ITP, focusing on microbiota-driven immune modulation, cytokine signaling, and platelet homeostasis. We assess microbiota-targeted interventions, including fecal microbiota transplantation (FMT), probiotics, and dietary modifications, while addressing key controversies and knowledge gaps. Advances in microbiome sequencing and artificial intelligence may facilitate personalized interventions. Standardizing microbiota-based diagnostics and validating their efficacy in clinical trials are crucial for their integration into ITP management. Bridging these gaps may lead to microbiota-driven strategies that enhance immune regulation and improve patient outcomes.},
}
@article {pmid40574696,
year = {2025},
author = {Biada, I and Tiezzi, F and Ibáñez-Escriche, N and Luz García, M and Argente, MJ and Santacreu, MA},
title = {Differential intestinal microbiome response to heat stress in two rabbit maternal lines: A comparative analysis using Random Forest, BayesC, and PLS-DA.},
journal = {Journal of animal science},
volume = {},
number = {},
pages = {},
doi = {10.1093/jas/skaf206},
pmid = {40574696},
issn = {1525-3163},
abstract = {Heat stress affects livestock productivity and health, particularly in rabbits, due to their physiological vulnerabilities. This study explores the relationship between environmental conditions, genetic lines backgrounds, and soft fecal microbiota. A 2×2 factorial design was used, involving two maternal rabbit lines: A (standard longevity line) and LP (high longevity line), exposed to heat stress and thermal comfort. Samples were analyzed with multiple models to assess the impact of heat stress on microbiota by comparing microbial diversity and evaluating the classification performance of Random Forest, Partial Least Squares Discriminant Analysis (PLS-DA), and Bayesian Regression (BayesC). Heat stress influenced microbial diversity in both lines, increasing alpha diversity and driving significant beta-diversity shifts (2.3% variance, p < 0.001). This could be due to intestinal barrier disruption, which facilitate pathogen proliferation. The high longevity line LP exhibited higher richness under thermal comfort, whereas heat stress equalized these differences between lines, possibly due to increased pathogen proliferation in the low longevity line A. These differences in response to heat stress may be influenced by the crosstalk between microbiota and host genetics, shaping distinct adaptive mechanisms in each line. Prediction accuracy and key selected variables distinguishing between lines A and LP varied across thermal conditions, with the Area Under the Curve (AUC) exceeding 0.92 under heat stress and 0.87 in thermal comfort. This reflects different microbiome regulations between the two lines under heat stress. Potential stress-associated taxa such as Erysipelatoclostridium and Monoglobus were more abundant in the low longevity line A. These results highlight LP's higher longevity and expected resilience, while line A's susceptibility is reflected in a higher abundance of heat stress-associated taxa in the latter. This underscores soft fecal microbiota as a potential biomarker for heat stress resilience and emphasizes the role of host-microbiota interactions in mediating genetic-environmental responses. Additionally, this study highlights the value of combining modeling approaches, which enhance accuracy and reveal key taxa driving heat stress responses. Among the models tested, PLS-DA achieved the highest accuracy, while Random Forest identified a smaller yet biologically relevant subset of taxa, providing valuable phylogenetic and taxonomic insights.},
}
@article {pmid40574683,
year = {2025},
author = {},
title = {Correction to: Human microbiome: Impact of newly approved treatments on C. difficile infection.},
journal = {American journal of health-system pharmacy : AJHP : official journal of the American Society of Health-System Pharmacists},
volume = {},
number = {},
pages = {},
doi = {10.1093/ajhp/zxaf137},
pmid = {40574683},
issn = {1535-2900},
}
@article {pmid40574533,
year = {2025},
author = {Baker, EJ and Cumberford, G and Hanaway, P},
title = {Recognizing the Health Benefits of Plant-Sourced Omega-3 Stearidonic Acid: Exploring Its Complementary Role to Preformed EPA/DHA.},
journal = {Lipids},
volume = {},
number = {},
pages = {},
doi = {10.1002/lipd.12452},
pmid = {40574533},
issn = {1558-9307},
abstract = {Very-long chain (VLC) omega-3 polyunsaturated fatty acids (PUFAs) like eicosapentaenoic acid (EPA), and docosahexaenoic acid (DHA) are crucial for optimal development, healthy aging, and disease management. Traditionally sourced from fatty fish, these omega-3 PUFAs face sustainability challenges, prompting increased exploration of plant-based alternatives, such as stearidonic acid (SDA). Recent studies highlight the efficient conversion of SDA to EPA, meaning that SDA may offer similar health benefits to EPA, including immune, joint, cognitive, and gut microbiome modulation (with distinct SDA-derived metabolites). This mini-review explores new research on SDA and its potential to deliver human health benefits. SDA-rich oils, notably Buglossoides arvensis oil (RBO; also known as Ahiflower oil) provide an eco-friendly, sustainable alternative to fish-derived omega-3 PUFAs. As concerns about marine omega-3 PUFA sources grow, SDA-rich oils present a viable option for clinicians and consumers seeking effective omega-3 PUFA supplementation.},
}
@article {pmid40574493,
year = {2025},
author = {Sun, J and Ren, C and Liu, N and Cao, X and Wang, C and Yao, S and Li, X and Wang, Z},
title = {Can Rhizosphere Effects Mitigate the Threat from Nanoplastics and Plastic Additives to Tomato (Solanum lycopersicum L.)?.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c01842},
pmid = {40574493},
issn = {1520-5851},
abstract = {Nanoplastics (NPs) and plastic additives inevitably coexist to threaten soil health and plant growth. Herein, in a root-box system isolating the rhizosphere and bulk soils, we explored the combined effects of NPs and a kind of typical plastic additive di-(2-ethylhexyl)phthalate (DEHP) on soil health via combining the evidence from in situ zymography, the microbiome, and metabolism. The plastic additive dominated the risks of plastic pollution to plants, and the coexistence of NPs did not mitigate the DEHP threat to microorganisms and increased that to food safety. Compared to single DEHP, combined NPs and DEHP inhibited β-glucosidase activity to limit soil organic carbon (C) decomposition and stimulated acid phosphatase activity to increase P uptake by tomato roots and enriched the relative abundance of C-fixed bacteria and P-dissolution bacteria, while inhibiting that of chemical heterotrophic bacteria in rhizosphere soils, which further stimulated the synthesis and metabolism of phospholipid and fatty acid and triphosphate cycle and increased nutrients bioavailability for plants. Therefore, rhizosphere effects optimized the root nutrient acquisition strategy, microbial community structure, and their metabolic processes to reduce the threat from NPs and plastic additives to plants. This study provides new insights for environmental risk control and agricultural management under plastic pollution.},
}
@article {pmid40574415,
year = {2025},
author = {Liu, X and Liang, Y and Li, Z and Xie, C and Zhang, Y and Wang, W and Ge, S and Li, J},
title = {Nano-Toothbrush for Noninvasive Control of Periodontitis.},
journal = {Journal of dental research},
volume = {},
number = {},
pages = {220345251335922},
doi = {10.1177/00220345251335922},
pmid = {40574415},
issn = {1544-0591},
abstract = {Periodontitis is a prevalent oral disease, and current clinical management remains limited to mechanical debridement of subgingival plaque and adjunctive antibiotic therapy. In this study, we introduced a piezocatalytic nanoparticle-constructed "nano-toothbrush" as a noninvasive strategy for oral biofilm removal. The dextran-mediated biofilm affinity of the nano-toothbrush induced localized oxidative stress under ultrasound irradiation, effectively disrupting biofilms and inhibiting pathogenic bacteria. This efficacy was evidenced by the removal of ex vivo biofilms from periodontitis patients. Importantly, the selective action of the nano-toothbrush minimized the damage to mouse fibroblasts and human immortalized oral epithelial cells, affirming its biosafety. In vivo studies showed that the nano-toothbrush significantly inhibited the cell viability of Porphyromonas gingivalis, effectively suppressed alveolar bone resorption, and alleviated inflammatory responses in a rat periodontitis model while concurrently preserving the diversity of the oral microbiome. This study presents a promising noninvasive and precise method for the removal of oral biofilms, offering new perspectives on the application of nanotherapeutics in the treatment of periodontitis and other plaque-induced diseases.},
}
@article {pmid40574306,
year = {2025},
author = {Shen, G and Xu, X and Li, M and Sun, Z and Wei, L and Deng, Z and Lin, Z and Huang, J and Qi, W and Xu, J},
title = {The Clinical Trials Landscape for Alzheimer's Disease.},
journal = {CNS neuroscience &amp; therapeutics},
volume = {31},
number = {6},
pages = {e70492},
doi = {10.1111/cns.70492},
pmid = {40574306},
issn = {1755-5949},
support = {202201010823//Guangzhou Science and Technology Program Project/ ; 2024A1515013041//Natural Science Foundation of Guangdong Province/ ; Y-zai2022/qn-0250//Beijing Xisike Clinical Oncology Research Foundation/ ; },
mesh = {*Alzheimer Disease/therapy/drug therapy ; Humans ; *Clinical Trials as Topic/methods ; },
abstract = {INTRODUCTION: Not only drug and non-drug development but also non-therapeutic research in Alzheimer's disease (AD) clinical trials is unclear.<br><br>METHODS: The participants were AD clinical trials obtained from the clinicaltrials.gov registry. The research objectives and interventions of those trials were analyzed. Bibliometric network analysis of those published articles in PubMed was also conducted.<br><br>RESULTS: A total of 1681 clinical trials and 565 corresponding published articles in the past 20&#x2009;years were included in the analysis. "Safety", "dose", "adverse events", and "biomarker" were the most frequently used words that appeared in the title or abstract of published articles. The top three classes of 362 drugs were anti-Amyloid, enhancing acetylcholine, neurotransmitter, or targeting its receptor. The physical therapy, diet, and cognitive training ranked as the first three classes of non-drug therapy. Imaging, risk factors, and molecular biomarkers were the three most abundant categories in non-therapeutic research, and three fields of prevention, risk factors, and the dental or intestinal microbiome showed an escalated trend (All Ptrend <&#x2009;0.05).<br><br>DISSUSION: The results described a comprehensive landscape for the clinical studies of AD. Although most drugs treated AD abortively, the success of lecanemab and decanemab provides confidence for us to further study the pathogenesis of AD and explore new therapeutic targets to develop anti-AD drugs. Rising non-drug and non-therapeutic research will provide more possible methods for the treatment and prevention of AD in thefuture.},
}
@article {pmid40573904,
year = {2025},
author = {Yang, H and Zhou, Y and Cheng, X and Qiu, C and Wang, S and Xia, Y and Huai, X and Xiu, Z and Wang, J and He, Y and Cao, G and Wei, Q and Wang, J and Ai, J and Zhang, H and Zhang, Y and Zhang, J and Zhang, W and Wang, B},
title = {Safety, Tolerability, and Immunogenicity of a DNA Vaccine (pGX9501) Against SARS-CoV-2 in Healthy Volunteers: A Single-Center, Randomized, Double-Blind, Placebo-Controlled, and Dose-Ranging Phase I Trial.},
journal = {Vaccines},
volume = {13},
number = {6},
pages = {},
doi = {10.3390/vaccines13060573},
pmid = {40573904},
issn = {2076-393X},
support = {92169212//National Natural Science Foundation of China/ ; HS2021SHZX001//Shanghai Municipal Science and Technology Major Project/ ; },
abstract = {Background: pGX9501 is a prophylactic DNA vaccine encoding the spike protein of SARS-CoV-2 and can induce immune response in the human body so as to prevent COVID-19. With respect to non-clinical studies, pGX9501 has been demonstrated to induce both cellular and humoral immune responses in various animal models. It was found that the level of antibody titers following a two-dose regimen was higher than that following a single-dose regimen in nonhuman primate challenge model. Methods: In China, a phase I, randomized, double-blind, placebo-controlled clinical trial has been conducted in Huashan Hospital, Shanghai, China to evaluate the safety, tolerability, and immunogenicity of DNA vaccine pGX9501 administered intradermally (ID) followed by electroporation (EP) in 45 Chinese healthy volunteers aged 18 to 59 years old. Results: No adverse events of special interest (AESIs), death, or treatment-related SAEs occurred in this study. All the treatment-related (vaccine or EP) adverse events (TRAEs) were of grade 1 and 2 in severity. The solicited AEs were reported in thirty-two (32/36, 88.9%) and nine (9/9, 100.0%) subjects, respectively, in the DNA vaccine and placebo group. The frequency of solicited AEs did not increase with vaccine dose level and frequency. The DNA vaccine pGX9501 effectively enhanced both humoral and cellular immune responses in a dose-dependent manner, with increased antibody GMTs and peak seroconversion rates observed on day 42. The significant rise in IFN-γ levels confirmed the vaccine's ability to induce cellular immune responses. Variations in the microbiome structure suggested a tangible impact of the gut microbiota on vaccine immunogenicity. Conclusions: The findings from this study confirm the immunogenicity and safety of the DNA vaccine pGX9501 and point to the potential role of the gut microbiota in vaccine immune responses. These insights provide practical references for the future design and development of DNA vaccines.},
}
@article {pmid40573878,
year = {2025},
author = {Ullah, F and Ali, S and Siraj, M and Akhtar, MS and Zaman, W},
title = {Plant Microbiomes Alleviate Abiotic Stress-Associated Damage in Crops and Enhance Climate-Resilient Agriculture.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {12},
pages = {},
doi = {10.3390/plants14121890},
pmid = {40573878},
issn = {2223-7747},
abstract = {Plant microbiomes, composed of a diverse array of microorganisms such as bacteria, fungi, archaea, and microalgae, are critical to plant health and resilience, playing key roles in nutrient cycling, stress mitigation, and disease resistance. Climate change is expected to intensify various abiotic stressors, such as drought, salinity, temperature extremes, nutrient deficiencies, and heavy metal toxicity. Plant-associated microbiomes have emerged as a promising natural solution to help mitigate these stresses and enhance agricultural resilience. However, translating laboratory findings into real-world agricultural benefits remains a significant challenge due to the complexity of plant-microbe interactions under field conditions. We explore the roles of plant microbiomes in combating abiotic stress and discuss advances in microbiome engineering strategies, including synthetic biology, microbial consortia design, metagenomics, and CRISPR-Cas, with a focus on enhancing their practical application in agriculture. Integrating microbiome-based solutions into climate-smart agricultural practices may contribute to long-term sustainability. Finally, we underscore the importance of interdisciplinary collaboration in overcoming existing challenges. Microbiome-based solutions hold promise for improving global food security and promoting sustainable agricultural practices in the face of climate change.},
}
@article {pmid40573860,
year = {2025},
author = {Luo, D and Liao, D and Han, T and Ji, C and He, C and Li, X},
title = {Regulatory Effects of Companion Plants (Maize (Zea mays) and Perilla frutescens) on American Ginseng Growth and Microbiome in Root Rot-Infested Field.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {12},
pages = {},
doi = {10.3390/plants14121871},
pmid = {40573860},
issn = {2223-7747},
support = {2022YFC3501501//National Key R&amp;D Program of China/ ; },
abstract = {American ginseng (AG) cultivation suffers from severe diseases, requiring heavy pesticide use. This study aimed to explore whether companion planting with maize (AG-maize) or Perilla frutescens (AG-perilla) could enhance AG growth and alter rhizosphere/root microbiomes in a root rot-infested field. Compared to monoculture (CK), companion planting significantly improved AG growth and survival rate at wither stage, with AG-maize showing the superior efficacy- increasing root length and fresh weight, and plant height by 39.04%, 46.10%, and 48.69%, respectively, while raising survival rate from 1.51% to 14.54%. Microbial analysis revealed that companion planting increased microbiome diversity and network complexity. At green fruit stage, AG-perilla increased rhizosphere fungal Chao1 index by 42.6%, while AG-maize and AG-perilla elevated endophytic fungal Shannon indices by 46.68% and 74.84%, respectively. At wither stage, AG-maize notably enriched beneficial microbes (e.g., soil Pseudomonas +108.49%, Bacillus +200.73%) while reducing pathogens (soil Fusarium -20.04%, root endophytic Alternaria -54.55%). Structural equation model indicated AG-maize improved AG survival via core species-driven antibiosis and nutrient regulation, with keystone species Lysobacter sp. RHLT3-4 and Verrucomicrobium sp. IMCC25902 significantly correlating with AG health. The AG-maize system fostered synergistic microbial networks, enriching beneficial taxa and suppressing pathogens. These findings provide a foundation for developing eco-friendly disease management and high-yield AG cultivation strategies.},
}
@article {pmid40573793,
year = {2025},
author = {Li, Y and Xiao, Y and Zhao, W and Kang, J and Yang, K and Fu, J},
title = {Characteristic Functional Genera (CFG) Mediate Nitrogen Priming Effect in the Microbiome of Saline-Alkaline Farmland.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {12},
pages = {},
doi = {10.3390/plants14121806},
pmid = {40573793},
issn = {2223-7747},
support = {LJGXCG2022-107//Heilongjiang Province "Double First-Class" Discipline Collaborative Innovation Achievement Construction Project "Green and Low-Carbon for Food Crops"/ ; YQJH2024171//Program for Young Talents of Basic Research in Universities of Heilongjiang Province/ ; YQ2024C043//Nature Scientific Foundation of Heilongjiang Province/ ; XDA28130103//Strategic Priority Research Program of the Chinese Academy of Science/ ; },
abstract = {This study aimed to investigate the impact of nitrogen priming effect on the makeup of the maize rhizosphere microbial community structure in saline-alkali agriculture, focusing on characteristic functional genera. In 2020, three nitrogen levels of 60 kg·ha[-1] (N1), 180 kg·ha[-1] (N2), and 300 kg·ha[-1] (N3), along with a control group, were established in the meadow saline-alkali soil farmland of Daqing in Heilongjiang Province. The maize cultivar was Xianyu 335. Rhizosphere soil was taken for nutritional analysis and high-throughput sequencing of the microbial population. The findings indicated that the bacterial community structure in the N1 and N2 treatment groups was comparable; however, the N3 treatment dramatically altered the community structure (p < 0.01). A notable disparity existed between the fungal nitrogen application group and the control group. Screening identified ten genera, including Lysobacter and Coniophora, as characteristic functional genera, with their habitats and functions dramatically altered during nitrogen priming effect. Nitrogen priming effect enhanced bacterial functionality for nitrogen source augmentation but diminished the capacity for nitrogen transformation, while also altering the nutritional preferences of fungus. Soil nitrogen and organic matter content showed distinct responses to different nitrogen application rates and exhibited significant interactions with the microbial community. The impacts of low, medium, and high nitrogen treatments on microbial and soil indicators varied, suggesting that effective nutrient management necessitates the regulation of microbial community function and accurate nitrogen administration. The research findings hold substantial importance and promotional potential for the sustainable advancement of saline-alkali agriculture.},
}
@article {pmid40573780,
year = {2025},
author = {Zhang, S and Luo, Z and Peng, J and Wu, X and Meng, X and Qin, Y and Zhu, F},
title = {Analysis of Cadmium Accumulation Characteristics Affected by Rhizosphere Bacterial Community of Two High-Quality Rice Varieties.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {12},
pages = {},
doi = {10.3390/plants14121790},
pmid = {40573780},
issn = {2223-7747},
support = {2024YFD2301400//the National Key Research and Development Program of China/ ; 2024CX09//the Agricultural Science and Technology Innovation Project of Hunan Province, China/ ; },
abstract = {Cadmium-contaminated rice poses serious health risks through the bioaccumulation of Cd (cadmium) from soil to edible grains. Cd contamination disrupts soil microbial ecology and alters microbial diversity. However, the role of cultivar-specific rhizosphere microbial communities in modulating Cd uptake remains unclear. In this study, we aimed to elucidate the mechanism underlying variety-dependent rhizosphere microecological remodeling and Cd accumulation in two independently selected late rice varieties, Yuzhenxiang (YZX) and Xiangwanxian 12 (XWX12). Combining physiological and metagenomic analyses, we revealed variety-specific correlations between root Cd accumulation and dynamic changes in soil pH, soil available phosphorus, and rhizosphere bacteria. The key bacterial genera (Variibacter, Nitrospira) showed differential enrichment patterns under Cd stress. In contrast, Galella and Anaeromyxobacter likely reduce Cd bioavailability by modulating phosphorus availability. Overall, this study elucidates that rice cultivars indirectly shape Cd accumulation patterns via rhizosphere microbial remodeling, providing novel insights for microbial remediation strategies in Cd-contaminated farmland.},
}
@article {pmid40573741,
year = {2025},
author = {Kruščić, K and Jelušić, A and Hladnik, M and Janakiev, T and Anđelković, J and Bandelj, D and Dimkić, I},
title = {The Influence of Bacterial Inoculants and a Biofertilizer on Maize Cultivation and the Associated Shift in Bacteriobiota During the Growing Season.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {12},
pages = {},
doi = {10.3390/plants14121753},
pmid = {40573741},
issn = {2223-7747},
support = {451-03-136/2025-03/200178//Ministry of Education, Science and Technological Development of Serbia/ ; TERRA_MADRE 7455//Program PRISMA of the Science Fund of the Republic of Serbia/ ; },
abstract = {Maize (Zea mays L.) relies heavily on nitrogen and phosphorus inputs, typically supplied through organic and inorganic fertilizers. However, excessive agrochemical use threatens soil fertility and environmental health. Sustainable alternatives, such as poultry manure (PM) and plant growth-promoting rhizobacteria (PGPR), offer promising solutions. This study examines the effects of a phytobiotic bacterial formulation (PHY), composed of Bacillus subtilis and Microbacterium sp., applied alone and in combination with PM, on maize's rhizosphere bacteriobiome across key growth stages. Field trials included four treatments: a control, PHY-coated seeds, PM, and combined PHY_PM. The results show that early in development, the PM-treated rhizospheres increased the abundance of beneficial genera such as Sphingomonas, Microvirga, and Streptomyces, though levels declined in later stages. The PHY_PM-treated roots in the seedling phase showed a reduced abundance of taxa like Chryseobacterium, Pedobacter, Phyllobacterium, Sphingobacterium, and Stenotrophomonas, but this effect did not persist. In the PM-treated roots, Flavisolibacter was significantly enriched at harvesting. Overall, beneficial bacteria improved microbial evenness, and the PHY_PM treatment promoted bacterial diversity and maize growth. A genome analysis of the PHY strains revealed plant-beneficial traits, including nutrient mobilization, stress resilience, and biocontrol potential. This study highlights the complementarity of PM and PGPR, showing how their integration reshapes bacteriobiome and correlates with plant parameters in sustainable agriculture.},
}
@article {pmid40573190,
year = {2025},
author = {Ruiz-Álvarez, BE and Cattero, V and Desjardins, Y},
title = {Prebiotic-like Effects of Proanthocyanidin-Rich Aronia Extract Supplementation on Gut Microbiota Composition and Function in the Twin-M-SHIME[®] Model.},
journal = {Pharmaceuticals (Basel, Switzerland)},
volume = {18},
number = {6},
pages = {},
doi = {10.3390/ph18060793},
pmid = {40573190},
issn = {1424-8247},
support = {NSERC-Symrise Industrial Chair on prebiotic Effects of Fruits and Vegetables//Symrise/ ; },
abstract = {Background: Phenolic compounds, particularly anthocyanins and proanthocyanidins (PACs), are poorly absorbed in the upper digestive tract and reach the colon largely intact, where they may influence gut microbiota (GM) composition and, in turn, impact host health. We hypothesized that a PAC-rich aronia extract would beneficially modulate the GM, promote the growth of health-associated bacteria, and enhance short-chain fatty acid (SCFA) production across different colon sections, with partial reversion effects after supplementation ends. Methods: The Twin-M-SHIME[®] system was used to simulate the digestion and colonic fermentation in two donors with contrasting microbiota profiles. The experimental design included four phases: stabilization (14 days), control (7 days), treatment with 500 mg/day PAC-rich aronia extract (21 days), and wash-out (10 days). SCFA production was monitored, and changes in microbiome composition were assessed using 16S rRNA gene sequencing. Results: PAC-rich aronia extract significantly modulated SCFA levels, increasing butyrate and reducing acetate, with some inter-donor variability. SCFA concentrations tended to return to baseline after the wash-out (WO) period. Metagenomic analysis revealed a decrease in Collinsella, Sutterella, Selenomonas, and Parabacteroides-genera linked to low-fiber diets and gut inflammation-while promoting Proteobacteria (e.g., Escherichia-Shigella, Klebsiella) and butyrate-associated Firmicutes such as Lactiplantibacillus. Although some microbial shifts partially reverted during the wash-out (e.g., Akkermansia, Bacteroides, and Bifidobacterium), other changes persisted. Conclusions: These findings suggest that PAC-rich aronia extract beneficially modulates GM and SCFA production, but continuous intake may be necessary to maintain these effects over time.},
}
@article {pmid40573134,
year = {2025},
author = {Wu, H and Witt, BL and van der Pol, WJ and Morrow, CD and Duck, LW and Tollefsbol, TO},
title = {Combined Phytochemical Sulforaphane and Dietary Fiber Inulin Contribute to the Prevention of ER-Negative Breast Cancer via PI3K/AKT/MTOR Pathway and Modulating Gut Microbial Composition.},
journal = {Nutrients},
volume = {17},
number = {12},
pages = {},
doi = {10.3390/nu17122023},
pmid = {40573134},
issn = {2072-6643},
support = {R01CA178441/NH/NIH HHS/United States ; },
mesh = {Animals ; *Isothiocyanates/pharmacology/administration &amp; dosage ; *Inulin/pharmacology/administration &amp; dosage ; Sulfoxides ; Female ; *Gastrointestinal Microbiome/drug effects ; *Dietary Fiber/administration &amp; dosage/pharmacology ; Mice ; TOR Serine-Threonine Kinases/metabolism ; Proto-Oncogene Proteins c-akt/metabolism ; *Breast Neoplasms/prevention &amp; control ; Mice, Transgenic ; Phosphatidylinositol 3-Kinases/metabolism ; Signal Transduction/drug effects ; Receptors, Estrogen/metabolism ; Phytochemicals/pharmacology/administration &amp; dosage ; Prebiotics ; Anticarcinogenic Agents ; },
abstract = {Background: Breast cancer (BC) is the second most common cancer among women in the United States. It has been estimated that one in eight women will be diagnosed with breast cancer in her lifetime. Various BC risk factors, such as age, physical inactivity, and smoking, play a substantial role in BC occurrence and development. Early life dietary intervention with plant-based bioactive compounds has been studied for its potential role in BC prevention. Sulforaphane (SFN), an isothiocyanate, is an antioxidant and anti-inflammatory agent extracted from broccoli sprouts (BSp) and other plants. Dietary supplementation of SFN suppresses tumor growth by inducing protective epigenetic changes and inhibiting cancer cell proliferation. Inulin, as a dietary fiber, has been studied for alleviating GI discomfort and weight loss by promoting the growth of beneficial bacteria in the gut. Objective: Early-life combinatorial treatment with both phytochemical SFN and potential prebiotic agent inulin at lower and safer dosages may confer more efficacious and beneficial effects in BC prevention. Methods: Transgenic mice representing estrogen receptor-negative BC were fed 26% (w/w) BSp and 2% (w/v) inulin supplemented in food and water, respectively. Results: The combinatorial treatment inhibited tumor growth, increased tumor onset latency, and synergistically reduced tumor weight. Gut microbial composition was analyzed between groups, where Ruminococcus, Muribaculaceae, and Faecalibaculum significantly increased, while Blautia, Turicibacter, and Clostridium sensu stricto 1 significantly decreased in the combinatorial group compared with the control group. Furthermore, combinatorial treatment induced a protective epigenetic effect by inhibiting histone deacetylases (HDACs) and DNA methyltransferases (DNMTs). Intermediates in the AKT/PI3K/MTOR pathway were significantly suppressed by the combinatorial treatment, including PI3K p85, p-AKT, p-PI3K p55, MTOR, and NF-κB. Cell cycle arrest and programmed cell death were induced by the combinatorial treatment via elevating the expression of cleaved-caspase 3 and 7 and inhibiting the expressions of CDK2 and CDK4, respectively. Orally administering F. rodentium attenuated tumor growth and induced apoptosis in a syngeneic triple-negative breast cancer (TNBC) mouse model. Conclusions: Overall, the findings suggest that early-life dietary combinatorial treatment contributed to BC prevention and may be a potential epigenetic therapy that serves as an adjunct to other traditional neoadjuvant therapies.},
}
@article {pmid40573129,
year = {2025},
author = {Ferrer, MF and Retuerto, M and Thavamani, A and San Valentin, EM and Sferra, TJ and Ghannoum, M and Sankararaman, S},
title = {Clinical and Gut Microbiome Characteristics of Medically Complex Patients Receiving Blenderized Tube Feeds vs. Standard Enteral Feeds.},
journal = {Nutrients},
volume = {17},
number = {12},
pages = {},
doi = {10.3390/nu17122018},
pmid = {40573129},
issn = {2072-6643},
support = {none//Fellowship Research Award Program, Rainbow Children's Foundation./ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Enteral Nutrition/methods/adverse effects ; Male ; Female ; Adolescent ; Child ; Child, Preschool ; Infant ; Young Adult ; Vomiting/etiology/epidemiology ; *Food, Formulated ; },
abstract = {Background: Diet is known to influence the composition of the gut microbiome. For patients who require enteral feeding, there has been a growing popularity of using blenderized tube feeds (BTFs) as an alternative to standard enteral formula (SEF). There is limited literature exploring the impact of BTFs on the gut microbiome. Methods: Twenty-eight patients 1 to 22 years of age who received their nutrition via gastrostomy tube for over 4 weeks were included and participants were divided into BTF and SEF groups. Demographics and clinical information were collected from the medical records, and all legal guardians completed a semi-structured interview using a questionnaire. 16SrRNA sequencing was used for bacteriome analysis. Results: Eleven patients in the BTF group and seventeen in the SEF group were included. No significant differences in the demographics were noted. Patients on BTFs had no emesis compared to seven (41%) in the SEF group, p = 0.02. There were no significant differences in other clinical characteristics and comorbidities. No significant differences in the gut microbiome between the groups were noted for alpha and beta diversities, richness, and evenness (at both genus and species levels). Differential abundance analysis showed only a few significant differences between the groups at all reported taxonomic levels. Conclusions: Patients on BTFs had a significantly decreased prevalence of emesis compared to the SEF group. No significant differences in the microbiome between the groups were noted for alpha and beta diversities, richness, and evenness. Prospective studies are recommended to verify our preliminary data and further evaluate the implications of our study results.},
}
@article {pmid40573072,
year = {2025},
author = {Wakino, S and Hasegawa, K and Tamaki, M and Minato, M and Inagaki, T},
title = {Kidney-Gut Axis in Chronic Kidney Disease: Therapeutic Perspectives from Microbiota Modulation and Nutrition.},
journal = {Nutrients},
volume = {17},
number = {12},
pages = {},
doi = {10.3390/nu17121961},
pmid = {40573072},
issn = {2072-6643},
mesh = {Humans ; *Renal Insufficiency, Chronic/microbiology/therapy/physiopathology ; *Gastrointestinal Microbiome/physiology ; *Dysbiosis/therapy/microbiology ; Probiotics/therapeutic use ; Prebiotics/administration &amp; dosage ; *Kidney/physiopathology ; Synbiotics/administration &amp; dosage ; Fecal Microbiota Transplantation ; Uremia/microbiology ; *Nutrition Therapy/methods ; },
abstract = {Chronic kidney disease (CKD) has a high prevalence worldwide, with an increasing incidence. One of the mechanisms of CKD progression involves a disordered inter-organ relationship between the kidneys and the intestine, known as the kidney-gut axis. In CKD, two pathological gut conditions-disturbed gut microbiota composition called uremic dysbiosis and leaky gut-contribute to the progression of CKD. Dysbiosis is associated with the increased production of gut-derived uremic toxins, leaky gut, and chronic systemic inflammation, leading to worsening uremia, which in turn aggravates the gut condition. This vicious cycle should be a target of the therapeutic strategy against CKD. The modulation of uremic dysbiosis, including prebiotics, probiotics, and synbiotics, has been a typical treatment approach, although clinical evidence for their efficacy has been insufficient. Some non-antibiotic drugs have an impact on human gut bacteria that are believed to play a role in their clinical efficacy on kidney function. Nutrition therapies, including a low-protein diet, dietary fiber, a Mediterranean diet, and whole grains, positively influence gut microbiota composition and have been linked to a decreased risk of CKD. Novel strategies are currently being explored, involving the use of postbiotics, microbiome sequencing techniques, and fecal microbiota transplantation, although clinical application remains to be tested. Human trials investigating the above-mentioned interventions remain inconclusive due to several limitations, including dietary variability and genetic factors. Future research should focus on the development of more effective probiotics, prebiotics, and microbial metabolism-modifying drugs, not only for CKD but for other systemic diseases as well.},
}
@article {pmid40572802,
year = {2025},
author = {Mackawy, AMH and Alturky, FS and Mohammed, AH and Alharbi, BF and Huq, M and Wasti, AZ and Ahmed, MAA and Alharbi, HOA},
title = {A Comparative Analysis of Feeding Practices and Oral Immunity in Infants.},
journal = {Medicina (Kaunas, Lithuania)},
volume = {61},
number = {6},
pages = {},
pmid = {40572802},
issn = {1648-9144},
mesh = {Humans ; Infant ; Female ; *Breast Feeding/statistics &amp; numerical data ; Male ; Interleukin-17/analysis ; Infant Formula ; Mouth Mucosa/microbiology/immunology ; },
abstract = {Background and Objectives: Infant feeding practices play a crucial role in shaping the oral microbiome, modulating inflammatory responses, and maintaining epithelial health during the first year of life. Breastfeeding promotes the growth of beneficial bacteria and supports a diverse, stable microbial community. In contrast, formula feeding is associated with increased colonization by potentially pathogenic bacteria, such as Staphylococcus and Escherichia coli, which may elevate the risk of infections, oral diseases, and inflammation. This study investigates the effects of breastfeeding versus formula feeding on oral bacterial growth, epithelial cell integrity, and interleukin-17 (IL-17) expression in infants aged 1-12 months. Materials and Methods: A total of 60 infants (30 breastfed and 30 formula-fed) were recruited from pediatric clinics in the Qassim region. Microbial cultures quantified bacterial colony-forming units (CFUs), and epithelial cell morphology was assessed through the microscopic analysis of mucosal scrapings. IL-17 concentrations were quantified from the oral mucosa through enzyme-linked immunosorbent assay. Statistical analyses, including t-tests and chi-square tests, compared bacterial loads, IL-17 levels, and indicators of epithelial health between groups. Adjustment for potential confounders was achieved through multivariate statistical analysis. Results: Formula-fed infants showed significantly higher IL-17 levels than breastfed infants (p < 0.001), indicating a stronger pro-inflammatory profile. Breastfed infants exhibited lower inflammation, improved epithelial health, and reduced cellular debris compared to formula-fed infants, who had higher bacterial loads. A significant correlation was found between epithelial health and bacterial clustering, with clearer epithelial cells associated with lower bacterial colonization. Conclusions: Formula feeding was associated with increased salivary IL-17 levels, greater bacterial colonization, and compromised epithelial integrity, indicating a heightened pro-inflammatory state and potential vulnerability to mucosal irritation or infection. Breastfeeding appeared to confer protective effects by promoting healthier microbial balance, epithelial integrity, and reducing inflammatory responses. These findings underscore the immunological and microbial benefits of breastfeeding in supporting oral health during infancy.},
}
@article {pmid40572315,
year = {2025},
author = {Kim, B and Lee, S and Lee, YJ and Kang, YM and Rhee, MH and Kwak, D and Yeo, YG and Kang, JW and Kim, T and Seo, MG},
title = {Preliminary Insights into the Gut Microbiota of Captive Tigers in Republic of Korea: Influence of Geographic and Individual Variation.},
journal = {Microorganisms},
volume = {13},
number = {6},
pages = {},
pmid = {40572315},
issn = {2076-2607},
support = {none//Baekdudaegan National Arboretum (Korean Tiger Conservation Center)./ ; },
abstract = {The gut microbiome plays a crucial role in the health and physiology of tigers (Panthera tigris), influencing digestion, immune function, and overall well-being. While numerous studies have characterized the gut microbiota of domestic carnivores and some wild felids, comparative analyses across different tiger subspecies under varying environmental contexts remain limited. In this exploratory study, we investigated the gut microbiome diversity and composition of 15 captive tigers, including both Siberian (P. tigris altaica) and Bengal (P. tigris tigris) subspecies, housed in two different regions in Korea. Using 16S rRNA gene sequencing of fecal samples, we analyzed microbial diversity across multiple taxonomic levels. Preliminary analyses revealed significant differences in microbial composition between geographic locations, whereas sex-based differences appeared minimal. Alpha and beta diversity metrics demonstrated substantial inter-individual variability, likely influenced by regional and environmental factors. Given the small sample size and the confounding between subspecies and housing location, the findings should be regarded as preliminary and not generalized beyond this specific cohort. Nevertheless, these insights highlight the potential utility of gut microbiome profiling for health monitoring and management in captive-tiger populations. Future research incorporating larger, more diverse cohorts will be essential to validate these trends and clarify the roles of diet, health status, and enrichment in shaping the gut microbiota.},
}
@article {pmid40572314,
year = {2025},
author = {Kim, MJ and Yoo, J and Yoo, S and Kwon, MY and Lee, S and Kim, M},
title = {The Clinically Significant Changes in the Composition and Functional Diversity of the Vaginal Microbiome in Women with Type 2 Diabetes Mellitus.},
journal = {Microorganisms},
volume = {13},
number = {6},
pages = {},
pmid = {40572314},
issn = {2076-2607},
support = {BCMC20LH03//Clinical Medicine Research of Bucheon St. Mary's Hospital/ ; },
abstract = {Type 2 diabetes mellitus (T2DM) significantly influences the composition and diversity of the vaginal microbiome, with implications for mucosal immunity, infection risk, and genitourinary health. This study aimed to investigate the vaginal microbiome profiles in women with T2DM, with a focus on differences according to menopausal status and associations with Candida colonization and the use of sodium-glucose cotransporter 2 (SGLT2) inhibitors. Compared to healthy controls, women with T2DM exhibited a decreased abundance of Lactobacillus species and increased microbial diversity. Community state of type (CST) IV, characterized by low Lactobacillus abundance and dominance of anaerobic taxa, was prevalent in the T2DM group. Among Candida-positive patients, Lactobacillus iners-dominant CST III was frequently observed, along with elevated levels of total and L-lactic acid. SGLT2 inhibitor users exhibited a different CST distribution pattern and slightly lower microbial richness and diversity, although these differences were not statistically significant. These findings underscore the impact of T2DM and its treatment on vaginal microbial composition and highlight the importance of considering vaginal health as part of comprehensive diabetes management in women.},
}
@article {pmid40572300,
year = {2025},
author = {Zhang, J and Tang, S and Wei, H and Yao, L and Chen, Z and Han, H and Ji, M and Yang, J},
title = {Reducing Cd Uptake by Wheat Through Rhizosphere Soil N-C Cycling and Bacterial Community Modulation by Urease-Producing Bacteria and Organo-Fe Hydroxide Coprecipitates.},
journal = {Microorganisms},
volume = {13},
number = {6},
pages = {},
pmid = {40572300},
issn = {2076-2607},
support = {42377039//National Natural Science Foundation of China/ ; },
abstract = {The bioavailability of heavy metals is profoundly influenced by their interactions with active soil components (microorganisms, organic matter, and iron minerals). However, the effects of urease-producing bacteria combined with organo-Fe hydroxide coprecipitates (OFCs) on Cd accumulation in wheat, as well as the mechanisms underlying these effects, remain unclear. In this study, pot experiments integrated with high-throughput sequencing were employed to investigate the impacts of the urease-producing bacterial strain TJ6, ferrihydrite (Fh), and OFCs on Cd enrichment in wheat grains, alongside the underlying soil-microbial mechanisms. The results demonstrate that the strain TJ6-Fh/OFC consortium significantly (p < 0.05) reduced (50.1-66.7%) the bioavailable Cd content in rhizosphere soil while increasing residual Cd fractions, thereby decreasing (77.4%) Cd accumulation in grains. The combined amendments elevated rhizosphere pH (7.35), iron oxide content, and electrical conductivity while reducing (14.5-21.1%) dissolved organic carbon levels. These changes enhanced soil-colloid-mediated Cd immobilization and reduced Cd mobility. Notably, the NH4[+] content and NH4[+]/NO3[-] ratio were significantly (p < 0.05) increased, attributed to the ureolytic activity of TJ6, which concurrently alkalinized the soil and inhibited Cd uptake via competitive ion channel interactions. Furthermore, the relative abundance of functional bacterial taxa (Proteobacteria, Gemmatimonadota, Enterobacter, Rhodanobacter, Massilia, Nocardioides, and Arthrobacter) was markedly increased in the rhizosphere soil. These microbes exhibited enhanced abilities to produce extracellular polymeric substances, induce phosphate precipitation, facilitate biosorption, and promote nutrient (C/N) cycling, synergizing with the amendments to immobilize Cd. This study for the first time analyzed the effect and soil science mechanism of urease-producing bacteria combined with OFCs in blocking wheat's absorption of Cd. Moreover, this study provides foundational insights and a practical framework for the remediation of Cd-contaminated wheat fields through microbial-organic-mineral collaborative strategies.},
}
@article {pmid40572296,
year = {2025},
author = {Schmidt, JE and Flores, J and Barragan, L and Amores, F and Khalsa, SDS},
title = {Optimizing Cocoa Productivity Through Soil Health and Microbiome Enhancement: Insights from Organic Amendments and a Locally Derived Biofertilizer.},
journal = {Microorganisms},
volume = {13},
number = {6},
pages = {},
pmid = {40572296},
issn = {2076-2607},
support = {n/a//Mars Wrigley/ ; },
abstract = {Despite growing interest in improving soil health on cocoa farms, applied research on the impacts of specific amendments on soil and plant outcomes is lacking. An integrated assessment of the impacts of two different organic amendments (compost and vermicompost) and a microbial biofertilizer on soil physical, chemical, and biological properties, as well as cocoa flowering, fruit set, and yield, was conducted in Guayaquil, Ecuador. Complementary culture-dependent and culture-independent methods were used to assess the impacts of amendments on microbial diversity, community composition, and specific taxa. Compost or vermicompost application affected soil chemical properties, including potassium, phosphorus, and sodium, and had small but significant effects on fungal beta diversity. Biofertilizer application slightly lowered soil pH and altered the total abundance of specific taxonomic groups including Azotobacter sp. and Trichoderma sp., with borderline significant effects on Azospirillum sp., Lactobacillus sp., Pseudomonas sp., calcium-solubilizing bacteria, and phosphorus-solubilizing bacteria. Amplicon sequencing (16S, ITS) identified 15 prokaryotic and 68 fungal taxa whose relative abundance was influenced by organic amendments or biofertilizer. Biofertilizer application increased cherelle formation by 19% and monthly harvestable pod counts by 11% despite no impact on flowering index or annual pod totals. This study highlights the tangible potential of microbiome optimization to simultaneously improve on-farm yield and achieve soil health goals on cocoa farms.},
}
@article {pmid40572287,
year = {2025},
author = {Dai, H and Jia, M and Xue, J and Liu, Z and Zhou, D and Hou, Z and Yu, J and Lu, S},
title = {Complementary Rhizosphere Microbial Strategies Drive Functional Specialization in Coastal Halophyte Succession: Differential Adaptation of Suaeda glauca and Phragmites communis to Saline-Alkali Stress.},
journal = {Microorganisms},
volume = {13},
number = {6},
pages = {},
pmid = {40572287},
issn = {2076-2607},
support = {BE2022306//Special Fund on Technology Innovation of Carbon Dioxide Peaking and Carbon Neutrality of Jiangsu Province/ ; LYKJ[2022]02//Jiangsu Provincial For-estry Science and Technology Innovation and Promotion Project/ ; JSPKLB202511//Scientific Fund of Nanjing Botanical Garden Mem Sun Yat-Sen/ ; },
abstract = {While rhizosphere microbiome functions in saline soils are well documented, complementary microbial strategies between pioneer and late-successional halophytes remain unexplored. Here, we used 16S rRNA sequencing and FAPROTAX functional prediction to compare the rhizosphere bacterial communities of two key halophytes-Suaeda glauca and Phragmites communis-in a reclaimed coastal wetland. The results demonstrate that both plants significantly restructured microbial communities through convergent enrichment of stress-tolerant taxa (Firmicutes, Pseudomonas, Bacillus, and Planococcus) while suppressing sulfur-oxidizing bacteria (Sulfurovum and Thiobacillus). However, they exhibited distinct microbial specialization: S. glauca uniquely enriched organic-matter-degrading taxa (Promicromonospora and Zhihengliuella) and upregulated aromatic compound degradation (2.29%) and ureolysis (0.86%) according to FAPROTAX analysis, facilitating carbon mobilization in early successional stages. Notably, P. communis selectively recruited nitrogen-cycling Serratia, with increased nitrate respiration (3.51% in P. communis vs. 0.91% in S. glauca) function, reflecting its higher nitrogen demand. Environmental factors also diverged: S. glauca's microbiome correlated with potassium and sodium, whereas P. communis responded to phosphorus and chloride. These findings uncover distinct microbial recruitment strategies by halophytes to combat saline stress-S. glauca-P. communis synergy through microbial carbon-nitrogen coupling-offering a template for consortia design in saline soil restoration.},
}
@article {pmid40572280,
year = {2025},
author = {Wang, Y and Diao, K and Li, H and Zhang, C and Zhang, G and Guo, C},
title = {Effects of Dietary Protein Levels on Production Performance, Meat Quality Traits, and Gut Microbiome of Fatting Dezhou Donkeys.},
journal = {Microorganisms},
volume = {13},
number = {6},
pages = {},
pmid = {40572280},
issn = {2076-2607},
support = {Grant Nos. 2019YFE0107700 and NRF-2019K1A3A1A20081146//This research was supported by the National Key R&amp;D Program of China-Korea Cooperative Project/ ; Grant No. SDAIT-30-02//the Shandong Province Modern Agricultural Technology System Donkey Industry Innovation Team/ ; Grant No. 2022TZXD0018//the Key R&amp;D Program of Shandong Province/ ; },
abstract = {This study aimed to investigate the effects of varying dietary protein levels on growth performance, meat quality traits, amino acid and fatty acid compositions, and hindgut microbiota in Dezhou donkeys. Eighteen 12-month-old male donkeys, weighing 188 ± 9 kg, were randomly allocated into three groups and fed diets containing 11.03% (LP), 12.52% (MP), and 14.06% (HP) protein. The average daily gain (ADG) was significantly higher (p < 0.05) in the HP and MP groups, while the feed conversion ratio (FCR) was lower (p < 0.05) compared to the LP group. The MP group exhibited superior performance in terms of serum albumin (ALB) and high-density lipoprotein (HDL) levels, as well as protein digestibility (p < 0.05). Improvements in meat tenderness, as well as increased levels of leucine, flavor amino acids (FAAs), and non-essential amino acids (NEAAs) (p < 0.05), were observed in the MP group compared to those in the LP and HP groups. The levels of total fatty acids (TFAs), saturated fatty acids (SFAs), unsaturated fatty acids (UFAs), and monounsaturated fatty acids (MUFAs) were higher (p < 0.05) in the LP and MP groups than in the HP group, with no significant differences (p > 0.05) observed between the LP and MP groups. The genera Prevotella, Clostridium_sensu_stricto_1, NK4A214_group, Oscillospiraceae_UCG-002, and Oscillospiraceae_UCG-005 in the rectum were identified as differential microbes associated with varying dietary protein levels. In conclusion, this study indicates that a dietary protein level of 12.52% could enhance the growth performance, dietary nutrient digestibility, slaughter performance, and meat quality of Dezhou donkeys by modulating hindgut microbial communities.},
}
@article {pmid40572254,
year = {2025},
author = {Park, Y and Kyung, S and Mun, S and Yu, BS and Yun, K and Baek, C and Lee, DG and Kang, S and Kim, SR and Kim, JH and Lee, Y and Park, BC and Han, K},
title = {Comparative Analysis of Bacteriome in Hair Follicle Layers of Patients with Female Pattern Androgenic Alopecia.},
journal = {Microorganisms},
volume = {13},
number = {6},
pages = {},
pmid = {40572254},
issn = {2076-2607},
abstract = {Androgenetic alopecia (AGA) is the most common form of patterned hair loss, exhibiting gender-specific clinical features. Recent studies highlight the importance of the skin microbiome in maintaining skin health, but the relationship between the hair follicle microbiome and hair loss, particularly AGA, remains understudied. Hair follicle layer samples were collected directly from the crown region of female pattern hair loss (FPHL), male pattern hair loss (MPHL), and healthy adult women (control) groups. Microbial DNA was extracted and analyzed using Illumina 16S rRNA V3-V4 gene amplicon sequencing. Alpha-diversity and beta-diversity analyses and taxonomic and functional profiling were conducted through relative abundance, LEfSe, and PICRUSt2 analyses. The alpha-diversity analysis showed a significant decrease in microbial richness in the hair loss groups. Unweighted UniFrac-based beta-diversity analysis revealed significant clustering between the control group and the FPHL group. Taxonomic profiling and LEfSe analysis identified differences in microbial composition and biomarkers. PICRUSt2 analysis further revealed altered pathways related to porphyrin metabolism, fatty acid biosynthesis, and steroid hormone metabolism. Additionally, differences in microbiome composition and potential functions were found between the FPHL and MPHL groups. This study provides comprehensive insights into the hair follicle microbiome, revealing unique microbial patterns and functional alterations associated with FPHL. Understanding these microbiome characteristics may contribute to targeted approaches for addressing AGA. Further research is warranted.},
}
@article {pmid40572244,
year = {2025},
author = {Roy, S and Alizadeh Bahmani, AH and Davids, M and Herrema, H and Nieuwdorp, M},
title = {Modulating the Gut-Muscle Axis: Increasing SCFA-Producing Gut Microbiota Commensals and Decreasing Endotoxin Production to Mitigate Cancer Cachexia.},
journal = {Microorganisms},
volume = {13},
number = {6},
pages = {},
pmid = {40572244},
issn = {2076-2607},
abstract = {Cancer cachexia is a multi-organ and multifactorial syndrome characterized by muscle wasting (with or without adipose tissue loss) and systemic inflammation in patients with advanced malignancies. Gut microbiota dysbiosis, particularly the depletion of short-chain fatty acid (SCFA)-producing bacteria, may contribute to the progression of cancer cachexia. Studies in both murine models and humans consistently associate cachexia with a decline in SCFA-producing gut microbiota commensals and an overgrowth of pro-inflammatory pathobionts. These microbial imbalances may lead to reduced levels of SCFAs and branched-chain amino acids (BCAAs) and alter the normal bile acid profile. BCAAs and the maintenance of a normal bile acid profile are associated with muscle synthesis and decreased breakdown. While SCFAs (acetate, propionate, and butyrate), contribute to intestinal barrier integrity and immune regulation. SCFA depletion may increase gut permeability, allowing bacterial endotoxins, such as lipopolysaccharide (LPS), to enter the bloodstream. This may lead to chronic inflammation, muscle catabolism, and impairment of anabolic pathways. Interventions targeting gut microbiota in preclinical models have mitigated inflammation and muscle loss. While clinical data are limited, it suggests an improvement in immune functions and better tolerance to anticancer therapies. Current evidence is predominantly derived from cross-sectional studies suggesting associations without causality. Thus, future longitudinal studies are needed to identify biomarkers and optimize personalized therapy.},
}
@article {pmid40572228,
year = {2025},
author = {Yue, C and Chai, Z and Li, F and Shang, L and Hu, Z and Deng, Y and Tang, YZ},
title = {Transitions of the Bacteria-Fungi Microbiomes Associated with Different Life Cycle Stages of Dinoflagellate Scrippsiella acuminata.},
journal = {Microorganisms},
volume = {13},
number = {6},
pages = {},
pmid = {40572228},
issn = {2076-2607},
support = {42376138//National Natural Science Foundation of China/ ; 42176207//National Natural Science Foundation of China/ ; },
abstract = {Dinoflagellates significantly contribute to the carbon fixation and microbial loop in the ocean with high ecological diversity. While the microbial communities associated with the HABs of dinoflagellates have attracted intensive attention in recent years, little attention has been paid to the microbiomes associated with resting cysts, an important stage in the life cycle and bloom initiation dynamics of dinoflagellates. Using Scrippsiella acuminata as a representative of cyst producers and cyst-relevant research in dinoflagellates, we surveyed the bacteria and fungi microbiomes long associated with different life cycle stages of the dinoflagellate culture through 16S and ITS rRNA amplicon sequencing, and predicted their possible functions using the PICRUSt2 algorithm. The results found high species diversity of the associated bacteria-fungi microbiomes, and species featured with diverse and flexible metabolic capabilities that have stably co-occurred with the laboratory culture of S. acuminata. The host-attached and the free-living groups of bacteria-fungi microbiomes, as operationally defined in the context, showed significant differences in terms of their nutritional preferences. The bacteria-fungi species diversity and community structure associated with cysts are also distinguished significantly from that with vegetative cells, with the latter attracting more bacteria-fungi species specializing in phosphate solubilization. These results suggest that the relative species abundance and thus the community structure of the host-associated microbiome shift with the transition of life cycle stages and environmental conditions. Our findings show the association tightness between bacteria-fungi microbiomes and dinoflagellate hosts and the different life stages of hosts shaping the bacteria-fungi communities, which result in dynamic and specific interactions between bacteria-fungi microbiomes and their hosts.},
}
@article {pmid40572225,
year = {2025},
author = {Jiang, Y and Li, W and Li, J and Hu, J and Wei, Y and Wang, Y and Yang, H and Zhou, Y and Wu, Y and Zhang, S},
title = {Co-Inoculating Burkholderia vietnamiensis B418 and Trichoderma harzianum T11W Reduced Meloidogyne incognita Infestation of Tomato Plants.},
journal = {Microorganisms},
volume = {13},
number = {6},
pages = {},
pmid = {40572225},
issn = {2076-2607},
support = {ZR2021MC085//Shandong Provincial Natural Science Foundation/ ; 2022TSGC2370//Shandong Provincial Innovation Capability Promotion Project for Sci-tech Small and Medium-sized Enterprises/ ; 2024GH15//Innovation Pilot Project of Integration of Science, Education, and Industry of Shandong Academy of Sciences (International Scientific and Technology Cooperation)/ ; },
abstract = {Root-knot nematodes (RKNs; Meloidogyne incognita) pose a significant threat to tomato crops, necessitating sustainable control methods. This study investigated the inoculation efficacy of co-cultured Burkholderia vietnamiensis B418 and Trichoderma harzianum T11W compared with single-strain treatments for RKNs suppression and their influence on the structure and function of the rhizosphere microbiome. Co-inoculation with B418 + T11W achieved a 71.42% reduction in the disease index, significantly outperforming single inoculations of B418 (54.46%) and T11W (58.93%). Co-inoculation also increased plant height by 38.51% and fresh weight by 76.02% compared to the RKNs infested plants control, promoting robust tomato growth. Metagenomic analysis reveals that co-inoculation enhanced bacterial diversity, with 378 unique bacterial species and a high Shannon index, while fungal diversity decreased with Trichoderma dominance (83.31% abundance). Actinomycetota (46.42%) and Ascomycota (97.92%) were enriched in the co-inoculated rhizosphere, showing negative correlations with RKNs severity. Functional analysis indicates enriched metabolic pathways, including streptomycin and unsaturated fatty acid biosynthesis, enhancing microbial antagonism. Single inoculations altered pathways like steroid degradation (B418) and terpenoid biosynthesis (T11W), but co-inoculation uniquely optimized the rhizosphere microenvironment. These findings highlight co-inoculation with B418 + T11W effectively suppressing RKNs and fostering plant health by reshaping microbial communities and functions, offering a promising approach for sustainable agriculture.},
}
@article {pmid40572215,
year = {2025},
author = {Ning, W and Luo, X and Zhang, Y and Li, S and Yang, X and Wang, X and Chen, Y and Xu, Y and Zhang, D and Zhang, S and Liu, Y},
title = {Comparative Analysis of Nano-Bactericides and Thiodiazole-Copper on Tomato Rhizosphere Microbiome.},
journal = {Microorganisms},
volume = {13},
number = {6},
pages = {},
pmid = {40572215},
issn = {2076-2607},
support = {2024AQ2036//2024AQ2036/ ; 2024CX04//2024CX04/ ; RCZ202505//RCZ202505/ ; },
abstract = {Vegetable crops such as tomato are highly susceptible to various pathogens. Nanoparticles (NPs) are emerging as effective nano-bactericides for managing plant pathogens. Communities of rhizosphere bacteria are essential for plant physiological health and also serve as a critical factor in evaluating the environmental compatibility of NPs. We evaluated the effects of a nano-bactericide (Cu-Ag nanoparticles) and a commercial bactericide (thiodiazole-copper) on the rhizosphere microbiome of tomato. The results show that low and high doses of the two bactericides induced alterations in the bacterial community structure to differing extents. Cu-Ag nanoparticles increased the relative abundance of potentially beneficial bacteria, including Bacteroidota, Gemmatimonadota, Acidobacteriota, and Actinobacteriota. Functional prediction revealed that Cu-Ag nanoparticles may affect the metabolic pathways of tomato root rhizosphere microorganisms and regulate the lacI/galR family, which controls virulence factors and bacterial metabolism. This study provides insight into the influence of metal nanoparticles on plant rhizosphere microbiomes and may lay a foundation for the application of nano-bactericides for the environmentally friendly control of plant diseases.},
}
@article {pmid40572205,
year = {2025},
author = {Chen, YC and Chiang, YF and Huang, KC and Wang, KL and Huang, YJ and Shieh, TM and Ali, M and Hsia, SM},
title = {The Vaginal Microbiome: Associations with Vaginal pH, Menopause and Metabolic Parameters.},
journal = {Microorganisms},
volume = {13},
number = {6},
pages = {},
pmid = {40572205},
issn = {2076-2607},
abstract = {The vaginal microbiota, a critical determinant of women's health, is influenced by hormonal and metabolic parameters across the lifespan. While Lactobacillus species are beneficial markers of vaginal health, microbial composition undergoes pronounced alterations after menopause. This study aimed to elucidate the associations between vaginal microbiota composition, vaginal pH, menopausal status, and metabolic parameters in Asian women. Vaginal secretion samples were collected from 40 women (20 premenopausal, 20 postmenopausal). Full-length 16S rRNA gene sequencing was used to characterize the microbiota, categorized into Community State Types (CSTs): CST-I + II (Lactobacillus crispatus/gasseri, protective), CST-III (Lactobacillus iners, neutral), and CST-IV (anaerobic bacteria, harmful). Vaginal pH and clinical data were assessed in relation to microbial profiles. CST distribution differed significantly by menopausal status and vaginal pH. Harmful-type CST-IV was more prevalent in postmenopausal women (70% vs. 40%, p < 0.05), while CST-III was dominant in premenopausal women (45% vs. 5%). CST-IV was associated with elevated pH (median 6.00, p = 0.026) and increased abundance of anaerobes including Bacteroides, Fusobacterium, Porphyromonas, Prevotella, and Streptococcus. Oral antibiotic use reduced both beneficial and harmful CSTs, shifting toward neutral CST-III (75%, p = 0.048). Use of sodium-glucose cotransporter-2 (SGLT2) inhibitors in postmenopausal women was associated with a higher prevalence of protective CST-I + II (57.14% vs. 8.33%, p < 0.05), though no significant impact on pathogen presence was observed. This study highlights the dynamic interplay between menopausal status, metabolic interventions, and vaginal microbiota composition. Findings may inform targeted strategies to maintain vaginal health in aging populations.},
}
@article {pmid40572201,
year = {2025},
author = {Bukša, A and Petrović, F and Maglica, &#x17d;},
title = {Fungal β-Glucans Enhance Lactic Acid Bacteria Growth by Shortening Their Lag Phase and Increasing Growth Rate.},
journal = {Microorganisms},
volume = {13},
number = {6},
pages = {},
pmid = {40572201},
issn = {2076-2607},
support = {Uniri-prirod-18-302//University of Rijeka/ ; },
abstract = {The gut microbiome has a significant role in general health and well-being. Novel types of prebiotics, such as fungal polysaccharides, show potential for the formulation of new synbiotic formulations. However, little is known about the underlying mechanisms of the prebiotic effects of such compounds. This study investigated the prebiotic properties of fungal glucan extracts from Pleurotus ostreatus, Lentinula edodes, and Saccharomyces cerevisiae, employing a novel high-throughput method based on optical density measurements. This approach enabled the simultaneous screening of the effects of multiple extracts on six different strains of probiotic bacteria. Experiments were conducted to evaluate the effect of the extracts on the growth dynamics (the duration of the lag phase and the growth rate) of probiotic strains of the genera Lactobacillus and Lacticaseibacillus and on pathogenic bacteria. Fungal polysaccharide supplementation, particularly with their β-glucans, significantly shortened the lag phase by an average of 7-8 h in all tested strains and increased the growth rate by 2-fold in four strains of lactic acid bacteria. Different magnitudes of effects were observed across the various strain-extract combinations. This study lays the groundwork for elucidating the mechanism by which fungal β-glucans stimulate growth in probiotic bacteria and for the rapid screening of optimal combinations for formulating innovative synbiotics.},
}
@article {pmid40572188,
year = {2025},
author = {Asao, K and Hashida, N},
title = {Overview of Microorganisms: Bacterial Microbiome, Mycobiome, Virome Identified Using Next-Generation Sequencing, and Their Application to Ophthalmic Diseases.},
journal = {Microorganisms},
volume = {13},
number = {6},
pages = {},
pmid = {40572188},
issn = {2076-2607},
support = {23K15906 [to K.A.]//the Japan Society for the Promotion of Science/ ; 21K09695 [to N.H.]//the Japan Society for the Promotion of Science/ ; },
abstract = {This review outlines technological advances in pathogen identification and describes the development and evolution of next-generation sequencers that can be applied to the ocular microbiome. Traditional methods such as culture and PCR have limitations in detecting the full spectrum of resident microorganisms, prompting a transition toward metagenomic analysis. As microbiome research expands across body systems, the comprehensive identification of ocular bacteria, fungi, and viruses has become possible. The commensal ocular microbiome may influence disease development through changes in the immune system and ocular environment. Next-generation sequencing enables detailed microbial profiling, aiding in disease diagnosis and treatment selection. Alterations in the microbiome may also induce metabolic changes, offering insights into novel treatment methods. This review outlines the evolution of next-generation sequencing technology, summarizes current knowledge of microorganisms found on the ocular surface and in intraocular fluid, and discusses future challenges and prospects. However, the large volume of microbiome data obtained must be interpreted with caution due to possible analytical biases. Furthermore, determining whether the microbiome is truly pathogenic requires comprehensive interpretation beyond the clinical findings and results of traditional identification methods.},
}
@article {pmid40572181,
year = {2025},
author = {Hansen, LHB and Lauridsen, C and Nielsen, B and Jørgensen, L and Schönherz, A and Canibe, N},
title = {Early Inoculation of a Multi-Species Probiotic in Piglets-Impacts on the Gut Microbiome and Immune Responses.},
journal = {Microorganisms},
volume = {13},
number = {6},
pages = {},
pmid = {40572181},
issn = {2076-2607},
support = {7038-00168B//Innovation Foundation, Denmark/ ; },
abstract = {Intestinal diseases in nursery pigs harm health and performance and drive antimicrobial resistance. This study evaluated whether early probiotic inoculation helps piglets to cope with weaning-related gut challenges. The probiotic, containing Lacticaseibacillus rhamnosus, Enterococcus lactis, Bifidobacterium longum subsp. infantis, and Bifidobacterium breve, was given orally to newborn piglets daily until day 4 and then every other day until weaning at day 28 (at 4 × 10[9] CFU/dose). The control piglets received a placebo. The results showed that the probiotic pigs had reduced fecal alpha-diversity on day 7 but greater Shannon diversity on day 28 (feces) and day 23 (intestinal contents) compared to those of the control pigs. Beta-diversity analysis showed microbial differences between the groups on day 35. Most zOTUs (zero-radius operational taxonomic units) found to significantly differentiate the two treatment groups were found pre weaning. Bifidobacterium breve, Ligilactobacillus salivarius, as well as Clostridium ramosum were significantly more abundant in the feces of the probiotic pigs more than once. The probiotic pigs had higher expression levels of mucin 2 (MUC2); solute carrier family 5, member 8 (SLC5A8); and interleukin 8 (IL-8) post weaning. In the early post-weaning period, the probiotic pigs had less diarrhea as well as lower cadaverine levels in digesta than the control pigs. In conclusion, early probiotic inoculation may induce lasting immunomodulation via microbial antigen changes, enhancing resilience during challenges, like weaning. Notably, the effects persisted beyond weaning and probiotic cessation.},
}
@article {pmid40572178,
year = {2025},
author = {Maniscalco, I and Bartochowski, P and Priori, V and Iancau, SP and De Francesco, M and Innamorati, M and Jagodzinska, N and Giupponi, G and Masucci, L and Conca, A and Mroczek, M},
title = {The Effects of Fecal Microbial Transplantation on the Symptoms in Autism Spectrum Disorder, Gut Microbiota and Metabolites: A Scoping Review.},
journal = {Microorganisms},
volume = {13},
number = {6},
pages = {},
pmid = {40572178},
issn = {2076-2607},
abstract = {The bilateral interaction between the brain and the gut has recently been on the spectrum of researchers' interests, including complex neural, endocrinological, and immunological signaling pathways. The first case reports and clinical studies have already reported that delivering microbes through fecal microbial transplantation (FMT) may alleviate symptoms of psychiatric disorders. Therefore, modifying the gut microbiota through FMT holds promise as a potential treatment for psychiatric diseases. This scoping review assessed studies from PubMed related to FMT in autism spectrum disorder and attention deficit hyperactivity disorder. The evaluation included nine clinical studies and case reports. The beneficial and persistent effect on the autism spectrum disorder (ASD) symptoms has been reported. Also, an increased microflora diversity and altered levels of neurometabolites in serum were identified, albeit with a tendency to return to baseline over time. The microbiome-gut-brain axis could provide new targets for preventing and treating psychiatric disorders. However, a recent large randomized clinical trial has shed light on the previously collected data and suggested a possible contribution of the placebo effect. This highlights the necessity of large randomized double-blind studies to reliably assess the effect of FMT in ASD.},
}
@article {pmid40572172,
year = {2025},
author = {Wiącek, J and Skonieczna-Żydecka, K and Łoniewski, I and Deli, CK and Fatouros, IG and Jamurtas, AZ and Moszczyńska, D and Karolkiewicz, J},
title = {Lactobacillus helveticus R0052 and Bifidobacterium longum R0175 Supplementation: An Exploratory, Randomized, Placebo-Controlled Trial of Endocannabinoid and Inflammatory Responses in Female Dancers.},
journal = {Microorganisms},
volume = {13},
number = {6},
pages = {},
pmid = {40572172},
issn = {2076-2607},
support = {Development of Young Researchers (Doctoral school of J. Wi&#x105;cek)//Poznan University of Physical Education/ ; },
abstract = {The anandamide (AEA) and lipopolysaccharide (LPS) interaction is gaining attention, but evidence on the influence of probiotics on endocannabinoid system (ECS) biomarkers remains limited. This study (NCT05567653) investigated the effects of 12-week supplementation with Lactobacillus helveticus R0052 and Bifidobacterium longum R0175 on AEA (main outcome) and inflammatory biomarkers in female dancers. Fifteen participants (5 probiotic, 10 placebo) were included in the final analysis. Serum levels of AEA, LPS, and cytokines (tumor necrosis factor-alpha-TNF-α, interleukin-1 beta-IL-1β, and interleukin-10-IL-10) were measured using an ELISA (enzyme-linked immunosorbent assay), and the psychological stress responses were evaluated using the Mini-COPE questionnaire. At the baseline, a correlation between AEA and LPS was observed (Spearman's r = 0.9677, p < 0.05). After 12 weeks, no statistically significant differences in the AEA, LPS, cytokine levels, or stress-coping strategies were observed between the probiotic and placebo groups (LPS-probiotic: +3.48 EU/L, p = 0.9361; placebo: +56.98 EU/L, p = 0.0694; AEA-probiotic: -1.11 ng/mL, p = 0.9538; placebo: +14.08 ng/mL, p = 0.4749). The direction of change may indicate a trend toward increased inflammation in the absence of probiotics, consistent with patterns described in previous literature. However, these results should be viewed as hypothesis generating and warrant confirmation in larger trials.},
}
@article {pmid40572124,
year = {2025},
author = {LaPoint, P and Banks, K and Bacorn, M and Prasad, R and Romero-Soto, HN and Namasivayam, S and Chen, Q and Patel, A and Levy, S and Hourigan, SK},
title = {Can Vaginal Seeding at Birth Improve Health Outcomes of Cesarean Section-Delivered Infants? A Scoping Review.},
journal = {Microorganisms},
volume = {13},
number = {6},
pages = {},
pmid = {40572124},
issn = {2076-2607},
abstract = {Although Cesarean section (C-section) delivery is often a necessary medical intervention, it also increases the risk of the infant developing chronic inflammatory, metabolic, and neurodevelopmental disorders. The association of C-section with the development of these conditions is thought to be partially mediated by the effects of the C-section on the infant's microbiome development and subsequent immune regulation. C-section-delivered infants acquire a different set of microbes compared with infants who are vaginally delivered. "Vaginal seeding" exposes C-section-delivered infants to the maternal vaginal microbiome directly after birth, partly replicating the microbial exposures they would have received during a vaginal delivery. Studies have shown that vaginal seeding at birth partially restores the infant microbiome towards that of a vaginally delivered infant. More recently, preliminary studies have shown a potential benefit of vaginal seeding on health outcomes. Here, we examine the evidence from observational studies and randomized controlled trials that have evaluated microbiome restoration after C-section, and we discuss new research assessing the potential impact of vaginal seeding on immune, metabolic, and neurodevelopmental outcomes and the underlying mechanisms. Collectively, we review the potential health benefits, safety risks, regulatory implications, and future directions for the use of vaginal seeding in infants delivered by C-section.},
}
@article {pmid40572122,
year = {2025},
author = {Fu, R and Zhu, M and Zhang, Y and Li, J and Feng, H},
title = {Harnessing the Rhizosphere Microbiome for Selenium Biofortification in Plants: Mechanisms, Applications and Future Perspectives.},
journal = {Microorganisms},
volume = {13},
number = {6},
pages = {},
pmid = {40572122},
issn = {2076-2607},
support = {242300421100; 242300421586//the Natural Science Foundation of Henan Province/ ; 242102320358//the Science and Technology Research Project of Henan Province/ ; 2024HYTP008//the Project for Youth Talent Lifting of Henan Province/ ; },
abstract = {The rhizosphere microbiome plays a critical role in promoting crop health and productivity. Selenium (Se), a beneficial trace element for plants, not only enhances resistance to both abiotic and biotic stresses but also modulates soil microbial communities. Se biofortification of crops grown in seleniferous soils using selenobacteria represents an eco-friendly and sustainable biotechnological approach. Crops primarily absorb selenium from the soil in its oxidized forms, selenate and selenite, and subsequently convert it into organic Se compounds. However, the role of Se-oxidizing bacteria in soil Se transformation, bioavailability, and plant uptake remains poorly understood. In this review, systematic collection and analysis of research on selenobacteria, including both Se-oxidizing and Se-reducing bacteria, are therefore essential to elucidate their functions in enhancing crop growth and health. These insights can (i) deepen our mechanistic understanding of microbially mediated Se cycling and stress resilience and (ii) offer a novel framework for nanomicrobiome engineering aimed at promoting sustainable food production.},
}
@article {pmid40572111,
year = {2025},
author = {Lucero, J and Nishiguchi, MK},
title = {Host-Associated Biofilms: Vibrio fischeri and Other Symbiotic Bacteria Within the Vibrionaceae.},
journal = {Microorganisms},
volume = {13},
number = {6},
pages = {},
pmid = {40572111},
issn = {2076-2607},
support = {1T32GM141862-24S3/NH/NIH HHS/United States ; DBI 2214038//National Science Foundation/ ; },
abstract = {Biofilm formation is important for microbial survival, adaptation, and persistence within mutualistic and pathogenic systems in the Vibironaceae. Biofilms offer protection against environmental stressors, immune responses, and antimicrobial treatments by increasing host colonization and resilience. This review examines the mechanisms of biofilm formation in Vibrio species, focusing on quorum sensing, cyclic-di-GMP signaling, and host-specific adaptations that influence biofilm structure and function. We discuss how biofilms differ between mutualistic and pathogenic species based on environmental and host signals. Recent advances in omics technologies such as transcriptomics and metabolomics have enhanced research in biofilm regulation under different conditions. Horizontal gene transfer and phase variation promote the greater fitness of bacterial biofilms due to the diversity of environmental isolates that utilize biofilms to colonize host species. Despite progress, questions remain regarding the long-term effects of biofilm formation and persistence on host physiology and biofilm community dynamics. Research integrating multidisciplinary approaches will help advance our understanding of biofilms and their implications for influencing microbial adaptation, symbiosis, and disease. These findings have applications in biotechnology and medicine, where the genetic manipulation of biofilm regulation can enhance or disrupt microbiome stability and pathogen resistance, eventually leading to targeted therapeutic strategies.},
}
@article {pmid40572102,
year = {2025},
author = {Fan, J and Yin, Y and Liu, Y and Chen, Y and Long, W and Liao, C},
title = {Age-Dependent Composition and Diversity of the Gut Microbiome in Endangered Gibbon (Nomascus hainanus) Based on 16S rDNA Sequencing Analysis.},
journal = {Microorganisms},
volume = {13},
number = {6},
pages = {},
pmid = {40572102},
issn = {2076-2607},
support = {31960703//The National Natural Science Foundation of China/ ; U22A20363//the National Natural Science Foundation of China/ ; ZDKJ2021035//The Major Science and Technology Plan of Hainan Province/ ; },
abstract = {The Hainan gibbon (Nomascus hainanus) is one of the most endangered primates globally, threatened by habitat destruction, genetic diversity loss, and ecological competition. In this study, given the critical role of the gut microbiota in host immune regulation and nutrient metabolism, we investigated the composition of and age-related variations in the gut microbiota in Hainan gibbons. Using 16S rRNA sequencing, we systematically investigated the gut microbial diversity of Hainan gibbons. We collected 41 fecal samples from Hainan Tropical Rainforest National Park, covering three age groups: juveniles (4-6 years), subadults (7-10 years), and elderly animals (≥13 years). This study found that microbiota composition changed significantly with age. Juveniles had higher microbial diversity and complexity, while subadults showed an increased abundance of Fibrobacter and Prevotella in their microbial communities, along with a Tax4Fun-predicted enrichment of functional genes related to energy metabolism, cell motility, and nervous system functions. LEfSe analysis identified statistically significant microbial taxa among different age groups, with Bacteroidota and Firmicutes being the dominant phyla across all groups with varying proportions. These results highlight the critical role of the gut microbiota in the health and adaptability of Hainan gibbons, offering insights for conservation strategies. The findings of this study are significant for understanding the changes in gut microbiota and their ecological functions across different life stages of endangered primates.},
}
@article {pmid40572090,
year = {2025},
author = {Jayasekera, V and Han, Y and Du, L},
title = {Identification of Pyrrole-2-Carboxylic Acid from the Biocontrol Agent Lysobacter Involved in Interactions with Fusarial Fungi.},
journal = {Microorganisms},
volume = {13},
number = {6},
pages = {},
pmid = {40572090},
issn = {2076-2607},
support = {P20 GM113126/GM/NIGMS NIH HHS/United States ; NA//University of Nebraska Collaboration Initiative Seed Grant/ ; },
abstract = {Lysobacter, a genus of Gram-negative bacteria, is known for producing antibiotic compounds, making it a promising biocontrol agent against crop pathogens. As part of the soil microbiome, Lysobacter species cooccur with a variety of microorganisms in the ecosystem. However, little is known about bioactive natural products involved in Lysobacter's interactions with other organisms. This study investigated interactions between Lysobacter sp. 3655 and two economically important fungal pathogens, Fusarium graminearum and Fusarium verticillioides. We discovered a Lysobacter molecule that is dramatically suppressed when co-culturing with the fungi, and the structure of this molecule was determined to be pyrrole-2-carboxylic acid (P2C). Chitin, a primary component of fungal cell walls, also suppressed P2C production in Lysobacter. Exogenous P2C addition promoted formation of Lysobacter biofilms within a range of concentrations, suggesting its potential role as a signaling molecule. Previously reported result showed that the mutation of the global regulator Clp in Lysobacter enzymogenes led to drastic increase of biofilm formation. Intriguingly, while P2C increased the biofilm formation in the wildtype of L. enzymogenes, it reduced the biofilms in the Clp mutant. Together, these findings reveal P2C as a novel signaling molecule mediating the interaction between Lysobacter and surrounding fungal species, highlighting its role in Lysobacter adaptation in response to environmental conditions.},
}
@article {pmid40572088,
year = {2025},
author = {Mauri, C and Giubbi, C and Consonni, A and Briozzo, E and Meroni, E and Luzzaro, F and Tonolo, S},
title = {The Emergence of Bacteroides pyogenes as a Human Pathogen of Animal Origin: A Narrative Review.},
journal = {Microorganisms},
volume = {13},
number = {6},
pages = {},
pmid = {40572088},
issn = {2076-2607},
abstract = {Bacteroides pyogenes is a Gram-negative obligate anaerobe rod. It is naturally found in the oral microbiome of cats and dogs, which represents a primary source of disease for humans. The present review provides an update on the role of B. pyogenes as a pathogen responsible for infections in humans. Indeed, an increasing number of B. pyogenes infections have been reported in recent years, including skin and soft tissue infections as well as severe diseases like osteomyelitis, Lemierre's syndrome, and bloodstream infection. Pre-analytical and analytical phases are crucial to guarantee the isolation of anaerobic bacteria, including B. pyogenes. Moreover, the introduction of MALDI-TOF mass spectrometry and 16S rRNA sequencing in clinical microbiology laboratories may be partially responsible for the increasing number of reports of B. pyogenes infections. However, the mechanisms underlying the pathogenicity of B. pyogenes remain poorly understood and require further investigations. Indeed, despite common antimicrobial susceptibilities, infections frequently persist and require multiple courses of antibiotics. In addition, based on literature data, this review indicates that treatment of skin and soft tissue infections often necessitates surgical procedures and hospitalization.},
}
@article {pmid40572084,
year = {2025},
author = {Vieira de Lima, R and Blanco, KC and Bagnato, VS},
title = {Control of Methicillin-Resistant Staphylococcus aureus Using Photodynamic Therapy in Synergy with Staphylococcus epidermidis: Role of Mixed Cultures in Developing Strategies to Inhibit Infections.},
journal = {Microorganisms},
volume = {13},
number = {6},
pages = {},
pmid = {40572084},
issn = {2076-2607},
support = {88887.928185/2023-00//CAPES/ ; 2013-07276-1//CEPOF-CEPID Program/ ; },
abstract = {Staphylococcus aureus is a Gram-positive bacterium living abundantly on our skin and mucous membranes. When there is an imbalance in microbiota, they are the main protagonists of various infections, such as soft tissue infections and bacteremia. However, Staphylococcus epidermidis also colonizes this microbiome, is able to compete with pathogenic bacteria, including methicillin-resistant Staphylococcus aureus (MRSA), and can contribute to treatments such as photodynamic inactivation (PDI) by inhibiting infection progression and restoring a healthy microbiota. In vitro photodynamic inactivation experiments were carried out using synthetic curcumin at a concentration of 5 μM as a photosensitizer and varying light doses (1, 2 and 5 J/cm[2]) at a wavelength of 450 nm, on pure cultures (S. aureus, S. epidermidis and MRSA) and mixed cultures, in which bacteria were placed together proportionally. This study revealed that pure cultures of these bacteria obtained statistically significant results with varying light doses of 2 and 5 J/cm[2]. In addition, in an attempt to bring infections closer to reality, experiments were carried out on mixed cultures. The results were not only significant but also increased reduction of bacteria, including resistant bacteria. Study offers new perspectives on the importance of themicrobiota for treatment of infections caused by the Staphylococcus genus.},
}
@article {pmid40572081,
year = {2025},
author = {Dietz, MW and Hsu, BY and van der Velde, M and Tieleman, BI},
title = {Gut Microbiome Development in Rock Pigeons: Effects of Food Restriction Early in Life.},
journal = {Microorganisms},
volume = {13},
number = {6},
pages = {},
pmid = {40572081},
issn = {2076-2607},
support = {Scolarship of overseas studies//Ministry of Education, Taiwan/ ; Personal Grant ot Prof A.G.G. Groothuis//University of Groningen/ ; },
abstract = {The developmental period is a critical phase in birds, influencing even lifetime reproductive success. The gut microbiome (GM) is important herein, affecting digestive capacity and immune function. Diet impacts the GM, but wild nestlings may experience resource limitations, which may also affect the GM. We investigated the effects of a week of food restriction early in life on the GM in captive rock pigeon nestlings (Columba livia). We sampled the GM at 0, 2, 4, 7, 8, 12, 20, 27, and 38 days and in foster parents. Alpha diversity varied only with age. However, differences in alpha diversity between nestlings and adults were larger during food restriction. Beta diversity varied with age, food treatment, and their interaction term. Four of the eleven major genera varied with age, while four others did not vary with age or food treatment. Major genera that contained potential pathogens (Escherichia-Shigella and Clostridium sensu stricto 1) were more abundant under food restriction. Food restriction thus affected GM development. The increase in alpha diversity and potential pathogens suggest that suppressed immune function may mediate the impact of food restriction on the GM. The effect diminished when food restriction was ended, suggesting that in wild nestlings, the impact of food restriction on the GM may be short-term.},
}
@article {pmid40572077,
year = {2025},
author = {Saha, P and Hartmann, P},
title = {Impact of Gut Microbiome on Gut Permeability in Liver and Gut Diseases.},
journal = {Microorganisms},
volume = {13},
number = {6},
pages = {},
pmid = {40572077},
issn = {2076-2607},
support = {K12 HD105271/GF/NIH HHS/United States ; KL2TR001444//University of California San Diego Altman Clinical and Translational Research Institute (ACTRI)/NIH grant/ ; #PNC22-159963//AASLD Pinnacle Research Award in Liver Diseases/ ; P30 DK120515/DK/NIDDK NIH HHS/United States ; },
abstract = {Hepatobiliary and gastrointestinal conditions, including chronic liver diseases and inflammatory bowel disease, are associated with significant morbidity and mortality globally. While the pathophysiology and symptoms vary from one disease to another, aberrations of the gut microbiome with deleterious microbial products affecting the intestinal barrier are common in patients suffering from these diseases. In this review, we summarize changes in the gut microbiome associated with various disease states and detail their role in gut barrier disruption and in modulating disease progression. Further, we discuss therapeutic interventions and precision medicine approaches targeting the microbiome, which have shown promise in alleviating these chronic illnesses in mouse models and patients.},
}
@article {pmid40572065,
year = {2025},
author = {Souza, DT and Moreira, ACS and Quevedo, HD and May, A},
title = {Evaluation of Microbial Transplantation from High-Productivity Soil to Improve Soybean Performance in Less Productive Farmland.},
journal = {Microorganisms},
volume = {13},
number = {6},
pages = {},
pmid = {40572065},
issn = {2076-2607},
abstract = {Microbial transplantation represents a sustainable strategy to address productivity gaps in agricultural soils by transferring microbiomes that enhance nutrient cycling, pathogen suppression, and stress tolerance. This study evaluates whether probiotic consortia from high-yield soybean soils (donor soil) could improve crop performance in less productive fields (recipient soil). We developed a host-adapted inoculant from soybean rhizospheres grown in donor soil and applied it to seeds at five concentrations (0.25-10 g/kg seed) in recipient soil, with untreated controls for comparison. To assess crop-specific microbial recruitment, we prepared a parallel bean-derived inoculant under identical conditions. Through 16S rRNA sequencing and growth/yield analysis, we found the following: (1) Distinct bacteriome assemblies between soybean- and bean-derived inoculants, confirming host specificity; (2) Successful enrichment of beneficial taxa (Enterobacteriaceae increased by 15-22%, Rhizobiaceae by 7-12%) despite native community resilience; and (3) Consistent yield improvement trends (4.8-6.2%), demonstrating potential to bridge productivity gaps. These results show that transplanted microbiomes can effectively modulate rhizosphere communities while maintaining ecological balance. This work establishes a scalable approach to address soil productivity limitations through microbiome transplantation. Future research should optimize (a) inoculant composition for specific productivity gaps; (b) delivery systems; and (c) compatibility with resident microbiomes, particularly in systems where niche-specific processes govern microbial establishment.},
}
@article {pmid40572063,
year = {2025},
author = {Shi, J and Su, H and He, S and Dai, S and Mao, H and Wu, D},
title = {Pan-Genomic Insights into Rumen Microbiome-Mediated Short-Chain Fatty Acid Production and Regulation in Ruminants.},
journal = {Microorganisms},
volume = {13},
number = {6},
pages = {},
pmid = {40572063},
issn = {2076-2607},
abstract = {The rumen microbiome represents a cornerstone of ruminant digestive physiology, orchestrating the anaerobic fermentation of plant biomass into short-chain fatty acids (SCFAs)-critical metabolites underpinning host energy metabolism, immune function, and environmental sustainability. This comprehensive review evaluates the transformative role of pan-genomics in deciphering the genetic and metabolic networks governing SCFA production in the rumen ecosystem. By integrating multi-omics datasets, pan-genomic approaches unveil unprecedented layers of microbial diversity, enabling precise identification of core functional genes and their dynamic contributions to carbohydrate degradation and SCFA biosynthesis. Notable advancements include the following: mechanistic insights into microbial community assembly and metabolic pathway regulation, highlighting strain-specific adaptations to dietary shifts; precision interventions for optimizing feed efficiency, such as rationally designing microbial consortia and screening novel feed additives through pan-genome association studies; and sustainability breakthroughs, demonstrating how targeted modulation of rumen fermentation can simultaneously enhance production efficiency and mitigate methane emissions. This synthesis underscores the potential of pan-genomics to revolutionize ruminant nutrition, offering a blueprint for developing next-generation strategies that reconcile agricultural productivity with environmental stewardship. The translational applications discussed herein position pan-genomics as a critical tool for advancing animal science and fostering a resilient livestock industry.},
}
@article {pmid40572060,
year = {2025},
author = {Dong, W and Zang, Q and Wang, Y and Ma, E and Ding, W and Yan, L and Hao, F},
title = {Synergistic Effects of Paenibacillus polymyxa NBmelon-1 Inoculation and Grafting Restructure of Rhizosphere Microbiome and Enhanced Disease Resistance in Melon Self-Rootstocks.},
journal = {Microorganisms},
volume = {13},
number = {6},
pages = {},
pmid = {40572060},
issn = {2076-2607},
support = {2021Z006//Development of Specific Germplasm and Breeding of New Multi-resistant Melon Rootstock Varieties/ ; CARS-25//National Watermelon and Melon Industry Technology System Construction Project/ ; },
abstract = {Rhizosphere microorganisms play pivotal roles in mitigating the challenges associated with continuous cropping in melon cultivation. While grafting and plant growth-promoting rhizobacteria (PGPR) independently influence rhizosphere microbial communities, their combined effects remain largely unexplored. This study investigates the synergistic regulation of Paenibacillus polymyxa NBmelon-1 inoculation and grafting on rhizosphere microbiome assembly, plant performance, and disease resistance in melon self-rootstocks. Field experiments demonstrated that NBmelon-1 inoculation significantly enhanced rootstock stem diameter (95.3% increase in spring) and root development, achieving a graft survival rate exceeding 95%. The combined treatment (NB+GJ) increased scion fruit yield by 29.8% in autumn and 36.5% in spring, as well as the single-fruit weight by 22.5% in autumn and 37.3% in spring, while maintaining fruit morphology. Integrated 16S rRNA and ITS sequencing revealed that the NB+GJ treatment selectively enriched antagonistic bacterial phyla (e.g., Firmicutes and Actinobacteriota) and suppressed pathogenic fungi (e.g., Fusarium and Melanconiella). Seasonal shifts in microbial diversity and functional gene profiles underscored the dynamic interplay between treatments and environmental factors. These findings establish a novel strategy for optimizing melon self-rootstock grafting systems and sustainably managing soil-borne diseases.},
}
@article {pmid40572023,
year = {2025},
author = {Silva, APV and Moloney, GM and Sequeira, AM and Liber, M and Bastiaanssen, T and Rea, K and Fitzgerald, P and Golubeva, A and Rodriguez-Aburto, M and Renes, IB and Knol, J and Dinan, T and Cryan, JF},
title = {Targeting the Microbiota Reverses C-Section-Induced Effects on Intestinal Permeability, Microbiota Composition, and Amygdala Gene Expression in the Mouse.},
journal = {Neurogastroenterology and motility},
volume = {},
number = {},
pages = {e70107},
doi = {10.1111/nmo.70107},
pmid = {40572023},
issn = {1365-2982},
support = {/SFI_/Science Foundation Ireland/Ireland ; },
abstract = {BACKGROUND: The microbiome significantly influences the development of the gastrointestinal and immune systems. The delivery method, whether Caesarean section (CS) or vaginal birth (VB), plays a crucial role in shaping microbiota composition, with CS babies exhibiting differences. Early-life nutritional interventions using probiotics or prebiotics may help restore this imbalance in CS infants. Our study aimed to assess gut permeability in CS mice compared to VB mice and explore whether prebiotics or probiotics could mitigate any deficiencies.<br><br>METHODS: Using a mouse model (NIH Swiss) for CS delivery, we measured plasma levels of a 4&#x2009;kDa macromolecule (FITC) at PND7, 14, 23, and 35. We evaluated ileal gene expression of tight junction proteins, profiled intestinal microbiome composition, and examined the expression of genes involved in neurotransmitter physiology in the amygdala. Additionally, we studied the impact of administering Bifidobacterium breve in drinking water and dietary administration of GOS/FOS on these outcomes.<br><br>KEY RESULTS: At PND7, CS-born mice exhibited increased ileal permeability, along with reduced expression of Tjp1, Occludin, Claudin 3, and Epcam compared to VB mice. Administration of B. breve or GOS/FOS alleviated changes in Epcam expression. During the pre-weaning period, beta diversity differed between VB and CS. Post-weaning, &#x3b2;-diversity increased following probiotic and prebiotic intervention. Additionally, CS mice showed changes in neurotransmitter gene expression in the amygdala, which were also mitigated by B. breve or GOS/FOS.<br><br>DISCUSSION: Our findings indicate that targeted microbiota-associated interventions can reverse deficits in intestinal permeability induced in CS mice.},
}
@article {pmid40571832,
year = {2025},
author = {Viswanathan, L and Moshiree, B},
title = {Advances in Diagnostics for the Evaluation of Neurogastroenterology &amp; Motility Disorders: Are They Ready for Prime Time?.},
journal = {Current gastroenterology reports},
volume = {27},
number = {1},
pages = {45},
pmid = {40571832},
issn = {1534-312X},
}
@article {pmid40571722,
year = {2025},
author = {Toit, AD},
title = {A misplaced microbiome.},
journal = {Nature reviews. Microbiology},
volume = {},
number = {},
pages = {},
pmid = {40571722},
issn = {1740-1534},
}
@article {pmid40571157,
year = {2025},
author = {Zhou, W and Ring, NG and Caldwell, R and Milstone, LM and Oh, J},
title = {Genotype-environment-driven dysbiosis in the skin microbiome of ichthyosis.},
journal = {The Journal of investigative dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jid.2025.06.1568},
pmid = {40571157},
issn = {1523-1747},
abstract = {Many factors might be expected to influence the cutaneous microbiome, especially on diseased skin. Yet few studies account for the complex interactions between host and environmental factors. To shed light on such interactions, we characterized the skin microbiome from seven types of ichthyosis and confirmed previous reports of genotype-related and barrier-related effects. We then focused on the TGM1 genotype and assessed the association between the microbiome features and the ichthyosis genotype and phenotype while adjusting for contextual host covariables, including clinical treatments. We showed that the ichthyosis genotype and phenotype interact - sometimes antagonistically - with treatment to influence the composition and metabolic potential of the skin microbiome at species, strain, and metabolic pathway levels. Notable interactions with the TGM1 genotype included transepidermal water loss (TEWL) and emollient and retinoid use. Larger groups of patients and additional measurements will be needed to unravel the complex interactions that impact host and environmental influences on skin microbiome.},
}
@article {pmid40571154,
year = {2025},
author = {Zhou, R and Chaskar, P and Patrick, MT and Wang, K and Piketty, C and Julia, V and Gudjonsson, JE and Krishnaswamy, JK and Tsoi, LC},
title = {Nemolizumab treatment normalizes dysregulated microbiome in lesional prurigo nodularis.},
journal = {The Journal of investigative dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jid.2025.06.1575},
pmid = {40571154},
issn = {1523-1747},
}
@article {pmid40571109,
year = {2025},
author = {Chen, H and Qiu, X and Lei, S and Zhao, Y and Zhang, M and Gao, M and Guo, R and Di, H and Huang, J and Yu, Z},
title = {Gut vs. Vaginal Microbiome in Diabetes Progression: Key Microbial Shifts and Implications.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {107833},
doi = {10.1016/j.micpath.2025.107833},
pmid = {40571109},
issn = {1096-1208},
abstract = {BACKGROUND: Dysiosis in gut and vaginal microbiome is implicated in type 2 diabetes (T2D) pathogenesis, but their contributions remain unclear. This study aims to compare their alterations and clinical relevance in diabetes development.<br><br>METHODS: Metagenomic sequencing was performed on vaginal and fecal samples from T2D patients. Differential feature selection and correlation model were used to dissect microbial contributions to diabetic markers.<br><br>RESULTS: Gut microbiota exhibited reduced diversity in T2D patients, with enrichment of Desulfovibrio desulfuricans and Adlercreutzia equolifaciens validated in public cohorts. Vaginal microbiota diversity remained unaffected. Furthermore, structural equation modeling revealed stronger gut microbiota associations with blood glucose and HbA1c. Notably, Romboutsia ilealis-derived pgm was enriched in the diabetes group, which could catalyze the production of glucose, suggesting that it may be involved in the progression of T2D.<br><br>CONCLUSION: Our findings establish the gut microbiome as the dominant driver of T2D progression, with R. ilealis emerging as a potential therapeutic target. This highlights the priority of gut-centric microbiota interventions in diabetes management.},
}
@article {pmid40571107,
year = {2025},
author = {Chen, J and Chen, Z and Xu, B and Huang, Z and Zhang, C},
title = {Skin microbiome of Asian elephants with skin diseases during seasonal transitions.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {107832},
doi = {10.1016/j.micpath.2025.107832},
pmid = {40571107},
issn = {1096-1208},
abstract = {INTRODUCTION: Wild Asian elephants (Elephas maximus), which are an endangered species, often suffer from skin diseases during seasonal transitions, which seriously affect their health. Understanding the pathogenesis of such skin diseases is critical for their prevention and treatment. It is known that skin microorganisms are closely related to host skin health.<br><br>OBJECTIVE: To compare the microbiotas and microbiomes of diseased and healthy skin of Asian elephants.<br><br>METHODS: DNA was extracted from skin swab samples from diseased and healthy Asian elephants for metagenomic sequencing. Various bioinformatic tools were used to process the raw sequencing data and identify gene sequences for functional annotation and species identification as well as to determine species abundance. Antibiotic resistance genes and virulence factors were also identified using DIAMOND.<br><br>RESULTS: Staphylococcus was highly enriched in the microbiota of diseased skin, whereas Leuconostoc predominated in that of healthy skin. Moreover, substantial differences existed between the two elephant skin groups in terms of metabolic pathways related to ATP-binding cassette transporters and TCSs and the abundance of antibiotic resistance genes and Staphylococcus-associated toxins. The substantial difference in Staphylococcus-related virulence factors was likely due to the significant enrichment of Staphylococcus in the diseased skin samples, suggesting that this bacterial genus is the causative agent of skin diseases in Asian elephants. Additionally, Leuconostoc mesenteroides, which was enriched in the healthy skin samples, has anti-inflammatory, antimicrobial, and other beneficial effects that have promising applications in the prevention, diagnosis, and treatment of skin diseases.<br><br>CONCLUSION: This study reveals the cause of skin diseases in Asian elephants and provides a theoretical basis for improving the skin health of wild animals and expanding wildlife conservation methods and technologies.},
}
@article {pmid40571019,
year = {2025},
author = {Wang, Y and Zhang, Z and Chen, S and Zhang, Y and Cao, Y and Zhao, J and Chen, A and Wu, Y},
title = {Integrated microbiome and metabolome analyses reveal effects of sodium alginate on the growth of Meretrix meretrix.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {145431},
doi = {10.1016/j.ijbiomac.2025.145431},
pmid = {40571019},
issn = {1879-0003},
abstract = {Sodium alginate (SA) has diverse biological activities, and its effects on the growth and intestinal health of Meretrix meretrix were evaluated over a 60-day feeding trial. The study tested five SA concentrations: 0 mg/L (SA0), 5 mg/L (SA5), 10 mg/L (SA10), 15 mg/L (SA15), and 20 mg/L (SA20). Results showed that 10 mg/L SA (SA10) significantly improved clam growth and intestinal health, enhancing villus length, goblet cell distribution, and digestive enzyme activity. However, higher SA concentrations (SA15 and SA20) degraded growth and intestinal health. Integrated microbiome-metabolome analysis revealed that sodium alginate at 10 mg/L could activate phenylalanine metabolism, tryptophan metabolism and lysine degradation pathway by optimizing the microbial community structure and specifically enriching functional bacteria (such as Xylanibacter, Achromobacter and Escherichia-Shigella), thus generating key metabolites such as phenaceturic acid, indole-3-acetamide and succinate, thus synergistically strengthening the intestinal barrier function, regulating the immune microenvironment and improving the energy metabolism efficiency. In a word, the appropriate concentration of sodium alginate (10 mg/L) can reshape the intestinal flora structure and metabolic network of M. meretrix, and then promote the growth of the clams.},
}
@article {pmid40571003,
year = {2025},
author = {Zhu, F and Xi, T and Liu, Q and Yu, N and Wang, F and Wen, Y and Wang, W},
title = {Asparagus polysaccharide attenuates atherosclerosis by modulating gut microbiota and metabolites.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {145492},
doi = {10.1016/j.ijbiomac.2025.145492},
pmid = {40571003},
issn = {1879-0003},
abstract = {Atherosclerosis remains a critical driver of cardiovascular morbidity; however, therapeutic strategies for halting its progression remain suboptimal. To date, there are no reports of asparagus polysaccharide (AP)-the active component of Asparagus cochinchinensis (Lour.) Merr.-promoting human health by modulating the gut microbiota. In the present study, we provided a high-fat diet (HFD) to an ApoE[-/-] murine model to investigate the mechanisms by which AP mitigates atherosclerotic pathogenesis. Our results demonstrated that AP significantly alleviated HFD-induced aortic lesions, decreased serum lipid levels (p < 0.01), and markedly decreased the mRNA levels of inflammatory factors in the aorta (p < 0.001). Using 16S rRNA sequencing, we observed that AP reversed HFD-induced alterations in the relative abundances of Bacteroidetes and Firmicutes at the phylum level, and remarkably increased the abundance of Actinobacteria (p < 0.01). Using untargeted metabolomics analysis, we identified 10 key metabolites associated with atherosclerosis. Furthermore, while L-glutaminyl-L-tryptophan levels increased in the faeces and decreased in the blood following HFD induction, AP treatment reversed this trend. This study provides the first evidence that AP exerts its anti-atherosclerotic effects through the gut microbiota-metabolite axis, with L-glutaminyl-L-tryptophan emerging as a potential, novel translational biomarker for therapeutic monitoring.},
}
@article {pmid40570997,
year = {2025},
author = {Liu, W and Lan, Z and Lin, Z and Zhao, Y and Lian, J and Yu, G},
title = {The microbiome-immune cell interaction network: Advancing tumor immunotherapy.},
journal = {Seminars in cancer biology},
volume = {114},
number = {},
pages = {128-137},
doi = {10.1016/j.semcancer.2025.06.009},
pmid = {40570997},
issn = {1096-3650},
abstract = {Tumor immunotherapy has achieved revolutionary advancements; however, owing to the complex interplay of multiple intrinsic and extrinsic tumor factors, the patient response rate remains suboptimal. Recent research has emphasized the pivotal role of microbiome in tumor progression. Under normal physiological conditions, microbiome enter orally and colonize sites such as the oral and intestinal mucosa, establishing a dynamic microbiome equilibrium that participates in essential physiological processes, including host metabolism and immune regulation. However, in pathological states, including dysbiosis, tumor initiation, or compromised mucosal barrier function, the microbiome can penetrate the mucosal barrier, infiltrate tumor tissues, and engage in intricate direct or indirect interactions with immune cells. These interactions play a pivotal role in reshaping the tumor immune microenvironment and modulating the host's anti-tumor immune response. This review elaborate the regulatory mechanisms involved in direct and indirect interactions between microbiome and immune cells within tumors, and their implications for tumor immunotherapy. We discuss the external factors that impact these interactions and outline the potential use of engineered bacteria in cancer treatment. From the perspective of the interaction network between microbiomes and immune cells, this review elucidates the mechanisms and potential of microbiomes in tumor immunotherapy, offering new insights and potential targets for innovative strategies in tumor prevention and treatment.},
}
@article {pmid40570852,
year = {2025},
author = {Janssen, E and Das, M and Butts, J and Alasharee, M and Mukherjee, S and Lozano, GL and Rao, C and Livingston, AF and Woods, B and Smith, E and Peters, Z and Milin, E and Beamer, MA and Wilkie, H and Leyva-Castillo, JM and Kam, C and Sobh, A and Dasouki, M and Wakim, RH and Dbaibo, G and Al-Herz, W and Chatila, TA and Finkelman, FD and Rakoff-Nahoum, S and Geha, RS},
title = {DOCK8 in T cells promotes Th17 and Treg cell functionality to restrain mucosal mast cells and limit susceptibility to oral anaphylaxis.},
journal = {Immunity},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.immuni.2025.06.004},
pmid = {40570852},
issn = {1097-4180},
abstract = {Immunoglobulin E (IgE)-mediated release of mediators from mast cells (MCs) drives food allergy, and intestinal MC load is an important determinant of disease severity. Dedicator of cytokinesis 8 (DOCK8)-deficient patients are highly susceptible to food allergy. We found that they exhibited elevated serum MC tryptase levels, suggesting increased MC load. Dock8[-/-] mice also had exaggerated IgE-mediated oral anaphylaxis, expansion of jejunal mucosal MCs (MMCs), and elevated serum levels of MMC-derived tryptase. This resulted in increased intestinal permeability, which promoted antigen absorption and thereby oral anaphylaxis. Mechanistically, these events were driven by an intestinal cascade in which reduced interleukin (IL)-17 cytokines led to dysbiosis, which drove IL-25 production. Increased IL-25 enhanced T helper (Th)2 production of IL-4 that expanded MMCs and exaggerated oral anaphylaxis. Furthermore, the failure of DOCK8-deficient T regulatory (Treg) cells to suppress intestinal IL-4 production and MC expansion left the exaggerated anaphylaxis unrestrained. These results suggest multi-faceted coordination between the microbiome, mucosal T cells, and MCs to restrict oral anaphylaxis.},
}
@article {pmid40570789,
year = {2025},
author = {Liu, W and Bo, T and Zhao, N and Hu, B and Li, G and Xiao, Z},
title = {Small mammal activities structure fine-scale soil microbial communities and coordinate rodenticide effects in the typical steppes of China.},
journal = {Ecotoxicology and environmental safety},
volume = {302},
number = {},
pages = {118560},
doi = {10.1016/j.ecoenv.2025.118560},
pmid = {40570789},
issn = {1090-2414},
abstract = {Soil microbial community is a diverse combination of microbial species that is influenced by soil moisture, physicochemical properties, biological activities, and other factors. Brandt's vole (Lasiopodomys brandtii) is a small rodent distributed in the typical steppes of China, Mongolia, and Russia, which often causes serious pest to the local areas when its population outbreaks. Yet the impacts of rodenticides on soil microbial diversity and ecosystem functions in Brandt's vole habitats are not well-known. In this study, we compared the microbial community composition and functional genes between the central and peripheral areas of undisturbed cave communities, as well as grasslands with and without rodenticides. The results showed that the activity of field voles and rodenticides had a significant impact on soil microbial communities, antibiotic resistance genes, and soil element cycling. The use of rodenticides reduces the activity of rodents, reduces pathogenic bacteria in the soil. The use of rodenticides inhibits N cycling, while rodent activity promotes the N cycling. Relative abundance of dissimilatory nitrate reduction nitrate (narGHI or napA), denitrification nitrous oxide (nosZ), nitrogen fixation nitrogen (nifH), denitrification nitric oxide (norB) were significantly decreased in rodenticide soil. The activity of rodents increases the abundance of specific antibiotic resistance genes (ARGs), while rodenticides reduce the abundance of AGRs in the soil. Our study for the first time explores the interaction effects of rodent activity and rodenticide use on soil, providing a reference for understanding the multifunctionality of soil ecosystems and the response of microbial communities to external disturbances (rodents and humans) in the future.},
}
@article {pmid40570762,
year = {2025},
author = {Pateriya, D and Malwe, AS and Sharma, VK},
title = {CRCpred: An AI-ML tool for colorectal cancer prediction using gut microbiome.},
journal = {Computers in biology and medicine},
volume = {195},
number = {},
pages = {110592},
doi = {10.1016/j.compbiomed.2025.110592},
pmid = {40570762},
issn = {1879-0534},
abstract = {Colorectal cancer (CRC) is a leading cause of death worldwide. A plethora of research shows the alteration of the gut microbiome and the association of bacterial taxa with CRC. Gaining insights into the health status through microbiome-based diagnosis is a rapidly growing area of research. Many studies have utilized machine learning (ML) to leverage gut microbial dysbiosis for CRC screening, yet most have been limited by their training data and algorithms. Here, using 1728 publicly available metagenomic samples from 11 studies across eight countries, we developed a web-based tool, "CRCpred," employing ML and deep learning-based hybrid algorithms for CRC prediction. The XGBoost algorithm demonstrated the highest performance, achieving an average area under the curve (AUC) of 0.90 on the test and 0.91 on the validation datasets. Our results highlight the utility of CRCpred in predicting CRC and healthy status using gut bacterial species relative abundance profile. CRCpred is publicly available at https://metabiosys.iiserb.ac.in/crcpred.},
}
@article {pmid40570700,
year = {2025},
author = {Chan, AA and Caron, C and Navarrete, M and Lee, CK and Noguti, J and Bui, JD and Lee, DJ},
title = {Mammary tissue microbiome analysis in PyMT mice reveals Methylobacteria as a commensal organism with potential therapeutic applications.},
journal = {Translational oncology},
volume = {59},
number = {},
pages = {102451},
doi = {10.1016/j.tranon.2025.102451},
pmid = {40570700},
issn = {1936-5233},
abstract = {Studies have reported differences in specific bacteria comparing the tissue microbiome in human breast cancer versus normal breast tissue, prompting hypotheses for potential therapies or theragnosis. To test these hypotheses using controlled experiments animal models are needed. Therefore, we investigated the microbiome in the gut and mammary tissue in a mouse model of breast cancer. C57BL/6 mice expressing the polyoma middle T antigen in the mammary gland (PyMT) develop spontaneous multifocal breast tumors. Microbiota in the gut and mammary tissue were studied prior to and after development of mammary gland tumors by amplicon and shotgun DNA sequencing. In parallel, RNA sequencing was performed on tumor and normal tissue to measure differences in gene expression associated with breast cancer. Bacteria identified in these studies were administered to mice to test their effects on cancer progression. Bacterial community composition in the gut of healthy or tumor-bearing mice showed wide fluctuation over time and did not organize into discrete clusters. In tumor versus healthy mammary gland tissue, relative abundances of six bacteria were significantly different: Ralstonia, Methylobacterium, Pelomonas, Staphylococcus and Tepidimonas. Methlyobacterium sequences were significantly higher (PERMANOVA, P = 0.013) in healthy tissue when compared to tumor, leading to a hypothesis that Methylobacterium may promote health. When co-transplanted with breast tumor cells, Methylobacterium reduced growth in immune competent mice. Here we describe the gut and mammary tissue microbial composition of healthy and breast tumor-bearing animals, identifying Methylobacterium sp as a commensal bacteria that might have therapeutic potential to reduce breast cancer progression.},
}
@article {pmid40570605,
year = {2025},
author = {Wu, Y and Liu, C and Shao, C and Huang, Q},
title = {Astaxanthin alleviates the microcystin-LR-induced intestinal inflammatory toxicity in zebrafish.},
journal = {Aquatic toxicology (Amsterdam, Netherlands)},
volume = {286},
number = {},
pages = {107462},
doi = {10.1016/j.aquatox.2025.107462},
pmid = {40570605},
issn = {1879-1514},
abstract = {Astaxanthin (AST), a potent natural antioxidant, has demonstrated promising therapeutic potential in mitigating inflammation. However, the precise anti-inflammatory mechanisms of AST, particularly in whole-organism contexts, remain incompletely understood. Given the zebrafish (Danio rerio)'s remarkable genomic, physiological, and immunological similarities to humans, it offers a uniquely advantageous vertebrate model for biomedical research. Therefore, in this study, we utilized adult zebrafish to investigate AST's capacity to attenuate microcystin-LR (MC-LR)-induced inflammatory toxicity and attempted to elucidate underlying mechanistic pathways. AST administration significantly alleviated intestinal inflammation, as evidenced by preservation of normal intestinal morphology, reduced intestinal permeability, and modulation of gene expression profiles linked to inflammation and intestinal homeostasis. Transcriptome sequencing coupled with bioinformatics analysis revealed that AST primarily suppressed inflammatory responses through regulation of peroxisome proliferator-activated receptor (PPAR) signaling axis. Notably, AST did not merely inhibit pro-inflammatory pathways but also enhanced the expression of genes critical for maintaining intestinal barrier integrity and metabolic homeostasis. Furthermore, the 16S rRNA gene amplicon sequencing of zebrafish microbiota revealed that AST treatment restructured the gut microbial community in the MC-LR-exposed fish. Specifically, AST promoted the expansion of beneficial flora, including Lactobacillus rhamnosus GG (LGG), which correlated with improved inflammatory outcomes. Collectively, these findings establish AST as an effective modulator of MC-LR-induced intestinal inflammation in zebrafish, acting via dual mechanisms: PPAR-mediated transcriptional regulation and optimization of the gut microbiome. These insights provide a robust preclinical rationale for exploring AST-based therapies in inflammatory disorders.},
}
@article {pmid40570459,
year = {2025},
author = {Qi, J and Li, J and Xi, Y and Yang, Z and Guo, S and Han, X and Wang, R and Li, L and Bai, L and Han, C and Wang, J and Liu, H},
title = {Multi-omics analysis provides new insights into molecular mechanisms for waterfowl fatty liver formation.},
journal = {Poultry science},
volume = {104},
number = {9},
pages = {105398},
doi = {10.1016/j.psj.2025.105398},
pmid = {40570459},
issn = {1525-3171},
abstract = {Waterfowl fatty liver has high nutritional value and offers benefits to human health. While previous research on fatty liver has focused on individual organs, this study explored fatty liver by examining the cecum, serum metabolites, and liver gene expression. This study integrated transcriptomic, metabolomic, and 16S rRNA microbiome analyses to analyze the molecular mechanism of waterfowl fatty liver formation. We identified seven core genes, five core metabolites, and three core microorganisms, which were significantly correlated. Overfeeding increased the abundance of Mucispirillum in the cecum, while Prevotella and Olsenella decreased. These microbial shifts, mediated by metabolites such as phthalic acid, influenced lipid metabolism, which induced changes in liver gene expression, including upregulation of ACBD4 and downregulation of HSP90B1 and HSPA5, thereby supporting fatty liver development. Additionally, ABC transporters, protein processing in the endoplasmic reticulum, and amino acid metabolism were important in fatty liver development. Our research findings provide new insights into the molecular mechanism of fatty liver with overfeeding in waterfowl from the perspective of the gut-liver axis.},
}
@article {pmid40570156,
year = {2025},
author = {Pyles, MB and Fowler, AL and Crum, AD and Hayes, SH and Schendel, RR and Lawrence, LM},
title = {Dietary nonstructural carbohydrates influence synthesis of mare milk carbohydrates and yield.},
journal = {Journal of animal science},
volume = {},
number = {},
pages = {},
doi = {10.1093/jas/skaf213},
pmid = {40570156},
issn = {1525-3163},
abstract = {Mare milk is the primary source of nutrients for neonatal foals and contains various carbohydrates. Milk oligosaccharides are complex carbohydrates that are resistant to enzymatic digestion and provide support for the immune system and developing microbiome in the neonate. However, factors influencing the synthesis of milk carbohydrates in the mare are not well understood. This study aimed to determine the effects of dietary non-structural carbohydrate (NSC) on mare milk composition and yield. Thoroughbred mares were paired by age and last breeding date then randomly assigned to one of two dietary treatments at 319 d of gestation: a High NSC concentrate (43.9% NSC; n=9; HC) or a Low NSC concentrate (17.8% NSC; n=7; LC). The mares were fed the concentrate feeds in addition to forage. Colostrum and milk samples were collected at the following time points postpartum: at parturition, 12 h, 3 d, 7 d, 14 d, and 21 d. Total milk carbohydrates (lactose and oligosaccharides) were analyzed using an infrared-based milk analyzer (MilkoScan FT+, Foss, Denmark). Milk oligosaccharides were separately quantified following defatting and deproteinization with chloroform and methanol, purification by solid phase extraction, and correction for residual lactose. Daily milk yield was measured at 6 and 7 d postpartum. Mixed model ANOVA with repeated measures was used to evaluate the effect of diet and time on milk components and total milk yield. Mares fed the HC concentrate tended to have higher total milk carbohydrates than mares fed the LC concentrate (P=0.059). There was no main effect of diet on milk oligosaccharides (P=0.34), however, this study was the first to report a change over time in total oligosaccharide concentrations in mare milk, which were highest after foaling and decreased over time (P=0.002). Daily milk yield, on a body weight (BW) basis, was higher in mares fed the HC concentrate (2.30% of BW) compared to the mares fed the LC concentrate (2.04% of BW; P=0.035). These results demonstrate the importance of the maternal diet to milk composition and production, and ultimately, the nutrients provided to the foal.},
}
@article {pmid40570071,
year = {2025},
author = {Savelieva, EI and Shachneva, MD},
title = {Problems and prospects of metabolomic studies in the alteration of the gut microbiome.},
journal = {Biomeditsinskaia khimiia},
volume = {71},
number = {3},
pages = {195-208},
doi = {10.18097/PBMCR1556},
pmid = {40570071},
issn = {2310-6972},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Metabolomics/methods ; *Metabolome ; Animals ; Bile Acids and Salts/metabolism ; *Renal Insufficiency, Chronic/microbiology/metabolism ; Fatty Acids, Volatile/metabolism ; },
abstract = {The review summarizes existing knowledge on the relationship between certain diseases and alteration (degeneration) of the intestinal microbiome. We consider major microbial metabolites firmly recognized as signaling molecules acting in communication between the microbiome and the host organism. These include short-chain fatty acids, bile acids, amines, amino acids, and their metabolites. Special attention is paid to metabolomic studies of the microbiome in chronic kidney diseases, in particular, immunoglobulin A nephropathy. The arguments supporting a concept of the microbiome of blood, previously considered an exclusively sterile environment in healthy humans, are considered. Metagenomic methods plays a key role in characterization of both the composition and potential physiological effects of microbial communities. The advantages and limitations of metabolomic analysis of blood serum/plasma and feces have been analyzed. Since the potential of clinical studies of the mutual impact of the microbiome-metabolome is limited by genetic and external factors, preclinical studies still employ both germ-free models and models based on the effects of antibiotics. The review considers the problems and prospects of metabolomics in studying the nature and mechanisms of the mutual impact of the microbiome and metabolome.},
}
@article {pmid40569902,
year = {2025},
author = {Belheouane, M and Kalsdorf, B and Niemann, S and Gaede, KI and Lange, C and Heyckendorf, J and Merker, M},
title = {Serratia sp. traits distinguish the lung microbiome of patients with tuberculosis and non-tuberculous mycobacterial lung diseases.},
journal = {PloS one},
volume = {20},
number = {6},
pages = {e0325362},
pmid = {40569902},
issn = {1932-6203},
mesh = {Humans ; *Microbiota/genetics ; Male ; Middle Aged ; *Lung/microbiology ; RNA, Ribosomal, 16S/genetics ; Female ; Adult ; *Serratia/genetics/isolation &amp; purification/classification ; Bronchoalveolar Lavage Fluid/microbiology ; Aged ; *Mycobacterium Infections, Nontuberculous/microbiology ; Nontuberculous Mycobacteria/genetics ; *Tuberculosis, Pulmonary/microbiology ; *Lung Diseases/microbiology ; },
abstract = {BACKGROUND: Pathogenic mycobacteria, such as Mycobacterium tuberculosis complex (Mtbc), and non-tuberculous mycobacteria (NTMs) can cause severe chronic pulmonary infections. However, not all infected patients develop active disease, and it remains unclear whether key lung microbiome taxa play a role in the pathogenesis of tuberculosis (TB) and NTM lung diseases (LD). Here, we aim to further define the lung microbiome composition in TB, and NTM-LD prior to the initiation of therapy.<br><br>STUDY DESIGN: We employed 16S rRNA amplicon sequencing to characterize the baseline microbiome in bronchoalveolar lavage fluid (BALF) from patients diagnosed with TB (n&#x2009;=&#x2009;23), NTM-LD (n&#x2009;=&#x2009;19), or non-infectious inflammatory disease (n&#x2009;=&#x2009;4). We applied depletion of human cells, removal of extracellular DNA, implementation of a decontamination strategy, and exploratory whole-metagenome sequencing (WMS) of selected specimens.<br><br>RESULTS: Genera Serratia and unclassified Yersiniaceae dominated the lung microbiome of most patients with a mean relative abundance of >15% and >70%, respectively. However, at the sub-genus level, as determined by amplicon sequence variants (ASVs), TB-patients exhibited increased community diversity, and distinct signatures of ASV_7, ASV_21 abundances which resulted in a significant association with disease state. Exploratory WMS, and ASV similarity analyses suggested the presence of Serratia liquefaciens, Serratia grimesii, Serratia myotis and/or Serratia quinivorans in TB and NTM-LD patients.<br><br>CONCLUSIONS: The lung microbiome of TB-patients harbored a distinct, and heterogenous structure, with specific occurrences of certain Serratia traits. Some of these traits may play a role in understanding the microbial interactions in the lung microbiome of patients infected with Mtbc.},
}
@article {pmid40569810,
year = {2025},
author = {Márquez, FJ and Granados, JE and Canet, LM and de Rojas, M and Caruz, AJ and Pérez, JM},
title = {The microbiome of the sucking louse Linognathus stenopsis (Phthiraptera, Anoplura, Linognathiidae).},
journal = {Journal of medical entomology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jme/tjaf060},
pmid = {40569810},
issn = {1938-2928},
support = {1380336//PAIDI/ ; },
}
@article {pmid40569694,
year = {2025},
author = {Kasmanas, JC and Magnúsdóttir, S and Zhang, J and Smalla, K and Schloter, M and Stadler, PF and de Leon Ferreira de Carvalho, ACP and Rocha, U},
title = {Integrating comparative genomics and risk classification by assessing virulence, antimicrobial resistance, and plasmid spread in microbial communities with gSpreadComp.},
journal = {GigaScience},
volume = {14},
number = {},
pages = {},
pmid = {40569694},
issn = {2047-217X},
support = {2019/03,396-9//S&#xe3;o Paulo Research Foundation/ ; 2022/03,534-5//S&#xe3;o Paulo Research Foundation/ ; //Deutsche Forschungsgemeinschaft/ ; //International Development Research Centre/ ; },
mesh = {*Plasmids/genetics ; Humans ; *Genomics/methods ; Virulence/genetics ; *Drug Resistance, Bacterial/genetics ; Gastrointestinal Microbiome/genetics ; Virulence Factors/genetics ; Computational Biology/methods ; Software ; Genome, Bacterial ; *Bacteria/genetics/pathogenicity/drug effects ; },
abstract = {BACKGROUND: Comparative genomics, genetic spread analysis, and context-aware ranking are crucial in understanding microbial dynamics' impact on public health. gSpreadComp streamlines the path from in silico analysis to hypothesis generation. By integrating comparative genomics, genome annotation, normalization, plasmid-mediated gene transfer, and microbial resistance-virulence risk-ranking into a unified workflow, gSpreadComp facilitates hypothesis generation from complex microbial datasets.<br><br>FINDINGS: The gSpreadComp workflow works through 6 modular steps: taxonomy assignment, genome quality estimation, antimicrobial resistance (AMR) gene annotation, plasmid/chromosome classification, virulence factor annotation, and downstream analysis. Our workflow calculates gene spread using normalized weighted average prevalence and ranks potential resistance-virulence risk by integrating microbial resistance, virulence, and plasmid transmissibility data and producing an HTML report. As a use case, we analyzed 3,566 metagenome-assembled genomes recovered from human gut microbiomes across diets. Our findings indicated consistent AMR across diets, with diet-specific resistance patterns, such as increased bacitracin in vegans and tetracycline in omnivores. Notably, ketogenic diets showed a slightly higher resistance-virulence rank, while vegan and vegetarian diets encompassed more plasmid-mediated gene transfer.<br><br>CONCLUSIONS: The gSpreadComp workflow aims to facilitate hypothesis generation for targeted experimental validations by the identification of concerning resistant hotspots in complex microbial datasets. Our study raises attention to a more thorough study of the critical role of diet in microbial community dynamics and the spread of AMR. This research underscores the importance of integrating genomic data into public health strategies to combat AMR. The gSpreadComp workflow is available at https://github.com/mdsufz/gSpreadComp/.},
}
@article {pmid40569658,
year = {2025},
author = {Yan, H and Wang, E and Wei, GS and Xu, X and Hurst, MRH and Zhang, B},
title = {Microbial dynamics across tri-trophic systems: insights from plant-herbivore-predator interactions.},
journal = {FEMS microbiology ecology},
volume = {101},
number = {7},
pages = {},
pmid = {40569658},
issn = {1574-6941},
support = {6222052//Beijing Natural Science Foundation/ ; 32070402//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Microbiota ; *Tetranychidae/microbiology/physiology ; *Food Chain ; RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/isolation &amp; purification ; *Herbivory ; Predatory Behavior ; *Mites/microbiology/physiology ; *Plants/microbiology ; },
abstract = {Microbes play a critical role in regulating tri-trophic interactions among plants, herbivores, and their natural enemies, influencing key ecological and evolutionary processes. To fully understand these interactions through the food chain, a well-defined tri-trophic system is required. We investigated microbial dynamics involving plants (beans, cucumbers, and eggplants), spider mites (Tetranychus urticae), and predatory mites (Phytoseiulus persimilis) through 16S rRNA gene sequencing. The results revealed significant variations in microbiota across different trophic levels. Source tracking analysis indicated that microbiota at each trophic level were rarely inherited from the previous one, and deterministic processes played a key role in shaping the endosphere communities of these levels. Most shared zero-radius operational taxonomic units across each trophic level belonged to Pseudomonas, Bacillus, and Staphylococcus. Leaf microbiota differed among plants, while spider mites harbored similar microbiota. Notably, the microbiota of predatory mites on eggplants differed significantly from those on the other two plants. Biomarker selection and correlation analyses revealed that the abundance of Methylobacterium and Stenotrophomonas was strongly correlated with the improved fitness of predatory mites across different plants. Our study highlights the complex and dynamic nature of microbial communities across different trophic levels in a well-defined plant-herbivore-predator system.},
}
@article {pmid40569514,
year = {2025},
author = {Villanueva-Millan, MJ and Leite, G and Mathur, R and Rezaie, A and Fajardo, CM and de Freitas Germano, J and Morales, W and Sanchez, M and Rivera, I and Parodi, G and Weitsman, S and Rashid, M and Hosseini, A and Brimberry, D and Barlow, GM and Pimentel, M},
title = {Hydrogen Sulfide and Methane on Breath Test Correlate with Human Small Intestinal Hydrogen Sulfide Producers and Methanogens.},
journal = {Digestive diseases and sciences},
volume = {},
number = {},
pages = {},
pmid = {40569514},
issn = {1573-2568},
abstract = {BACKGROUND: Evidence indicates that 3 gas breath testing (BT) correlates with stool microbial populations. Breath methane (CH4) levels correlate with stool Methanobrevibacter smithii levels and constipation, while hydrogen sulfide (H2S) levels correlate with stool H2S producers and diarrhea. However, their relationships to small bowel microbes are unknown.<br><br>AIMS: To assess relationships between small bowel microbes and breath gases.<br><br>METHODS: REIMAGINE study subjects completed a fasting single-sample BT for CH4 and H2S. During esophagogastroduodenoscopy without colon preparation, duodenal aspirates were obtained using double-lumen sterile aspiration catheters. Microbial DNAs underwent shotgun sequencing (NovaSeq6000).<br><br>RESULTS: Duodenal bacterial profiles differed significantly in subjects with breath H2S&#x2009;&#x2265;&#x2009;1.5&#xa0;ppm vs. those with&#x2009;<&#x2009;1.5&#xa0;ppm, with 2.08-log2fold greater prevalence of phylum Thermodesulfobacteriota. Higher breath H2S levels correlated with greater duodenal prevalences of H2S producers, including Proteus mirabilis (P&#x2009;=&#x2009;0.002), Desulfosarcina widdelii (P&#x2009;=&#x2009;0.027), and Desulfobulbus oligotrophicus (P&#x2009;=&#x2009;0.041); co-occurrence of all 3 species correlated with&#x2009;~&#x2009;50% higher breath H2S levels (P&#x2009;=&#x2009;0.0001). Duodenal archaeal profiles differed significantly in subjects with intestinal methanogen overgrowth (IMO, CH4&#x2009;&#x2265;&#x2009;10&#xa0;ppm), with 2.94-log2fold greater prevalence of family Methanobacteriaceae vs. non-IMO&#xa0;subjects. Higher breath CH4 correlated with greater prevalences of methanogens including M. smithii (P&#x2009;=&#x2009;0.02), Halarchaeum sp. CBA1220 (P&#x2009;=&#x2009;0.003), Desulfurococcus mucosus (P&#x2009;=&#x2009;0.046), and Halobaculum rubrum (P&#x2009;=&#x2009;0.049). IMO was more common in subjects with co-occurrence of all 4 species (P&#x2009;=&#x2009;0.04). In IMO-positive subjects, CH4 levels correlated with greater constipation severity (P&#x2009;=&#x2009;0.019); P. mirabilis (P&#x2009;=&#x2009;0.021) and D. oligotrophicus (P&#x2009;=&#x2009;0.003) correlated with looser stool in IMO-negative subjects. M. smithii prevalence correlated with known hydrogen-producing syntrophs, e.g., Christensenella minuta (P&#x2009;<&#x2009;0.001).<br><br>CONCLUSION: This study demonstrates that duodenal prevalences of H2S-producing bacteria and methanogenic archaea contribute to H2S and CH4 levels, respectively, on BT.},
}
@article {pmid40569502,
year = {2025},
author = {Mortezaee, K},
title = {Microbiota interaction with Tregs: a target for colitis.},
journal = {Clinical &amp; translational oncology : official publication of the Federation of Spanish Oncology Societies and of the National Cancer Institute of Mexico},
volume = {},
number = {},
pages = {},
pmid = {40569502},
issn = {1699-3055},
abstract = {Gut-resident microbiota associate with host immune system to promote homeostasis, and regulatory T cells (Tregs) are critical in the maintenance of immune balance. Tregs have immunosuppressive activity, and their presence hampers the development of inflammatory diseases. This review aims to unravel microbiome impact on Tregs in bowel inflammation and harnessing such interaction to combat colitis as a separate disease or a consequence of immune checkpoint inhibitor (ICI) therapy of cancer. Short-chain fatty acids (SCFAs) are microbial-derived metabolites associated positively with Treg generation and maintenance and being effective for hampering bowel inflammation. Treg induction shapes gut microbiota profile and support microorganism colonization in their niche and protect the host from inflammation, while suppression of Treg differentiation and activity directs microbiota-induced Th17 expansion and inducing inflammation. Thus, balancing Treg representation with Th17 cells and Treg reprogramming through manipulation of gut microbiota can offer therapy. Microbiota epithelial attachment/detachment and interaction with antigen-presenting cells (APCs) are important for the final fate of T cell signature. Fecal microbial transplantation (FMT) is a strategy for promoting normobiosis and represents a navel approach to targeting colitis. FMT with appropriate microbiota from healthy donors can reinforce microbial diversity, density and persistence to enrich their environment with transforming growth factor (TGF)-β, induce IL-10 producing APCs and reinforce gut barrier, with all these being effective for recovering Tregs, restoring intestinal homeostasis and hampering colitis. ICI therapy of cancer may predispose subjects to colitis due to the impact on microbiome and reducing Treg population. FMT promotes local Treg reorchestration, being advantageous in cancer patients.},
}
@article {pmid40569263,
year = {2025},
author = {Darlington, DN and Berger, RB and Keesee, JD and Nicholson, SE and Wu, X},
title = {Trauma and Hemorrhage Lead to an Elevation in Fecal Short-Chain Fatty Acids.},
journal = {Shock (Augusta, Ga.)},
volume = {},
number = {},
pages = {},
doi = {10.1097/SHK.0000000000002645},
pmid = {40569263},
issn = {1540-0514},
abstract = {INTRODUCTION: Severe trauma and hemorrhage in rats lead to changes in the beta diversity of the commensal bacteria found in the gut. Because Short-Chain Fatty Acids (SCFA) are produced by these bacteria, SCFA concentration may also change following trauma and hemorrhage and reflect these alterations in the microbiome.<br><br>OBJECTIVE: To determine whether changes in SCFA occur after trauma and hemorrhage in the feces and plasma of rodents.<br><br>MATERIALS AND METHODS: Polytrauma was induced in isoflurane-anesthetized Sprague-Dawley rats by damage to the small intestine, liver, right leg skeletal muscle, and femur, followed by 20% hemorrhage. Whole blood resuscitation was performed at 1 hour (20%). Rats were euthanized at 2 hours and feces and plasma were analyzed for short-chain fatty acids (SCFA) by liquid chromatography tandem mass spectroscopy.<br><br>RESULTS: Of twenty-one SCFA analyzed in the feces and plasma, 11 were measurable. In feces, five demonstrated a significant elevation after 2 hours of severe trauma and hemorrhage (n-8) including propionic (37775 &#xb1; 8919 vs. 146591 &#xb1; 46734 nM/mg protein: mean &#xb1; SEM), pentanoic (10975 &#xb1; 2981 vs. 41828 &#xb1; 10645), 2-methyl propionic (2621 &#xb1; 523 vs. 13798 vs. 2083), 4-methyl pentanoic (1134 &#xb1; 302 vs. 4320 &#xb1; 1029) and 3-phenyl propionic acid (42194 &#xb1; 4863 vs. 153024 &#xb1; 38473). The addition of whole blood resuscitation did not change these responses, but led to an additional significant elevation in butyric (68551 &#xb1; 10786 vs. 369951 &#xb1; 79515) and hexanoic acid (24548 &#xb1; 6791 vs. 102002 &#xb1; 32069). There was no change in SCFA after trauma, hemorrhage or resuscitation in the plasma (n = 6).<br><br>CONCLUSION: Two hours of severe trauma and hemorrhage lead an elevation in many SCFAs in rat feces. No change in SCFA was found in plasma. Because SCFA are primarily derived from commensal bacteria in the gut, these data suggest that the measurement of SCFA could be used as an index of changes in the gut microbiome in pathological condition including trauma and hemorrhage.},
}
@article {pmid40569166,
year = {2025},
author = {Agudelo, FAG and Leblanc, N and Bourdeau-Julien, I and St-Arnaud, G and Dahhani, F and Flamand, N and Veilleux, A and Di Marzo, V and Raymond, F},
title = {Dietary Manganese Modulates Microbiota and Intestinal N-Acylethanolamines in a Sex-Specific Manner in Mice With Diet-Induced Obesity.},
journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology},
volume = {39},
number = {13},
pages = {e70763},
pmid = {40569166},
issn = {1530-6860},
support = {//Canada Excellence Research Chairs, Government of Canada (CERC)/ ; RGPIN 03922//Canadian Government | Natural Sciences and Engineering Research Council of Canada (NSERC)/ ; //Canadian Government | Canadian Institutes of Health Research (CIHR)/ ; //UL | Sentinelle Nord, Universit Laval (Sentinel North)/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Female ; Male ; Mice ; *Obesity/metabolism/etiology/microbiology ; *Manganese/pharmacology/administration &amp; dosage ; Mice, Inbred C57BL ; *Ethanolamines/metabolism ; Diet, High-Fat/adverse effects ; Endocannabinoids/metabolism ; Sex Factors ; Intestines/microbiology ; Diet ; },
abstract = {Obesity is characterized by low-grade inflammation, changes in gut microbiota, and increased tone of the expanded endocannabinoid system (eCBome). The gut is a complex ecosystem that serves as an interface between the diet and its ultimate conversion to nutrients and energy for all cells of the organism. Manganese (Mn) is an essential micronutrient from the diet required for normal cell function and physiological processes. Moreover, it is an indispensable trace mineral for some microbial species since it is a cofactor in several metabolic enzymes. Therefore, we aimed to identify possible interactions between gut microbiota composition and the eCBome during dietary variations of Mn in the context of diet-induced obesity. Female and male mice were fed Mn-depleted and Mn-enriched diets in combination with Low Fat-Low Sucrose (LFLS) or High Fat-High Sucrose (HFHS) diets for 28 days to assess intestinal microbiota and eCBome levels. Mn-enriched diets enhanced the circulating levels of N-docosapentaenoyl-ethanolamine (DPEA) and anandamide (AEA), while they reduced the intestinal concentrations of other N-acylethanolamines, particularly in the caecum. Besides, we found a strong sex effect of Mn on the intestinal levels of 2-monoacylglycerols (2-MAGs), which were lower in females. Other endocannabinoid-like molecules involved in the immune response were impacted by dietary Mn enrichment, such as N-palmitoyl-glycine and N-oleoyl-L-serine. Concomitantly, Mn enrichment promoted segment-specific changes in the relative abundance of several taxa in intestinal microbiota following the HFHS diet. Microbial families such as Peptostreptococcaceae, Muribaculaceae, and Erysipelotrichaceae responded differentially to dietary variations in Mn. This study hints at potential interactions between Mn levels and diet composition with the eCBome and intestinal bacteria during dietary Mn variations within HFHS-induced dysmetabolic processes in a sex-dependent manner. These results will eventually contribute to identifying members of the gut microbiome and mediators of the eCBome useful for improving metabolic health.},
}
@article {pmid40569073,
year = {2025},
author = {Kobiałka, M and Świerczewski, D and Walczak, M and Urbańczyk, W},
title = {Extremely distinct microbial communities in closely related leafhopper subfamilies: Typhlocybinae and Eurymelinae (Cicadellidae, Hemiptera).},
journal = {mSystems},
volume = {},
number = {},
pages = {e0060325},
doi = {10.1128/msystems.00603-25},
pmid = {40569073},
issn = {2379-5077},
abstract = {UNLABELLED: Among the Hemiptera insects, a widespread way of feeding is sucking sap from host plants. Due to their nutrient-poor diet, these insects enter into obligate symbiosis with their microorganisms involved in the synthesis of components essential for host survival. However, within the Cicadellidae family, there is a relatively large group of mesophyll feeders-Typhlocybinae-that is considered to be devoid of obligate symbiotic companions. In this work, we examine the composition of microorganisms in this subfamily and compare the results with their close relatives-the Eurymelinae subfamily. To study the microbiome, we used high-throughput next-generation sequencing (NGS, Illumina) and advanced microscopic techniques, such as transmission electron microscopy (TEM) and fluorescence in situ hybridization (FISH), in a confocal microscope. In the bodies of Typhlocybinae insects, we did not detect the presence of microorganisms deemed to be obligate symbionts. Their microbial communities consist of facultative symbionts, mainly alphaproteobacteria such as Wolbachia or Rickettsia as well as others that can be considered as facultative, including Spiroplasma, Acidocella, Arsenophonus, Sodalis, Lariskella, Serratia, Cardinium, and Asaia. On the other hand, the Eurymelinae group is characterized by a high diversity of microbial communities, both obligate and facultative, similar to other Cicadomorpha. We find co-symbionts involved in the synthesis of essential amino acids such as Karelsulcia, betaproteobacteria Nasuia, or gammaproteobacteria Sodalis. In other representatives, we observed symbiotic yeast-like fungi from the family Ophiocordycipitaceae or Arsenophonus bacteria inhabiting the interior of Karelsulcia bacteria. Additionally, we investigated some aspects of symbiont transmission and the phylogeny of symbiotic organisms and their hosts.<br><br>IMPORTANCE: The Typhlocybinae and Eurymelinae leafhoppers differ significantly in their symbiotic communities. They have different diets, as Typhlocybinae insects feed on parenchyma, which is richer in nutrients, while Eurymelinae, like most representatives of Auchenorrhyncha, consume sap from the phloem fibers of plants. Our work presents comprehensive studies of 42 species belonging to the two above-mentioned, and so far poorly known, Cicadomorpha subfamilies. Phylogenetic studies indicate that the insects from the studied groups have a common ancestor. The diet shift in the Typhlocybinae leafhoppers contributed to major changes in the composition of microorganisms inhabiting the body of these insects. Research on the impact of diet on the microbiome and the subsequent consequences on the evolution and adaptation of organisms plays an important role in the era of climate change.},
}
@article {pmid40569063,
year = {2025},
author = {Bolino, M and Duman, H and Avcı, &#x130; and Kayili, HM and Petereit, J and Zundel, C and Salih, B and Karav, S and Frese, SA},
title = {Proteomic and N-glycomic comparison of synthetic and bovine whey proteins and their effect on human gut microbiomes in vitro.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0020025},
doi = {10.1128/spectrum.00200-25},
pmid = {40569063},
issn = {2165-0497},
abstract = {UNLABELLED: Advances in food production systems and customer acceptance have led to the commercial launch of dietary proteins produced via modern biotechnological approaches as alternatives to traditional agricultural sources. At the same time, a deeper understanding of how dietary components interact with the gut microbiome has highlighted the importance of understanding the nuances underpinning diet-microbiome interactions. Novel food proteins with distinct post-translational modifications resulting from their respective production systems have not been characterized, nor how they may differ from their traditionally produced counterparts. Here, we have characterized the protein composition and N-glycome of a yeast-synthesized and commercially available whey protein ingredient and compared this novel ingredient to whey protein isolate powder derived from bovine milk. Despite strong similarities in protein composition, we found that the N-glycome significantly differs between the two protein sources, reflecting the biosynthetic machinery of the production systems. Furthermore, the diversity of proteins found in yeast-synthesized whey protein were lower relative to bovine whey protein, despite both being predominantly β-lactoglobulin. Finally, to understand whether these differences in N-glycome profiles may affect the human gut microbiome, we compared these proteins in an in vitro fecal fermentation model. The two whey protein sources generated significant differences among three representative gut microbiomes in vitro, most likely due to differences in N-glycan composition and degradation by these representative microbial communities. This work highlights the need to understand how differences in novel biotechnological systems affect the bioactivity of synthesized proteins and how these differences impact the human gut microbiome.<br><br>IMPORTANCE: Recent advances in food technology have led to the production of animal-free products from yeast that are traditionally derived from animals, such as milk proteins. These new processes raise important questions about the use of synthetic proteins as a replacement for traditionally sourced protein, especially in the context of the gut microbiome. Importantly, yeast produce N-glycans comprised primarily of mannose, while animals synthesize structurally and compositionally complex N-glycan structures. Given these differences, we characterized a new, yeast-derived whey protein ingredient and compared it to bovine whey protein. We found that yeast-derived whey protein differs in its impact on human gut microbiomes because of differences in N-glycan structures, despite similarity in protein composition. These findings raise important questions as to whether these differences in synthetic proteins lead to significant changes to the gut microbiome in vivo, and whether this may impact the utility of these novel ingredients.},
}
@article {pmid40569025,
year = {2025},
author = {Celik, E and Ozcan, G and Vatansever, C and Paerhati, E and Uygur, L and Unal, C and Guler Cekic, S and Ozten, MA and Gürsoy, A and Keskin, &#xd6; and Turgal, M and Gursoy, T and Can, F},
title = {Alterations in vaginal microbiome in women with short cervix: longitudinal study of microbial diversity and impact of vaginal progesterone treatment.},
journal = {Ultrasound in obstetrics &amp; gynecology : the official journal of the International Society of Ultrasound in Obstetrics and Gynecology},
volume = {},
number = {},
pages = {},
doi = {10.1002/uog.29269},
pmid = {40569025},
issn = {1469-0705},
support = {119S463//T&#xfc;rkiye Bilimsel ve Teknolojik Ara&#x15f;t&#x131;rma Kurumu/ ; },
abstract = {OBJECTIVES: A short cervix is a known risk factor for preterm birth, and imbalances in the vaginal microbiome, such as low relative abundance of Lactobacillus, may be associated with an increased risk of preterm birth. The aim of this study was to evaluate differences in the vaginal microbiome between women with a short cervix and those with normal cervical length in the second trimester. Additionally, we aimed to assess longitudinal changes in microbial diversity during pregnancy, as well as the impact of vaginal progesterone treatment on vaginal microenvironment in women with a short cervix.<br><br>METHODS: This was a prospective, longitudinal study conducted at Koc University Hospital between January 2020 and May 2023, in women with a singleton pregnancy with a short cervical length (&#x2264;&#x2009;25&#x2009;mm) in the second trimester (20&#x2009;+&#x2009;0 to 24&#x2009;+&#x2009;6&#x2009;weeks' gestation). After diagnosis of short cervix, administration of 200&#x2009;mg vaginal progesterone daily was initiated. The control group comprised women with a normal cervical length (>&#x2009;25&#x2009;mm) in the second trimester, matched for age and body mass index (BMI). Cervicovaginal swabs were collected from the posterior fornix at three gestational-age ranges: in the first trimester (11&#x2009;+&#x2009;0 to 13&#x2009;+&#x2009;6&#x2009;weeks), the second trimester (20&#x2009;+&#x2009;0 to 24&#x2009;+&#x2009;6&#x2009;weeks) and the third trimester (28&#x2009;+&#x2009;0 to 34&#x2009;+&#x2009;6&#x2009;weeks), and cervical length was measured following sample collection. DNA was extracted and the 16S rRNA bacterial gene was sequenced to analyze and compare the vaginal microbiome between women with a short cervix and controls. We also assessed the microbiome longitudinally in each group, across the first, second and third trimesters. In the short-cervix group, we also compared the microbiome before initiation of progesterone treatment in the second trimester and 4&#x2009;weeks after its initiation.<br><br>RESULTS: Among 490 pregnant women who underwent first-trimester screening during the study period and had vaginal swabs collected, short cervical length was detected in 31 at the second-trimester scan. These women formed the study group. A further 27 women, with a normal cervical length, were matched for BMI and age and assigned to the control group. During the second trimester, women with a short cervix exhibited greater species diversity compared with the control group; this was suggested by the higher Shannon index (0.45 vs 0.33; P&#x2009;=&#x2009;0.135), which reflects species richness and evenness, and further demonstrated by the higher Chao index (20.2 vs 13.8; P&#x2009;=&#x2009;0.018), which estimates species richness. In the second trimester, Lactobacillus was less abundant in women with a short cervix than in the control group, although the difference did not reach significance (86.8% vs 95.5%; P&#x2009;=&#x2009;0.091). At the phylum level, in women with a short cervix compared to those with normal cervical length, the relative abundance of Firmicutes, to which the genus Lactobacillus belongs, was significantly lower (90.7% vs 97.6%; P&#x2009;=&#x2009;0.041), while the relative abundances of both Bacteroidota (1.73% vs 0.4%; P&#x2009;=&#x2009;0.004) and Proteobacteria (0.2% vs 0.01%; P&#x2009;=&#x2009;0.007) were higher. In the second trimester, the relative abundance of Lactobacillus gasseri was significantly lower in women with a short cervix compared to controls (4.7% vs 13.8%; P&#x2009;=&#x2009;0.023). In the longitudinal analysis of the vaginal microbiome, there were no significant differences among the trimesters in the control group. In contrast, in those with a short cervix, there was a notable decrease in the amount of Lactobacillus crispatus, from 55.0% in the first trimester to 36.1% in the second trimester (P&#x2009;=&#x2009;0.052). In women with a short cervix, there was no significant difference in bacterial diversity after vs before progesterone treatment (Chao index, 22.6 vs 20.5; P&#x2009;=&#x2009;0.609).<br><br>CONCLUSION: These findings highlight the significant alterations in the vaginal microbiome of pregnant women with a short cervix in comparison to those with normal cervical length, particularly in terms of higher species diversity and distinct community composition. The study also shows that vaginal progesterone treatment in women with a short cervix does not alter the vaginal microbiome, suggesting that it is a safe and effective intervention without disrupting the vaginal microbial balance. Understanding the relationship between cervical length and the vaginal microbiome is essential for developing strategies to reduce the risk of preterm birth in high-risk populations. &#xa9; 2025 The Author(s). Ultrasound in Obstetrics &amp; Gynecology published by John Wiley &amp; Sons Ltd on behalf of International Society of Ultrasound in Obstetrics and Gynecology.},
}
@article {pmid40568872,
year = {2025},
author = {Han, J and Fan, DJ and Jiang, LC and Lu, Z and Ye, T and Wei, Z and Feng, YQ},
title = {In Situ Dynamic Molecular Monitoring of Single Seed Exudates by Induced Electrospray Ionization Mass Spectrometry.},
journal = {Analytical chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.analchem.5c01437},
pmid = {40568872},
issn = {1520-6882},
abstract = {Seed exudates are essential for seed germination and shaping the microbiome. However, analyzing single seed exudates in situ is challenging due to their low volume and complexity. This study utilized tapered glass capillary emitters as miniature Petri dishes as well as induced electrospray ionization mass spectrometry (iESI-MS) for in situ collection and real-time analysis of single seed exudates. Through this innovative platform, we observed dynamic changes in amino acids (AAs) and organic acids (OAs) in the central carbon metabolism pathway of single Arabidopsis seed exudates during the imbibition process. Quantitative results revealed that the levels of AAs and OAs exhibited a pattern of an initial increase followed by a decrease. Furthermore, the onset and peak levels of AAs occurred earlier than those of OAs, suggesting that the seeds may adopt a two-step defense mechanism to regulate the composition of the microbiome. This study provides a valuable tool for gaining insight into seed exudates and microbiome interactions.},
}
@article {pmid40568744,
year = {2025},
author = {Sabu Kattuman, EE and Teegala, LR and Darzi, S and Thodeti, CK and Paruchuri, S},
title = {Leukotrienes: Bridging the Inflammatory Gap in Asthma and Inflammatory Bowel Diseases (IBD).},
journal = {Comprehensive Physiology},
volume = {15},
number = {3},
pages = {e70022},
pmid = {40568744},
issn = {2040-4603},
support = {R01AI144115/NH/NIH HHS/United States ; R01HL148585/NH/NIH HHS/United States ; 25PRE1373953//American Heart Association/ ; 971237//American Heart Association/ ; },
mesh = {Humans ; *Inflammatory Bowel Diseases/metabolism/immunology ; *Asthma/metabolism/immunology ; *Leukotrienes/metabolism ; Animals ; Inflammation/metabolism ; Gastrointestinal Microbiome ; },
abstract = {Leukotrienes are potent inflammatory lipid mediators produced primarily by immune cells. Inflammation, being the center stone of two major disease conditions, namely, asthma and inflammatory bowel disease (IBD), has led researchers to study the role of leukotrienes (LTs) in both these disease settings extensively. Several studies indicate a crucial role for LTs in the development and progression of IBD, whereas LTs, especially cysteinyl leukotrienes (cys-LTs), have been identified as the major contributors to asthma initiation and progression for over three decades. Additionally, the lungs and the gut share several common characteristics, including their exposure to the external environment, similar microbiome composition, and inflammatory responses. These similarities suggest a bidirectional relationship, supported by the increased risk of IBD in asthma patients and vice versa. However, the specific role of LTs in this lung-gut connection remains unclear. This review will examine how several common factors, such as physiology, microbiome, environment, and inflammatory mediators, especially LTs, modulate this crosstalk. The review also highlights in detail how altered leukotriene biosynthesis and signaling contribute to the pathogenesis of both asthma and IBD. Furthermore, we will consider the therapeutic implications of targeting leukotriene pathways for patients with concurrent asthma and IBD in the hope of developing more efficient treatment outcomes for these interconnected conditions. Finally, this review will very briefly explore the involvement of neuronal connections in mediating the lung-gut crosstalk.},
}
@article {pmid40466811,
year = {2025},
author = {Healy, HG and Pawluk, E and Dieter, L and Roberts, SC and Tanner, W and Mathew, T and Peaper, D and Martinello, RA and Peccia, J},
title = {Bacterial recolonization of hospital sink biofilms.},
journal = {The Journal of hospital infection},
volume = {162},
number = {},
pages = {95-105},
doi = {10.1016/j.jhin.2025.05.013},
pmid = {40466811},
issn = {1532-2939},
abstract = {BACKGROUND: Hospital sink drains are known reservoirs for many pathogens that cause healthcare-associated infections (HAIs). Drain bacteria can migrate up to the drain cover and then spread to surrounding surfaces and patients through droplet dispersal during sink use. Therefore, cleaning sink surfaces represents a key intervention strategy to limit transmission between drains and patients.<br><br>AIMS: In this study, we aimed to: (1) characterize microbial community taxonomy and abundance in sink components and (2) evaluate the kinetics and sources of bacterial recolonization onto sink surfaces after cleaning.<br><br>METHODS: Drainpipes, drain covers, sink basins, drinking water, and p-trap liquid from hospital sinks in New Haven, CT, USA were sampled before and after intervention surface cleaning/disinfection (N = 251). Bacterial abundance and taxonomy were assessed via culture counts, digital droplet PCR, MALDI-ToF, and 16S rRNA gene amplicon sequencing.<br><br>FINDINGS: Drain biofilms had median bacterial abundance of 1.80 &#xd7; 10[8] 16S rRNA gene copies/cm[2] and 2.06 &#xd7; 10[6] cfu/cm[2], which correlated with bacterial abundance on sink surfaces. Hallway sinks, which were used more frequently than patient room sinks, had higher bacterial abundance. Drain microbial communities largely consisted of novosphingobium and sphingobium, with detection of acinetobacter, pseudomonas, legionella, and stenotrophomonas. Sink surfaces had abundant mycobacterium, methylobacterium-methylorubrum, and sphingobium, as well as genera common to skin microbiomes (e.g., corynebacterium, staphylococcus, streptococcus). Immediately after cleaning/disinfection, culturable bacteria were generally undetectable on drain covers; bacterial gene copies were reduced but rebounded to over 80% of pre-cleaning levels within 24 h. After seven days, 9.2% of recolonizing bacteria were derived from drains, and 15.7% were from tap water.<br><br>CONCLUSION: This study contributes to our understanding of factors that influence pathogen abundance on hospital sink surfaces and limitations of routine cleaning and disinfection.},
}
@article {pmid40568741,
year = {2025},
author = {Pinder, LF and Bertrand, P and Fertitta, V and Cahais, V and Mwanahamuntu, M and Nyambe, N and Chisele, S and Shibemba, AL and McKay-Chopin, S and Cuenin, C and Lucas, E and Korenjak, M and Muwonge, R and Ghantous, A and Herceg, Z and Parham, GP and Zavadil, J and Basu, P and Gheit, T},
title = {Vaginal microbiome composition in women with HIV undergoing treatment of cervical transformation zone in a screen and treat program in Zambia.},
journal = {AIDS (London, England)},
volume = {39},
number = {9},
pages = {1303-1306},
doi = {10.1097/QAD.0000000000004187},
pmid = {40568741},
issn = {1473-5571},
mesh = {Humans ; Female ; Zambia ; *Vagina/microbiology ; *HIV Infections/complications/drug therapy ; *Microbiota ; Adult ; RNA, Ribosomal, 16S/genetics ; Treatment Outcome ; Sequence Analysis, DNA ; Lactobacillus/isolation &amp; purification/genetics/classification ; DNA, Ribosomal/chemistry/genetics ; DNA, Bacterial/genetics/chemistry ; Young Adult ; Middle Aged ; },
abstract = {This study assessed the vaginal microbiome in women with HIV undergoing cervical transformation zone treatment in Zambia. 16S rRNA sequencing showed lower microbial diversity in successful outcomes (N = 18) than those with treatment failure (N = 17) treatment outcome, with Lactobacillus abundance correlated with success. Moreover, HPV-negative women (N = 12) had higher Lactobacillus levels and less pathogens than HPV-positive women (N = 12). These findings suggest a Lactobacillus-dominated microbiome may be associated with positive treatment outcomes.},
}
@article {pmid40568698,
year = {2025},
author = {Hernández-Luna, MA},
title = {Editorial: Bacteria-host interactions: from infection to carcinogenesis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1634299},
doi = {10.3389/fcimb.2025.1634299},
pmid = {40568698},
issn = {2235-2988},
}
@article {pmid40568683,
year = {2025},
author = {Wang, C and Fan, Y and Zhang, L and Zhao, Z and Luo, F and Sun, K and Zeng, M and Tian, H and Peng, M and Luo, Y and Zhao, H and He, S and Sun, H},
title = {Deciphering the contributions of fecal microbiota from patients with high-grade glioma to tumor development in a humanized microbiome mouse model of glioma.},
journal = {Neuro-oncology advances},
volume = {7},
number = {1},
pages = {vdaf085},
pmid = {40568683},
issn = {2632-2498},
abstract = {BACKGROUND: Recent studies have revealed associations between gut microbiota and glioma. However, the underlying mechanisms remain poorly understood. This study primarily aims to elucidate the impact of altered gut microbiota on tumor progression in glioma-bearing mice.<br><br>METHODS: Fecal samples were collected from glioma patients and healthy controls to compare the effects of human-derived gut microbiota on glioma development in mice. We also analyzed the associations between these microbiota profiles and plasma metabolites.<br><br>RESULTS: Significant differences were observed in both the composition and diversity of the gut microbiota between glioma patients and healthy controls. Mice transplanted with gut microbiota from high-grade glioma patients (HGG-FMT) exhibited accelerated glioma progression compared to those transplanted with microbiota from healthy individuals (HC-FMT). Specifically, Eisenbergiella, Mailhella, and Merdimonas were significantly enriched in HGG-FMT mice, while Limosilactobacillus and Anaerospora increased in HC-FMT mice. Furthermore, Merdimonas showed a positive correlation with sphingosine, sphingosine 1-phosphate, and D-sphingosine in HGG-FMT mice. Conversely, Limosilactobacillus was positively correlated with stearidonic acid and eicosapentaenoic acid in HC-FMT mice.<br><br>CONCLUSIONS: Our findings demonstrate that gut microbiota from high-grade glioma patients can promote glioma progression in mice, potentially through mechanisms involving sphingosine 1-phosphate. This metabolite may enter the bloodstream and accelerate glioma growth, offering novel insights into glioma pathogenesis and potential treatment options.},
}
@article {pmid40568577,
year = {2025},
author = {Qiu, X and Li, D},
title = {Multi-omics analysis untangles the crosstalk between intratumor microbiome, lactic acid metabolism and immune status in lung squamous cell carcinoma.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1603822},
pmid = {40568577},
issn = {1664-3224},
mesh = {Humans ; *Lung Neoplasms/immunology/metabolism/genetics/microbiology/pathology ; *Carcinoma, Squamous Cell/immunology/metabolism/genetics/microbiology ; *Lactic Acid/metabolism ; *Microbiota/immunology ; Transcriptome ; Biomarkers, Tumor/genetics ; Tumor Microenvironment/immunology ; Multiomics ; },
abstract = {INTRODUCTION: Cancer development is intricately linked with metabolic dysregulation, including lactic acid metabolism (LM), which plays a pivotal role in tumor progression and immune evasion. However, its specific implications in lung squamous cell carcinoma (LUSC) remain unclear.<br><br>METHODS: We used numerous datasets encompassing bulk and single-cell transcriptome, genome, intratumor microbiome, and digital pathome to systematically investigate the LM patterns in LUSC. Multiple machine learning algorithms were used to generate the LUSC classification. Histopathology image-based deep learning model was used to predict the classification. Casual mediation analysis was conducted to uncover the association among intratumor microbiota, LM, and immunity.<br><br>RESULTS: Two LM-based subtypes were discovered endowed with distinct clinical outcomes and biological peculiarities, such as overall survival, somatic mutations, and intratumor microbiota structure. Moreover, the histopathology image-based deep learning model accurately predicted our LM-based LUSC taxonomy, significantly improving its clinical utility. Machine learning models based on seven LM-related genes (CHEK2, LIPT1, TUFM, NDUFA10, AGK, PNPLA2, and GFM1) accurately predicted immunotherapy outcomes for multiple cancer types, including LUSC, and outperformed other currently known biomarkers. Furthermore, mediation analysis identified potential association pathways involving tumor-resident microbes, LM-related gene signatures, and antitumor immune cells.<br><br>DISCUSSION: Overall, this study advanced the understanding of the relationship between LM patterns and LUSC tumor biology, as well as its potential clinical implications, which might advance the tailored management of LUSC.},
}
@article {pmid40568547,
year = {2025},
author = {Tatarko, AR and Vannette, RL and Frese, S and Leonard, A},
title = {A wild bumble bee shows intraspecific differences in sensitivity to multiple pesticides.},
journal = {Royal Society open science},
volume = {12},
number = {6},
pages = {250281},
pmid = {40568547},
issn = {2054-5703},
abstract = {Wild pollinator declines are increasingly linked to pesticide exposure, yet it is unclear how intraspecific differences contribute to observed variation in sensitivity, and the role gut microbes play in the sensitivity of wild bees is largely unexplored. Here, we investigate site-level differences in survival and microbiome structure of a wild bumble bee exposed to multiple pesticides, both individually and in combination. We collected wild Bombus vosnesenskii foragers (N = 175) from an alpine meadow, a valley lake shoreline and a suburban park and maintained them on a diet containing a herbicide (glyphosate), a fungicide (tebuconazole), an insecticide (imidacloprid) or a combination of these chemicals. Alpine bees had the highest overall survival, followed by shoreline bees then suburban bees. This was in part explained by body size differences across sites and the presence of conopid parasitoids at two of the sites. Notably, site of origin impacted bee survival on the herbicide, fungicide and combination treatment. We did not find evidence of gut microbiome differences across pesticide treatment, nor a site-by-treatment interaction. Regardless, the survival differences we observed emphasize the importance of considering population of origin when studying pesticide toxicity of wild bees.},
}
@article {pmid40568349,
year = {2025},
author = {Aghara, H and Patel, M and Chadha, P and Parwani, K and Chaturvedi, R and Mandal, P},
title = {Unraveling the Gut-Liver-Brain Axis: Microbiome, Inflammation, and Emerging Therapeutic Approaches.},
journal = {Mediators of inflammation},
volume = {2025},
number = {},
pages = {6733477},
pmid = {40568349},
issn = {1466-1861},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Brain/metabolism ; *Inflammation/metabolism ; *Liver/metabolism ; Animals ; Dysbiosis/metabolism ; Probiotics/therapeutic use ; },
abstract = {The gut-liver-brain axis (GLB axis) plays a crucial role in maintaining metabolic, immune, and neurological homeostasis. The gut microbiota influences systemic health through its metabolites, including short-chain fatty acids (SCFAs), bile acids (BAs), and tryptophan (Trp) derivatives, which regulate immune function, lipid metabolism, and neurotransmitter balance. Dysbiosis is an imbalance in gut microbiota that has been implicated in metabolic dysfuntion associated fatty liver disease (MAFLD), alcohol-associated liver disease (AALD), and neuroinflammatory conditions such as schizophrenia. Increased gut permeability allows microbial byproducts like lipopolysaccharides (LPSs) to enter the liver and brain, activating inflammatory pathways that contribute to disease progression. Moreover, hepatic dysfunction can lead to neuroinflammation and cognitive impairments. Understanding the interplay between microbial metabolites and host physiology provides insight into novel therapeutic interventions. Strategies such as probiotics, prebiotics, synbiotics, fecal microbiota transfer (FMT), and postbiotics offer potential treatments to restore gut eubiosis and mitigate disease severity. This review highlights the mechanistic role of the GLB axis in health and disease, emphasizing microbiome-targeted therapies as a promising avenue for managing metabolic and neuropsychiatric disorders. Trial Registration: ClinicalTrials.gov identifier: NCT04823676, NCT02496390, NCT06024681, NCT02721264.},
}
@article {pmid40568303,
year = {2025},
author = {Wiederkehr, F and Engelhardt, KE and Vetter, J and Ruscheweyh, HJ and Salazar, G and O'Brien, J and Priest, T and Ziegler, M and Sunagawa, S},
title = {Host-level biodiversity shapes the dynamics and networks within the coral reef microbiome.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf097},
pmid = {40568303},
issn = {2730-6151},
abstract = {Coral reefs face severe threats from human activity, resulting in drastic biodiversity loss. Despite the urgency of safeguarding these ecosystems, we know little about the ecological impacts of losing coral reef host-associated microbial communities (microbiomes). Here, we experimentally studied the microbiomes attached to or released from seven benthic reef hosts belonging to the functional groups of stony corals, soft corals, macroalgae, and sponges while manipulating the coral reef metacommunity to mimic biodiverse or degraded reef habitats. Developing an ecological framework, we found host species and functional groups to show distinct patterns of interacting with the environment (i.e. by exuding, maintaining, acquiring, or exchanging microbiome members), with habitat biodiversity primarily influencing microbial acquisition. In a degraded compared to a biodiverse habitat, the microbiomes of stony corals were less connected to soft corals and sponges, while those of soft corals, macroalgae, and sponges became more tightly linked. Our study demonstrates that a decline in metacommunity biodiversity is not merely associated with a proportional loss in microbial diversity; rather, it triggers complex changes in the microbial interactions among the persisting hosts with each other and the environment. These results emphasize the importance of conserving coral reef host biodiversity to preserve the intricately linked microbiomes-and with them the ecosystem functions and services coral reefs provide.},
}
@article {pmid40568126,
year = {2025},
author = {Kumar, R and Sykes, DJ and Band, VI and Schaller, ML and Patel, R and Vitvitsky, V and Sajjakulnukit, P and Singhal, R and Wong, HKA and Hourigan, SK and Ichinose, F and Lyssiotis, CA and Shah, YM and Banerjee, R},
title = {Gut sulfide metabolism modulates behavior and brain bioenergetics.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.04.09.647962},
pmid = {40568126},
issn = {2692-8205},
abstract = {UNLABELLED: The host-microbiome interface is rich in metabolite exchanges and exquisitely sensitive to diet. Hydrogen sulfide (H 2 S) is present at high concentrations at this interface, and is a product of both microbial and host metabolism. The mitochondrial enzyme, sulfide quinone oxidoreductase (SQOR), couples H 2 S detoxification to oxidative phosphorylation; its inherited deficiency presents as Leigh disease. Since an estimated two thirds of systemic H 2 S metabolism originates in gut, it raises questions as to whether impaired sulfide clearance in this compartment contributes to disease, and whether it can be modulated by dietary sulfur content. In this study, we report that SQOR deficiency confined to murine intestinal epithelial cells, perturbs colon bioenergetics that is reversed by antibiotics, establishing a significant local contribution of microbial H 2 S to host physiology. We also find that a 2.5-fold higher methionine intake, mimicking the difference between animal and plant proteins, synergized with intestinal SQOR deficiency to adversely impact colon architecture and alter microbiome composition. In serum, increased thiosulfate, a biomarker of H 2 S oxidation, revealed that intestinal SQOR deficiency combined with high dietary methionine, affects sulfide metabolism globally and perturbs energy metabolism as indicated by higher ketone bodies. The mice exhibited lower exploratory locomotor activity while brain MRI revealed an atypical reduction in ventricular volume, which was associated with lower aquaporin 1 that is important for cerebrospinal fluid secretion. Our study reveals the dynamic interaction between dietary sulfur intake and sulfide metabolism at the host-microbe interface, impacting gut health, and the potential for lower dietary methionine intake to modulate pathology.<br><br>SIGNIFICANCE STATEMENT: The host-microbiome interface is rich in metabolite-based communications that are modulated by diet. Hydrogen sulfide (H 2 S), which is a respiratory poison at high concentrations, is enriched at this interface, and is detoxified by the host enzyme, sulfide quinone oxidoreductase (SQOR). Given the quantitatively significant contribution of gut to systemic H 2 S metabolism, we examined how SQOR deficiency restricted to murine intestinal epithelial cells, interacts with high dietary methionine, designed to approximate the difference between plant versus animal protein levels, to affect local and global bioenergetics. Our study revealed profound short- and long-range impacts resulting from the synergy between decreased H 2 S clearance capacity in gut and high dietary methionine on global energy metabolism, brain pathology, and behavior.},
}
@article {pmid40567942,
year = {2025},
author = {Zheng, W and Su, M and Hong, N and Ye, P},
title = {Gut-eye axis.},
journal = {Advances in ophthalmology practice and research},
volume = {5},
number = {3},
pages = {165-174},
pmid = {40567942},
issn = {2667-3762},
abstract = {BACKGROUND: The gut microbiome, colonizing the human gastrointestinal tract, is increasingly recognized for its symbiotic relationship with the immune system in maintaining overall host health. This emerging understanding raises intriguing questions about potential connections between the gut microbiome and anatomically distant organs, such as the eye, possibly mediated through immune pathways.<br><br>MAIN TEXT: This review synthesizes contemporary research on ocular diseases with the framework of the burgeoning "gut-eye axis" concept. Investigations spanning from the ocular surface to the fundus suggest correlations between the gut microbiome and various ocular disorders. By elucidating the putative pathogenic mechanisms underlying these ocular conditions, we offer novel perspectives to inform future diagnostic and therapeutic interventions in ophthalmology.<br><br>CONCLUSIONS: By presenting a critical analysis of current knowledge regarding the role of gastrointestinal microbiota in ocular health, this review shed light on the complex interplay between gut dysbiosis and eye disorders. Our work endeavors to catalyze interdisciplinary research and foster innovative clinical applications, thereby bridging the gap between the gut microbiota and the ocular well-being.},
}
@article {pmid40567545,
year = {2025},
author = {Tang, J and Wang, Y and Zhou, Q and Fang, Z and Lin, Y and Xu, S and Feng, B and Zhuo, Y and Jiang, X and Zhao, H and Wu, D and Che, L},
title = {Effects of maternal and post-weaning supplementation with microbe-derived antioxidants on sow and piglet performance, oxidative status, and gut microbiota.},
journal = {Frontiers in veterinary science},
volume = {12},
number = {},
pages = {1574259},
pmid = {40567545},
issn = {2297-1769},
abstract = {The antioxidants were found to improve inflammatory responses and redox status. This study investigated the effects of maternal and post-weaning supplementation with microbe-derived antioxidants (MA) on sow performance, redox status, and fecal microorganisms, as well as the growth performance, inflammatory responses and intestinal microbiota of weaned piglets. Sixty multiparous sows were randomly allocated to the control group (CON, basal diet) and the MA group (basal diet supplemented with 2.0 g MA/kg) from d 90 of gestation to d 24 of lactation, according to the parity and body condition. At weaning, a total of 80 piglets per group were selected and randomly assigned to either the basal diet or the MA-supplemented diet, with 10 pens per group and 4 piglets per pen, for a period of 21-day trial. Results showed that maternal MA supplementation increased litter size at weaning (p < 0.05) and the milk contents of dry matter (p = 0.08) and fat (p = 0.09), while decreasing the plasma activities of alanine aminotransferase and aspartate aminotransferase in sows on d 24 of lactation (p < 0.05). Moreover, maternal MA supplementation reduced plasma malondialdehyde concentration (p ≤ 0.01) in sows at farrowing and weaning, as well as catalase activity at weaning (p = 0.01), and tended to increase total antioxidant capacity at farrowing (p = 0.08). Additionally, the fecal contents of butyrate (p = 0.04) and propionate (p = 0.09) were higher in sows receiving the MA diet at d 24 of lactation. In post-weaning piglets, maternal MA supplementation increased average daily gain (p = 0.07) and average daily feed intake (p < 0.05) throughout the period, and increased plasma immunoglobulin G and interleukin-10 concentrations (p < 0.05). Additionally, either maternal or post-weaning MA supplementation positively influenced the gut microbiome of both sows and weaned piglets. In conclusion, maternal MA supplementation during late gestation and lactation increased litter size at weaning, which may be associated with the improved milk quality and redox status. Furthermore, maternal MA supplementation may enhance the growth performance of post-weaning piglets, potentially linking to the improvements in immunological parameters and gut microbiome.},
}
@article {pmid40567024,
year = {2025},
author = {Ueta, R and Imai, H and Saijo, K and Kawamura, Y and Kodera, S and Ishioka, C},
title = {Influence of Citrobacter freundii on NINJ2 Expression and Oxaliplatin Resistance in Colorectal Cancer.},
journal = {Cancer medicine},
volume = {14},
number = {13},
pages = {e70940},
doi = {10.1002/cam4.70940},
pmid = {40567024},
issn = {2045-7634},
support = {JP22K07293//Japan Society for the Promotion of Science/ ; },
mesh = {*Oxaliplatin/pharmacology/therapeutic use ; Humans ; *Colorectal Neoplasms/drug therapy/genetics/pathology/microbiology/metabolism ; *Citrobacter freundii ; Animals ; *Drug Resistance, Neoplasm/genetics ; Mice ; Cell Line, Tumor ; Xenograft Model Antitumor Assays ; Apoptosis/drug effects ; Gene Expression Regulation, Neoplastic/drug effects ; *Antineoplastic Agents/pharmacology ; Reactive Oxygen Species/metabolism ; Mice, Nude ; Female ; Mice, Inbred BALB C ; },
abstract = {BACKGROUND: Oxaliplatin, a third-generation platinum-based chemotherapeutic agent, is widely used in the treatment of colorectal cancer (CRC). However, some patients do not respond effectively to oxaliplatin, and intrinsic resistance to the drug poses a significant challenge. Recent studies have revealed an association between the gut microbiome and the progression of CRC. We hypothesized that Citrobacter freundii, a component of the gut microbiome, contributes to oxaliplatin resistance by regulating specific gene expression in CRC cells.<br><br>METHODS: A bacterial culture filtrate from Citrobacter freundii was employed in the experiments. The CRC cell line RKO, following exposure to this filtrate, was analyzed using high-throughput RNA sequencing. Candidate genes were identified through MTT assays, siRNA knockdown, and overexpression experiments. Apoptosis and reactive oxygen species (ROS) assays were performed to investigate the underlying mechanisms. Finally, a xenograft mouse model was used to evaluate oxaliplatin resistance in vivo.<br><br>RESULTS: Exposure to bacterial culture filtrate from Citrobacter freundii induced oxaliplatin resistance in RKO cells with downregulation of the NINJ2 gene as a possible molecular mechanism. ReducedNINJ2 gene expression suppressed oxaliplatin-induced apoptosis and ROS generation. A tendency toward reduced oxaliplatin efficacy was observed in vivo when NINJ2 gene expression was suppressed.<br><br>CONCLUSION: This study demonstrates that Citrobacter freundii promotes oxaliplatin resistance in CRC through downregulation of NINJ2 gene. NINJ2 gene may serve as a predictive biomarker and therapeutic target to overcome oxaliplatin resistance in CRC.},
}
@article {pmid40566930,
year = {2025},
author = {Liu, Q and Wu, Y and Fan, Q and Liu, J and Chen, Y and He, Y and Wei, W and Zhang, H and Zhao, Y and He, Y and Du, X and Guo, J},
title = {Oral Nanoarmored Live Bacterial Biotherapeutics Bearing Polyphenol-Based Supraparticles Enhance Chemotherapy via Reestablishing Immuno-Oncology-Microbiome Axis.},
journal = {ACS nano},
volume = {},
number = {},
pages = {},
doi = {10.1021/acsnano.5c01158},
pmid = {40566930},
issn = {1936-086X},
abstract = {The immuno-oncology-microbiome (IOM) axis, referring to the gut microbiota-regulated immune interactions on the tumor microenvironment and systemic immunity, is essential for cancer therapies. However, the cytotoxicity of chemotherapeutic agents (Chemos) disrupts the gut microbiota- and gut microbiota-manipulated IOM axis, further diminishing the therapeutic efficacy. Here, we developed oral nanoarmored live bacterial biotherapeutics (supraLBT), to reshape the tumor microenvironment and enhance chemotherapy via reestablishing the IOM axis. The cyto-adhesive polyphenol-based supraparticles, made from green tea polyphenol and food-grade milk protein, attached on microbes (Escherichia coli Nissle1917, EcN) resisted a range of clinically relevant Chemos via phenolic-mediated noncovalent interactions, enhancing supraLBT survival by 27-fold compared with bare EcN. SupraLBT restored the intestinal microbiota and the disrupted IOM axis, thereby reducing the infiltration of regulatory T cells, increasing the recruitment of cytotoxic CD8[+] T cells to the tumor bed, and further inhibiting tumor proliferation and demonstrating enhanced systemic immune responses. Notably, oral supraLBT combined with chemotherapy (doxorubicin) exhibited 2.35-fold greater tumor regression than that of doxorubicin alone, indicating that oral supraLBT can enhance the chemotherapeutic effect. Further investigations revealed that supraLBT reprogrammed the immune tumor microenvironment by upregulating antitumor cytokines and altering the gut microbial composition. Given the intricate interplay between gut microbiota, host immune system, and tumor microenvironment, this work presents a facile and biomaterial-engineered microorganism-based strategy to enhance the synergistic immuno-chemotherapy effects.},
}
@article {pmid40566601,
year = {2025},
author = {Bednarek, K and Wszołek, K and Szewc, M and Gałęcka, M and Mruczyński, A and Bruszewski, A and Wierzchowski, M and Wilczak, M and Chmaj-Wierzchowska, K},
title = {Microbiota of Cervical Canal in Nine Patients Diagnosed with Ectopic Pregnancy: Case Series.},
journal = {Life (Basel, Switzerland)},
volume = {15},
number = {6},
pages = {},
doi = {10.3390/life15060949},
pmid = {40566601},
issn = {2075-1729},
abstract = {Dysbiosis, or an altered microbiota composition, has been implicated in chronic endometrial inflammation and recurrent implantation failure. Despite growing research on the relationship between the genital microbiome and reproductive health, few studies have examined its role in ectopic pregnancy. Therefore, our study focuses on the microbiota of the cervical canal in women diagnosed with an ectopic pregnancy. Material and methods: The study group consisted of nine women of a reproductive age who were hospitalized at the Department of Maternal and Child Health, Gynecology and Obstetrics, Clinical Hospital of the University of Poznań, between February and September 2023. In nine patients, an ectopic pregnancy was diagnosed based on a transvaginal ultrasound examination. The swabs were collected for quantitative microbiological culture (using Amies transport medium). The microbiological analyses involved quantitative culture on selected selective and differential media, following the Standard Operating Procedure developed by the Institute of Microecology. Results: A reduced Lactobacillus spp. count (≤5 × 10[7] CFU/mL) was observed in 78% of the patients participating in the study, including those that produce H2O2, i.e., with strong protective properties for the environment of the female reproductive tract. The molecular analyses revealed Ureaplasma spp. (U. parvum and U. urealyticum) in 33% of the samples (three patients). However, Chlamydia trachomatis and Mycoplasma genitalium were not detected in any of the analyzed samples. Conclusions: The ease of obtaining material and the minimally invasive nature of lower reproductive tract examinations may allow for the evaluation of microbiota imbalances, helping to identify individuals at an increased risk of reproductive complications.},
}
@article {pmid40566568,
year = {2025},
author = {Papakonstantinou, A and Moustakli, E and Potiris, A and Zikopoulos, A and Tsarna, E and Christodoulaki, C and Tsakiridis, I and Dagklis, T and Panagopoulos, P and Drakakis, P and Stavros, S},
title = {Behind-the-Scenes Actors in Fertility: A Comprehensive Review of the Female Reproductive Tract Microbiome and Its Clinical Relevance.},
journal = {Life (Basel, Switzerland)},
volume = {15},
number = {6},
pages = {},
doi = {10.3390/life15060916},
pmid = {40566568},
issn = {2075-1729},
abstract = {The study of the microbiome has rapidly progressed over the past few decades, capturing the interest of both scientists and the general public. Nevertheless, there is still no widely agreed-upon definition for the term "microbiome" despite tremendous advances in our knowledge. The international scientific literature consistently underscores the difference between the human microbiome and human microbiota. Recent research has emphasized the importance of the female reproductive tract microbiome in fertility, impacting natural conception and assisted reproductive technologies (ARTs). This review explores the relationship between infertility and the microbiota of the female reproductive tract through a thorough evaluation of research papers and large-scale studies published up to 2024. The objective of this review is to critically assess current evidence on the role of the reproductive tract microbiome in female infertility and ART outcomes. Relevant papers were identified and analyzed through the electronic medical databases PubMed/MEDLINE and Scopus. A comprehensive synthesis of data from 36 original studies was performed, including observational, case-control, cohort, and randomized trials. By focusing on the vagina, cervix, and endometrium, this study offers a comprehensive overview of the microbiome throughout the female reproductive tract. RIF and poor reproductive outcomes are strongly linked to dysbiosis, which is characterized by a reduction in Lactobacillus species. Lactobacillus crispatus, in particular, plays a significant role in protecting against bacterial vaginosis and infertility. A thorough understanding of how the microbiome impacts fertility and the development of clinical strategies to improve reproductive outcomes requires standardized microbiome investigation techniques and larger, randomized trials that account for diverse patient characteristics.},
}
@article {pmid40566488,
year = {2025},
author = {Borrego-Ruiz, A and Borrego, JJ},
title = {The Bidirectional Interplay Between Substances of Abuse and Gut Microbiome Homeostasis.},
journal = {Life (Basel, Switzerland)},
volume = {15},
number = {6},
pages = {},
doi = {10.3390/life15060834},
pmid = {40566488},
issn = {2075-1729},
abstract = {Specific gut microorganisms and their metabolic by-products have been identified as key regulators of host physiology, contributing to the modulation of the immune system, inflammatory processes, brain function, and behavior, which highlights the gut microbiome as a potential modulator of the neurobiological mechanisms involved in substance use disorders. This narrative review provides an updated overview of how drugs of abuse influence the composition and dynamics of the human gut microbiome and how bacterial dysbiosis may be a contributing factor to substance use disorders by modulating the communication between the gut and the brain. Thus, by examining commonly abused substances such as alcohol, psychostimulants, opioids, cannabinoids, and nicotine, this review aimed to deepen the understanding of the bidirectional relationship between the gut microbiome and substance use. There is evidence indicating that gut microbiome alterations may influence addiction through changes in gut-brain signaling. Furthermore, changes in the gut microbiome and its metabolites may not only result from substance use disorders, but could also modulate behavioral responses to drugs of abuse. Although the exact mechanisms by which the gut microbiome modulates behavioral responses to drugs of abuse are not fully understood, microbial products such as short-chain fatty acids, tryptophan metabolites, bile acids, and neurotransmitters have been suggested to play a role in this process by influencing the blood-brain barrier permeability, host immune activation, neural signaling, and gene expression. Therefore, manipulating the gut microbiome or its by-products may represent a promising approach for enhancing substance use disorder treatments, identifying individuals at increased risk of pathological drug use, and elucidating its role in substance-related behaviors.},
}
@article {pmid40565936,
year = {2025},
author = {Grafanaki, K and Maniatis, A and Anastogianni, A and Bania, A and Pasmatzi, E and Stathopoulos, C},
title = {Nutrition and Diet Patterns as Key Modulators of Metabolic Reprogramming in Melanoma Immunotherapy.},
journal = {Journal of clinical medicine},
volume = {14},
number = {12},
pages = {},
doi = {10.3390/jcm14124193},
pmid = {40565936},
issn = {2077-0383},
abstract = {Background: Melanoma, one of the most aggressive forms of skin cancer, has seen significant therapeutic advances with immune checkpoint inhibitors (ICIs). However, many patients fail to respond or develop resistance, creating the need for adjunct strategies. Objective: The objective of this study is to critically evaluate how specific dietary patterns and nutrient-derived metabolites modulate melanoma metabolism and immunotherapy outcomes, emphasizing translational implications. Methods: We performed an integrative review of preclinical and clinical studies investigating dietary interventions in melanoma models and ICI-treated patients. Mechanistic insights were extracted from studies on nutrient transport, immunometabolism, and microbiome-immune interactions, including data from ongoing nutritional clinical trials. Results: Diets rich in fermentable fibers, plant polyphenols, and unsaturated lipids, such as Mediterranean and ketogenic diets, seem to contribute to the reprogramming of tumor metabolism and enhance CD8+ T-cell activity. Fasting-mimicking and methionine-restricted diets modulate T-cell fitness and tumor vulnerability via nutrient stress sensors (e.g., UPR, mTOR). High fiber intake correlates with favorable gut microbiota and improved ICI efficacy, while excess protein, methionine, or refined carbohydrates impair immune surveillance via lactate accumulation and immunosuppressive myeloid recruitment. Several dietary molecules act as network-level modulators of host and microbial proteins, with parallels to known drug scaffolds. Conclusions: Integrating dietary interventions into melanoma immunotherapy can significantly influence metabolic reprogramming by targeting metabolic vulnerabilities and reshaping the tumor-immune-microbiome axis. When combined with AI-driven nutrient-protein interaction mapping, this approach offers a precision nutrition paradigm that supports both physicians and patients, emerging as a novel layer to enhance and consolidate existing therapeutic strategies.},
}
@article {pmid40565688,
year = {2025},
author = {Yang, X and Kang, X and Li, L and Zhang, S},
title = {Highland Barley Tartary Buckwheat Coarse Grain Biscuits Ameliorated High-Fat Diet-Induced Hyperlipidaemia in Mice Through Gut Microbiota Modulation and Enhanced Short-Chain Fatty Acid Secretion Mice.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {12},
pages = {},
doi = {10.3390/foods14122079},
pmid = {40565688},
issn = {2304-8158},
abstract = {Dietary modification plays a crucial role in managing and preventing hyperlipidemia. This study examined the combination of highland barley, tartary buckwheat, mung beans, Ormosia hosiei, black rice, and corn germ oil in multi-grain biscuit form. This formulation leverages the synergistic interactions among bioactive compounds, which exert preventive and therapeutic effects against lipid disorders. C57BL/6N mice were fed a high-fat diet for 12 weeks to establish a hyperlipidemia model, followed by feeding with highland barley tartary buckwheat coarse-grain biscuits for 4 weeks. The experimental outcomes revealed that the highland barley tartary buckwheat coarse-grain biscuits effectively controlled body weight and reduced fasting blood sugar levels: body weight was restored to approximately 29 g, and the fasting blood sugar level returned to the normal range of 6 mmol/L. We also observed improved organ indices and regulated blood lipids in hyperlipidemic mice. The total cholesterol of high-fat mice was reduced to 5 mmol/L and the triglyceride level to 1 mmol/L. A significant reduction in inflammatory markers and histopathological improvement in hepatic and adipose tissues were also observed. The intervention enhanced leptin and adiponectin secretion while elevating concentrations of acetic, propionic, butyric, valeric, and caproic acids. Microbiome analysis demonstrated favorable shifts in bacterial populations, characterized by increased Bacteroidetes and Verrucomicrobia abundance and a decreased Firmicutes-to-Proteobacteria ratio, promoting beneficial genera while suppressing potentially pathogenic taxa. These findings suggest that the developed highland barley tartary buckwheat coarse-grain biscuits are a promising dietary intervention for hyperlipidemia management. The effects were potentially mediated through gut microbiota modulation and enhanced short-chain fatty acid production. This research provides novel insights into functional food development for hyperlipidemia.},
}
@article {pmid40565559,
year = {2025},
author = {Vohra, J and Barbosa, G and Pascoal, LB and Reis, LO},
title = {Advances in Genitourinary Tumor Genomics and Immunotherapy.},
journal = {Genes},
volume = {16},
number = {6},
pages = {},
doi = {10.3390/genes16060667},
pmid = {40565559},
issn = {2073-4425},
support = {304747/2018-1//National Council for Scientific and Technological Development/ ; 310135/2022-2//National Council for Scientific and Technological Development/ ; },
mesh = {Humans ; *Immunotherapy/methods ; *Genomics/methods ; *Urogenital Neoplasms/genetics/therapy/immunology ; Precision Medicine ; },
abstract = {Advancements in immune monitoring and modulation technologies are driving transformative changes in cancer immunotherapy. These innovations are crucial for assessing patient-specific immune responses, enabling more accurate predictions of therapeutic efficacy and enhancing treatment outcomes. This review provides a comprehensive overview of current technologies used in immune monitoring, such as flow cytometry, single-cell RNA sequencing, and multiplex cytokine profiling. It also explores cutting-edge immune modulation methods, such as biomaterials that activate immune cells and genetically engineered cell-based therapies. We examine the strengths and limitations of these techniques and identify areas where further progress is needed. In particular, we explore how personalized therapies, real-time monitoring systems, and artificial intelligence shape the future of immune-based treatments. Through a comparative analysis of existing platforms and emerging solutions, this paper underscores the importance of integrating diverse scientific approaches-from immunology and bioengineering to data science-in advancing safer, more effective cancer treatments. This interdisciplinary approach promises to enhance the precision and accessibility of immune-based therapies, offering new hope for improved cancer care.},
}
@article {pmid40565444,
year = {2025},
author = {Wang, X and Sun, Z and Xue, H and An, R},
title = {Artificial Intelligence Applications to Personalized Dietary Recommendations: A Systematic Review.},
journal = {Healthcare (Basel, Switzerland)},
volume = {13},
number = {12},
pages = {},
doi = {10.3390/healthcare13121417},
pmid = {40565444},
issn = {2227-9032},
abstract = {Background/Objectives: Personalized dietary recommendations are essential for managing chronic conditions such as diabetes and irritable bowel syndrome (IBS). However, traditional approaches often fall short in accounting for individual metabolic variability. This systematic review evaluates the effectiveness of artificial intelligence (AI)-generated dietary interventions in improving clinical outcomes among adults. Methods: Following PRISMA guidelines, we searched six electronic databases for peer-reviewed studies published between 19 November 2015 to 6 September 2024. Eligible studies included adults aged 18 to 91 who received AI-generated dietary recommendations based on biomarkers such as blood glucose, gut microbiome composition, and self-reported data. Study designs included randomized controlled trials (RCTs), pre-post studies, and cross-sectional analyses. The GRADE system was used to assess the quality of evidence. Results: Eleven studies met inclusion criteria (five RCTs, five pre-post designs, one cross-sectional). Most AI methods used in the included studies were based on machine learning (ML), including conventional ML algorithms, deep learning (DL), and hybrid approaches integrating ML with IoT-based systems. Interventions led to improved glycemic control, metabolic health, and psychological well-being. Notable outcomes included a 39% reduction in IBS symptom severity and a 72.7% diabetes remission rate. Among nine studies with comparison groups, six reported statistically significant improvements in AI groups, two found comparable or better outcomes, and one found no difference. Mild side effects such as fatigue and constipation were observed. Conclusions: AI-generated dietary interventions show promise in surpassing traditional approaches by providing personalized, data-driven recommendations. Further research is needed to validate long-term effects, refine intervention protocols, and enhance user adherence in both clinical and public health settings.},
}
@article {pmid40565331,
year = {2025},
author = {Karasalih, B and Duman, H and Bechelany, M and Karav, S},
title = {Osteopontin: Its Properties, Recent Studies, and Potential Applications.},
journal = {International journal of molecular sciences},
volume = {26},
number = {12},
pages = {},
doi = {10.3390/ijms26125868},
pmid = {40565331},
issn = {1422-0067},
mesh = {*Osteopontin/metabolism/chemistry/genetics ; Humans ; Animals ; Gastrointestinal Microbiome ; Neoplasms/metabolism ; },
abstract = {OPN is a phosphorylated glycoprotein found in all vertebrate organisms and expressed in many tissues and secretions. It is a pleiotropic protein that plays diverse roles in various pathological and physiological processes. OPN is involved in many tissue transformation events such as intestinal and brain development, the regulation of immune system activity, immune cell activation, and inflammatory responses. This protein increases the functionality of the digestive system by regulating the intestinal microbiome and may help strengthen the intestinal barrier. OPN can also influence cognitive development and behavior. In addition, its recent association with cancer has gained critical importance. The increased expression of OPN has been observed in many cancer types, which may promote tumor cell metastasis. OPN is also effective in bacterial interaction and infections; it can prevent bacterial adhesion, supporting the development of new therapeutic approaches for oral care. Furthermore, the supplementation of OPN in infant formula has positively influenced the immune and intestinal health of infants. Many recent studies have focused on these aspects. This article provides a review and comparison of the existing knowledge on the structure and functions of OPN. It emphasizes how milk-derived OPN impacts human and infant health and disease.},
}
@article {pmid40565291,
year = {2025},
author = {Uceda, S and Reiriz, M and Echeverry-Alzate, V and Beltrán-Velasco, AI},
title = {The Interplay Between Exosomes and Gut Microbiota in Neuroinflammation: A New Frontier in Alzheimer's Disease.},
journal = {International journal of molecular sciences},
volume = {26},
number = {12},
pages = {},
doi = {10.3390/ijms26125828},
pmid = {40565291},
issn = {1422-0067},
mesh = {Humans ; *Alzheimer Disease/metabolism/microbiology/pathology/etiology ; *Exosomes/metabolism ; *Gastrointestinal Microbiome ; Animals ; *Neuroinflammatory Diseases/metabolism/microbiology ; Dysbiosis ; Biomarkers/metabolism ; },
abstract = {Alzheimer's disease (AD) is a complex neurodegenerative condition that is characterized by the accumulation of amyloid-β, the hyperphosphorylation of tau, and persistent neuroinflammation. However, these hallmarks alone do not fully capture the intricacies of AD pathology, thus necessitating the investigation of emerging mechanisms and innovative tools. Exosomes (nanoscale vesicles involved in cell communication and immune modulation) have emerged as pivotal cellular vehicles due to their dual role-both in the propagation of pathological proteins and the regulation of inflammatory responses. Furthermore, these vesicles have been demonstrated to play a crucial role in the mediation of the effects of microbiota-derived metabolites and the reflection of systemic influences such as dysbiosis, thereby establishing a link between the gut-brain axis and the progression of AD. A comprehensive narrative literature review was conducted using the following databases: ScienceDirect, Scopus, Wiley, Web of Science, Medline, and PubMed, covering studies published between 2015 and 2025. Inclusion and exclusion criteria were established to select research addressing exosomal biogenesis, their functional and diagnosis role, their therapeutic potential, and the emerging evidence on microbiota-exosome interplay in Alzheimer's disease. Exosomes have been identified as integral mediators of intercellular communication, reflecting the molecular state of the central nervous system. These particles have been shown to promote the propagation of pathological proteins, modulate neuroinflammatory responses, and serve as non-invasive biomarkers due to their detectability in peripheral fluids. Advances in exosomal engineering and microbiome-based interventions underscore the potential for targeting systemic and CNS-specific mechanisms to develop integrative therapies for AD. Exosomes present a promising approach for the early diagnosis and personalized treatment of Alzheimer's disease. However, methodological challenges and ongoing controversies, including those related to the influence of systemic factors such as dysbiosis, necessitate multidisciplinary research to optimize and standardize these strategies.},
}
@article {pmid40565274,
year = {2025},
author = {Zhang, M and Dong, C},
title = {Molecular Mechanisms of Cadmium Stress Resistance in Vegetable Crops.},
journal = {International journal of molecular sciences},
volume = {26},
number = {12},
pages = {},
doi = {10.3390/ijms26125812},
pmid = {40565274},
issn = {1422-0067},
support = {2023YFD2300704//the National Key R&amp;D Program of China/ ; 32372795//the National Natural Science Foundation of China/ ; CAAS-ASTIP-IVFCAAS//the Science and Technology Innovation Project of Chinese Academy of Agricultural Sciences/ ; CAAS-ZDRW202302//the Science and Technology Innovation Project of Chinese Academy of Agricultural Sciences/ ; },
mesh = {*Cadmium/toxicity ; *Stress, Physiological/drug effects ; *Crops, Agricultural/genetics/drug effects/metabolism ; *Vegetables/drug effects/genetics/metabolism/growth &amp; development ; Gene Expression Regulation, Plant/drug effects ; Plant Growth Regulators/metabolism ; Oxidative Stress/drug effects ; Plant Proteins/genetics/metabolism ; },
abstract = {Cadmium (Cd) stress poses significant threats to vegetable crops, impacting their growth, physiological processes, and safety as part of the human food chain. This review systematically summarizes the latest advances in the molecular mechanisms of vegetable crops' resistance to Cd stress. First, physiological and biochemical responses are outlined, including growth inhibition, impaired photosynthesis, oxidative stress, disrupted nutrient absorption, altered phytohormone levels, and gene expression changes. Next, key molecular mechanisms are discussed, focusing on the roles of transporter-related genes (e.g., NRAMP, HIPP, ABCG), transcription factors (e.g., HsfA1a, WRKY, ERF), enzyme-related genes (e.g., E3 ubiquitin ligase, P-type ATPase), microRNAs (e.g., miR398), and potential functional genes in Cd uptake, translocation, and detoxification. Additionally, the regulatory roles of phytohormones and their analogues (e.g., brassinosteroids, gibberellin, salicylic acid) in mitigating Cd toxicity are analyzed, highlighting their involvement in antioxidant defense, gene regulation, and stress signaling pathways. Finally, future research directions are proposed, emphasizing species-specific defense mechanisms, root hair-specific Cd exclusion mechanisms, and interdisciplinary approaches integrating AI and microbiome manipulation. This review provides a comprehensive reference for enhancing Cd stress resistance in vegetable crops and promoting safe crop production.},
}
@article {pmid40565268,
year = {2025},
author = {Dragomanova, S and Kalfin, R and Tancheva, L and Mehan, S and Stanciu, D and Panaiotov, S},
title = {Pathological Alterations in Human Blood Microbiome-An Updated Review.},
journal = {International journal of molecular sciences},
volume = {26},
number = {12},
pages = {},
doi = {10.3390/ijms26125807},
pmid = {40565268},
issn = {1422-0067},
support = {K&#x3a0;-06-H73/5-05.12.2023//National Science Fund, Sofia, Bulgaria./ ; },
mesh = {Humans ; *Microbiota ; Cardiovascular Diseases/microbiology/blood ; Metabolic Diseases/microbiology/blood ; },
abstract = {The main source of microorganisms in the blood is the intestinal and oral microflora through the route of atopobiosis. It is clear that the blood microbiome undergoes significant changes in response to various pathological conditions within the human body. In this review, we summarized data from studies of the human blood microbiome in diseases of the nervous system and cardiovascular, respiratory, liver, kidney, and metabolite disorders. Links between the blood microbiome and the above mentioned diseases are demonstrated. In support of this understanding, it is evident that analogous alterations in microbiome composition occur across various disease categories; however, the microbial signatures associated with the blood microbiome exhibit specificity. For instance, an elevated abundancy of Proteobacteria has been identified in cardiovascular, renal, and metabolic disorders. Conversely, while Firmicutes are found to be abundant in renal and metabolic conditions, their levels are diminished in cardiovascular diseases. Additionally, patients suffering from respiratory and liver ailments typically show a heightened presence of Bacteroidetes; notably, Flavobacterium is prevalent in respiratory diseases, whereas Enterobacteriaceae is associated with liver diseases. Hence, the human blood microbiome could be considered as a potential biomarker in certain diseases.},
}
@article {pmid40565258,
year = {2025},
author = {Duda-Madej, A and Viscardi, S and Stecko, J and Szymańska, N and Topola, E and Pacyga, K and Szandruk-Bender, M},
title = {Can Nature Overcome Invasive Gastrointestinal Infections?.},
journal = {International journal of molecular sciences},
volume = {26},
number = {12},
pages = {},
doi = {10.3390/ijms26125795},
pmid = {40565258},
issn = {1422-0067},
mesh = {Humans ; Gastrointestinal Microbiome/drug effects ; Animals ; *Gastrointestinal Diseases/drug therapy/microbiology ; *Alkaloids/therapeutic use/pharmacology ; *Bacterial Infections/drug therapy/microbiology ; *Anti-Bacterial Agents/therapeutic use/pharmacology ; Intestinal Mucosa/microbiology/drug effects ; },
abstract = {Invasive bacterial gastrointestinal infections represent a substantial clinical burden worldwide, contributing to significant morbidity and, in severe cases, mortality. The causative bacterial agents of these infections include Shigella spp., enteroinvasive Escherichia coli, Salmonella spp., Campylobacter jejuni, Yersinia enterocolitica, and Listeria monocytogenes. Given the growing challenges of therapy failures and rising antibiotic resistance, there is still an unmet need to identify novel, effective, and safe compounds exhibiting antimicrobial, anti-inflammatory, and immunomodulatory activities. In the present review, we aimed to compile current data regarding three alkaloids-berberine, sanguinarine, and cheleritrin-which hold significant promise in treating bacterial invasive gastrointestinal diseases. Our review extended beyond the direct antimicrobial properties of these compounds against pathogens capable of breaching the intestinal epithelial barrier. We also presented their modulatory effects on intestinal barrier integrity and their influence on the composition and function of the resident gut microbiota, thereby highlighting their potential indirect role in attenuating pathogen invasion and disease progression. Thus, our review presents alkaloids as potential preparations that potentiate the activity of classic anti-infective drugs, as well as substances that, by affecting the microbiome and intestinal mucosa, could be used for inflammatory bowel diseases.},
}
@article {pmid40565108,
year = {2025},
author = {Tkaczyk, M and Mertas, A and Kuśka-Kiełbratowska, A and Fiegler-Rudol, J and Bobela, E and Cisowska, M and Morawiec, T and Skaba, D and Wiench, R},
title = {In Vitro Evaluation of Candida spp. and Staphylococcus aureus Sensitivity to 450 nm Diode Laser-Mediated Antimicrobial Photodynamic Therapy with Curcumin and Riboflavin.},
journal = {International journal of molecular sciences},
volume = {26},
number = {12},
pages = {},
doi = {10.3390/ijms26125645},
pmid = {40565108},
issn = {1422-0067},
mesh = {*Curcumin/pharmacology ; *Photochemotherapy/methods ; *Staphylococcus aureus/drug effects/radiation effects ; *Candida/drug effects/radiation effects ; *Riboflavin/pharmacology ; *Lasers, Semiconductor ; *Photosensitizing Agents/pharmacology ; Microbial Sensitivity Tests ; Microbial Viability/drug effects/radiation effects ; },
abstract = {Oral candidiasis, commonly caused by Candida (C.) albicans and other non-albicans Candida species, increases resistance to conventional antifungal therapies. This study aimed to evaluate the in vitro efficacy of antimicrobial photodynamic therapy (aPDT) using a 450 nm diode laser in combination with curcumin and riboflavin against Candida spp. and Staphylococcus (S.) aureus. Reference strains of C. albicans, C. glabrata, C. krusei, and S. aureus were exposed to aPDT under varying incubation times and laser parameters, then viable microorganism cells (CFU) counts were assessed the microbial reduction, and statistical analyses were performed to evaluate significance. aPDT significantly reduced microbial viability in a time- and dose-dependent manner. Optimal incubation times were 20 min for Candida spp. and 10 min for S. aureus, with the highest efficacy observed at 400 mW and 120 s irradiation. The photosensitizer or laser alone had no significant antimicrobial effect. Curcumin/riboflavin-mediated aPDT is a promising alternative or adjunctive approach to conventional antimicrobial therapy, particularly for resistant oral infections.},
}
@article {pmid40565024,
year = {2025},
author = {Mitrović, M and Stanković Popović, V and Erceg, S and Perišić Mitrović, M and Dobrosavljević, A and Stupar, A and Vuković, P and Zlatković, D and Svorcan, P},
title = {Exploring the Potential of Oral Butyrate Supplementation in Metabolic Dysfunction-Associated Steatotic Liver Disease: Subgroup Insights from an Interventional Study.},
journal = {International journal of molecular sciences},
volume = {26},
number = {12},
pages = {},
doi = {10.3390/ijms26125561},
pmid = {40565024},
issn = {1422-0067},
mesh = {Humans ; Male ; Female ; Middle Aged ; *Butyric Acid/administration &amp; dosage/therapeutic use ; *Dietary Supplements ; Gastrointestinal Microbiome/drug effects ; *Fatty Liver/drug therapy/metabolism ; Aged ; Adult ; *Butyrates/administration &amp; dosage ; Administration, Oral ; Liver/drug effects/metabolism ; Fatty Acids, Volatile/metabolism ; },
abstract = {Metabolic dysfunction-associated steatotic liver disease (MASLD) is a common cause of chronic liver disease and is closely associated with metabolic abnormalities and cardiovascular risks. Butyrate, a short-chain fatty acid produced by gut microbiota, has the potential to enhance liver health by modulating inflammation and supporting gut barrier integrity. This study aimed to investigate and compare the effects of sodium butyrate and calcium butyrate in patients with MASLD. In this single-center, randomized clinical trial, 181 patients with MASLD were enrolled and assigned to receive either sodium butyrate (n = 121) or calcium butyrate (n = 60) supplementation at a daily dose of 1000 mg. The primary endpoint was the change in liver steatosis, measured using the Controlled Attenuation Parameter (CAP) via FibroScan[®]. Secondary endpoints included liver stiffness, biochemical parameters, hepatic steatosis and fatty liver indices, fecal calprotectin levels, stool short-chain fatty acid levels, and microbiome composition. A subgroup analysis compared responders (a ≥ 5% reduction in CAP) to non-responders. There were no significant changes in CAP values for either group (ΔCAP: sodium butyrate, 0.84; calcium butyrate, -0.23; p = 0.70). Sodium butyrate significantly reduced serum trimethylamine N-oxide and fatty liver index, while calcium butyrate led to a decrease in fecal calprotectin levels. Responders demonstrated a lower body mass index, higher levels of high-sensitivity C-reactive protein and HbA1c, and distinct microbiome profiles, characterized by lower abundance of Subdoligranulum and higher abundance of Catenibacterium. Although butyrate supplementation did not significantly improve liver steatosis as measured by CAP, the differing effects on metabolic and inflammatory markers suggest that there may be potential benefits for specific subgroups of patients with MASLD.},
}
@article {pmid40564985,
year = {2025},
author = {Jannati, S and Patel, A and Patnaik, R and Banerjee, Y},
title = {Oleocanthal as a Multifunctional Anti-Cancer Agent: Mechanistic Insights, Advanced Delivery Strategies, and Synergies for Precision Oncology.},
journal = {International journal of molecular sciences},
volume = {26},
number = {12},
pages = {},
doi = {10.3390/ijms26125521},
pmid = {40564985},
issn = {1422-0067},
mesh = {Humans ; *Antineoplastic Agents/pharmacology/therapeutic use/chemistry ; *Neoplasms/drug therapy/metabolism ; Precision Medicine/methods ; Animals ; *Cyclopentane Monoterpenes/pharmacology/therapeutic use/chemistry ; *Aldehydes/pharmacology/chemistry/therapeutic use ; Drug Delivery Systems ; Phenols ; },
abstract = {Oleocanthal (OC), a secoiridoid phenolic compound exclusive to extra virgin olive oil (EVOO), has emerged as a promising nutraceutical with multifaceted anti-cancer properties. Despite its well-characterized anti-inflammatory and antioxidant effects, the mechanistic breadth and translational potential of OC in oncology remain underexplored and fragmented across the literature. This comprehensive review synthesizes and critically analyzes recent advances in the molecular, pharmacological, and translational landscape of OC's anti-cancer activities, providing an integrative framework to bridge preclinical evidence with future clinical application. We delineate the pleiotropic mechanisms by which OC modulates cancer hallmarks, including lysosomal membrane permeabilization (LMP)-mediated apoptosis, the inhibition of key oncogenic signaling pathways (c-MET/STAT3, PAR-2/TNF-α, COX-2/mPGES-1), the suppression of epithelial-to-mesenchymal transition (EMT), angiogenesis, and metabolic reprogramming. Furthermore, this review uniquely highlights the emerging role of OC in modulating drug resistance mechanisms by downregulating efflux transporters and sensitizing tumors to chemotherapy, targeted therapies, and immunotherapies. We also examine OC's bidirectional interaction with gut microbiota, underscoring its systemic immunometabolic effects. A major unmet need addressed by this review is the lack of consolidated knowledge regarding OC's pharmacokinetic limitations and drug-drug interaction potential in the context of polypharmacy in oncology. We provide an in-depth analysis of OC's poor bioavailability, extensive first-pass metabolism, and pharmacogenomic interactions, and systematically compile preclinical evidence on advanced delivery platforms-including nanocarriers, microneedle systems, and peptide-drug conjugates-designed to overcome these barriers. By critically evaluating the mechanistic, pharmacological, and translational dimensions of OC, this review advances the field beyond isolated mechanistic studies and offers a strategic blueprint for its integration into precision oncology. It also identifies key research gaps and outlines the future directions necessary to transition OC from a nutraceutical of dietary interest to a viable adjunctive therapeutic agent in cancer treatment.},
}
@article {pmid40564914,
year = {2025},
author = {Wong, JKC and Patel, BK and Tai, YK and Tan, TZ and Khine, WWT and Chen, WC and Kukumberg, M and Ching, J and Lee, LS and Chua, KV and Tan, TY and Wu, KY and Bai, X and Iversen, JN and Purnamawati, K and Abdul Jalil, R and Kumar, AP and Lee, YK and Moochhala, SM and Franco-Obregón, A},
title = {Fecal Microbiota Transplantation from Mice Receiving Magnetic Mitohormesis Treatment Reverses High-Fat Diet-Induced Metabolic and Osteogenic Dysfunction.},
journal = {International journal of molecular sciences},
volume = {26},
number = {12},
pages = {},
doi = {10.3390/ijms26125450},
pmid = {40564914},
issn = {1422-0067},
support = {A-0001177-01-00//iHealthtech Microbiome in Health, Disease and Aging 2018 Joint Research Grant/ ; MOE-T2EP30120-0016//Ministry of Education/ ; NUHSRO/2023/039/RO5+6/Seed-Mar/04//National University Health System/ ; },
mesh = {Animals ; *Diet, High-Fat/adverse effects ; Mice ; *Fecal Microbiota Transplantation/methods ; Male ; *Osteogenesis ; Mice, Inbred C57BL ; Ceramides/metabolism ; Gastrointestinal Microbiome ; *Magnetic Field Therapy/methods ; Liver/metabolism ; *Metabolic Diseases/therapy/etiology/metabolism ; Bone Density ; },
abstract = {This study compared the metabolic consequences of fecal microbiota transplantation (FMT) from donor mice that had been either administered pulsed electromagnetic field (PEMF) therapy or exercised to recipient mice fed a high-fat diet (HFD). Eight weeks of PEMF treatment (10 min/week) enhanced PGC-1α-associated mitochondrial and metabolic gene expression in white and brown adipose to a greater degree than eight weeks of exercise (30-40 min/week). FMT from PEMF-treated donor mice recapitulated these adipogenic adaptations in HFD-fed recipient mice more faithfully than FMT from exercised donors. Direct PEMF treatment altered hepatic phospholipid composition, reducing long-chain ceramides (C16:0) and increasing very long-chain ceramides (C24:0), which could be transferred to PEMF-FMT recipient mice. FMT from PEMF-treated mice was also more effective at recovering glucose tolerance than FMT from exercised mice. PEMF treatment also enhanced bone density in both donor and HFD recipient mice. The gut Firmicutes/Bacteroidetes (F/B) ratio was lowest in both the directly PEMF-exposed and PEMF-FMT recipient mouse groups, consistent with a leaner phenotype. PEMF treatment, either directly applied or via FMT, enhanced adipose thermogenesis, ceramide levels, bone density, hepatic lipids, F/B ratio, and inflammatory blood biomarkers more than exercise. PEMF therapy may represent a non-invasive and non-strenuous method to ameliorate metabolic disorders.},
}
@article {pmid40564903,
year = {2025},
author = {Chung, BS and Yang, K and Park, C and Ryu, T},
title = {Prolonged Intestinal Ethanol Absorption and Oxidative Stress: Revisiting the Gut-Liver Axis in Alcohol-Associated Disease.},
journal = {International journal of molecular sciences},
volume = {26},
number = {12},
pages = {},
doi = {10.3390/ijms26125442},
pmid = {40564903},
issn = {1422-0067},
support = {RS-2023-00238039//National Research Foundation of Korea/ ; },
mesh = {Humans ; *Oxidative Stress/drug effects ; *Ethanol/pharmacokinetics/metabolism ; *Intestinal Absorption ; Animals ; *Liver/metabolism/drug effects ; Gastrointestinal Microbiome ; *Liver Diseases, Alcoholic/metabolism ; Intestinal Mucosa/metabolism ; *Alcoholism/metabolism ; Dysbiosis ; },
abstract = {Chronic alcohol consumption induces oxidative stress not only in the liver but also in the gastrointestinal tract, where prolonged intestinal ethanol absorption plays a pivotal and underrecognized role. This review reframes ethanol pharmacokinetics to emphasize sustained jejunal and ileal uptake, which maintains elevated blood alcohol levels and perpetuates redox imbalance across the gut-liver axis. We integrate recent findings on ethanol-induced barrier dysfunction, CYP2E1-mediated ROS production, microbial dysbiosis, and mitochondrial disruption, proposing that the intestine is an active site of injury and a driver of systemic inflammation. Key mechanistic insights reveal that gut-derived endotoxins, compromised epithelial integrity, and microbiome-mitochondria interactions converge to exacerbate hepatic and extrahepatic damage. We further explore emerging therapeutic strategies-ranging from NAD[+] repletion and probiotics to fecal microbiota transplantation-that target this upstream pathology. Recognizing prolonged intestinal ethanol absorption as a clinically meaningful phase offers new directions for early intervention and redox-based treatment in alcohol-associated disease.},
}
@article {pmid40564803,
year = {2025},
author = {Kunnathodi, F and Arafat, AA and Alhazzani, W and Mustafa, M and Azmi, S and Ahmad, I and Selan, JS and Anvarbatcha, R and Alotaibi, HF},
title = {Unraveling the Genetic Architecture of Obesity: A Path to Personalized Medicine.},
journal = {Diagnostics (Basel, Switzerland)},
volume = {15},
number = {12},
pages = {},
doi = {10.3390/diagnostics15121482},
pmid = {40564803},
issn = {2075-4418},
abstract = {Obesity is a global health challenge characterized by significant heterogeneity in causes and treatment responses, complicating sustainable management. This narrative review explores the genomic architecture of obesity and its implications for personalized interventions, focusing on how genetic variations influence key biological pathways and treatment outcomes. A comprehensive literature search, guided by the authors' expertise, was conducted to identify key publications on the genomics of obesity and personalized approaches. The selection of articles prioritized those that provided direct insights into the genomic basis of obesity and its potential for informing tailored strategies. Genomic studies reveal both monogenic and polygenic influences on obesity, identifying numerous susceptibility loci. Genome-wide association studies (GWASs) have linked common variants in genes like FTO and MC4R to increased BMI and appetite dysregulation, respectively. Epigenetic research highlights the role of DNA methylation and other modifications in gene-environment interactions. Genetic and polygenic risk scores (GRSs and PRSs) show potential for refining risk stratification and predicting treatment response. The gut microbiome and metabolome also contribute to obesity pathogenesis, offering novel targets for intervention. Personalized medicine offers significant potential for improving obesity management through tailored interventions based on an individual's genetic and 'omics' profile. Future research should focus on elucidating the functional consequences of identified variants, exploring gene-environment interactions, and developing strategies to overcome current limitations in clinical translation. With continued advancements, precision medicine can enhance treatment efficacy, increase sustainability, and help reduce the global burden of obesity-related diseases.},
}
@article {pmid40564683,
year = {2025},
author = {Mania, L and Nanobashvili, K and Manjavidze, T and Benashvili, M and Bzishvili, N and Astamadze, I},
title = {Impact of Symptomatic COVID-19 on the Oral Health of Pediatric Patients in Tbilisi City.},
journal = {Children (Basel, Switzerland)},
volume = {12},
number = {6},
pages = {},
doi = {10.3390/children12060725},
pmid = {40564683},
issn = {2227-9067},
support = {PHDF - 22 - 2374//Shota Rustaveli National Science Foundation/ ; },
abstract = {BACKGROUND/PURPOSE: Coronavirus disease 2019 (COVID-19) has become the cause of a global health crisis during the pandemic. This research aimed to study the impact of symptomatic COVID-19 on children's oral health indices and salivary microbiome composition during the post-COVID-19 period.<br><br>METHODS: An observational, cross-sectional study was conducted in Tbilisi (Georgia) among children aged 7-12 years. A total of 421 children included in the study had a history of laboratory-confirmed COVID-19 within one year of exposure. No participants met the criteria for comorbid conditions or for PCC. A stratified simple random selection of schools and among selected clusters was used. The selected children were divided into two groups: the exposed group, who were patients with a history of symptomatic COVID-19, and the control group, who were patients with a history of asymptomatic COVID-19. The data were collected from August 2022 to December 2023. Oral screening, microbiological examination of saliva, and administration of questionnaires were also performed. Logistic regression was used to calculate ORs with 95% confidence intervals. The statistical processing of the data was performed with SPSS 23.0. This study was approved by the Biomedical Research Ethical Council of the University of Georgia (UGREC-04-22/9 March 2022).<br><br>RESULTS: Statistically significant differences in the means of the oral health indicators between the studied groups were detected (exposed: DMFT + deft = 5.9; MGI = 0.92; S-OHI = 1.9; control: DMFT + deft = 3.8; MGI = 0.56; S-OHI = 1.4). According to the logistic regression, symptomatic COVID-19 had a significant effect on the following oral health indicators: DMFT + deft (OR = 1.26; 95% CI = 1.14-1.39), MGI (OR = 2.31; 95% CI = 1.50-3.55), and S-OHI (OR = 3.43; 95% CI = 2.03-5.76). The effect of symptomatic COVID-19 on the frequency of eradication of the studied microbiome was also significant (OR = 2.12; 95% CI = 1.23-3.63).<br><br>CONCLUSIONS: A close association was established between symptomatic COVID-19 and microbiome changes in the oral saliva of children, as well as between oral health indicators and symptomatic COVID-19. Considering the research results, it is assumed that a symptomatic course of COVID-19 may be an additional risk factor associated with poor oral health in the pediatric population in the post-COVID-19 period.},
}
@article {pmid40564364,
year = {2025},
author = {Li, M and Ma, C and Li, Y and An, Z and Yang, Y and Gao, F and Li, C and Liu, Y},
title = {Effect of Adding Alkaline Metal Ions Complexes Rumen Microbiota and Metabolome of Hu Lambs.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {12},
pages = {},
doi = {10.3390/ani15121816},
pmid = {40564364},
issn = {2076-2615},
support = {CARS-38;2021ZD0024//Changqin Li/ ; },
abstract = {This study aimed to evaluate the effects of studying the effects of the alkali metal ion complexes (AMIC) on the rumen of lambs. Eighteen 3-month-old male Hu lambs (30 ± 2.5 kg) were randomly assigned to three groups (n = 6). Dietary treatments were: control group (CG, base diet), group C1 (base diet + 0.15% AMIC), and group C2 (base diet + 0.30% AMIC). After 60 days of feeding, samples were collected for analysis. Compared with CG, rumen weight significantly increased in both C1 and C2 (p < 0.05). In C2, average daily gain (ADG), bacterial crude protein (BCP), propionic acid concentration, and rumen papillary length were significantly higher than in CG (p < 0.05). Rumen microbiota analysis showed that AMIC supplementation changed the microbial community composition, increasing the relative abundance of fiber-degrading bacteria (e.g., Prevotellaceae_UCG-001) and decreasing pathogenic Proteobacteria. In particular, rumen papillary length positively correlated with Unclassified Oscillospiraceae, Candidatus Saccharimonas, and Unclassified Clostridia vadinBB60 group. Metabolomic analysis revealed that quercetin 3-O-glucuronide levels increased in a dose-dependent manner with higher AMIC. This metabolite positively correlated with Prevotellaceae_UCG-001 abundance and ADG. At 0.30% AMIC, phospholipids PC(18:0/18:4(6Z,9Z,12Z,15Z)) and PE(18:0/16:1(9Z)) were significantly upregulated, and both positively correlated with Candidatus Saccharimonas, Unclassified Clostridia vadinBB60 group, and papillary morphology. In summary, AMIC supplementation affected metabolism by modulating the rumen microbiota, thereby promoting energy absorption and growth. The 0.30% AMIC inclusion significantly enhanced rumen papilla growth, increased the absorption area, promoted propionic acid production, reduced the acetic acid to propionic acid ratio, and ultimately improved the growth rate of Hu lambs. Thus, adding 0.30% AMIC was associated with improved growth performance.},
}
@article {pmid40564325,
year = {2025},
author = {Jiang, K and Ma, J and Xu, J and Zhang, Y and Niu, H},
title = {Multi-Omics Revealed the Effects of Different Feeding Systems on Rumen Microorganisms, Cellulose Degradation, and Metabolites in Mongolian Cattle.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {12},
pages = {},
doi = {10.3390/ani15121774},
pmid = {40564325},
issn = {2076-2615},
support = {This research was funded by the National Natural Science Foundation of China (32460813), the Inner Mongolia Natural Science Foundation Project (2022MS03074), and the Program for Young Talents of Science (NJYT22054) and Technology in Universities (GXKY2204//Xinhua Niu,Ying Zhang/ ; },
abstract = {Rumen microbiota is crucial for cellulose degradation and nutrient metabolism in ruminants. Different feeding systems like grazing and housed feeding can significantly impact it. Mongolian cattle show unique cellulose degradation ability, but functional changes under different feeding conditions are unclear. This study aims to investigate the effects of grazing and housed feeding on rumen microbiota, cellulose degradation, and metabolism in Mongolian cattle. In a 90-day trial, 12 female Mongolian cattle were divided into grazing (F group) and housed feeding (S group). Rumen samples were collected to analyze fermentation parameters, enzyme activities, microbiomes, and metabolomes. The F group had higher acetate, cellulase, xylanase, and β-glucosidase activities (p < 0.05). Bacteroidota and Prevotella were more abundant (p < 0.05), while Firmicutes and Ruminococcus were less abundant (p < 0.05) in the F group. Carbohydrate metabolic pathways and CAZymes (GH2, GH10) were upregulated in the F group, while the S group had enriched purine metabolic pathways and CAZyme (GH31). A total of 64 differential metabolites were found, with subaphylline upregulated in the F group and L-arogenate in the S group (p < 0.05). Grazing increased cellulose degradation and subaphylline production in Mongolian cattle, while housed feeding improved starch utilization efficiency and fat synthesis. These findings provide a basis for optimizing feeding strategies and improving fibrous feed resource utilization in Mongolian cattle.},
}
@article {pmid40564310,
year = {2025},
author = {Zeng, S and Shao, L and Zhao, M and Wang, L and Cheng, J and Zhang, T and Lu, H},
title = {Effects of Different Rearing Methods on the Intestinal Morphology, Intestinal Metabolites, and Gut Microbiota of Lueyang Black-Bone Chickens.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {12},
pages = {},
doi = {10.3390/ani15121758},
pmid = {40564310},
issn = {2076-2615},
abstract = {The Lueyang black-bone chicken represents a distinct indigenous avian breed native to China and it is a slow-growing broiler breed. The gut, whose primary function is to digest food and absorb nutrients, is also home to a large and diverse microbial community. The intestinal morphology, intestinal metabolites, and gut microbiota are critical determinants of nutrient utilization efficiency and immune health in poultry. This study investigates the impact of two distinct rearing modalities-cage-raised (CR) and cage-free (CF)-on the intestinal morphology, intestinal metabolites, and gut microbiota of the duodenum and cecum in Lueyang black-bone chickens. Additionally, we have integrated metabolomics and microbiome analyses. Morphological assessments revealed that, in comparison to the CR group, the CF group exhibited a significant increase in duodenal villi height (VH) and crypt depth (CD) (p < 0.01). Furthermore, there was a notable increase in the number of intestinal inflammatory cells within the CF group. Non-targeted metabolomics indicated an upregulation of omega-3 series polyunsaturated fatty acids and bile acid metabolites in the CR group. Conversely, the CF group demonstrated significantly elevated levels of lysophosphatidylcholine (LPC) and phosphatidylcholine (PE) in the intestine. Microbiome analysis revealed that in the duodenum, beneficial bacteria (e.g., Lactobacillus) were the dominant genera in the CF group, while the Bacteroides predominate in the CR group. Correlation analyses indicated a positive association between LPC levels and the presence of eight bacterial genera, including Ureaplasma. The omega-3 series polyunsaturated fatty acids were positively correlated with three bacterial genera, such as Flavobacterium. Notably, bile acid metabolites exhibited a significant positive correlation with Rikenellaceae_RC9_gut_group. In conclusion, this study provides novel insights into how rearing methods influence intestinal morphology, intestinal metabolites, and gut microbiota, offering a new perspective for the scientific management of poultry with the premise of ensuring animal health and welfare.},
}
@article {pmid40564300,
year = {2025},
author = {Boughey, I and Samsing, F and Hall, E and Rodney, R and Bush, R},
title = {Characterisation of the Faecal Microbiome of Alpacas Raised in South Eastern Australia.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {12},
pages = {},
doi = {10.3390/ani15121748},
pmid = {40564300},
issn = {2076-2615},
abstract = {There is limited investigation of the alpaca microbiome on a global scale, with no previous research conducted in Australia characterising the faecal microbiome. The microbiome composition in other ruminants has been shown to impact feed efficiency, average daily gain and methane production. This study aimed to characterise the faecal microbiome of alpacas raised in south-eastern Australia and identify variation across geographic regions. Faecal samples were collected from 59 healthy adult female alpacas, aged between 15 months and 17 years in NSW, Australia. Firmicutes were identified as the dominant phyla, accounting for 57.78% of the cumulative abundance, followed by Bacteroidota (29.12%). These two phyla accounted for 90% of the taxa, with the cumulative abundance of Firmicutes and Bacteriodota significantly differing (p < 0.05) across locations. There was no effect of age on the frequency of microbes identified at either phyla or class levels. The alpaca's production status only significantly affected the abundance of Firmicutes Clostridia Oscillospirales (p = 0.0026). The breakdown of the alpaca faecal microbiome identified here is consistent with previous ruminant and camelid studies. This study provides a valuable baseline for the microbiome characterisation of alpacas in south-eastern Australia and can be used as a baseline for further microbiome studies.},
}
@article {pmid40564287,
year = {2025},
author = {Steinberger, AJ and de Campos, JL and Kates, AE and Goldberg, TL and Ruegg, PL and Safdar, N and Sethi, AK and Shutske, JM and Suen, G},
title = {Assessing the Impacts of Dairy Farm Antimicrobial Use on the Bovine Fecal Microbiome.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {12},
pages = {},
doi = {10.3390/ani15121735},
pmid = {40564287},
issn = {2076-2615},
support = {20017-68003-26500//United States Department of Agriculture/ ; WIS04039//United States Department of Agriculture/ ; },
abstract = {Rising rates of antimicrobial-resistant infections have prompted increased scrutiny on antimicrobial use (AMU) in livestock agriculture. Dairy farms primarily use antimicrobials to maintain animal health and welfare by treating and preventing infectious diseases. However, the impact of dairy farm AMU practices on the cattle fecal microbiome remains largely unclear, partly due to difficulties in quantifying AMU. This study leveraged quantitative AMU data from 40 large commercial dairy farms to identify farms with low (n = 4) and high (n = 4) AMU. Using 16S rRNA gene amplicon sequencing, we compared the fecal bacterial communities of dairy calves and cows (healthy, cull, sick) by both AMU designation (high/low) and by individual farm AMU, summarized by animal defined daily dose (DDD) and mg/kg. We found significant differences in beta-diversity between cattle from high- and low-AMU groups using either method and found that Corynebacterium and Clostridium abundances increased with farm AMU. Additionally, we found fecal bacterial communities differed across farms within high- and low-AMU groupings, highlighting the need to account for farm-to-farm variation when assessing AMU impacts. These findings suggest that dairy farm AMU influences the fecal microbiome and identifies specific taxa that warrant further investigation as potential reservoirs for antimicrobial resistance genes.},
}
@article {pmid40564277,
year = {2025},
author = {Nistelberger, R and Gibler, P and Barones, L and Absenger, A and Kral-Pointner, JB and Salzmann, M and Hartmann, B and Podesser, BK and Hohensinner, PJ and Plasenzotti, R},
title = {Non-Invasive Analyses of Altered Schaedler Flora in C57Bl/6J and Balb/c Mice to Monitor Hygiene Status of a Housing Facility.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {12},
pages = {},
doi = {10.3390/ani15121725},
pmid = {40564277},
issn = {2076-2615},
abstract = {The composition of the gut microbiome, defined by environmental factors, significantly affects research outcomes, with variations observed across animal facilities. Efforts to standardize led to the definition of the 'Altered Schaedler flora' (ASF), comprising eight bacterial groups. Our data highlights the variability of ASF under pathogen contact. Feces from two wild-type strains (C57Bl/6J and Balb/c mice) with and without proven infection was collected in two different animal facilities and analyzed. The data show a significant difference in the quantity (either reduction or increase) of the eight ASF bacterial groups when comparing infected and non-infected mice across different housing areas (SPF-specific pathogen-free, quarantine, and conventional-experimental areas) within a facility, as well as in comparison to another facility. Furthermore, strain-specific differences are also evident, with certain ASF groups showing a reduction in quantity at one facility but an increase at the other, comparing the same housing area. Comparative studies across facilities confirmed the necessity of baseline determination for accurate ASF analysis. Performing ASF analysis, facilitated by in-house qPCR (quantitative polymerase chain reaction) kits, offers prompt and precise microbiome profiling, enhancing experimental accuracy and health monitoring in animal research settings.},
}
@article {pmid40564234,
year = {2025},
author = {Jia, J and Bao, P and Li, N and Kong, S and Chu, M and Chen, Q and Yan, P},
title = {Lactobacillus Supplementation Modulates Rumen Microbiota and Metabolism in Yaks Under Fattening Feeding Conditions: A Comprehensive Multi-Omics Analysis.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {12},
pages = {},
doi = {10.3390/ani15121681},
pmid = {40564234},
issn = {2076-2615},
support = {TCYC-TP2023//Xinjiang Tianchi Talent Research Program/ ; KCXFZ20201221173205015//Shenzhen Science and Technology Program/ ; CARS-37//National Beef Cattle Industry Technology and System/ ; 2022KJ137//Shandong Natural Science Foundation/ ; },
abstract = {The rumen is a critical organ that facilitates nutrient digestion in ruminant animals. However, the biological mechanisms by which rumen microbiota and its metabolites enable Lactobacillus to modulate rumen structure and maintain functional homeostasis under fattening feeding conditions remain poorly understood. In this study, 80 male Pamir yaks were selected, and a 170-day data collection phase was implemented. Correlation phenotypic data and multi-omics analyses (rumen microbial sequencing and rumen epithelial metabolomics) were conducted to investigate the regulatory effects of Lactobacillus supplementation on rumen microbiota and metabolic processes in a concentrate-based rearing yak model. The results demonstrated that feeding a high-energy diet may impair yak ruminal histomorphology, microbiota composition, and function while negatively modulating rumen microbiota-metabolic profiles associated with specific ruminal microbial communities and functions. Lactobacillus intervention treatment optimized the yak ruminal microbiome composition (mucous layer maturation was promoted, Prevotella and Ruminococcus abundance were reduced, and Fibrobacter and Muribaculaceae abundance were increased), thereby altering metabolite concentrations involved in various metabolic pathways under a high-energy feeding pattern (fatty acid metabolism pathways were upregulated). These alterations elucidated the beneficial impacts of the Lactobacillus supplementation strategy on yak ruminal health without compromising the high-energy intensive rearing pattern. Furthermore, the regulated ruminal microbiome metabolites may serve as potential biomarkers for future investigations into the functional impacts of Lactobacillus intervention treatment on healthy feeding strategies for yaks.},
}
@article {pmid40564230,
year = {2025},
author = {Dahadha, R and Hundam, S and Al-Zghoul, MB and Alanagreh, L and Ababneh, M and Mayyas, M and Alghizzawi, D and Mustafa, MA and Gerrard, DE and Dalloul, RA},
title = {Embryonic Thermal Manipulation Affects Body Performance Parameters and Cecum Microbiome in Broiler Chickens in Response to Post-Hatch Chronic Heat Stress Challenge.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {12},
pages = {},
doi = {10.3390/ani15121677},
pmid = {40564230},
issn = {2076-2615},
support = {grant numbers 552/2023 and 400/2024//Deanship of Research at Jordan University of Science and Technology/ ; },
abstract = {Rising global temperatures challenge poultry production by disrupting the cecal microbiota, which is essential for chicken health. Thermal manipulation (TM) during embryogenesis is a potential strategy to enhance thermotolerance in broilers. This study examined TM's effects on the cecal microbiome, body weight (BW), and body temperature (BT) under chronic heat stress (CHS). Fertile Indian River eggs (n = 800) were incubated under control (37.8 °C, 56% RH) or TM conditions (39 °C, 65% RH for 18 h per day from embryonic day 10 to 18). On post-hatch day 18, male chicks were assigned to either CHS (35 ± 0.5 °C for five days) or thermoneutral conditions (24 ± 0.5 °C). The CHS-TM group showed a significantly higher BW than the CHS-CON group (p < 0.05). Under thermoneutral conditions, TM chicks had a lower BT on day 1 (p < 0.05), while the CHS-TM group exhibited a non-significant BT reduction compared to the CHS-CON group under heat stress (p > 0.05). An analysis of the gut microbiome showed that the beta diversity analysis (PERMANOVA, p < 0.05) indicated distinct microbial shifts. Firmicutes and Bacteroidota dominated the phylum level, with CHS increased Bacilli and Lactobacillus while reducing Lachnospirales in the CHS-TM group. These findings suggest that TM modulates gut microbiota and mitigates BW loss, offering a potential strategy to enhance broilers' resilience to heat stress.},
}
@article {pmid40564214,
year = {2025},
author = {Popa, EC and Maghiar, L and Maghiar, TA and Brihan, I and Georgescu, LM and Toderaș, BA and Sachelarie, L and Huniadi, A},
title = {Hashimoto's Thyroiditis and Female Fertility: Endocrine, Immune, and Microbiota Perspectives in Assisted Reproduction-A Narrative Review.},
journal = {Biomedicines},
volume = {13},
number = {6},
pages = {},
doi = {10.3390/biomedicines13061495},
pmid = {40564214},
issn = {2227-9059},
abstract = {Hashimoto's thyroiditis is the most prevalent autoimmune thyroid disorder, and it disproportionately affects women of reproductive age. Its impact on fertility and assisted reproductive technologies [ART] has become an area of growing clinical interest. Thyroid autoimmunity can influence female reproductive health through multiple interconnected mechanisms, including subtle thyroid hormone imbalances, reduced ovarian reserve, altered endometrial receptivity, and dysregulated immune responses. Subclinical hypothyroidism and the presence of anti-thyroid antibodies have been linked to increased miscarriage risk and reduced success rates in ART, particularly in intracytoplasmic sperm injection (ICSI) cycles. Although levothyroxine supplementation is widely used, its benefits in euthyroid women remain uncertain. Recent studies suggest that gut microbiota may modulate immune function and affect fertility outcomes among women with autoimmune thyroid conditions. This narrative review synthesizes findings from a broad literature base of over 40 peer-reviewed publications published between 2010 and 2025, with 30 of the most relevant and methodologically robust studies selected for detailed analysis. The review integrates clinical, endocrine, immunological, and microbiome-related perspectives. The evidence supports the need for personalized fertility management in women with Hashimoto's thyroiditis and highlights directions for future research into immune and microbiota-targeted therapies.},
}
@article {pmid40564196,
year = {2025},
author = {Schoppmeier, CM and Classen, GL and Contini, S and Rebmann, P and Brendlen, D and Wicht, MJ and Barbe, AG},
title = {Introducing a Novel Paper Point Method for Isolated Apical Sampling-The Controlled Apical Sampling Device: A Methodological Study.},
journal = {Biomedicines},
volume = {13},
number = {6},
pages = {},
doi = {10.3390/biomedicines13061477},
pmid = {40564196},
issn = {2227-9059},
abstract = {Objectives: To introduce a novel method for apical lesion sampling using a protected paper point device and to evaluate its effectiveness and robustness during the sampling process in vitro. Methods: A prototype for apical sample collection was developed as an adaptation of the Micro-Apical Placement System-the device features a highly tapered screw head with a thin, hollow, stainless-steel tube and an internal wire piston. Standardized 5 mm paper points (ISO 10; PD Dental, Switzerland) served as carrier material. The prototype was tested using 30 × 3D-printed, single-rooted tooth models inoculated using two bacterial strains (Staphylococcus epidermidis and Escherichia coli) to simulate apical and intraradicular bacterial infections, respectively. The sampling process involved collecting and analyzing samples at specific timepoints, focusing on the presence or absence of E. coli contamination. Following sample collection, cultural detection of bacterial presence was performed by incubating the samples on agar plates to confirm the presence of E. coli. Samples were collected as follows: S0 (sterility control of the prototype), P0 (sterility control of the tooth model), P1 (apical sample collected with the CAPS (controlled apical sampling) device, and P2 (contamination control sample to check for the presence of E. coli inside the root canal). Results: Handling of the CAPS prototype was straightforward and reproducible. No loss of paper points or complications were observed during sample collection. All sterility samples (P0, S0) were negative for tested microorganisms, confirming the sterility of the setup. P2 samples confirmed the presence of E. coli in the root canal in all trials. The P1 samples were free from contamination in 86.67% of trials. Conclusions: The CAPS method for apical sampling demonstrated advances in the successful and precise sample collection of apically located S. epidermidis and will be a useful tool for endodontic microbiological analysis. Its user-friendly design and consistent performance highlight its potential for clinical application, contributing to more accurate microbial diagnostics and later patient-specific therapeutic approaches in endodontic treatments.},
}
@article {pmid40564149,
year = {2025},
author = {Fei, Q and Huang, J and He, Y and Zhang, Y and Zhang, X and Wang, J and Fu, Q},
title = {Immunometabolic Interactions in Obesity: Implications for Therapeutic Strategies.},
journal = {Biomedicines},
volume = {13},
number = {6},
pages = {},
doi = {10.3390/biomedicines13061429},
pmid = {40564149},
issn = {2227-9059},
abstract = {Obesity is characterized by excessive fat accumulation that triggers chronic low-grade inflammation and systemic immune dysregulation, significantly increasing the risk of metabolic disorders including insulin resistance, type 2 diabetes, and cardiovascular disease. This review examines the bidirectional relationship between obesity and immune dysfunction, focusing on how immune cell infiltration in adipose tissue drives inflammatory processes. We highlight the phenotypic shifts in key immune populations-macrophages polarized toward proinflammatory M1 phenotypes, T cell exhaustion occurrs, and alterations appear in B cells, natural killer (NK) cells, and dendritic cells-that collectively contribute to metabolic deterioration. The gut microbiome emerged as a critical mediator in this relationship, influencing both immune responses and metabolic regulation through gut-liver and gut-brain axes. We explore emerging immunomodulatory therapeutic strategies, including anti-inflammatory agents, microbiota interventions, and targeted immune therapies such as innovative nanomedicine approaches. The review also addresses the challenges of immunotherapy in obesity, particularly the paradoxical effects observed in cancer immunotherapy outcomes and the need for personalized treatment approaches. Artificial intelligence is highlighted as a potential tool to enhance patient stratification and treatment optimization in future immunomodulatory interventions. Understanding these immunometabolic interactions provides a foundation for developing more effective therapeutic strategies that could transform obesity management and reduce the burden of obesity-related metabolic diseases.},
}
@article {pmid40564116,
year = {2025},
author = {Lin, W and Liang, Z and Fang, J and Liu, Y and Lei, L and Lin, J and Xia, B and Zheng, Z and Yuan, J and Tang, C},
title = {Association Between Gut Microbiota and Chronic Kidney Disease: A Two-Sample Mendelian Randomization Study in a Chinese Population.},
journal = {Biomedicines},
volume = {13},
number = {6},
pages = {},
doi = {10.3390/biomedicines13061397},
pmid = {40564116},
issn = {2227-9059},
support = {A2402020//Shenzhen Medical Research Fund/ ; JCYJ20210324123414040 and JCYJ20230807110715030//Shenzhen Municipal Science and Technology Innovation Commission/ ; No. A2403069, C2401002//Shenzhen Medical Research Fund/ ; Gastrointestinal Surgery, No.LCYSSQ20220823091203008//the Funding of Shenzhen Clinical Research Center for Gastroenterology/ ; No. 82473707//the Natural Science Foundation of China/ ; No. ZSQYRSSFAR0004//the Research Supporting Start-up Fund for Associate researcher, of SAHSYSU/ ; No. 392012//the Startup Fund for the 100 Top Talents Program, SYSU/ ; },
abstract = {Background: Population differences in gut microbiota composition and related metabolites may influence their potential causal relationship with chronic kidney disease (CKD); however, this relationship remains poorly understood in the Chinese population. Materials and Methods: We conducted a two-sample Mendelian randomization (MR) study using summary statistics of 500 gut microbial features (9 phyla, 3 classes, 14 orders, 32 families, 95 genera, 248 species, and 99 gut metabolic modules (GMMs)) from the 4D-SZ (from Shenzhen, China) discovery cohort (n = 1539). CKD summary statistics were obtained from the China Kadoorie Biobank (CKB) (489 cases and 75,531 controls). Associations between gut microbiota and CKD were evaluated via inverse variance weighted, MR-Egger, weighted median, and MR-PRESSO. To validate our findings, we replicated the analyses in two independent East Asian CKD GWAS datasets: the Biobank of Japan (BBJ) dataset (2117 cases and 174,345 controls) and the J-Kidney-Biobank (JKB) dataset (382 cases and 3471 controls). We further validated the results via a meta-GWAS of BUN and eGFR in Biobank Japan (BBJ) and the Taiwan Biobank (TWB). Additionally, we analyzed 304 serum proteins from the Guangzhou Nutrition and Health Study (GNHS) and conducted mediation MR analyses to explore potential mediators. Result: At the locus-wide significance threshold, we identified 18 gut microbiome features associated with CKD onset in the China Kadoorie Biobank (CKB). Genus Alistipes (OR 1.02, 95% CI 1.00-1.03, p = 0.03) was associated with incident CKD risk in the JKB cohort. Species Bifidobacterium catenulatum-Bifidobacterium pseudocatenulatum complex (OR 1.0074, 95% CI 1.0070-1.0142, p = 0.01) was associated with incident CKD risk in a meta-GWAS of BUN. Sensitivity analyses, including Cochran's Q test, MR-Egger intercept analysis, leave-one-out analysis, and funnel plots, yielded consistent results. Mediation analysis revealed that 26.7% (95% CI: 0.006-0.6700, p = 0.04) of the effect of Alistipes on CKD risk was mediated through the serum protein FBLN1. Conclusions: Our study provides Mendelian randomization-based evidence supporting a potential causal relationship between gut microbiota and CKD, highlighting the potential mediating role of FBLN1 in the association between genus Alistipes and CKD. Further studies are needed to explore whether and how genus Alistipes and FBLN1 contribute to CKD development.},
}
@article {pmid40564111,
year = {2025},
author = {Bieganska, EA and Kosinski, P and Wolski, M},
title = {Possible Applications of Fecal Microbiota Transplantation in the Pediatric Population: A Systematic Review.},
journal = {Biomedicines},
volume = {13},
number = {6},
pages = {},
doi = {10.3390/biomedicines13061393},
pmid = {40564111},
issn = {2227-9059},
abstract = {Background: The potential therapeutic role of fecal microbiota transplantation (FMT) in various diseases has been thoroughly studied over the last few decades. However, the majority of studies focus on the adult population, therefore, conclusions regarding the application of FMT in the pediatric population are much less clear. This systematic review aims to summarize the research conducted so far on the efficacy and safety of FMT in the pediatric population, assess the quality of the evidence of its effectiveness, and outline the most promising areas for future research. Methods: We performed a systematic literature search from the index date to 8 June 2024 on the Embase, PubMed, and Web of Science databases. One author screened the resulting 121 articles. Eventually, 35 eligible studies that reported FMT use in seven different diseases were identified. Results: All of the studies assessed FMT as a safe procedure without many serious adverse effects. The best-documented application, which is the only one recommended in official guidelines, is recurrent Clostridioides difficile infection. Other disease entities in which the use of FMT has been studied with good clinical effects are inflammatory bowel disease, allergic colitis, autism, Tourette syndrome, and colonization with multi-drug-resistant organisms. However, it should be noted that the majority of studies are cohort and case-control studies, without randomization, which translates into low evidence quality. In one randomized, controlled trial focusing on the effect of FMT on weight loss in obese individuals, a lack of effect was found. Conclusions: While FMT and subsequent iterations of gut microbiota-targeted interventions hold promising therapeutic potential for various disease entities in the pediatric population, the current evidence behind this conclusion is of low quality. Based on current studies, these methods appear to be both effective and safe. However, further randomized clinical trials are necessary, especially within the pediatric population, for which such studies remain scarce.},
}
@article {pmid40564077,
year = {2025},
author = {Theis, BF and Park, JS and Kim, JSA and Zeydabadinejad, S and Vijay-Kumar, M and Yeoh, BS and Saha, P},
title = {Gut Feelings: How Microbes, Diet, and Host Immunity Shape Disease.},
journal = {Biomedicines},
volume = {13},
number = {6},
pages = {},
doi = {10.3390/biomedicines13061357},
pmid = {40564077},
issn = {2227-9059},
abstract = {The human gut microbiome is intricately linked to systemic and organ-specific immune responses and is highly responsive to dietary modulation. As metagenomic techniques enable in-depth study of an ever-growing number of gut microbial species, it has become increasingly feasible to decipher the specific functions of the gut microbiome and how they may be modulated by diet. Diet exerts both supportive and selective pressures on the gut microbiome by regulating a multitude of factors, including energy density, macronutrient and micronutrient content, and circadian rhythm. The microbiome, in turn, contributes to local and systemic immune responses by providing colonization resistance against pathogens, shaping immune cell activity and differentiation, and facilitating the production of bioactive metabolites. Emerging research has strengthened the connections between the gut microbiome and cardiometabolic disorders (e.g., cardiovascular disease, obesity, type-2 diabetes), autoimmune conditions (e.g., type-1 diabetes, rheumatoid arthritis, celiac disease), respiratory disease, chronic kidney and liver disease, inflammatory bowel disease, and neurological disorders (e.g., Alzheimer's, Parkinson's disease, depressive disorders). Here, we outline ways in which dietary factors impact host response in diseases through alterations of gut microbiome functionality and composition. Consideration of diet-mediated microbial effects within the context of the diseases discussed highlights the potential of microbiome-targeted treatment strategies as alternative or adjunct therapies to improve patient outcomes.},
}
@article {pmid40564016,
year = {2025},
author = {Paraskevaidis, I and Tsougos, E and Kourek, C},
title = {The Microbiome Connection: A Common Pathway Linking Cancer and Heart Failure.},
journal = {Biomedicines},
volume = {13},
number = {6},
pages = {},
doi = {10.3390/biomedicines13061297},
pmid = {40564016},
issn = {2227-9059},
abstract = {In humans, heart failure (HF) and cancer are among the leading causes of morbidity and mortality. A growing body of evidence highlights a bidirectional relationship between these conditions, underpinned by shared risk factors and overlapping pathophysiological pathways. This review aims to explore the emerging role of the intestinal microbiome as a common mechanistic link between HF and cancer. Specifically, we examine how microbial dysbiosis and its metabolic products-such as trimethylamine N-oxide (TMAO), short-chain fatty acids (SCFAs), bile acids, lipopolysaccharides (LPS), and branched-chain amino acids (BCAAs)-contribute to inflammation, immune dysregulation, oxidative stress, and metabolic dysfunction. These mechanisms promote multiorgan impairment and establish a vicious cycle that fuels both tumorigenesis and cardiac deterioration. HF, cancer, and the gut microbiome are not isolated entities but are deeply interconnected through shared biological mechanisms-including chronic inflammation, microbial dysbiosis, immune and neurohumoral modulation, and metabolic derangement. These findings support the concept of a microbiome-centered axis involving the gut, heart, and tumors, which may underlie many chronic disease processes. Understanding these interactions may provide novel insights into disease pathogenesis and uncover promising therapeutic targets that leverage microbiome modulation to prevent or treat HF, cancer, and other systemic diseases.},
}
@article {pmid40563985,
year = {2025},
author = {Klinsoda, J and Thurakit, T and Tongkhao, K and Treesuwan, K and Yodin, K and Kantrong, H},
title = {Exploring the Bacterial Microbiome of High-Moisture Plant-Based Meat Substituted Soybean Flour with Mung Bean Protein and Duckweed Powder.},
journal = {Biology},
volume = {14},
number = {6},
pages = {},
doi = {10.3390/biology14060735},
pmid = {40563985},
issn = {2079-7737},
support = {grant number FF(KU)11.67//Kasetsart University Research and Development Institute (KURDI), Thailand/ ; },
abstract = {(1) Background: This study aimed to investigate the bacterial microbiomes in the ingredients and final PBM products during a storage period of 28 days at 2-4 °C for food safety and quality. (2) Methods: DNA from raw ingredients (i.e., defatted soy flour, potato starch, wheat gluten, mung bean protein, and duckweed) and three PBM formulations were extracted and sequenced using 16S rRNA gene sequencing. (3) Results: Alpha diversity (Simpson and Shannon) was high in the raw ingredients (p ≤ 0.05). Beta diversity showed dissimilarities between the samples. Firmicutes and Proteobacteria were the core microflora in these ingredients. The heat-stable microbes in PBM (e.g., Nostocaceae in SF and Cyanobacteriale in MB and DW) survived after extrusion. After the ingredients were stored at room temperature, the bacterial communities shifted, with Paucibacter being the majority population in raw ingredients and PBM in the 2nd batch. The predictions of Potential_Pathogens related to the abundance of Aeromonadaceae and Enterobacteriaceae need to be monitored during storage. (4) Conclusions: Our results showed that the bacterial community in PBM containing 30% MB and 3% DW did not drastically change during 28 days of storage at cold temperatures. Uncovering bacterial microbiomes in the ingredients should be emphasized for quality and safety, as ingredients influence the microbiome in the final products.},
}
@article {pmid40563973,
year = {2025},
author = {Qumsani, AT},
title = {Gut Microbiome Engineering for Diabetic Kidney Disease Prevention: A Lactobacillus rhamnosus GG Intervention Study.},
journal = {Biology},
volume = {14},
number = {6},
pages = {},
doi = {10.3390/biology14060723},
pmid = {40563973},
issn = {2079-7737},
abstract = {The gut microbiota has emerged as a critical modulator in metabolic diseases, with substantial evidence supporting its role in attenuating diabetes-related nephropathy. Recent investigations demonstrate that strategic manipulation of intestinal microflora offers novel therapeutic avenues for safeguarding renal function against diabetic complications. This investigation sought to determine the nephroprotective potential of Lactobacillus rhamnosus GG (LGG) administration in diabetic nephropathy models. Six experimental cohorts were evaluated: control, probiotic-supplemented control, diabetic, diabetic receiving probiotic therapy, diabetic with antibiotics, and diabetic treated with both antibiotics and probiotics. Diabetic conditions were established via intraperitoneal administration of streptozotocin (50 mg/kg) following overnight fasting, according to validated protocols for experimental diabetes induction. Probiotic therapy (3 × 10[9] CFU/kg, bi-daily) began one month before diabetes induction and continued throughout the study duration. Glycemic indices were monitored at bi-weekly intervals, inflammatory biomarkers, renal function indices, and urinary albumin excretion. The metabolic profile was evaluated through the determination of HOMA-IR and the computation of metabolic syndrome scores. Microbiome characterization employed 16S rRNA gene sequencing alongside metagenomic shotgun sequencing for comprehensive microbial community mapping. L. rhamnosus GG supplementation substantially augmented microbiome richness and evenness metrics. Principal component analysis revealed distinct clustering of microbial populations between treatment groups. The Prevotella/Bacteroides ratio, an emerging marker of metabolic dysfunction, normalized following probiotic intervention in diabetic subjects. Results: L. rhamnosus GG administration markedly attenuated diabetic progression, achieving glycated hemoglobin reduction of 32% compared to untreated controls. Pro-inflammatory cytokine levels (IL-6, TNF-α) decreased significantly, while anti-inflammatory mediators (IL-10, TGF-β) exhibited enhanced expression. The renal morphometric analysis demonstrated preservation of glomerular architecture and reduced interstitial fibrosis. Additionally, transmission electron microscopy confirmed the maintenance of podocyte foot process integrity in probiotic-treated groups. Conclusions: The administration of Lactobacillus rhamnosus GG demonstrated profound renoprotective efficacy through multifaceted mechanisms, including microbiome reconstitution, metabolic amelioration, and inflammation modulation. Therapeutic effects suggest the potential of a combined probiotic and pharmacological approach to attenuate diabetic-induced renal pathology with enhanced efficacy.},
}
@article {pmid40563920,
year = {2025},
author = {Zambuzzi, WF and Ferreira, MR and Wang, Z and Peppelenbosch, MP},
title = {A Biochemical View on Intermittent Fasting's Effects on Human Physiology-Not Always a Beneficial Strategy.},
journal = {Biology},
volume = {14},
number = {6},
pages = {},
doi = {10.3390/biology14060669},
pmid = {40563920},
issn = {2079-7737},
support = {KICH2.V4P.22.015/NWO_/Dutch Research Council/Netherlands ; },
abstract = {Intermittent fasting (IF) has emerged as a widely practiced dietary regimen, increasingly utilized in both clinical and non-clinical settings for its potential health benefits. Evidence suggests that IF can improve metabolic health by enhancing insulin sensitivity, reducing inflammation, and aiding weight management. Recent studies have also explored its role in mitigating obesity-related diseases, such as type 2 diabetes and non-alcoholic fatty liver disease, and its ability to support cardiovascular health and mental function. The effects of IF, however, vary depending on individual health conditions. Some patients show no clinical improvement, while others experience worsened outcomes. Mechanistically, IF induces metabolic switching and activates adenosine monophosphate-activated protein kinase (AMPK), both of which contribute to its therapeutic potential. These responses are influenced by factors such as underlying pathology, baseline metabolic state, and dietary composition. While preclinical data indicate potential therapeutic effects in diseases like cancer, rheumatoid arthritis, and neurodegenerative conditions, these findings are not yet sufficiently supported by human studies. This review argues that IF holds promise as a disease-modifying intervention. However, its implementation should be personalized according to patient-specific characteristics, and future clinical trials must prioritize identifying optimal fasting protocols to maximize therapeutic outcomes.},
}
@article {pmid40563918,
year = {2025},
author = {Dildar, T and Cui, W and Ikhwanuddin, M and Ma, H},
title = {Aquatic Organisms in Response to Salinity Stress: Ecological Impacts, Adaptive Mechanisms, and Resilience Strategies.},
journal = {Biology},
volume = {14},
number = {6},
pages = {},
doi = {10.3390/biology14060667},
pmid = {40563918},
issn = {2079-7737},
support = {32473150//National Natural Science Foundation of China/ ; 2024-SPY-00-013//Agricultural and Rural Department of Guangdong Province/ ; STKJ202209029//Guangdong Provincial Department of Science and Technology/ ; },
abstract = {Salinity stress presents a major ecological challenge for aquatic organisms, particularly in environments where salinity levels fluctuate. These fluctuations are becoming more pronounced due to climate change, further destabilizing aquatic ecosystems. Understanding how organisms adapt to such variability is essential for biodiversity conservation and the sustainable management of aquatic resources. This review examines the physiological, molecular, and behavioral adaptations that enable aquatic organisms to survive and thrive under salinity stress. Specifically, it explores mechanisms of osmotic regulation, ion transport, and oxidative stress responses, highlighting key signaling pathways-such as AMP-activated protein kinase (AMPK), Phosphatidylinositol 3-kinase-protein kinase (PI3K-AKT), Mitogen-activated protein kinase (MAPK), and the Hippo pathway-that facilitate these adaptive processes. The review also emphasizes the genetic and epigenetic modifications that contribute to resilience, underscoring the importance of genetic diversity for species survival in fluctuating salinity conditions. Furthermore, the interactions between host organisms and their microbiomes are discussed as critical factors influencing resilience. The review addresses the impact of salinity fluctuations on species distribution and biodiversity, with a focus on the implications of climate change for aquatic ecosystems. Finally, strategies for mitigating salinity stress, such as nutritional interventions and the development of salinity-resistant varieties, are explored, particularly in aquaculture. Overall, this review consolidates current knowledge on organismal adaptations, molecular mechanisms, and environmental challenges, offering valuable insights for ecological research and aquaculture practices in the face of climate change.},
}
@article {pmid40563880,
year = {2025},
author = {Tayyab, M and Islam, W and Waqas, W and Zhang, Y},
title = {Probiotic-Vaccine Synergy in Fish Aquaculture: Exploring Microbiome-Immune Interactions for Enhanced Vaccine Efficacy.},
journal = {Biology},
volume = {14},
number = {6},
pages = {},
doi = {10.3390/biology14060629},
pmid = {40563880},
issn = {2079-7737},
abstract = {The rapid expansion of aquaculture is vital for global food security, yet it faces persistent threats from disease outbreaks, vaccine inefficacy, and antibiotic overuse, all of which undermine sustainability. Conventional vaccines often fail to induce robust mucosal immunity, spurring interest in probiotics as adjuvants to enhance immunogenicity. Probiotics such as Bacillus subtilis and Lactobacillus casei modulate fish microbiomes, fortify mucosal barriers, and activate innate immune responses via mechanisms including Toll-like receptor signaling and cytokine production. These actions prime the host environment for prolonged adaptive immunity, improving antigen uptake and pathogen clearance. Experimental advances-such as Bacillus subtilis-engineered spores increasing survival rates to 86% in Vibrio anguillarum-challenged European seabass-demonstrate the potential of this synergy. Innovations in delivery systems, including chitosan-alginate microcapsules and synbiotic formulations, further address oral vaccine degradation, enhancing practicality. Probiotics also suppress pathogens while enriching beneficial gut taxa, amplifying mucosal IgA and systemic IgM responses. However, challenges such as strain-specific variability, environmental dependencies, and unresolved ecological risks persist. Optimizing host-specific probiotics and advancing multi-omics research is critical to unlocking this synergy fully. Integrating probiotic mechanisms with vaccine design offers a pathway toward antibiotic-free aquaculture, aligning with One Health principles. Realizing this vision demands interdisciplinary collaboration to standardize protocols, validate field efficacy, and align policies with ecological sustainability. Probiotic-vaccine strategies represent not merely a scientific advance but an essential evolution for resilient, ecologically balanced aquaculture systems.},
}
@article {pmid40563845,
year = {2025},
author = {Busayli, AM and Xu, W and Raffah, GA and Chen, G},
title = {Gut Microbiome, Neuroinflammation, and Fetal Alcohol Spectrum Disorders: Insights from Rodent Models.},
journal = {Biology},
volume = {14},
number = {6},
pages = {},
doi = {10.3390/biology14060593},
pmid = {40563845},
issn = {2079-7737},
support = {1013179575//University of Kentucky College of Medicine/ ; },
abstract = {Fetal alcohol spectrum disorder (FASD) is a significant public health issue that affects children. It results from ethanol exposure during pregnancy, leading to considerable physical, neurodevelopmental, behavioral, and cognitive deficits. The exact mechanism is not well understood. Recently, considerable attention has been focused on the influence of gut microbiome on brain development through the gut-brain axis. Changes in the gut microbiome resulting from ethanol exposure may contribute to the pathology of FASD, potentially involving neuroinflammation. This literature review summarizes the existing research and primary animal studies on the impact of early ethanol exposure on the gut microbiome, neuroinflammation, brain development, and behavioral consequences. The evidence suggests that early ethanol exposure alters the gut microbiome, which may induce neuroinflammation, brain damage, and cognitive impairment. However, a clear causal relationship among these factors remains to be fully elucidated.},
}
@article {pmid40563824,
year = {2025},
author = {Hasan, A and Scuderi, SA and Capra, AP and Giosa, D and Bonomo, A and Ardizzone, A and Esposito, E},
title = {An Updated and Comprehensive Review Exploring the Gut-Brain Axis in Neurodegenerative Disorders and Neurotraumas: Implications for Therapeutic Strategies.},
journal = {Brain sciences},
volume = {15},
number = {6},
pages = {},
doi = {10.3390/brainsci15060654},
pmid = {40563824},
issn = {2076-3425},
abstract = {The gut-brain axis (GBA) refers to the biochemical bidirectional communication between the central nervous system (CNS) and the gastrointestinal tract, linking brain and gut functions. It comprises a complex network of interactions involving the endocrine, immune, autonomic, and enteric nervous systems. The balance of this bidirectional pathway depends on the composition of the gut microbiome and its metabolites. While the causes of neurodegenerative diseases (NDDs) vary, the gut microbiome plays a crucial role in their development and prognosis. NDDs are often associated with an inflammation-related gut microbiome. However, restoring balance to the gut microbiome and reducing inflammation may have therapeutic benefits. In particular, introducing short-chain fatty acid-producing bacteria, key metabolites that support gut homeostasis, can help counteract the inflammatory microbiome. This strong pathological link between the gut and NDDs underscores the gut-brain axis (GBA) as a promising target for therapeutic intervention. This review, by scrutinizing the more recent original research articles published in PubMed (MEDLINE) database, emphasizes the emerging notion that GBA is an equally important pathological marker for neurological movement disorders, particularly in Alzheimer's disease, Parkinson's disease, multiple sclerosis, amyotrophic lateral sclerosis, Huntington's disease and neurotraumatic disorders such as traumatic brain injury and spinal cord injury. Additionally, the GBA presents a promising therapeutic target for managing these diseases.},
}
@article {pmid40563782,
year = {2025},
author = {Hong, SH and Roh, HW and Nam, YJ and Kim, TW and Cho, YH and Son, SJ and Hong, CH},
title = {Age- and Sex-Specific Gut Microbiota Signatures Associated with Dementia-Related Brain Pathologies: An LEfSe-Based Metagenomic Study.},
journal = {Brain sciences},
volume = {15},
number = {6},
pages = {},
doi = {10.3390/brainsci15060611},
pmid = {40563782},
issn = {2076-3425},
support = {2024-ER0505-00//Korea National Institute of Health (KNIH)/ ; GRRCAjou2023-B02//Gyeonggi-do Regional Research Center program of Gyeonggi province/ ; RS-2022-KH130309//Korea Health Technology R&amp;D Project through the Korea Health Industry Development Institute (KHIDI), funded by the Ministry of Health &amp; Welfare, Republic of Korea/ ; RS-2021-KH113821//Korea Health Technology R&amp;D Project through the Korea Health Industry Development Institute (KHIDI), funded by the Ministry of Health &amp; Welfare, Republic of Korea/ ; },
abstract = {BACKGROUND/OBJECTIVES: Emerging evidence suggests that gut microbiota composition is influenced by both age and sex and may contribute to dementia-related brain pathologies. However, comprehensive microbiome-based biomarker discovery stratified by these factors remains limited.<br><br>METHODS: We performed a metagenomic analysis of the gut microbiota of participants stratified by sex (female vs. male) and age (<75 vs. &#x2265;75 years). Alpha diversity (observed operational taxonomic unit, Chao1, Shannon, and Simpson) and linear discriminant analysis effect size analyses were conducted to identify dominant taxa associated with Alzheimer's pathology, vascular pathology, and dementia-related structural brain changes.<br><br>RESULTS: Females and non-elderly participants (aged < 75 years) exhibited higher gut microbial diversity, characterized by an increased abundance of Bifidobacterium spp. and Blautia spp., whereas males and elderly participants (aged &#x2265; 75 years) exhibited increased levels of Bacteroides spp. and Bacteroidia, which have been associated with inflammation and dysbiosis. Several taxa, including Bifidobacterium spp. were consistently identified as potential protective biomarkers, while Bacteroides spp. was linked to a higher risk of dementia-related brain pathologies.<br><br>CONCLUSIONS: Our findings demonstrate distinct age- and sex-specific differences in gut microbiota composition that may be closely associated with the pathophysiology of dementia-related brain pathologies. These results demonstrate that gut microbiota may serve as potential biomarkers for monitoring cerebrovascular conditions, potentially contributing to the development of personalized therapeutic strategies.},
}
@article {pmid40563710,
year = {2025},
author = {Kazen, AB and Umfleet, LG and Aboulalazm, FA and Cohen, AD and Terhune, S and Mason, L and Obarski, S and Franczak, M and Kindel, TL and Wang, Y and Kirby, JR},
title = {Gut Microbiota and Neurovascular Patterns in Amnestic Mild Cognitive Impairment.},
journal = {Brain sciences},
volume = {15},
number = {6},
pages = {},
doi = {10.3390/brainsci15060538},
pmid = {40563710},
issn = {2076-3425},
support = {1R21AG075501-24A1/NH/NIH HHS/United States ; },
abstract = {Background/Objectives: The interplay between the gut microbiome (GMB) and neurovascular function in neurodegeneration is unclear. The goal of this proof-of-concept, cross-sectional study is to identify relationships between the GMB, neurovascular functioning, and cognition in amnestic mild cognitive impairment (aMCI), the prototypical prodromal symptomatic stage of Alzheimer's disease (AD). Methods: Participants (n = 14 aMCI and 10 controls) provided fecal samples for GMB sequencing (16S and shotgun metagenomics), underwent MRI, and completed cognitive testing. Cerebral vascular reactivity (CVR), cerebral blood flow (CBF), and arterial transit time (ATT) were assessed. Statistical analyses evaluated the relationships between discriminatory taxa, cerebrovascular metrics, and cognition. Results: Sequencing revealed differentially abundant bacterial and viral taxa distinguishing aMCI from controls. Spearman correlations revealed that bacteria known to induce inflammation were negatively associated with CVR, CBF, and cognition, and positively associated with ATT. A reciprocal pattern emerged for the association of taxa with gut health. Conclusions: Our results provide preliminary evidence that pro-inflammatory gut bacterial and viral taxa are associated with neurovascular dysfunction and cognitive impairment in prodromal AD, highlighting their potential as candidate microbial biomarkers and targets for early intervention.},
}
@article {pmid40563519,
year = {2025},
author = {Ahmad, MF and Ahmad, FA and Alsayegh, AA and Zeyaullah, M and Babalghith, AO and Faidah, H and Ahmed, F and Khanam, A and Mozaffar, B and Kambal, N and Bantun, F},
title = {Probiotics and Cancer: Mechanistic Insights and Organ-Specific Impact.},
journal = {Biomolecules},
volume = {15},
number = {6},
pages = {},
doi = {10.3390/biom15060879},
pmid = {40563519},
issn = {2218-273X},
mesh = {*Probiotics/therapeutic use/pharmacology ; Humans ; *Neoplasms/microbiology/prevention &amp; control/drug therapy ; Gastrointestinal Microbiome/drug effects ; Animals ; },
abstract = {Probiotics have been revealed in various studies to modulate the gut microbiome and have a substantial impact on cancers, comprising oesophageal, lung, liver, and colorectal cancer. These properties are endorsed by a diverse mechanism, including the modulation of the gut microbiome; preventing the metabolism of carcinogenic substances; exertion of anti-inflammatory action, immunopotentiator properties, and antioxidant activities; prevention of tumour growth; and decreasing the adverse effects of chemotherapy. There are promising perspectives regarding the new and developing field of probiotic research in relation to cancer treatment. This review demonstrates the recent findings of probiotics efficacy in cancer prevention and treatment and organ-specific impact along with protection from chemotherapy-induced side effects. The present evidence specifies that strategic probiotics application may be an effective complementary approach for the management of numerous kinds of cancer; still, additional studies and clinical trials are required to comprehend the relationships between cancer and probiotics.},
}
@article {pmid40563478,
year = {2025},
author = {Lo, Y and Cheng, TT and Huang, CJ and Cheng, YC and Chyuan, IT},
title = {Advancing Therapeutic Strategies in Atopic Dermatitis: Emerging Targets and Personalized Approaches.},
journal = {Biomolecules},
volume = {15},
number = {6},
pages = {},
doi = {10.3390/biom15060838},
pmid = {40563478},
issn = {2218-273X},
mesh = {Humans ; *Dermatitis, Atopic/immunology/drug therapy/therapy/metabolism ; *Precision Medicine/methods ; Cytokines/metabolism ; Thymic Stromal Lymphopoietin ; Animals ; Immunity, Innate ; Adaptive Immunity ; Molecular Targeted Therapy ; },
abstract = {Atopic dermatitis (AD) is a chronic inflammatory skin disorder marked by intricate interplay among skin barrier dysfunction, immune dysregulation, and microbial dysbiosis. While therapeutic advancements targeting T helper 2 (Th2) cytokines, such as interleukin (IL)-4 and IL-13, and the Janus kinase/signal transducer and activator of transcription (JAK/STAT) pathway have yielded promising outcomes, a significant proportion of patients still experience inadequate relief, particularly from persistent pruritus. Achieving minimal disease activity remains an unmet clinical priority and a cornerstone of effective AD management. This review provides an in-depth analysis of current therapeutic approaches and integrates findings from recent biologic studies, with a particular focus on innovative strategies under active investigation. These approaches include targeting components of the innate immune system, such as thymic stromal lymphopoietin (TSLP) and IL-1 family cytokines; the adaptive immune system, including OX40-OX40L interactions and Th17- and Th22-related cytokines; and mechanisms associated with pruritus, such as IL-31, histamine receptors, and neurokinin 1 receptor. Emerging insights underscore the transformative potential of personalized therapeutic regimens tailored to the distinct endotypes and severity of AD. Advances in deciphering the pathogenesis of AD are unlocking unprecedented opportunities for precision medicine, offering renewed hope for improved outcomes in this multifaceted and heterogeneous condition.},
}
@article {pmid40563474,
year = {2025},
author = {Kushawaha, B and Rem, TT and Pelosi, E},
title = {Harnessing Microbiome, Bacterial Extracellular Vesicle, and Artificial Intelligence for Polycystic Ovary Syndrome Diagnosis and Management.},
journal = {Biomolecules},
volume = {15},
number = {6},
pages = {},
doi = {10.3390/biom15060834},
pmid = {40563474},
issn = {2218-273X},
mesh = {*Polycystic Ovary Syndrome/diagnosis/microbiology/therapy ; Humans ; Female ; *Artificial Intelligence ; *Extracellular Vesicles/metabolism ; *Microbiota ; *Gastrointestinal Microbiome ; Dysbiosis/microbiology ; Bacteria/metabolism ; },
abstract = {Polycystic ovary syndrome (PCOS) affects 6-19% of reproductive-age women worldwide, yet diagnosis remains challenging due to heterogeneous presentations and symptoms overlapping with other endocrine disorders. Recent studies have shown that gut dysbiosis plays a significant role in PCOS pathophysiology, with bacterial extracellular vesicles (BEVs) functioning as critical mediators of the gut-ovary axis. BEVs carry distinct cargos in PCOS patients-including specific miRNAs and inflammatory proteins-and show promise for both diagnostic and therapeutic applications. Artificial intelligence (AI) is emerging as a promising significant tool in PCOS research due to improved diagnostic accuracy and the capability to analyze complex datasets combining microbiome, BEV, and clinical parameters. These integrated approaches have the potential to better address PCOS multifactorial nature, enabling improved phenotypic classification and personalized treatment strategies. This review examines recent advances in the last 25 years in microbiome, BEV, and AI applications in PCOS research using PubMed, Web of Science, and Scopus databases. We explore the diagnostic potential of the AI-driven analysis of microbiome and BEV profiles, and address ethical considerations including data privacy and algorithmic bias. As these technologies continue to evolve, they hold increasing potential for the improvement of PCOS diagnosis and management, including the development of safer, more precise, and effective interventions.},
}
@article {pmid40563468,
year = {2025},
author = {Pagliaro, R and Scialò, F and Schiattarella, A and Cianci, R and Campbell, SFM and Perrotta, F and Bianco, A and Castaldo, G},
title = {Mechanisms of Lung Cancer Development in Cystic Fibrosis Patients: The Role of Inflammation, Oxidative Stress, and Lung Microbiome Dysbiosis.},
journal = {Biomolecules},
volume = {15},
number = {6},
pages = {},
doi = {10.3390/biom15060828},
pmid = {40563468},
issn = {2218-273X},
mesh = {Humans ; *Cystic Fibrosis/complications/microbiology/pathology/metabolism ; *Dysbiosis/microbiology/complications ; *Oxidative Stress ; *Inflammation/pathology/metabolism ; *Lung Neoplasms/pathology/etiology/microbiology/metabolism ; *Microbiota ; *Lung/microbiology/pathology ; Animals ; },
abstract = {Cystic fibrosis (CF) is a genetic disorder caused by mutations in the CFTR gene, leading to defective ion transport and impaired function of various organs. Chronic inflammation, oxidative stress, and microbial dysbiosis are key pathological features of CF patients, contributing to disease progression, lung damage, and an increased susceptibility to infections. Emerging evidence suggests that in CF patients these factors can promote cancer development, especially lung cancer. Chronic inflammation in CF, driven by immune cell dysfunction, results in the release of pro-inflammatory cytokines and reactive oxygen species (ROSs), fostering an environment conducive to cancer initiation. Oxidative stress can amplify cellular damage and hinder airway remodeling. ROSs not only damage cellular components such as lipids, proteins, and DNA but also disrupt lung homeostasis, creating a favorable environment for cancer development. Furthermore, the lung microbiome in CF patients is often dysbiotic, with a reduced diversity and the predominance of pathogenic bacteria such as Pseudomonas aeruginosa, which exacerbate inflammation and may contribute to carcinogenesis. This review explores the mechanisms linking CF to lung cancer, examining the potential clinical implications of these mechanisms for early detection, monitoring, and targeted therapies for lung cancer prevention in CF patients.},
}
@article {pmid40563386,
year = {2025},
author = {Zeng, M and Li, Y and Cheng, J and Wang, J and Liu, Q},
title = {Prebiotic Oligosaccharides in Skin Health: Benefits, Mechanisms, and Cosmetic Applications.},
journal = {Antioxidants (Basel, Switzerland)},
volume = {14},
number = {6},
pages = {},
doi = {10.3390/antiox14060754},
pmid = {40563386},
issn = {2076-3921},
support = {MZGC20240028//Sichuan Science and Technology Innovation Seedling Project/ ; 22208111//National Natural Science Foundation of China/ ; 22378077//National Natural Science Foundation of China/ ; 2023A1515010064//Guangdong Basic and Applied Basic Research Foundation/ ; 2023QNRC001//Young Elite Scientists Sponsorship Program by CAST/ ; },
abstract = {Prebiotic oligosaccharides have attracted significant interest in dermatology and skin health due to their ability to modulate the skin microbiome and microbiota-host interactions. This review offers a novel dual perspective, systematically examining the benefits of both oral intake and topical application of prebiotic oligosaccharides, including well-established prebiotics (e.g., human milk oligosaccharides, galacto- and fructo-oligosaccharides) and emerging prebiotic candidates (e.g., gluco-oligosaccharides, chitosan-oligosaccharides, agaro-oligosaccharides). First, cutting-edge synthetic processes for producing diverse oligosaccharides and their structural chemistry are introduced. Then, we discuss in vitro studies demonstrating their efficacy in promoting skin commensals, inhibiting pathogens, and conferring protective effects, such as antioxidant, anti-inflammatory, anti-melanogenic, and wound-healing properties. Furthermore, we emphasize in vivo animal studies and clinical trials revealing that prebiotic oligosaccharides, administered orally or topically, alleviate atopic dermatitis, enhance skin hydration, attenuate acne, and protect against photo-aging by modulating skin-gut microbiota and immune responses. Mechanistically, we integrate genetic and molecular insights to elucidate how oligosaccharides mediate these benefits, including gut-skin axis crosstalk, immune regulation, and microbial metabolite signaling. Finally, we highlight current commercial applications of oligosaccharides in cosmetic formulations while addressing scientific and practical challenges, such as structure-function relationships, clinical scalability, and regulatory considerations. This review bridges mechanistic understanding with practical applications, offering a comprehensive resource for advancing prebiotic oligosaccharides-based skincare therapies.},
}
@article {pmid40563357,
year = {2025},
author = {Clemente-Suárez, VJ and Martín-Rodríguez, A and Beltrán-Velasco, AI and Rubio-Zarapuz, A and Martínez-Guardado, I and Valcárcel-Martín, R and Tornero-Aguilera, JF},
title = {Functional and Therapeutic Roles of Plant-Derived Antioxidants in Type 2 Diabetes Mellitus: Mechanisms, Challenges, and Considerations for Special Populations.},
journal = {Antioxidants (Basel, Switzerland)},
volume = {14},
number = {6},
pages = {},
doi = {10.3390/antiox14060725},
pmid = {40563357},
issn = {2076-3921},
abstract = {BACKGROUND: Type 2 diabetes mellitus (T2DM) is a chronic metabolic disorder characterized by persistent hyperglycemia, oxidative stress, and inflammation, contributing to insulin resistance and long-term complications. Dietary antioxidants from plant sources, such as polyphenols, flavonoids, carotenoids, and phenolic acids, have been increasingly studied for their potential to modulate these pathophysiological mechanisms.<br><br>OBJECTIVE: This review aims to summarize and critically analyze the current evidence on the biological effects, therapeutic potential, and translational challenges of plant-derived antioxidants in the prevention and management of T2DM.<br><br>METHODS: This narrative review was conducted using peer-reviewed literature from PubMed, Scopus, and Web of Science. Emphasis was placed on mechanistic studies, clinical trials, bioavailability data, and advances in formulation technologies related to antioxidant compounds in the context of T2DM.<br><br>RESULTS: Plant antioxidants exert beneficial effects by modulating oxidative stress, reducing systemic inflammation, and improving insulin signaling pathways. However, their clinical application is limited by low bioavailability, chemical instability, and high interindividual variability. Recent developments, such as nanoencapsulation, synergistic functional food formulations, and microbiome-targeted strategies, have shown promise in enhancing efficacy. Additionally, personalized nutrition approaches and regulatory advances are emerging to support the integration of antioxidant-based interventions into diabetes care.<br><br>CONCLUSIONS: Plant-derived antioxidants represent a promising complementary tool for T2DM management. Nonetheless, their effective clinical use depends on overcoming pharmacokinetic limitations and validating their long-term efficacy in well-designed trials. Integrating food technology, microbiome science, and precision nutrition will be crucial to translate these compounds into safe, scalable, and personalized therapeutic options for individuals with or at risk of T2DM.},
}
@article {pmid40563352,
year = {2025},
author = {He, J and Tang, Q and Liu, YC and Wang, LJ and Chai, YF},
title = {Impact of Diquat on the Intestinal Health and the Composition and Function of the Gut Microbiome.},
journal = {Antioxidants (Basel, Switzerland)},
volume = {14},
number = {6},
pages = {},
doi = {10.3390/antiox14060721},
pmid = {40563352},
issn = {2076-3921},
support = {TJYXZDXK-007A//Tianjin Municipal Medical Key Construction Project/ ; PUMF01010010-2024-18//Beijing Union Medical Foundation-Rui E Emergency Medicine Research/ ; },
abstract = {Diquat (DQ) is extensively utilized as a herbicide in farming, and its intake can result in serious systemic toxicity due to its induction of oxidative stress (OS) and disruption of intestinal homeostasis. The gastrointestinal tract is one of the first systems exposed to DQ, and damage to this system can influence the general health of the host. Our review summarizes the toxic effects of DQ on the intestinal barrier integrity, gut microbiome, and microbial metabolites (e.g., short-chain fatty acids [SCFAs], bile acids). By elucidating the mechanisms linking DQ-induced OS to gut dysbiosis, mitochondrial dysfunction, and inflammation, our work provides critical insights into novel therapeutic strategies, including probiotics, antioxidants (e.g., hydroxytyrosol, curcumin), and selenium nanoparticles. These findings address a pressing gap in understanding environmental toxin-related gut pathology and offer potential interventions to mitigate systemic oxidative damage.},
}
@article {pmid40563329,
year = {2025},
author = {Shoham, S and Pintel, N and Avni, D},
title = {Oxidative Stress, Gut Bacteria, and Microalgae: A Holistic Approach to Manage Inflammatory Bowel Diseases.},
journal = {Antioxidants (Basel, Switzerland)},
volume = {14},
number = {6},
pages = {},
doi = {10.3390/antiox14060697},
pmid = {40563329},
issn = {2076-3921},
support = {101000501//European Commission/ ; },
abstract = {Oxidative stress is a recognized contributor to the pathophysiology of inflammatory bowel disease (IBD), exacerbating chronic inflammation and tissue damage. While traditional IBD therapies primarily focus on immune modulation, alternative approaches that address oxidative stress and promote gut microbial health present new opportunities for symptom relief and disease management. Microalgae, known for their potent antioxidant, anti-inflammatory, and prebiotic properties, show promise in alleviating oxidative damage and supporting beneficial gut bacteria. This review explores the multifaceted role of oxidative stress in IBD and highlights the therapeutic potential of microalgae-derived compounds. In addition, it examines the synergistic benefits of combining microalgal antioxidants with probiotics to promote gut homeostasis. Advances in delivery systems, including nanotechnology and symbiotic bacteria-microalgae interactions, are also discussed as emerging approaches for targeted treatment. The review concludes by identifying future research priorities focused on clinical translation and microalgae-based bioengineering innovations to enhance the efficacy and accessibility of therapeutics for IBD patients.},
}
@article {pmid40563316,
year = {2025},
author = {Martins-Green, M and Kim, J and Aziz, K},
title = {The Impact of the Skin Microbiome and Oxidative Stress on the Initiation and Development of Cutaneous Chronic Wounds.},
journal = {Antioxidants (Basel, Switzerland)},
volume = {14},
number = {6},
pages = {},
doi = {10.3390/antiox14060682},
pmid = {40563316},
issn = {2076-3921},
abstract = {Wound healing is a very complex process composed of several phases in which precise events occur, both temporally and specially. However, when these processes go awry, biofilm-forming bacteria become installed in the healing tissue, and the patient has comorbidities, so the wounds do not heal and become chronic. In this review, we describe the importance of high levels of oxidative stress (OS) and bacteria from the skin microbiome in the initiation and development of chronic wounds. The skin microbiome is diverse in humans, and its composition is dependent on the environment in the specific areas of the body. OS is critical for wound healing as it stimulates the immune system to destroy pathogens and secrete cytokines and growth factors that stimulate healing. When OS levels become high in the wound and the bacteria of the skin install themselves in the wound, chronicity ensues. However, neither OS nor the bacteria of the skin alone can initiate chronicity. However, when present together, chronic wounds develop. Given the complexity of chronic wound initiation, developing treatment for these wounds has been difficult. Here, we also discuss the challenges of treating chronic wounds and offer a potential sequence of approaches to treating these wounds after debridement.},
}
@article {pmid40563121,
year = {2025},
author = {Wang, X and Liu, J and Huoshen, W and Liu, J and Qiao, X and Zhang, H and Zhou, XJ},
title = {Causal relationships between gut microbiota and IgA nephropathy: evidence from Mendelian randomization and microbiome validation.},
journal = {Renal failure},
volume = {47},
number = {1},
pages = {2522979},
doi = {10.1080/0886022X.2025.2522979},
pmid = {40563121},
issn = {1525-6049},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Glomerulonephritis, IGA/microbiology/genetics ; Mendelian Randomization Analysis ; RNA, Ribosomal, 16S/genetics ; Genome-Wide Association Study ; },
abstract = {BACKGROUND: Emerging evidence links gut microbiota strongly with IgA Nephropathy (IgAN). However, the causal role of specific gut microbiota in IgAN remains unclear. This study used a two-sample Mendelian randomization (MR) approach, validated with 16S rRNA datasets, to identify these causal relationships.<br><br>METHODS: We performed MR analysis using genetic instruments for 412 gut microbiota taxa from genome-wide association studies (GWAS) as exposures and IgAN GWAS data as outcomes. The inverse-variance weighted method was used as the primary analysis, supplemented by MR-Egger regression, weighted median methods, and Cochran's Q test to assess pleiotropy and heterogeneity. Significant findings were validated using reverse, multivariable, and mediation MR analyses. Results were validated using genus-level 16S rRNA datasets with batch correction (ConQuR), and microbial function was inferred via PICRUSt2.<br><br>RESULTS: Three gut microbiota species were protective against IgAN: s_Alistipes_senegalensis (OR = 0.64, p&#x2009;=&#x2009;.002), s_Ruminococcus_bromii (OR = 0.75, p&#x2009;=&#x2009;.040), and s_Bilophila_unclassified (OR = 0.68, p&#x2009;=&#x2009;.040). Six species were associated with increased IgAN risk, including g_Barnesiella (OR = 1.32, p&#x2009;=&#x2009;.030) and s_Rothia_mucilaginosa (OR = 1.52, p&#x2009;=&#x2009;.040). After multiple-testing correction, significant associations persisted for s_Alistipes_senegalensis (p&#x2009;=&#x2009;.043), s_Bacteroides_clarus (p&#x2009;=&#x2009;.035), and s_Bilophila_unclassified (p&#x2009;=&#x2009;.002). Sensitivity analyses confirmed robust results without pleiotropy or heterogeneity. Genus-level validation confirmed consistent microbial shifts. Functional predictions showed upregulation of carbohydrate/fatty acid metabolism and downregulation of the urea cycle.<br><br>CONCLUSIONS: This study reveals specific gut microbes and metabolic pathways potentially driving IgAN, offering novel biomarkers and therapeutic targets for microbiome-based interventions.},
}
@article {pmid40563092,
year = {2025},
author = {Amimo, JO and Kunyanga, CN and Raev, SA and Kick, M and Micheal, H and Saif, LJ and Vlasova, AN},
title = {Stunting is associated with persistent and transferable alterations in the gut microbiome.},
journal = {Gut pathogens},
volume = {17},
number = {1},
pages = {49},
pmid = {40563092},
issn = {1757-4749},
support = {OPP1117467//Bill and Melinda Gates Foundation/ ; R01A1099451//National Institute of Allergy and Infectious Diseases/ ; },
abstract = {As robust animal models to study the pathophysiology of stunting are absent, we have comparatively characterized the gut microbiota of malnourished/stunted vs. clinically healthy/normal Kenyan toddlers (12-24 months old) and established a gnotobiotic (Gn) pig fecal transplant model to gain understanding of microbial community structure associated with stunting. As expected, the bacterial composition between the two toddler groups was distinct: Actinobacteria was most prevalent in healthy toddlers, whereas Proteobacteria dominated in stunted toddlers. Although the diversity indices showed no significant differences, unique bacterial genera were found in each toddler group: three genera unique to stunted toddlers and ten unique to healthy toddlers, with eight genera shared between the groups. We observed a higher number of enriched bacterial virulence genes in healthy vs. stunted toddlers suggesting that the microbiome plasticity and functional characteristics of the healthy toddlers allow for the pathogen/pathobiont control. In contrast, we noted the presence of more genes associated with antimicrobial-resistance (AMR) bacteria in stunted toddlers, possibly due to early-life antibiotic treatments. Of interest, functional analysis showed that CAZymes associated with carbohydrate biosynthesis, and a few metabolic pathways related to protein/amino acid, carbohydrate and fat catabolism were enriched in stunted toddlers. In contrast carbohydrate degradation CAZymes and numerous anabolic pathways were prevalent in healthy toddlers. These patterns were also evident in the Gn pigs transplanted with stunted/healthy human fecal microbiota (HFM). Overall, our findings suggest that the microbiota transplanted Gn pigs represent a valuable model for studying the infant microbial community structure and the impacts of stunting on the child gut microbiota. Additionally, this is the first study to demonstrate that the healthy vs. stunted microbiota composition and function remained different in the Gn pigs throughout the study. This information and the Gn pig model are vital for developing and testing targeted interventions for malnourished/stunted populations, consequently advancing microbiome-based diagnosis and personalized medicine.},
}
@article {pmid40562845,
year = {2025},
author = {Shiner, YA and Caplan, S and Doweck, I},
title = {Actinomyces findings in tonsillectomy specimens- comparison between adults and pediatrics populations.},
journal = {European archives of oto-rhino-laryngology : official journal of the European Federation of Oto-Rhino-Laryngological Societies (EUFOS) : affiliated with the German Society for Oto-Rhino-Laryngology - Head and Neck Surgery},
volume = {},
number = {},
pages = {},
pmid = {40562845},
issn = {1434-4726},
abstract = {BACKGROUND: Tonsillectomy is a common surgical procedure primarily performed for obstructive sleep apnea (OSA) and recurrent acute tonsillitis. Actinomyces are gram-positive, anaerobic bacteria commonly found in the oral cavity and known to form part of the human microbiome, occasionally associated with localized infections. While Actinomyces bacterial colonization in tonsils has been previously studied, its correlation with surgical indications and outcomes remains unclear.<br><br>OBJECTIVES: The study aimed to investigate the relationship between Actinomyces colonization in tonsillar specimens and surgical indications, and to examine whether Actinomyces presence influences tonsillectomy outcomes, specifically post-operative hemorrhage and hospital stay.<br><br>METHODS: This retrospective cohort study analyzed electronic medical records from Lady Davis Carmel Medical Centre between 2011 and 2021. The study included 1,333 patients who underwent extra-capsular tonsillectomies. Patient demographics, surgical indications, length of hospital stay, post-surgical complications, and pathological reports were collected and analyzed using IBM SPSS Statistics 28.0.<br><br>RESULTS: The study population consisted of 760 (57%) males and 573 (43%) females, with an age range of 0.98 to 67.5&#xa0;years (mean 9.1&#xa0;years). Actinomyces was present in 13.2% of specimens from patients with infectious indications compared to 4.5% in patients with obstructive indications (p&#x2009;<&#x2009;0.001). A statistically significant age difference was observed between patients with (17.78&#xa0;years) and without (8.55&#xa0;years) Actinomyces. Multivariate analysis revealed that age was the most significant predictor of Actinomyces presence (OR 1.047, p&#x2009;<&#x2009;0.0001).<br><br>CONCLUSIONS: The study found a significant correlation between Actinomyces presence, older age, and infectious surgical indications. While Actinomyces colonization did not demonstrate a direct influence on surgical complications, the findings suggest potential clinical relevance that merits further research to elucidate the bacterium's role in tonsillar pathology.},
}
@article {pmid40562776,
year = {2025},
author = {Davidson, S and So, Y and Oscarsson, E and Håkansson, &#xc5; and Sjöberg, K},
title = {Presence of viable gram-positive bacteria in blood of patients with inflammatory bowel disease is not affected by treatment.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {20283},
pmid = {40562776},
issn = {2045-2322},
mesh = {Humans ; Female ; Male ; Adult ; Middle Aged ; *Gram-Positive Bacteria/isolation &amp; purification/genetics ; *Colitis, Ulcerative/microbiology/blood/drug therapy ; *Inflammatory Bowel Diseases/microbiology/blood/drug therapy ; *Crohn Disease/microbiology/blood/drug therapy ; C-Reactive Protein/metabolism ; Young Adult ; Anti-Bacterial Agents/therapeutic use ; },
abstract = {In inflammatory bowel disease (IBD) the pathogenetic process is characterized by dysbiosis, increased permeability, translocation, and immune activation. The aim of the present study was to assess the presence of viable bacteria in the blood of patients with IBD and to correlate the findings with clinical characteristics. The study included 28 patients with Crohn's disease (CD) (median age 38 years, 50% female, biological treatment in 71%) and 19 patients with ulcerative colitis (UC) (median age 45 years, 33% female, biological treatment in 84%). Identification of viable bacteria in the blood was evaluated by optimized cultivation and Sanger sequencing and for quantification real-time PCR was performed. Viable Gram-positive bacteria were detected in 34 IBD patients (72.3%). There were no associations between the presence of bacteria and gender, antibiotic treatment, intake of alcohol, use of PPI, steroids, or biological treatment. The number of bacterial copies was correlated with higher C-reactive protein (CRP) (p = 0.013). In ¾ of the patients, viable bacteria were identified in the blood despite treatment with biologicals, which indicates a vast barrier defect. This observation also indicates that the disease is still active. To obtain a true deep mucosal healing an intact barrier function is required.},
}
@article {pmid40562421,
year = {2025},
author = {Supasitdikul, T and Mazariegos, JRR and Nhat, NN and Tung, YT and Yang, DF and Lee, LJ and Gunawan, SP and Chen, YC},
title = {Sleep Deprivation Alters Gut Microbiome Diversity and Taxonomy: A Systematic Review and Meta-Analysis of Human and Rodent Studies.},
journal = {Journal of sleep research},
volume = {},
number = {},
pages = {e70125},
doi = {10.1111/jsr.70125},
pmid = {40562421},
issn = {1365-2869},
support = {NSTC 112-2314-B-038-051-MY3//National Science and Technology Council/ ; },
abstract = {Sleep deprivation (SD) affects the gut microbiome, but findings across studies vary in terms of microbiota changes, SD induction methods and gut measurements. The effects of SD on the gut microbiome in humans and rodents have not been comprehensively reviewed. This meta-analysis investigated SD-related factors and their effects on the gut microbiome in human and rodent models. We analysed data from studies published before February 28, 2024, and calculated standardised mean differences (SMDs). Subgroup analyses were conducted for rodents and humans. A total of 20 studies (4 human, 5 rat, 8 mouse and 3 combined human and rodent) were included. SD significantly reduced alpha diversity (Shannon and Simpson indices) and increased the Firmicutes-to-Bacteroidetes ratio. In rodents, the Shannon index was lower (SMD = -1.27, 95% CI: -2.20 to -0.34), and the Firmicutes/Bacteroidetes ratio was higher (SMD = 2.60, 95% CI: 1.61-3.59). Human studies showed nonsignificant trends, limited by small sample sizes. Analysis at the phylum, family and genus levels showed a modest decrease in Actinobacteria and Tenericutes and a minor increase in Bacteroidetes, Firmicutes and Proteobacteria. Reductions in Lactobacillaceae and Erysipelotrichaceae and increases in Ruminococcaceae and Lachnospiraceae were observed. A2, Lactobacillus and Ruminococcus_1 were less abundant in the SD group. Overall, SD alters gut microbiome composition. Standardised human studies are needed to clarify translational relevance.},
}
@article {pmid40562254,
year = {2025},
author = {Martelli, A and Mohamed, Y and Gallego-Ferrer, G and Gentile, P and Girón-Hernández, J},
title = {Revolutionizing gut health: Advances in encapsulation strategies for probiotics and bioactive molecules.},
journal = {Biotechnology advances},
volume = {},
number = {},
pages = {108630},
doi = {10.1016/j.biotechadv.2025.108630},
pmid = {40562254},
issn = {1873-1899},
abstract = {Advancements in biotechnology underscore the critical role of gastrointestinal microbiome in health and disease. Probiotic supplementation offers therapeutic potential, particularly for functional gastrointestinal disorders, which affect over 40 % of the global population and impair quality of life. Despite a rapidly growing probiotics market, many formulations suffer from poor efficacy due to challenges such as gastric survival, temperature sensitivity and poor colonization of the gut lining. Encapsulation technologies have emerged as potential solutions, offering protection for probiotics but introducing complexities related to biopolymer coatings and adhesion efficiency. Moreover, reactive oxygen species (ROS) significantly influence gut health, with excess ROS contributing to dysbiosis, intestinal barrier disruption and inflammation. While dietary antioxidants offer some benefits, their rapid clearance and nonspecific biodistribution limit therapeutic efficacy. Encapsulation strategies integrating probiotics with phenolic antioxidants have demonstrated enhanced survival, adhesion, and antioxidant activity, presenting a promising avenue for gut health interventions. This review primarily aims to explore innovative approaches to encapsulated probiotic formulations, emphasizing their potential to address current limitations and improve gut health. Specifically, the review examines key areas of focus including the design and manufacturing of systems incorporating live microorganisms and bioactive molecules; evaluation of their digestion, release and bioactivity; and their in vitro and in vivo efficacy. Finally, regulatory considerations and future research directions, focused on advancing smart encapsulation strategies and novel delivery systems to enhance therapeutic efficacy and address current challenges in gut health interventions are also explored.},
}
@article {pmid40562244,
year = {2025},
author = {Costa, BF and Sawaya, C and Buren, JV and Smith, AL},
title = {Investigating anaerobic digestion microbiome resilience to high PFOA and PFOS mixtures during cometabolism.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {132877},
doi = {10.1016/j.biortech.2025.132877},
pmid = {40562244},
issn = {1873-2976},
abstract = {Anaerobic digestion (AD) is a reducing environment with high microbial diversity and potential for biotransformation of PFAS. Yet, their fate and impact on the microbial community remains poorly understood. This study evaluated the long-term impact (100 d) of perfluorooctanoic acid (PFOA) and perfluorooctane sulfonate (PFOS) spiked at10 mg/L (low) and 100 mg/L (high), respectively. Although resilient to complete system failure, high PFAS concentrations disrupted AD, evidenced by 25-50 % reduction in methane content, 45 %-48 % reduction in cumulative biogas production, and accumulation of butyric acid. No significant decrease in PFAS concentration was observed in the liquid fraction after 100 d relative to the kill controls, indicating PFAS adsorption behavior. However, PFAS concentrations were temporally variable. Microbial community analysis revealed enrichment of notable AD groups, such as Firmicutes, Synergistetes, and Methanomassillicoccus phyla in high PFAS reactors, which underscores the potential for the microbiome adaptation and informs future strategies for PFAS-contaminated sludge treatment.},
}
@article {pmid40562242,
year = {2025},
author = {Jiang, F and Ye, C and Wang, F and Dong, T and Wei, J and Kapelan, Z and Hofman, J and Xu, Z and Chu, W},
title = {Enhanced thioether formation in stormwater pipes induced by nitrogen-containing pollutants: The role of the sediment microbiome.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {132878},
doi = {10.1016/j.biortech.2025.132878},
pmid = {40562242},
issn = {1873-2976},
abstract = {The illicit connections between sewage and stormwater pipes result in the discharge of untreated sewage into receiving rivers, posing significant odor and health hazards. While thioethers are recognized as key odorants in sewage systems, their distribution in stormwater systems remain poorly characterized. This study analyzed 12 types of thioethers in stormwater pipes sampled at 21 sites in China. Advanced analytical techniques, including Mantel analysis and Structural Equation Modeling, were employed to examine the relationships between overlying water properties, sediment microbial characteristics, and thioether concentrations. Results showed that sediment thioether loads (36.77 ± 50.14 μg S/m; range: 7.24-99.96 μg S/m) were substantially higher than those in the overlying water (12.02 ± 42.52 μg S/m; range: 0.03-92.76 μg S/m), highlighting sediment as a critical pollution reservoir. Dissolved oxygen, NH3-N, and terrestrial-derived dissolved organic nitrogen were identified as key factors shaping sediment microbiome composition, particularly fermentative, sulfate-reducing, and denitrifying bacteria, which in turn drives thioether formation. Specifically, dominant compounds like dimethyl disulfide and dimethyl trisulfide were found to be produced through the anaerobic fermentation of methionine and redox conversion of methanethiol, as well as the anaerobic fermentation of cysteine and methylation of polysulfides. Humic substances could facilitate methanethiol redox conversion and polysulfide methylation by serving as methyl donors and enhancing electron transfer efficiency. Additionally, NH3-N may promote microbial metabolism by providing amino groups essential for the synthesis of metabolic precursors. Therefore, effective mitigation of odorous thioethers in stormwater systems necessitates integrated strategies targeting both sulfur-containing organic precursors and nitrogen-rich pollutants.},
}
@article {pmid40562170,
year = {2025},
author = {Gallagher, K and Halperin-Goldstein, S and Paller, AS},
title = {New Treatments in Atopic Dermatitis Update.},
journal = {Annals of allergy, asthma &amp; immunology : official publication of the American College of Allergy, Asthma, &amp; Immunology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.anai.2025.06.020},
pmid = {40562170},
issn = {1534-4436},
abstract = {This review evaluates the efficacy and safety of novel and emerging topical and systemic therapies for atopic dermatitis (AD) across pediatric and adult populations with an emphasis on recent advancements and future directions. Data were sourced from peer-reviewed publications (PubMed), scientific meeting abstracts, ClinicalTrials.gov, and industry press releases. Several new agents have received Food and Drug Administration approval, expanding therapeutic options for patients. Non-steroidal topical treatments, such as roflumilast and tapinarof creams, are approved for adults and children down to 6 and 2 years, respectively. Topical Janus kinase (JAK) inhibitors, including ruxolitinib, leverage inhibition of the JAK1 pathway with low concern for toxicity. The use of biologics targeting the interleukin (IL)-4/IL-13 pathway has expanded; dupilumab is approved for patients 6 months and older and tralokinumab and lebrikizumab are approved for 12 years and above. Most recently, nemolizumab, targeting the IL-31 receptor, which mediates nonhistaminergic itch, has been approved for those 12 years and above. Although baricitinib is approved in Europe and Japan, upadacitinib and abrocitinib remain the only oral JAK inhibitors approved for U.S. patients 12 years and older. Promising investigational therapies, particularly through topically altering the microbiome (bacteriotherapy) and systemic agents targeting the OX40/OX40L pathway and multispecific antibodies, are in development. These innovations represent a shift toward personalized AD management. As the treatment landscape evolves, ongoing research is essential to assess long-term safety and efficacy, as well as to develop predictive models that optimize treatment strategies, ultimately improving patient outcomes and quality of life.},
}
@article {pmid40561434,
year = {2025},
author = {Cultrera, G and Franco, S and Spoto, G and Libra, M and Falzone, L},
title = {Review Article: Disrupted Oral Microbiota and Its Implications in Cancer Onset and Progression: A Narrative Review.},
journal = {Critical reviews in oncogenesis},
volume = {30},
number = {2},
pages = {83-106},
doi = {10.1615/CritRevOncog.2025059551},
pmid = {40561434},
issn = {0893-9675},
mesh = {Humans ; *Microbiota ; *Neoplasms/microbiology/pathology/etiology ; *Dysbiosis/microbiology/complications ; *Mouth/microbiology ; Disease Progression ; Carcinogenesis ; },
abstract = {The oral microbiota plays a pivotal role in maintaining oral health, but its dysbiosis has been increasingly implicated in the development of systemic diseases, including cancer. Emerging evidence highlights the potential contribution of oral microorganisms to carcinogenesis in the oral cavity and distant organs, such as the lungs, pancreas, and genitourinary tract. This review explores the mechanisms through which the oral microbiota influences cancer development and treatment response, mainly driven by microbial translocation, systemic inflammation, immune modulation, and the release of carcinogenic metabolites. Additionally, the review discusses how oral microbiota perturbations interact with host factors, such as diet, systemic diseases, genetics, and cancer therapies, to influence tumor initiation, progression, and response to treatment. A critical analysis of past and emerging literature shows that specific microbial taxa potentially influence tumor progression and immune responses, including Fusobacterium, Porphyromonas, Aggregatibacter and Treponema. The detection of these microorganisms and the study of oral microbiome profiling in cancer care may offer new diagnostic and therapeutic strategies; however, further studies with homogeneous patient populations are needed to fully understand the contributions of oral dysbiosis in cancer development and treatment responses.},
}
@article {pmid40561433,
year = {2025},
author = {Vivarelli, S and Marconi, A and Matera, S and Falzone, L and Fenga, C},
title = {Review Article: Night Shift Work, Circadian Disruption, and the Gut Microbiome: Implications for Human Health.},
journal = {Critical reviews in oncogenesis},
volume = {30},
number = {2},
pages = {67-81},
doi = {10.1615/CritRevOncog.2025059579},
pmid = {40561433},
issn = {0893-9675},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Shift Work Schedule/adverse effects ; *Circadian Rhythm/physiology ; *Work Schedule Tolerance/physiology ; Dysbiosis ; },
abstract = {The gut microbiome (GM) plays a critical role in regulating a number of physiological processes within the human host, including metabolism, immune function, and protection from pathogens. Emerging evidence suggests that occupational exposures, particularly working night shifts or during irregular hours, significantly influence the GM composition and functionality. These disruptions are closely tied to the misalignment between the host's circadian rhythms and the GM's internal clocks, leading to dysbiosis and increased systemic inflammation. This misalignment has been linked to the development of several health conditions, including dysmetabolism, type 2 diabetes, obesity, cardiovascular diseases, and gastrointestinal disorders. This review provides a thorough analysis of the current research on workers who are exposed to night shifts, highlighting the profound impact of circadian misalignment on both the GM wellbeing and the overall human health. Innovative interventions, such as dietary supplementation with probiotics, prebiotics, circadian-aligned nutrition, and time-restricted eating, offer promising strategies for restoring the GM balance and synchronizing the microbiome with the host's circadian rhythms affected by occupational stressors. Precision-based interventions tailored to specific occupational exposures and circadian patterns may provide effective solutions for improving worker's health and preventing long-term chronic diseases associated with detrimental exposures. In light of these findings, integrating microbiome-targeted approaches into occupational health policies could lead to better health outcomes, reduce the risk of chronic diseases, and enhance the overall well-being of at-risk workers. Occupational research should continue to explore these personalized approaches, together with novel assessment strategies, to optimize health interventions and mitigate the long-term effects of night shift work.},
}
@article {pmid40561432,
year = {2025},
author = {Leyva, BK and Bonavida, B},
title = {Review Article: Probiotics and Oncogenesis: Clinical Implications.},
journal = {Critical reviews in oncogenesis},
volume = {30},
number = {2},
pages = {49-66},
doi = {10.1615/CritRevOncog.2025058336},
pmid = {40561432},
issn = {0893-9675},
mesh = {*Probiotics/therapeutic use/administration &amp; dosage ; Humans ; *Neoplasms/therapy/etiology/prevention &amp; control/microbiology ; Gastrointestinal Microbiome ; *Carcinogenesis/drug effects ; Tumor Microenvironment/immunology ; Animals ; Immunotherapy/methods ; },
abstract = {The interplay between probiotics and cancer development has emerged as a complex but important field in oncology research. While probiotics are known gut microbiome modulators and have the ability to modulate an immune response, their role in the prevention and treatment of cancer are inadequately understood. Evidence from peer-reviewed literature suggests that probiotics-mediated effects contribute to cancer prevention and treatment. Such effects include the enhancement of barrier function, production of anti-inflammatory agents, modulation of immune responses, and regulation of the tumor microenvironment. Clinical studies offer promising results in terms of therapeutic applications in certain cancers where probiotic bacteria may help reduce risk factors while enhancing treatment efficacy. Emerging evidence indicates potential benefits in the combination of probiotics with immunotherapy, including improved response rates and reduced side effects. Significant challenges remain, however, including the standardization of probiotic bacterial constituents, the route of administration, optimal delivery methods and safety concerns. Future research should focus on personalized treatment plans with emphasis on strain-specific effects and the development of next-generation probiotics specifically targeted for cancer applications, in combination with current treatment therapeutics.},
}
@article {pmid40561431,
year = {2025},
author = {Ho, M and Bonavida, B},
title = {Review Article: Probiotics-Mediated Enhancement of Checkpoint Inhibitor Blockade for HER2+ Breast Cancer.},
journal = {Critical reviews in oncogenesis},
volume = {30},
number = {2},
pages = {37-47},
doi = {10.1615/CritRevOncog.2025058633},
pmid = {40561431},
issn = {0893-9675},
mesh = {Humans ; *Breast Neoplasms/drug therapy/metabolism/pathology/immunology ; *Immune Checkpoint Inhibitors/therapeutic use/pharmacology ; *Probiotics/therapeutic use/administration &amp; dosage ; *Receptor, ErbB-2/metabolism/antagonists &amp; inhibitors ; Female ; Gastrointestinal Microbiome/drug effects/immunology ; Animals ; Immunotherapy/methods ; },
abstract = {Immune checkpoint inhibitors (ICIs) have significantly improved survival rates for many types of cancer, giving patients survival prognoses that had been previously unattainable. Unfortunately, in many advanced cancers, including breast cancer (BC), objective response rates (ORRs) have been reported to be between 5% and 25% and immune-related adverse events (irAEs) can be severe, emphasizing the need to improve the effectiveness of ICIs while minimizing irAEs. In recent years, probiotics and various bacteria consortia have gained growing recognition for their application in immunotherapies for various cancers. Many preclinical models have demonstrated that probiotics significantly influence the gut microbiome, enhancing the production of beneficial metabolites and promoting interactions with cytotoxic T cells to amplify the antitumor effects of ICIs. For the treatment of HER2+ BC, current clinical trials have administered ICIs in combination with anti-HER2 agents (e.g., trastuzumab) to enhance treatment efficacy. Thus far, this combination has shown promising results, especially in patients with advanced PDL1-positive disease. However, as these trials are still ongoing, the efficacy of immune checkpoint blockade (ICB) therapy for HER2+ BCs remains inconclusive and requires further investigation. Thus, this review discusses the use of probiotics in ICB therapy, focusing on the potential role of probiotics in HER2+ BC response to ICIs, their underlying mechanisms and challenges.},
}
@article {pmid40561430,
year = {2025},
author = {Ung, W and Bonavida, B},
title = {Review Article: Fecal Microbiota Transplantation in Melanoma: Mechanisms-Mediated Enhancement of Anti-Tumor Immunotherapy.},
journal = {Critical reviews in oncogenesis},
volume = {30},
number = {2},
pages = {23-35},
doi = {10.1615/CritRevOncog.2025058249},
pmid = {40561430},
issn = {0893-9675},
mesh = {Humans ; *Fecal Microbiota Transplantation/methods ; *Melanoma/therapy/immunology/microbiology/etiology ; *Immunotherapy/methods ; *Gastrointestinal Microbiome/immunology ; Immune Checkpoint Inhibitors/therapeutic use ; Animals ; *Skin Neoplasms/therapy/immunology/microbiology ; },
abstract = {The gut microbiota is integral to human health, influencing nutrition, metabolism, and immunity. Dysbiosis has been implicated in cancer development and resistance to therapies, highlighting the potential of microbiota modulation as a therapeutic strategy. Melanoma, while comprising only 1% of skin cancer diagnoses, accounts for over 80% of skin cancer related deaths, emphasizing the need for innovative approaches to enhance treatment efficacy. Although immune checkpoint inhibitors (ICIs) such as anti-programmed cell death protein (PD-1) and cytotoxic T-lymphocyte associated protein 4 (CTLA-4) blockade therapies have significantly improved survival for some melanoma patients, the majority fails to achieve durable responses and often develops long-term resistance to these treatments. Fecal microbiota transplantation (FMT) is emerging as a promising intervention to restore microbial balance and enhance treatment efficacy. This review explores the historical evolution and current applications of FMT in oncology, with a focus on its ability to modulate the gut microbiome, augment antitumor immunity, and overcome resistance to checkpoint blockade therapy in melanoma. Despite its promise, significant challenges remain, including ensuring the safety of the procedure, selecting suitable donors, and addressing regulatory hurdles. Future research aimed at optimizing FMT protocols, identifying key microbial strains, and understanding the mechanisms underlying microbiota-immune interactions will be essential to fully harness the potential of FMT as a transformative adjunct in cancer treatment.},
}
@article {pmid40561429,
year = {2025},
author = {Navasardyan, I},
title = {Review Article: Involvement of the Gut Microbiome and Probiotic Interventions in Pediatric Acute Lymphoblastic Leukemia.},
journal = {Critical reviews in oncogenesis},
volume = {30},
number = {2},
pages = {13-21},
doi = {10.1615/CritRevOncog.2025058176},
pmid = {40561429},
issn = {0893-9675},
mesh = {Humans ; *Probiotics/therapeutic use ; *Precursor Cell Lymphoblastic Leukemia-Lymphoma/microbiology/therapy ; *Gastrointestinal Microbiome/drug effects/immunology ; Child ; Child, Preschool ; },
abstract = {Acute lymphoblastic leukemia (ALL) is a common pediatric cancer marked by uncontrolled proliferation of lymphoblasts, primarily affecting children aged two to five years. While treatment success rates have reached 90% in children, challenges such as therapy toxicity and relapse persist. The gut microbiome, known to impact immune function, is often disrupted in ALL patients, potentially worsening with treatments like chemotherapy and antibiotics. Research suggests probiotics may help restore microbial balance and mitigate side effects, with certain strains showing promise in reducing gastrointestinal symptoms; however, their use requires caution in immunocompromised patients due to infection risks. Probiotics could improve treatment outcomes in ALL, but further research is needed to establish safe, standardized protocols for use in this sensitive population.},
}
@article {pmid40561428,
year = {2025},
author = {Kumari, S and Srilatha, M and Nagaraju, GP},
title = {Review Article: Understanding the Role of the Microbiome in Breast Cancer Progression.},
journal = {Critical reviews in oncogenesis},
volume = {30},
number = {2},
pages = {1-11},
doi = {10.1615/CritRevOncog.2024056468},
pmid = {40561428},
issn = {0893-9675},
mesh = {Humans ; *Breast Neoplasms/pathology/microbiology/therapy/etiology/metabolism ; Female ; *Dysbiosis/microbiology ; Disease Progression ; *Gastrointestinal Microbiome ; *Microbiota ; Animals ; },
abstract = {The breast cancer fatality rate poses a global health concern. Dysbiosis of the gut and breast microbiome plays a crucial role in both the onset and metastasis of breast cancer by influencing immune response and hormone metabolism. Probiotics, antibiotics, and KEY WORDS: breast cancer, immunotherapy, microbiome, exosomes, gut microbiota are used in microbiome-targeted drugs as therapy alternatives. Metabolic alterations accelerate the development of cancer. For instance, 27-hydroxycholesterol promotes tamoxifen resistance and estrogen receptor-positive (ER+) breast cancer. Malignant breast tissues differ from healthy breast tissues by their unique microbial profiles. The microbiome influences metabolic pathways such as lipid and glucose metabolism and microbial compounds like β-glucuronidases and short-chain fatty acids (SCFAs) influence metabolism, drug resistance, and progression of cancer. New approaches to treating breast cancer include immunotherapies, nanoparticle drug delivery systems, and emerging therapeutics based on interactions among the microbiome, the immune system, and exosomes. These approaches may improve immune responses, decrease chemotherapy resistance, and stop the spread of cancer. Here, we discuss dysbiosis in breast cancer and therapeutic approaches.},
}
@article {pmid40560629,
year = {2025},
author = {Zhou, Y and Chai, L and Wang, Y and Zhang, H},
title = {Multi-dimensional characterization of the tumor microenvironment profiles in lung squamous cell carcinoma.},
journal = {Physiological genomics},
volume = {},
number = {},
pages = {},
doi = {10.1152/physiolgenomics.00042.2025},
pmid = {40560629},
issn = {1531-2267},
abstract = {Tumor microenvironment (TME) plays an important role in tumorigenesis, development, metastasis and drug sensitivity, but little is known about it in lung squamous cell carcinoma (LUSC). Here, the RNA-sequencing data, clinical and survival data of patients with LUSC in The Cancer Genome Atlas and six independent datasets were collected. Based on the unsupervised clustering of knowledge-based functional gene expression signatures, LUSC was classified into four subtypes. Cluster1 and cluster3 exhibited substantial tumor immune infiltration, suggesting a better response to immunotherapy. Relatively worse survival was observed in cluster4, probably due to higher angiogenesis. Besides, differentially expressed genes in cluster1, cluster2 and cluster3 were prominently enriched in immune-related pathways, while extracellular matrix-related pathways were enriched for cluster4. Genomic data analyses showed significant variations in tumor mutational burden and mutational frequency of several genes, such as TP53, among the four subtypes. Additionally, the four subtypes exhibited heterogeneity in the sensitivity of commonly used chemotherapy drugs for lung cancer and the intratumor microbiome profile. Finally, a prognostic model was developed and its performance and generalization ability were independently validated in multiple datasets. Overall, our study advances the understanding of the TME in LUSC and proposes a prognostic model that facilitates clinical decision-making.},
}
@article {pmid40560537,
year = {2025},
author = {Stummer, BE and Moghaddam, MJ and Roohani-Dezfouli, M and Nidumolu, B and Zhang, X and Harvey, PR},
title = {Wheat rhizosphere persistence of Trichoderma gamsii A5MH during suppression of a Fusarium-Pythium root disease complex differentially impacts the soil fungal and oomycete microbiome.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxaf158},
pmid = {40560537},
issn = {1365-2672},
abstract = {AIMS: Determine the impacts of inoculant strain Trichoderma gamsii A5MH and crop phenology on the structure of fungal and oomycete communities in wheat rhizosphere soil.<br><br>METHODS AND RESULTS: Over two consecutive wheat crops, A5MH inoculation suppressed an oomycete (Globisporangium)-fungal (Fusarium) root disease complex. Amplicon sequencing determined the impacts of A5MH-treatment and crop phenology on the structure of rhizosphere soil fungal and oomycete communities. Culture-dependent (C-D) techniques quantified inoculant impacts on non-target root endophytic fungi, previously co-isolated with strain A5MH and the fungal and oomycete pathogens. Inoculant treatment differentiated the structure of the fungal microbiome in both years, primarily due to increased Trichoderma abundance and decreases in cereal pathogenic, root endophytic and saprophytic taxa. Strain A5MH did not impact the structure of the oomycete microbiome. Crop phenology altered fungal and oomycete community structure, these impacts greater at tillering and grain harvest, respectively. A5MH-induced decreases in rhizosphere abundance (C-D) of root endophytic fungi were associated with increased crop biomass at tillering.<br><br>CONCLUSIONS: Whilst the structure of rhizosphere soil fungal and oomycete communities altered as the wheat crop matured, only fungal communities were impacted by A5MH-treatment due to increased Trichoderma and decreased abundance of recognized and emerging plant pathogenic fungi.},
}
@article {pmid40560509,
year = {2025},
author = {Andersen, C and Ebsen, TS and Thorup, CA and Reinholdt, KB and Kjaerulff, AMG and Udholm, N and Khalid, V and Madzak, A and Duez, C and Münch, H and Pauli, S and Danstrup, CS and Petersen, NK and Greve, T and Klug, TE},
title = {Next-generation sequencing of the tonsillar microbiome in severe acute tonsillitis: comparison with healthy controls and culture-based findings.},
journal = {European journal of clinical microbiology &amp; infectious diseases : official publication of the European Society of Clinical Microbiology},
volume = {},
number = {},
pages = {},
pmid = {40560509},
issn = {1435-4373},
abstract = {PURPOSE: Previous culture-based studies suggest three significant pathogens in acute tonsillitis (AT): Streptococcus pyogenes, Fusobacterium necrophorum, and Streptococcus dysgalactiae. Next-generation sequencing (NGS) provides further insights into the human microbiome and may pinpoint additional pathogens in bacterial infections. We aimed to investigate the tonsillar microbiome and identify pathogens associated with AT by applying NGS to tonsillar swabs from patients with severe AT, comparing the findings with both healthy controls and culture-based results.<br><br>METHODS: Full-length sequencing of the 16S rRNA gene (16S tNGS) was performed on tonsillar swabs from 64 AT patients and 55 controls, who were prospectively enrolled at two Danish Ear-Nose-Throat Departments between June 2016 and December 2019.<br><br>RESULTS: The mean number of detected bacteria was significantly higher in patients analysed with 16S tNGS (36) than with culture methods (6.5, p&#x2009;<&#x2009;0.001). The alpha diversity was lower in patients compared to controls (p&#x2009;<&#x2009;0.001) and beta diversity showed separation of the two groups (p&#x2009;=&#x2009;0.001). S. pyogenes (p&#x2009;=&#x2009;0.001) and Bifidobacteriaceae (p&#x2009;=&#x2009;0.002) were significantly more abundant in patients compared to controls. The three suggested pathogens were detected more frequently using 16S tNGS compared to culture: S. pyogenes (38% vs. 27%, p&#x2009;=&#x2009;0.26), F. necrophorum (19% vs. 11%, p&#x2009;=&#x2009;0.32), and S. dysgalactiae (14% vs. 11%, p&#x2009;=&#x2009;0.79).<br><br>CONCLUSION: The tonsillar microbiome differed significantly between AT patients and healthy controls. Our findings confirm the role of S. pyogenes in AT, but did not identify additional likely pathogens. The addition of 16S tNGS to cultures increased the collective detection rate of three previously suggested pathogens from 48 to 70%.},
}
@article {pmid40560314,
year = {2025},
author = {Rojas-Chacón, JA and Echeverría-Beirute, F and Jiménez-Madrigal, JP and Varela-Benavides, I and Faggioli, V and Berkelmann, D and Gatica-Arias, A},
title = {Deciphering soil nematode-bacteria-fungi community composition and functional dynamics in coffee agroecosystems under conventional and sustainable management practices in Costa Rica.},
journal = {World journal of microbiology &amp; biotechnology},
volume = {41},
number = {7},
pages = {220},
pmid = {40560314},
issn = {1573-0972},
support = {801-C3-501//UKRI-BBSRC Capacity Building for Bioinformatics in Latin America Network (CABANA-net) grant, between the Chan Zuckerberg Initiative (CZI) and the University of Costa Rica/ ; 801-C3-501//UKRI-BBSRC Capacity Building for Bioinformatics in Latin America Network (CABANA-net) grant, between the Chan Zuckerberg Initiative (CZI) and the University of Costa Rica/ ; 801-C3-501//UKRI-BBSRC Capacity Building for Bioinformatics in Latin America Network (CABANA-net) grant, between the Chan Zuckerberg Initiative (CZI) and the University of Costa Rica/ ; 2022-316296//The Chan Zuckerberg Initiative DAF/ ; 2022-316296//The Chan Zuckerberg Initiative DAF/ ; 2022-316296//The Chan Zuckerberg Initiative DAF/ ; },
mesh = {Costa Rica ; *Soil Microbiology ; Animals ; *Nematoda/classification/genetics/physiology ; Soil/chemistry/parasitology ; *Fungi/classification/genetics/isolation &amp; purification ; *Bacteria/classification/genetics/isolation &amp; purification ; Agriculture/methods ; *Coffee/growth &amp; development ; Coffea/growth &amp; development ; High-Throughput Nucleotide Sequencing ; },
abstract = {Understanding the interactions between soil bacteria, fungi, and nematodes in coffee agroecosystems is crucial for optimizing sustainable agriculture. This study investigated the composition and functional dynamics of these communities under conventional and sustainable management systems. Soil samples were collected from three major coffee-growing regions in Costa Rica, representing different agricultural regimes. Nematode community was analyzed using optical microscopy, while microbial communities were analyzed using high-throughput sequencing. In both cases, bioinformatic tools were used for functional prediction based on taxonomy.. Herbivorous nematodes dominated both systems, while bacterivores (Rhabditidae, Cephalobidae) and fungivores (Aphelenchoidae) were significantly more abundant in soils subject to sustainable practice (p < 0.05). Nematode maturity indices and food web diagnostics showed no significant differences between systems, even though metabolic footprints related to organic matter decomposition varied (p < 0.05). Bacterial communities were dominated by the phyla Proteobacteria, Acidobacteria, and Chloroflexi, while the fungal community was largely composed of Ascomycota (53.21% in both systems). The fungal genus Mortierella was particularly prevalent. Soil pH, along with Ca, Mg, K, and extractable acidity, influenced community composition. Functional profiles revealed higher gene abundances linked to nutrient and energy cycling in sustainable systems, particularly phosphorus and sulfur metabolism. Saprotroph-symbiotroph fungi were more common in sustainable soils, while pathotrophic fungi dominated conventional systems. This is the first comprehensive analysis of bacteria, fungi, and nematodes across different agricultural practices in coffee agroecosystems in Costa Rica.},
}
@article {pmid40560287,
year = {2025},
author = {Zhuang, Y and Lyu, T and Chen, Y and Li, W and Tang, L and Xian, SP and Yang, PF and Wang, L and Zhang, QQ and Mei, C and Lin, YJ and Yan, Z and Li, Z and He, JZ and Zeng, FM},
title = {Mechanistic insights into endometriosis: roles of Streptococcus agalactiae and L-carnitine in lesion development and angiogenesis.},
journal = {Angiogenesis},
volume = {28},
number = {3},
pages = {38},
pmid = {40560287},
issn = {1573-7209},
support = {202401AY070001-120//Yunnan Province Applied Basic Research Program Kunming Medical University Joint Project/ ; WYYXQN-2021016//the Excellent Young Researchers Program of the Fifth Affiliated Hospital of Sun Yat-sen University/ ; 2023080017//the Excellent Young Researchers Program of the Fifth Affiliated Hospital of Sun Yat-sen University/ ; 82102689//National Natural Science Foundation of China/ ; 2022A1515220187//The Guangdong Basic and Applied Basic Research Foundation/ ; 22qntd3502//Fundamental Research Funds for the Central Universities, Sun Yat-sen University/ ; 2018-016//Project of Guiyang Health and Family Planning Commission/ ; },
mesh = {Female ; Humans ; *Streptococcus agalactiae/metabolism ; Animals ; *Carnitine/metabolism/pharmacology ; *Neovascularization, Pathologic/microbiology/pathology/metabolism ; Mice ; *Endometriosis/microbiology/pathology/metabolism ; Adult ; *Streptococcal Infections/microbiology/pathology ; Cell Movement ; Angiogenesis ; },
abstract = {Retrograde menstruation is a widely recognized etiological factor for endometriosis (EMs); however, it is not the sole cause, as not all affected women develop EMs. Emerging evidence suggests a significant association between the vaginal microbiota and EMs. Nonetheless, the precise mechanisms by which microbial communities influence the pathophysiology and progression of EMs remain unclear. In this study, the cervical mucus from patients with EMs showed significantly greater microbial abundance compared with that of controls, with Streptococcus agalactiae (S. agalactiae) exhibiting the most substantial increase as determined by 16S rRNA gene sequencing. In a murine model, elevated S. agalactiae levels significantly increased the lesion number and colonization, whereas antibiotic treatment reduced lesion formation. Metabolomic analyses showed elevated L-carnitine levels in the cervical secretions and serum of patients with EMs, a finding corroborated in murine tissues. Exogenous L-carnitine administration similarly increased the number and weight of endometriotic lesions. Meanwhile, the inhibition of L-carnitine synthesis suppressed lesion formation induced by S. agalactiae. In vitro, both S. agalactiae and L-carnitine promoted EMs cell proliferation, migration, and invasion. L-carnitine synthesis inhibition attenuated cell motility stimulated by S. agalactiae. Mechanistically, S. agalactiae enhanced angiogenesis through L-carnitine by upregulating vascular endothelial growth factor expression and increasing human umbilical vein endothelial cell motility. These findings identify S. agalactiae as a key cervical microbiome component in EMs development and reveal a microbiota-metabolite-angiogenesis axis that may offer novel therapeutic targets.},
}
@article {pmid40560276,
year = {2025},
author = {Sharma, A and Bora, P},
title = {Engineering synthetic microbial communities to restructure the phytobiome for plant health and productivity.},
journal = {World journal of microbiology &amp; biotechnology},
volume = {41},
number = {7},
pages = {228},
pmid = {40560276},
issn = {1573-0972},
mesh = {*Plants/microbiology ; *Microbiota ; Soil Microbiology ; Agriculture/methods ; Bacteria/genetics/metabolism ; *Synthetic Biology/methods ; *Microbial Consortia ; },
abstract = {Global agriculture stands at a critical juncture, facing the dual challenge of sustaining food production for a rapidly growing population while mitigating the environmental consequences of intensive farming. The overuse of chemical fertilizers and pesticides has accelerated soil degradation, biodiversity loss, and ecological imbalances, threatening long-term viability. Synthetic microbial communities (SynComs) have emerged as a promising approach to reshape plant-microbe interactions, offering a precise, scalable, and ecologically sustainable alternative to conventional agrochemicals. Unlike native microbial communities, which form naturally and vary with environmental conditions, SynComs are deliberately assembled consortium of multiple microbial strains selected for their complementary functions, ecological compatibility, and ability to perform targeted roles within a host or environment. By engineering microbes with targeted functional traits, SynComs enhance nutrient assimilation, bolster plant defence, and fortify resilience against biotic and abiotic stresses. The understanding of SynCom design, exploring their composition, functional dynamics, and mechanisms for optimizing plant health is crucial for effective synthesis and application, alongside cutting-edge computational tools and genomic databases that enable precision engineering of microbial communities. Despite their transformative potential, large-scale application of SynComs remains constrained by challenges related to field efficacy, regulatory frameworks, and long-term microbial persistence. Addressing these barriers through interdisciplinary research and policy innovation is imperative. As environmental microbiome moves towards sustainability-driven solutions, SynComs hold the key to revolutionizing farming practices, reducing chemical dependence, and ensuring global food security in an era of mounting environmental stressors.},
}
@article {pmid40560225,
year = {2025},
author = {Li, T and Tian, Y and Wang, Y and Yang, J and Chen, Z and Li, Y},
title = {Elucidation of novel diagnostic biomarkers and therapeutic targets in colorectal carcinoma: an integrative approach leveraging multi-omics, computational biology, and single-cell sequencing technologies.},
journal = {Mammalian genome : official journal of the International Mammalian Genome Society},
volume = {},
number = {},
pages = {},
pmid = {40560225},
issn = {1432-1777},
support = {82104012, 82202950, 82303681//The National Natural Science Foundation of China/ ; 2021-I2M-1-042//the Chinese Academy of Medical Sciences Innovation Fund for Medical Sciences/ ; 3332022063//the Fundamental Research Funds for the Central Universities/ ; },
abstract = {This study employs a comprehensive, multi-layered analytical approach to comprehensively investigate the pathogenesis, diagnostic methodologies, and potential therapeutic targets of colorectal cancer. Integrating data from the Global Burden of Disease (GBD) database, transcriptomics, proteomics, and single-cell sequencing technologies, this study elucidates both the epidemiological characteristics and molecular mechanisms of colorectal cancer. Our findings indicate that VEGFA, ICAM1, and IL6R play prominent roles in cancer progression. Proteomics analysis has identified multiple potential drug targets, and molecular docking and dynamic simulations have provided a theoretical foundation for developing drugs targeting VEGFA. Multi-omics studies have revealed that colorectal cancer progression involves intricate microbiome-host interactions, metabolic regulation, and immune response mechanisms, with factors such as Clostridia, 4E-BP1, AIFM1, and CXCL5 exhibiting dual roles. These discoveries not only deepen our understanding of colorectal cancer pathogenesis but also offer novel insights for optimizing diagnostic and therapeutic strategies, thereby laying the groundwork for developing personalized treatment regimens. Future research should focus on further validating these findings and exploring their potential clinical applications.},
}
@article {pmid40560060,
year = {2025},
author = {Dinakis, E and Xu, C and Muralitharan, R and Jama, H and Xie, L and Leung, C and Mirabito Colafella, K and McArdle, Z and Salimova, E and Camargo Tavares, L and Snelson, M and Johnson, C and Gaspari, T and Mackay, C and O'Donnell, J and Marques, F},
title = {pH-sensor GPR68 plays a role in how dietary fibre lowers blood pressure in a preclinical model of hypertension.},
journal = {Clinical science (London, England : 1979)},
volume = {},
number = {},
pages = {},
doi = {10.1042/CS20243009},
pmid = {40560060},
issn = {1470-8736},
support = {102927, 105663, 106698//National Heart Foundation of Australia/ ; GTN2017382, GNT2017382, GNT1124288//National Health and Medical Research Council/ ; Not applicable//Sylvia and Charles Viertel Charitable Foundation/ ; },
abstract = {Dietary fibre lowers blood pressure (BP) via short-chain fatty acids, acidic metabolites released from fibre fermentation by bacteria in the large intestine. This acidic microenvironment may activate the pH-sensing receptor GPR68, primarily expressed in immune cells. Here, we aimed to investigate whether GPR68 confers the BP-lowering effects of a high-fibre diet in hypertension by regulating inflammatory responses. Baseline BP parameters were measured using telemetry in C57BL/6J wildtype (WT) and GPR68-deficient (Gpr68-/-) male and female mice. Moreover, male mice were fed a control or high-fibre diet following minipump implantation with saline or Angiotensin II (Ang II), where BP was measured weekly by tail-cuff. Cardiac ultrasounds, histological, flow cytometric and gut microbiome (16S) analyses were performed. No BP differences were detected in untreated male and female mice, irrespective of genotype. Similarly to WT mice, Gpr68-/- male mice were susceptible to Ang II-induced hypertension. High-fibre-fed WT mice exhibited blunted elevations in BP and improved cardiac collagen deposition and aortic elastin content compared to control-fed WT mice. These were not observed in high-fibre-fed Gpr68-/- mice. A high-fibre diet decreased pro-inflammatory renal and aortic immune cell counts independently of GPR68. Dietary fibre, rather than GPR68 or Ang II, was the primary factor influencing differences in the gut microbiota. This study provides novel insight into how the pH-sensing receptor GPR68 may be implicated in the protective effects of a high-fibre diet. However, these effects are likely immune-independent.},
}
@article {pmid40560035,
year = {2025},
author = {Shan, L and Xu, X and Huang, L and Li, D and Deng, Y and Xue, X and Guo, S and Huang, Y and Zhang, X and Yu, Y and Ma, L and Qian, K and Wang, J},
title = {A Novel nor@DHB Matrix for Direct Microbial Analysis in Lung Cancer Tissues.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e04038},
doi = {10.1002/advs.202504038},
pmid = {40560035},
issn = {2198-3844},
support = {2022YFC2406600//National Key Research and Development; and Technology Plan of the Ministry of Science/ ; 82302641//National Natural Science Foundation of China/ ; 82472771//National Natural Science Foundation of China/ ; 23XD1423200//Science and Technology Commission of Shanghai Municipality/ ; 21140902800//Science and Technology Commission of Shanghai Municipality/ ; YG2022ZD024//Shanghai Jiao Tong University STAR Grant/ ; },
abstract = {Dynamic changes occurring in the lung microbiota can impact the initiation, progression, and prognosis of lung cancer (LC). Consequently, the development of suitable intratumoral microbiota analysis methods is crucial. Although matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) involves straightforward operations and provides precise results, the "direct smear method" limits the identification of bacterial subspecies. Furthermore, the issue of inadequate quantification with MALDI MS renders it unsuitable for direct analysis of intratumoral bacteria. To address these challenges, a novel ionic liquid in this study is employed, called norharmane conjugated to 2,5-dihydroxybenzoic acid (Nor@DHB) for the direct detection of intratumoral bacteria using MALDI MS. Because gram-negative bacteria are dominant within cancer cells, lipid A is selected as the chemical fingerprint for bacterial identification. The results demonstrated that using Nor@DHB can enhance the lipid A signal by an order of magnitude and achieved a good linear relationship within a concentration range of 0.01-80 ng mL[-1]. Here, this method is successfully applied to the direct analysis of lipid A in actual clinical samples. Subsequent machine learning and nomogram models further confirmed the correlation between characteristic lipid A ions and LC patient clinicopathological features, which are further validated through both in vitro and in vivo experiments.},
}
@article {pmid40559977,
year = {2025},
author = {Tomuța, RA and Moldovan, AF and Matiș, L and Maris, L and Ghitea, TC and Banica, F},
title = {The Paradox of Clean Eating: Neuroactive Dysbiosis and Pesticide Residues in Fruit- and Vegetable-Based Diets.},
journal = {Toxics},
volume = {13},
number = {6},
pages = {},
pmid = {40559977},
issn = {2305-6304},
support = {410068//University of Oradea/ ; },
abstract = {(1) Background: Exposure to pesticide residues through food remains a critical issue in public health, especially given their potential cumulative neurotoxic effects. (2) Methods: This study investigated the presence of pesticide residues in commonly consumed vegetables, fruits, and cereals based on official laboratory reports and evaluated the intestinal microbiome profiles of individuals whose diets consisted of over 50% plant-based foods. (3) Results: Analytical results from accredited laboratories in Romania demonstrated that all tested food samples were compliant with European regulations (Regulation (EC) 396/2005), with either undetectable or below-quantification-limit pesticide residues. However, organophosphates such as chlorpyrifos and diazinon were frequently tested, indicating persistent regulatory concern due to their known neurotoxic potential. A parallel analysis of stool samples revealed significant imbalances in neuroactive gut bacteria, including consistently low levels of Bifidobacterium and Lactobacillus species, and elevated levels of Oscillibacter and Alistipes, which are implicated in modulating GABA and serotonin pathways. Markers of proinflammatory activity, such as LPS-positive bacteria and histamine producers, were also elevated. (4) Conclusions: These findings suggest that even in diets rich in plant-based foods, microbial dysbiosis with neuroactive relevance can occur, potentially linked to environmental or dietary factors. The study underscores the need for a comprehensive evaluation of food safety and microbiome function as interconnected determinants of neurological health.},
}
@article {pmid40559883,
year = {2025},
author = {Jasemi, S and Molicotti, P and Fais, M and Cossu, I and Simula, ER and Sechi, LA},
title = {Biological Mechanisms of Enterotoxigenic Bacteroides fragilis Toxin: Linking Inflammation, Colorectal Cancer, and Clinical Implications.},
journal = {Toxins},
volume = {17},
number = {6},
pages = {},
pmid = {40559883},
issn = {2072-6651},
support = {legge 22//Regione Autonoma della Sardegna legger regionale 2022/ ; },
mesh = {*Colorectal Neoplasms/chemically induced/microbiology ; *Bacterial Toxins/chemistry/genetics/toxicity ; *Metalloendopeptidases/toxicity ; *Bacteroides fragilis ; Virulence Factors/chemistry/genetics/toxicity ; Gastrointestinal Microbiome ; Structure-Activity Relationship ; Humans ; Molecular Structure ; },
abstract = {Enterotoxigenic Bacteroides fragilis (ETBF) has emerged as a gut microbiome pathogen that can promote intestinal inflammation and contribute to colorectal cancer (CRC). Its principal virulence factor, the Bacteroides fragilis toxin (BFT), is a zinc-dependent metalloprotease that disrupts epithelial barrier integrity, initiates inflammatory signaling pathways, and enhances epithelial proliferation. Although growing evidence supports a link between ETBF and CRC, some inconsistencies across studies highlight the need for further investigation into the molecular mechanisms underpinning BFT-mediated pathogenesis. This review examines the biological structure and activity of BFT, with a focus on its role in epithelial injury, inflammatory responses, and tumorigenesis. In addition, we discuss current challenges in the detection and characterization of ETBF and BFT, including technical limitations in clinical diagnostics and methodological variability across studies. Recent advances in multi-omics technologies, molecular diagnostics, nanobody-based detection platforms, and probiotic intervention are also highlighted as promising avenues for improving ETBF identification and therapeutic targeting. Future research integrating systematic molecular profiling with clinical data is essential to enhance diagnostic accuracy, elucidate pathophysiological mechanisms, and develop effective interventions against ETBF-associated diseases.},
}
@article {pmid40559850,
year = {2025},
author = {Shi, L and Niu, QJ and Xu, HH and Huang, YX and Zhao, YW and Refaie, A and Sun, LH and Deng, ZC},
title = {Dietary Supplementation of Zinc Oxide Quantum Dots Protective Against Clostridium perfringens Induced Negative Effects in Broilers.},
journal = {Toxins},
volume = {17},
number = {6},
pages = {},
pmid = {40559850},
issn = {2072-6651},
support = {2023TZXD038//Key R&amp;D Program of Shandong Province, China/ ; 2662023DKPY002//Fundamental Research Funds for the Central Universities/ ; NA//a research gift from Sichuan Chelota Biotech Corporation Limited/ ; },
mesh = {Animals ; *Zinc Oxide/administration &amp; dosage/pharmacology ; *Chickens/growth &amp; development ; *Quantum Dots/administration &amp; dosage ; *Clostridium perfringens ; *Clostridium Infections/veterinary/microbiology/prevention &amp; control ; *Poultry Diseases/microbiology/prevention &amp; control ; *Dietary Supplements ; Gastrointestinal Microbiome/drug effects ; Intestines/drug effects/microbiology/pathology ; Animal Feed ; },
abstract = {Clostridium perfringens is a major cause of necrotizing enteritis in chickens. This study aimed to investigate the effects of zinc oxide quantum dots (ZnO-QDs) on growth performance, redox status, and gut microbiota in broilers challenged with C. perfringens. A total of 320 1-day-old chicks were divided into five groups: negative control (NC) without treatment; positive control (PC) infected with C. perfringens; and the other three groups (40, 80, and 120 Zn) were given ZnO-QDs at doses of 40, 80, and 120 mg/kg, respectively, under C. perfringens infection, respectively. The results show that, compared to the NC group, the PC group exhibited negative effects on growth performance, intestinal morphology, and antioxidant status in broilers. However, compared to the PC group, 120 mg Zn increased (p < 0.05) the body weight of broilers at 21 days, while 40 mg Zn reduced (p < 0.05) serum diamine oxidase activity. The intestinal macroscopic evaluation showed that the PC group had the highest lesion scores, whereas the 120 mg Zn group exhibited the lowest lesion score. Meanwhile, compared to the PC group, the 40 mg Zn group had higher (p < 0.05) CAT and GPX activities and a lower (p < 0.05) MDA concentration. Moreover, the 40 mg Zn group up-regulated (p < 0.05) the gene expression of Cathelicidin-1, IL-10, Claudin-1, and MLCK in the jejunum. Furthermore, the 120 mg Zn group increased (p < 0.05) the abundance of Blautia, Parasutterella, and Lachnospiraceae FCS020 in the cecum. In conclusion, ZnO-QDs exerted a beneficial effect on improving growth performance and overall health in broilers under C. perfringens infection, potentially by regulating redox balance and gut microbiota.},
}
@article {pmid40559796,
year = {2025},
author = {Popov, IV and Peshkova, DA and Lukbanova, EA and Tsurkova, IS and Emelyantsev, SA and Krikunova, AA and Malinovkin, AV and Chikindas, ML and Ermakov, AM and Popov, IV},
title = {Gut Microbiota Dynamics in Hibernating and Active Nyctalus noctula: Hibernation-Associated Loss of Diversity and Anaerobe Enrichment.},
journal = {Veterinary sciences},
volume = {12},
number = {6},
pages = {},
pmid = {40559796},
issn = {2306-7381},
support = {23-14-00316//Russian Science Foundation/ ; 075-10-2025-017//Ministry of Science and Higher Education of the Russian Federation/ ; },
abstract = {Hibernation in mammals entails profound physiological changes that are known to impact host-associated microbial communities, yet its effects on the gut microbiota of synanthropic bats remain underexplored. In this study, we investigated the gut bacterial composition and diversity of Nyctalus noctula before and during hibernation using high-throughput 16S rRNA amplicon sequencing. Fecal samples from individually banded bats were collected under controlled conditions at a rehabilitation center and analyzed for alpha and beta diversity, as well as differential taxonomic abundance. Hibernation was associated with a marked reduction in microbial diversity according to the Shannon and Simpson indices and a distinct restructuring of gut communities based on the Bray-Curtis dissimilarity index. Active bats exhibited a diverse microbiota enriched in facultative anaerobes, including Lactococcus, Enterococcus, and Escherichia-Shigella, while hibernating individuals were dominated by obligate anaerobes, such as Romboutsia and Paeniclostridium. These findings suggest a contraction and functional specialization of the gut microbiota during torpor, potentially reflecting adaptations to fasting, hypothermia, and reduced gut motility. Our results demonstrate that the bat's gut microbiome is highly responsive to physiological status and underscore the importance of microbial ecology for understanding the host's energy balance and health under seasonal contexts.},
}
@article {pmid40559778,
year = {2025},
author = {Nishigaki, A and Marchesi, JR and Previdelli, RL},
title = {Faecal Microbiota Transplantation as an Adjuvant Treatment for Extraintestinal Disorders: Translating Insights from Human Medicine to Veterinary Practice.},
journal = {Veterinary sciences},
volume = {12},
number = {6},
pages = {},
pmid = {40559778},
issn = {2306-7381},
abstract = {Faecal microbiota transplantation (FMT) has emerged as a transformative therapy in human medicine, particularly for managing recurrent Clostridioides difficile infections and other gastrointestinal (GI) disorders. Beyond the GI tract, FMT has shown potential in addressing extraintestinal conditions in people, including metabolic, immune-mediated, dermatological, neurological, and infectious diseases. Research in people has highlighted its efficacy in decolonising multidrug-resistant organisms in infection, mitigating autoimmune diseases, and improving outcomes in metabolic disorders such as obesity and diabetes. Furthermore, FMT has also been linked to enhanced responses to immunotherapy in cancer and improved management of hepatic and renal conditions. These findings underscore the intricate connections between the gut microbiome and systemic health, opening novel therapeutic avenues. In veterinary medicine, while FMT has demonstrated benefits for GI disorders, its application in extraintestinal diseases remains largely unexplored. Emerging evidence suggests that conditions such as atopic dermatitis, chronic kidney disease, immune-mediated diseases, and behavioural disorders in companion animals could benefit from microbiome-targeted therapies. However, significant gaps in knowledge persist, particularly regarding the long-term safety and efficacy for veterinary applications. This review synthesises findings from human medicine to assess their relevance for veterinary applications and future research.},
}
@article {pmid40559763,
year = {2025},
author = {Sun, N and Xie, L and Chao, J and Xiu, F and Zhai, H and Zhou, Y and Yu, X and Shui, Y},
title = {Study on the Correlation Between Aggressive Behavior and Gut Microbiota and Serum Serotonin (5-HT) in Working Dogs.},
journal = {Veterinary sciences},
volume = {12},
number = {6},
pages = {},
doi = {10.3390/vetsci12060526},
pmid = {40559763},
issn = {2306-7381},
support = {No.D2024005//Fundamental Research Funds for the Central Universities/ ; },
abstract = {Aggressive canine behavior poses a significant threat to public health. Understanding aggressive behavior is crucial for canine socialization and human-dog interactions. This study conducted an exploratory analysis of working dogs to investigate changes in gut microbiota and neurotransmitters associated with aggressive behavior. Notably, it represents the first research to systematically differentiate canine aggression into offensive and defensive subtypes for investigation. In this study, 56 working dogs from three regions of China, comprising different breeds (11 Spaniels, 13 German Shepherds, and 32 Belgian Malinois), aged 4.89 ± 1.54 years, and of both sexes (38 males and 18 females), were assessed and grouped for aggressive behavior using a C-BARQ-based questionnaire. Then, 16S rRNA sequencing and ELISA were employed to compare differences in gut microbiota and serotonin concentrations between aggressive (n = 35) and non-aggressive (n = 21) groups, as well as between offensive (n = 26) and defensive (n = 9) aggression subgroups. β-diversity analysis confirmed no significant correlation between aggressive behavior and gut microbiota composition (p > 0.05), suggesting a limited role of gut microbiota in modulating host behavior. Comparative analysis of gut microbiota composition revealed no significant differences in phylum-level abundance among different aggression types (p > 0.05). Notably, the non-aggressive group exhibited significantly higher relative abundances of Escherichia-Shigella, Erysipelotrichaceae_UCG-003, and Clostridium_sensu_stricto_1 compared to the aggressive group (p < 0.05). Random forest analysis identified Lactobacillus as a biomarker for canine aggressive behavior and Turicibacter as a discriminatory factor between offensive and defensive aggression. The results demonstrated a strong correlation between aggression and 5-HT neurotransmission. Serum serotonin levels were significantly lower in both the defensive (39.92 ± 2.58 ng/mL) and offensive (50.07 ± 3.90 ng/mL) aggression groups compared to the non-aggressive group (59.49 ± 2.76 ng/mL), with the lowest levels found in defensively aggressive dogs. The defensive group showed significantly lower serotonin levels than the offensive group (p < 0.001). The results demonstrate that different behavioral phenotypes in aggressive dogs lead to distinct gut microbiome compositions. This suggests that microbiome analysis may facilitate early diagnosis and preventive intervention before aggressive behavior manifests. As such, 5-HT shows potential as a monitoring tool for diagnosing canine aggression, with significant practical applications in canine behavior management.},
}
@article {pmid40559651,
year = {2025},
author = {Wimmer, BC and Dwan, C and De Medts, J and Duysburgh, C and Rotsaert, C and Marzorati, M},
title = {Undaria pinnatifida Fucoidan Enhances Gut Microbiome, Butyrate Production, and Exerts Anti-Inflammatory Effects in an In Vitro Short-Term SHIME[®] Coupled to a Caco-2/THP-1 Co-Culture Model.},
journal = {Marine drugs},
volume = {23},
number = {6},
pages = {},
doi = {10.3390/md23060242},
pmid = {40559651},
issn = {1660-3397},
support = {n.a.//Marinova Pty Ltd., 249 Kennedy Drive, Cambridge, TAS 7170, Australia/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Polysaccharides/pharmacology/isolation &amp; purification ; *Undaria/chemistry ; *Anti-Inflammatory Agents/pharmacology ; Caco-2 Cells ; Coculture Techniques ; *Butyrates/metabolism ; THP-1 Cells ; Colon/microbiology/drug effects ; Feces/microbiology ; Cytokines/metabolism ; Adult ; Fatty Acids, Volatile/metabolism ; Edible Seaweeds ; },
abstract = {Fucoidans have demonstrated a wide range of bioactivities including immune modulation and benefits in gut health. To gain a deeper understanding on the effects of fucoidan from Undaria pinnatifida (UPF) on the colonic microbiome, the short-term Simulator of the Human Intestinal Microbial Ecosystem[®], a validated in vitro gut model, was applied. Following a three-week intervention period on adult faecal samples from three healthy donors, microbial community activity of the colonic microbiota was assessed by quantifying short-chain fatty acids while composition was analysed utilising 16S-targeted Illumina sequencing. Metagenomic data were used to describe changes in community structure. To assess the secretion of cytokines, co-culture experiments using Caco-2 and THP1-Blue™ cells were performed. UPF supplementation over a three-week period had a profound butyrogenic effect while also enriching colonic microbial diversity, consistently stimulating saccharolytic genera, and reducing genera linked with potentially negative health effects in both regions of the colon. Mild immune modulatory effects of UPF were also observed. Colonic fermentation of UPF showed anti-inflammatory properties by inducing the secretion of the anti-inflammatory cytokines IL-6 and IL-10 in two out of three donors in the proximal and distal colon. In conclusion, UPF supplementation may provide significant gut health benefits.},
}
@article {pmid40559436,
year = {2025},
author = {Domilescu, I and Miutescu, B and Horhat, FG and Popescu, A and Nica, C and Ghiuchici, AM and Gadour, E and Sîrbu, I and Hutanu, D},
title = {Gut-Microbiome Signatures Predicting Response to Neoadjuvant Chemoradiotherapy in Locally Advanced Rectal Cancer: A Systematic Review.},
journal = {Metabolites},
volume = {15},
number = {6},
pages = {},
doi = {10.3390/metabo15060412},
pmid = {40559436},
issn = {2218-1989},
abstract = {BACKGROUND AND OBJECTIVES: Rectal cancer management increasingly relies on watch-and-wait strategies after neoadjuvant chemoradiotherapy (nCRT). Accurate, non-invasive prediction of pathological complete response (pCR) remains elusive. Emerging evidence suggests that gut-microbiome composition modulates radio-chemosensitivity. We systematically reviewed primary studies that correlated baseline or on-treatment gut-microbiome features with nCRT response in locally advanced rectal cancer (LARC).<br><br>METHODS: MEDLINE, Embase and PubMed were searched from inception to 30 April 2025. Eligibility required (i) prospective or retrospective human studies of LARC, (ii) faecal or mucosal microbiome profiling by 16S, metagenomics, or metatranscriptomics, and (iii) response assessment using tumour-regression grade or pCR. Narrative synthesis and random-effects proportion meta-analysis were performed where data were homogeneous.<br><br>RESULTS: Twelve studies (n = 1354 unique patients, median sample = 73, range 22-735) met inclusion. Four independent machine-learning models achieved an Area Under the Receiver Operating Characteristic curve AUROC &#x2265; 0.85 for pCR prediction. Consistently enriched taxa in responders included Lachnospiraceae bacterium, Blautia wexlerae, Roseburia spp., and Intestinimonas butyriciproducens. Non-responders showed over-representation of Fusobacterium nucleatum, Bacteroides fragilis, and Prevotella spp. Two studies linked butyrate-producing modules to radiosensitivity, whereas nucleotide-biosynthesis pathways conferred resistance. Pooled pCR rate in patients with a "butyrate-rich" baseline profile was 44% (95% CI 35-54) versus 21% (95% CI 15-29) in controls (I[2] = 18%).<br><br>CONCLUSIONS: Despite heterogeneity, convergent functional and taxonomic signals underpin a microbiome-based radiosensitivity axis in LARC. Multi-centre validation cohorts and intervention trials manipulating these taxa, such as prebiotics or live-biotherapeutics, are warranted before clinical deployment.},
}
@article {pmid40559414,
year = {2025},
author = {Moustakli, E and Stavros, S and Katopodis, P and Potiris, A and Drakakis, P and Dafopoulos, S and Zachariou, A and Dafopoulos, K and Zikopoulos, K and Zikopoulos, A},
title = {Gut Microbiome Dysbiosis and Its Impact on Reproductive Health: Mechanisms and Clinical Applications.},
journal = {Metabolites},
volume = {15},
number = {6},
pages = {},
doi = {10.3390/metabo15060390},
pmid = {40559414},
issn = {2218-1989},
abstract = {The human gut microbiome is integral to maintaining systemic physiological balance, with accumulating evidence emphasizing its critical role in reproductive health. This review investigates the bidirectional interactions between the gut microbiota and the female reproductive system, mediated by neuroendocrine, immune, and metabolic pathways, constituting the gut-reproductive axis. Dysbiosis, characterized by microbial imbalance, has been linked to reproductive disorders such as polycystic ovary syndrome (PCOS), endometriosis, infertility, impaired spermatogenesis, and pregnancy complications. These associations can be explained by immunological dysregulation, systemic inflammation, altered sex hormone metabolism, and hypothalamic-pituitary-gonadal (HPG) axis disturbances. This review aims to clarify the molecular and cellular mechanisms underpinning gut-reproductive interactions and to evaluate the feasibility of microbiome-targeted therapies as clinical interventions for improving reproductive outcomes.},
}
@article {pmid40559413,
year = {2025},
author = {Malcangi, G and Marinelli, G and Inchingolo, AD and Trilli, I and Ferrante, L and Casamassima, L and Nardelli, P and Inchingolo, F and Palermo, A and Inchingolo, AM and Dipalma, G},
title = {Salivaomics: New Frontiers in Studying the Relationship Between Periodontal Disease and Alzheimer's Disease.},
journal = {Metabolites},
volume = {15},
number = {6},
pages = {},
doi = {10.3390/metabo15060389},
pmid = {40559413},
issn = {2218-1989},
abstract = {BACKGROUND: This study explores the link between oral biofluids, microbial dysbiosis, and Alzheimer's disease (AD), highlighting saliva and gingival crevicular fluid (GCF) as non-invasive diagnostic sources. AD onset and progression appear to be influenced not only by genetic and environmental factors but also by changes in the oral microbiome and related inflammatory and metabolic alterations. As global populations age, the incidence of AD is projected to rise significantly. Emerging evidence implicates the oral microbiome and salivary metabolites in neurodegenerative pathways, suggesting that oral health may mirror or influence brain pathology.<br><br>MATERIALS AND METHODS: A systematic review of recent multi-omics studies was performed, focusing on salivary and GCF analysis in patients with AD, those with mild cognitive impairment (MCI), and cognitively healthy individuals. Databases searched included PubMed, Web of Science, and Scopus, following PRISMA guidelines.<br><br>RESULTS: Across the 11 included studies, significant alterations were reported in both the salivary microbiome and metabolome in AD patients. Notable microbial shifts involved increased abundance of Veillonella parvula and Porphyromonas gingivalis, while key metabolites such as L-tyrosine, galactinol, and mannitol were consistently dysregulated. These biomarkers correlated with cognitive performance and systemic inflammation.<br><br>CONCLUSIONS: Oral biofluids represent promising, accessible sources of biomarkers for early AD detection. Multi-omics integration reveals the oral-brain axis as a potential target for diagnosis, monitoring, and therapeutic strategies.},
}
@article {pmid40559396,
year = {2025},
author = {Corral-Guerrero, IA and Martínez-Medina, AE and Alvarado-Mata, LY and Chávez, ACF and Muñoz-García, R and Luévanos-Escareño, MP and Sosa-Martínez, JD and Castro-Alonso, MJ and Nimmakayala, P and Reddy, UK and Balagurusamy, N},
title = {Capsaicin as a Microbiome Modulator: Metabolic Interactions and Implications for Host Health.},
journal = {Metabolites},
volume = {15},
number = {6},
pages = {},
doi = {10.3390/metabo15060372},
pmid = {40559396},
issn = {2218-1989},
support = {2025-03710//the United States Department of Agriculture/ ; 2023-09267//National Institute of Food and Agriculture (USDA-NIFA)/ ; 2242771//the National Science Foundation (NSF)/ ; },
abstract = {Background/Objectives: Capsaicin is the principal pungent compound in chili peppers and is increasingly recognized as a multifunctional phytochemical with systemic effects beyond its sensory properties. It has been linked to metabolic regulation, neuroprotection, inflammation control, and cancer modulation. This review aims to provide an integrative synthesis of capsaicin's metabolism, its interaction with the gut microbiome, and its physiological implications across organ systems. Methods: We conducted a critical literature review of recent in vivo and in vitro studies exploring capsaicin's metabolic fate, biotransformation by host enzymes and gut microbes, tissue distribution, and molecular pathways. The literature was analyzed thematically to cover gastrointestinal absorption, hepatic metabolism, microbiota interactions, and systemic cellular responses. Results: Capsaicin undergoes extensive hepatic metabolism, producing hydroxylated and dehydrogenated metabolites that differ in transient receptor potential vanilloid type 1 (TRPV1) receptor affinity and tissue-specific bioactivity. It crosses the blood-brain barrier, alters neurotransmitter levels, and accumulates in brain regions involved in cognition. In addition to its systemic effects, capsaicin appears to undergo microbial transformation and influences gut microbial composition, favoring short-chain fatty acid producers and suppressing pro-inflammatory taxa. These changes contribute to anti-obesity, anti-inflammatory, and potentially anticancer effects. Dose-dependent adverse outcomes, such as epithelial damage or tumor promotion, have also been observed. Conclusions: Capsaicin represents a diet-derived bioactive molecule whose systemic impact is shaped by dynamic interactions between host metabolism and the gut microbiota. Clarifying its biotransformation pathways and context-specific effects is essential for its safe and effective use in metabolic and neurological health strategies.},
}
@article {pmid40559387,
year = {2025},
author = {Zong, J and Wu, H and Hu, X and Yao, A and Zhu, W and Dou, G and Liu, S and Zhu, X and Gu, R and Sun, Y and Wu, Z and Wang, S and Gan, H},
title = {Plasma and Fecal Metabolites Combined with Gut Microbiome Reveal Systemic Metabolic Shifts in [60]Co Gamma-Irradiated Rats.},
journal = {Metabolites},
volume = {15},
number = {6},
pages = {},
doi = {10.3390/metabo15060363},
pmid = {40559387},
issn = {2218-1989},
abstract = {Background: High-dose γ-ray exposure (≥7 Gy) in nuclear emergencies induces life-threatening acute radiation syndrome, characterized by rapid hematopoietic collapse (leukocytes <0.5 × 10[9]/L) and gastrointestinal barrier failure. While clinical biomarkers like leukocyte depletion guide current therapies targeting myelosuppression, the concomitant metabolic disturbances and gut microbiota dysbiosis-critical determinants of delayed mortality-remain insufficiently profiled across the 28-day injury-recovery continuum. Methods: This study investigates the effects of [60]Co γ-ray irradiation on metabolic characteristics and gut microbiota in Sprague Dawley rats using untargeted metabolomics and 16S rRNA sequencing. Meanwhile, body weight and complete blood counts were measured. Results: Body weight exhibited significant fluctuations, with the most pronounced deviation observed at 14 days. Blood counts revealed a rapid decline in white blood cells, red blood cells, and platelets post-irradiation, reaching nadirs at 7-14 days, followed by gradual recovery to near-normal levels by 28 days. Untargeted metabolomics identified 32 upregulated and 33 downregulated plasma metabolites at 14 days post-irradiation, while fecal metabolites showed 47 upregulated and 18 downregulated species at 3 days. Key metabolic pathways impacted included Glycerophospholipid metabolism, alpha-linolenic acid metabolism, and biosynthesis of unsaturated fatty acids. Gut microbiota analysis demonstrated no significant change in α-diversity but significant β-diversity shifts (p < 0.05), indicating a marked alteration in the compositional structure of the intestinal microbial community following radiation exposure. Principal coordinate analysis confirmed distinct clustering between control and irradiated groups, with increased abundance of Bacteroidota and decreased Firmicutes in irradiated rats. These findings highlight dynamic metabolic and microbial disruptions post-irradiation, with recovery patterns suggesting a 28-day restoration cycle. Spearman's rank correlation analysis explored associations between the top 20 fecal metabolites and 50 abundant bacterial taxa. Norank_f_Muribaculaceae, Prevotellaceae_UCG-001, and Bacteroides showed significant correlations with various radiation-altered metabolites, highlighting metabolite-microbiota relationships post-radiation. Conclusions: This study provides insights into potential biomarkers for radiation-induced physiological damage and underscores the interplay between systemic metabolism and gut microbiota in radiation response.},
}
@article {pmid40559197,
year = {2025},
author = {Prisco, SZ and Oliveira, SD and Weir, EK and Thenappan, T and Al Ghouleh, I},
title = {Gut Microbiome in Pulmonary Arterial Hypertension-An Emerging Frontier.},
journal = {Infectious disease reports},
volume = {17},
number = {3},
pages = {},
doi = {10.3390/idr17030066},
pmid = {40559197},
issn = {2036-7430},
support = {5K08HL168166-02A1/NH/NIH HHS/United States ; 5K01HL159037-04A1/NH/NIH HHS/United States ; },
abstract = {Pulmonary arterial hypertension (PAH) is an irreversible disease characterized by vascular and systemic inflammation, ultimately leading to right ventricular failure. There is a great need for adjunctive therapies to extend survival for PAH patients. The gut microbiome influences the host immune system and is a potential novel target for PAH treatment. We review the emerging preclinical and clinical evidence which strongly suggests that there is gut dysbiosis in PAH and that alterations in the gut microbiome may either initiate or facilitate the progression of PAH by modifying systemic immune responses. We also outline approaches to modify the intestinal microbiome and delineate some practical challenges that may impact efforts to translate preclinical microbiome findings to PAH patients. Finally, we briefly describe studies that demonstrate contributions of infections to PAH pathogenesis. We hope that this review will propel further investigations into the mechanisms by which gut dysbiosis impacts PAH and/or right ventricular function, approaches to modify the gut microbiome, and the impact of infections on PAH development or progression.},
}
@article {pmid40559193,
year = {2025},
author = {Anselmo, A and Rizzo, F and Gervasi, E and Corrent, L and Ciammaruconi, A and Fillo, S and Fortunato, A and Marella, AM and Costantini, S and Baldassari, L and Lista, F and Ciervo, A},
title = {Tropheryma whipplei and Giardia intestinalis Co-Infection: Metagenomic Analysis During Infection and the Recovery Follow-Up.},
journal = {Infectious disease reports},
volume = {17},
number = {3},
pages = {},
doi = {10.3390/idr17030062},
pmid = {40559193},
issn = {2036-7430},
support = {B1519 ESM4 GP//Italian General Secretariat of Defense and the National Armaments Directorate within the "Eu-ropean Biodefence Laboratory Network 2 (EBLN2) project",/ ; },
abstract = {BACKGROUND: Whipple's disease (WD) is a rare infection caused by Tropheryma whipplei. Diagnosis is challenging and requires a combination of several data sets, such as patient history, clinical and laboratory investigations, and endoscopy with histology analyses. While persistent diarrhea is a common symptom, WD can affect multiple organs.<br><br>CASE DESCRIPTION: We present the case of a 66-year-old immunocompetent patient with WD and a history of Helicobacter pylori infection who developed chronic diarrhea. Colonoscopy and histopathological analysis revealed the presence of foamy macrophages with periodic acid-Schiff-positive particles. Subsequently, molecular methods confirmed the clinical WD diagnosis and metagenomic analyses further identified a co-infection with Giardia intestinalis. The patient fully recovered after 14 months of antibiotic therapy. During pharmacological treatment, clinical and laboratory follow-ups were conducted at 6 and 12 months, and microbiome profiles were also analyzed to identify the most abundant species in the samples.<br><br>CONCLUSION: The metagenomic analyses showed the eradication of the two pathogens and a progressive restoration to a healthy/balanced status after antibiotic therapy.},
}
@article {pmid40559130,
year = {2025},
author = {Chaple-Gil, AM and Santiesteban-Velázquez, M and Urbizo Vélez, JJ},
title = {Association Between Oral Microbiota Dysbiosis and the Risk of Dementia: A Systematic Review.},
journal = {Dentistry journal},
volume = {13},
number = {6},
pages = {},
doi = {10.3390/dj13060227},
pmid = {40559130},
issn = {2304-6767},
abstract = {Background/Objectives: Growing evidence suggests that oral microbiota dysbiosis may contribute to the development of systemic conditions, including neurodegenerative diseases. This dysregulation promotes immunoinflammatory responses that are increasingly associated with dementia. This systematic review aimed to evaluate the association between oral microbiota dysbiosis and the risk of dementia in older adults. Methods: Eligible studies evaluated oral microbial composition using validated methods such as genetic sequencing, bacterial culture, or metagenomic analysis. Following PRISMA guidelines and a PICO framework, the review included cohort, case-control, and cross-sectional studies. Searches were conducted across PubMed, Scopus, Web of Science, Embase, and Cochrane Library. Two independent reviewers screened and selected studies, resolving disagreements through a third evaluator. Results: This systematic review revealed that Tannerella forsythia, Fusobacterium nucleatum, Porphyromonas, Prevotella, Leptotrichia, Fusobacteriota, Peptostreptococcaceae, and Candida spp. were consistently associated with Alzheimer's disease and mild cognitive impairment, indicating their potential role in neurodegeneration. In contrast, Streptococcus gordonii, Gemella haemolysans, Rothia, Neisseria, and Haemophilus were reduced in cognitively impaired individuals, suggesting a link with healthy cognition. Studies also showed decreased microbial diversity in Alzheimer's disease and the possible modifying effect of the APOE4 allele. Oral health interventions improved microbial composition and slowed cognitive decline, supporting the diagnostic and therapeutic potential of oral microbiota modulation. Conclusions: The findings suggest that oral microbiota dysbiosis may not only result from cognitive decline but also contribute to its pathogenesis. Future studies with larger and more diverse cohorts are recommended to validate these associations.},
}
@article {pmid40559033,
year = {2025},
author = {Zhang, X and Cao, Q and Wang, F and Du, Y and Zhao, W and Guo, Y and Rueppell, O},
title = {Diverse Sublethal Effects of a Common Fungicide Impact the Behavior and Physiology of Honey Bees.},
journal = {Insects},
volume = {16},
number = {6},
pages = {},
doi = {10.3390/insects16060603},
pmid = {40559033},
issn = {2075-4450},
support = {RGPIN-2022-03629//Natural Sciences and Engineering Research Council/ ; 202103021223142//Shanxi Provincial Applied Basic Research Plan (Youth) Project/ ; 2021BQ53//Shanxi Agricultural University Doctoral Fund Project/ ; CARS-44-KXJ2//Modern Agro-Industry Technology Research System/ ; 202208140055//China Scholarship Council/ ; NA//Alberta Beekeepers Commission/ ; },
abstract = {Honey bees and other pollinators are key to functioning natural and managed ecosystems. However, their health is threatened by many factors, including pesticides. Spraying fungicides during flowering of fruit trees is widespread even though it directly exposes pollinators to these fungicides. Here, we report a series of experiments designed to understand how the combination of propiconazole and carbendazim, marketed in China as Chunmanchun[®], affects honey bee health. With an acute oral toxicity of 23.8 μg a.i./bee over 24 h in the laboratory, we considered the acute mortality risk from normal Chunmanchun[®] applications as relatively low. However, our comprehensive studies revealed other diverse effects: Chunmanchun[®] reduced memory after classic conditioning by approximately 25% and altered the activity of protective enzymes and the composition of the honey bees' gut microbiota. Specifically, the genus Lactobacillus was decreased by ~13%, and Bartonella and Snodgrassella were increased by ~10% and ~7.5%, respectively. The gut metabolome was also disrupted in diverse ways, possibly as a functional consequence of the microbiome changes. Thus, we demonstrated numerous sublethal effects of the combination of propiconazole and carbendazim, which adds to the growing evidence that agrochemicals and fungicides in particular can harm pollinator health in subtle ways that are not captured in simple mortality assays.},
}
@article {pmid40559017,
year = {2025},
author = {Danmek, K and Praphawilai, P and Ghosh, S and Jung, C and Mohamadzade Namin, S and Aedtem, P and Chuttong, B},
title = {Evaluation of Red Palm Weevils (Rhynchophorus ferrugineus: Curculionidae) for Putative Oxidation of Ingested Polystyrene and Polyurethane and Their Gut Microbiota Response.},
journal = {Insects},
volume = {16},
number = {6},
pages = {},
doi = {10.3390/insects16060587},
pmid = {40559017},
issn = {2075-4450},
support = {208210//National Research Council of Thailand (NRCT)/ ; 2024K2A9A1A06003640//National Research Foundation of Korea/ ; //Chiang Mai University/ ; },
abstract = {This study assessed the growth performance of red palm weevil (RPW) (Rhynchophorus ferrugineus: Curculionidae) larvae on a liquid diet of yeast-enriched potato dextrose broth (control) and on diets with added polystyrene and polyurethane. For 15 days of diet exposure, the growth and survival, plastic degradation, and gut microbiota of larvae were examined. RPWs showed higher survival rates under polystyrene and polyurethane treatments than in the control group. Head diameter showed a higher trend under polyurethane treatment than under the other treatments. Treated plastics were partly degraded after a 15-day exposure. Further analysis of plastic residues from frass revealed significant differences in Fourier Transform Infrared Spectroscopy (FTIR), with decreased intensity of characteristic peaks compared to frass from larvae fed in the control. Gut bacterial communities in the gut of RPW larvae showed that plastic feeding did not significantly alter the presence of key microbial taxa, but members of Firmicutes and Proteobacteria were higher in the plastic treatment, showing preliminary signs of plastic oxidation and degradation. Overall, these findings provide evidence that ingestion of PS and PU by RPW larvae supports their survival and alters their gut microbiota, possibly due to plastic degradation, paving the way for further research into the interactions between RPWs, their microbiome, and key functional activities, with implications for plastic waste management and recycling.},
}
@article {pmid40558984,
year = {2025},
author = {Crane, YM and Crane, CF and Subramanyam, S and Schemerhorn, BJ},
title = {Shotgun Metagenome Analysis of Two Schizaphis graminum Biotypes over Time With and Without Carried Cereal Yellow Dwarf Virus.},
journal = {Insects},
volume = {16},
number = {6},
pages = {},
doi = {10.3390/insects16060554},
pmid = {40558984},
issn = {2075-4450},
support = {5020-21000-000-D//USDA-ARS Research Project/ ; },
abstract = {The greenbug aphid (Schizaphis graminum (Rondani)) is a major pest of wheat and an important vector of wheat viruses. An RNA-seq study was conducted to investigate the microbial effects of two greenbug genotypes, the presence or absence of cereal yellow dwarf virus, and the condition of the wheat host over a 20-day time course of unrestricted greenbug feeding. Messenger RNA reads were mapped to ca. 47,000 bacterial, 1218 archaeal, 14,165 viral, 571 fungal, and 94 protozoan reference or representative genomes, plus greenbug itself and its wheat host. Taxon counts were analyzed with QIIME2 and DESeq2. Distinct early (days 1 through 10) and late (days 15 and 20) communities differed in the abundance of typical enteric genera (Shigella, Escherichia, Citrobacter), which declined in the late community, while the ratio of microbial to greenbug read counts declined 50% and diversity measures increased. The nearly universal aphid endosymbiont, Buchnera aphidicola, accounted for less than 25% of the read counts in both communities. There were 302 differentially expressed (populated) genera with respect to early and late dates, while 25 genera differed between the greenbug genotypes and nine differed between carrier and virus-free greenbugs. The late community was likely responding to starvation as the wheat host succumbed to aphid feeding. Our results add to basic knowledge about aphid microbiomes and offer an attractive alternative method to assess insect microbiomes.},
}
@article {pmid40558498,
year = {2025},
author = {Ahmad, I and Omura, S and Khadka, S and Sato, F and Park, AM and Rimal, S and Tsunoda, I},
title = {Gut Microbiota in a Viral Model of Multiple Sclerosis: Modulation and Pitfalls by Oral Antibiotic Treatment.},
journal = {Cells},
volume = {14},
number = {12},
pages = {},
doi = {10.3390/cells14120871},
pmid = {40558498},
issn = {2073-4409},
support = {JP22K07527//Japan Society for the Promotion of Science/ ; JP23K06493//Japan Society for the Promotion of Science/ ; JP21K07287//Japan Society for the Promotion of Science/ ; JP24K10500//Japan Society for the Promotion of Science/ ; JP22K18378//Japan Society for the Promotion of Science/ ; JP23K08901//Japan Society for the Promotion of Science/ ; JP24K10163//Japan Society for the Promotion of Science/ ; KD2303//2023 Kindai University Research Enhancement Grant/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Anti-Bacterial Agents/pharmacology/administration &amp; dosage/therapeutic use ; *Multiple Sclerosis/microbiology/virology/drug therapy ; Mice ; *Theilovirus ; Administration, Oral ; Disease Models, Animal ; Mice, Inbred C57BL ; Female ; },
abstract = {Viral infections have been associated with multiple sclerosis (MS), an immune-mediated disease in the central nervous system (CNS). Since Theiler's murine encephalomyelitis virus (TMEV) can induce MS-like demyelination, TMEV infection is the most widely used viral model for MS. Although the precise pathophysiology is unknown, altered fecal bacterial populations were associated with distinct immune gene expressions in the CNS. We aimed to determine the role of gut microbiota in TMEV infection by administering an antibiotic cocktail in drinking water before (prophylactic administration) or after (therapeutic administration) TMEV infection. The antibiotic administration reduced total eubacteria, including the phyla Bacillota and Bacteroidota, but increased the phylum Pseudomonadata in feces. Prophylactic administration did not alter TMEV-induced inflammatory demyelination clinically or histologically, without changes in anti-viral IgG1/IgG2c levels or lymphoproliferative responses; therapeutic administration temporarily suppressed the neurological signs. Although antibiotic treatment had minimal effects on TMEV infection, adding metronidazole and ampicillin in drinking water substantially reduced water intake in the antibiotic group of mice, resulting in significant body weight loss. Since dehydration and stress could affect immune responses and gut microbiota, caution should be exercised when planning or evaluating the oral antibiotic cocktail treatment in experimental animals.},
}
@article {pmid40558392,
year = {2025},
author = {Xu, Y and Sha, Y and Chen, X and Chen, Q and Liu, X and He, Y and Huang, W and He, Y and Gao, X},
title = {Interaction Between Rumen Microbiota and Epithelial Mitochondrial Dynamics in Tibetan Sheep: Elucidating the Mechanism of Rumen Epithelial Energy Metabolism.},
journal = {Biotech (Basel (Switzerland))},
volume = {14},
number = {2},
pages = {},
doi = {10.3390/biotech14020043},
pmid = {40558392},
issn = {2673-6284},
support = {32260820//National Natural Science Foundation of China/ ; GAU-XKTD-2022-21//Discipline Team Project of Gansu Agricultural University/ ; GAU-QDFC-2022-06//Gansu Agricultural University Youth Mentor Support Fund project/ ; 2025CXZX-824//Post-graduate Innovation Star Project of Gansu Province/ ; },
abstract = {Investigating the functional interactions between rumen microbial fermentation and epithelial mitochondrial dynamics/energy metabolism in Tibetan sheep at different altitudes, this study examined ultrastructural changes in rumen epithelial tissues, expression levels of mitochondrial dynamics-related genes (fusion: Mfn1, Mfn2, OPA1, Mic60; fission: Drp1, Fis1, MFF), and ketogenesis pathway genes (HMGS2, HMGCL) in Tibetan sheep raised at three altitudes (TS 2500m, TS 3500m, TS 4500m). Correlation analysis was performed between rumen microbiota/metabolites and mitochondrial energy metabolism. Results: Ultrastructural variations were observed across altitudes. With increasing altitude, keratinized layer became more compact; desmosome connections between granular layer cells increased; mitochondrial quantity and distribution in spinous and basal layers increased. Mitochondrial dynamics regulation: Fission genes (FIS1, DRP1, MFF) showed significantly higher expression at TS 4500m (p < 0.01); fusion genes (Mfn1, OPA1) exhibited altitude-dependent upregulation. Energy metabolism markers: Pyruvate (PA) decreased significantly at TS 3500m/TS 4500m (p < 0.01); citrate (CA) increased with altitude; NAD[+] peaked at TS 3500m but decreased significantly at TS 4500m (p < 0.01); Complex II (SDH) and Complex IV (CO) activities decreased at TS 4500m (p < 0.01). Ketogenesis pathway: β-hydroxybutyrate increased significantly with altitude (p < 0.01); acetoacetate peaked at TS 2500 m/TS 4500 m; HMGCS2 expression exceeded HMGCL, showing altitude-dependent upregulation at TS 4500m (p < 0.01). Microbiome-metabolism correlations: Butyrivibrio_2 and Fibrobacter negatively correlated with Mic60 (p < 0.01); Ruminococcaceae_NK4A214_Group positively correlated with Mfn1/OPA1 (p < 0.05); WGCNA identified 17 metabolite modules, with MEturquoise module positively correlated with DRP1/Mfn2/MFF (p < 0.05). Conclusion: Altitude-induced ultrastructural adaptations in rumen epithelium correlate with mitochondrial dynamics stability and ketogenesis upregulation. Mitochondrial fission predominates at extreme altitudes, while microbiota-metabolite interactions suggest compensatory energy regulation mechanisms.},
}
@article {pmid40558199,
year = {2025},
author = {He, M and Kolhoff, F and Mont, MA and Parvizi, J},
title = {Is Osteoarthritis a State of Joint Dysbiosis?.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {6},
pages = {},
doi = {10.3390/antibiotics14060609},
pmid = {40558199},
issn = {2079-6382},
abstract = {Osteoarthritis (OA) has traditionally been defined as a degenerative joint disease driven by mechanical wear, aging, and metabolic disturbances. However, emerging evidence suggests that joint dysbiosis, a dysregulation in the joint microbiome, may play an important role in OA pathogenesis. This review explores the mechanisms linking dysbiosis to OA. We examine the presence and origin of joint dysbiosis, also highlighting the gut-joint and oral-joint axes as potential routes for microbial translocation. However, challenges remain in distinguishing causation from correlation and addressing microbial contaminants in microbiome studies. Future research should prioritize longitudinal studies and multiomics integration to elucidate the complex interplay between microbial communities and joint health.},
}
@article {pmid40558145,
year = {2025},
author = {Kline, A and Cobián Güemes, AG and Yore, J and Ghose, C and Van Tyne, D and Whiteson, K and Pride, DT},
title = {Current Clinical Laboratory Challenges to Widespread Adoption of Phage Therapy in the United States.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {6},
pages = {},
doi = {10.3390/antibiotics14060553},
pmid = {40558145},
issn = {2079-6382},
abstract = {The resurgence of phage therapy in Western societies has been in direct response to recent increases in antimicrobial resistance (AMR) that have ravaged many societies. While phage therapy as a concept has been around for over 100 years, it has largely been replaced by antibiotics due to their relative ease of use and their predictability in spectrum of activity. Now that antibiotics have become less reliable due to greater antibiotic resistance and microbiome disruption, phage therapy has once again become a viable and promising alternative, but it is not without its challenges. Much like the development of antibiotics, with deployment of phage therapeutics there will be a simultaneous need for diagnostics in the clinical laboratory. This review provides an overview of current challenges to widespread adoption of phage therapy with a focus on adoption in the clinical diagnostic laboratory. Current barriers include a lack of standard methodology and quality controls for phage susceptibility testing and selection, the absence of phage-antibiotic synergy testing, and the absence of standard methods to assay phage activity on biofilms. Additionally, there are a number of lab-specific administrative and regulatory barriers to widespread phage therapy adoption including the need for pharmacokinetic (PK) and pharmacodynamic (PD) assays, methods to account for changes in phages after passaging, an absence of regulatory guidance on what will be required for agency approvals of phages and how broad that approval will apply, and the increased need for lab personnel or automation to account for the work of testing large phage libraries against bacteria isolates.},
}
@article {pmid40558084,
year = {2025},
author = {Brumfield, KD and Enke, S and Swan, BK and Carrasquilla, L and Lee, MD and Stern, DB and Gieser, L and Hasan, NA and Usmani, M and Jutla, AS and Huq, A and Caviness, K and Goodrich, JS and Bull, R and Colwell, RR},
title = {Hybridization capture sequencing for Vibrio spp. and associated virulence factors.},
journal = {mBio},
volume = {},
number = {},
pages = {e0051625},
doi = {10.1128/mbio.00516-25},
pmid = {40558084},
issn = {2150-7511},
abstract = {Proliferation of Vibrio spp. in aquatic ecosystems is associated with climate change and, concomitantly, increased incidence of vibriosis. They are autochthonous to aquatic environments globally, but traditional metagenomic methods for detecting and typing pathogenic Vibrio spp. are challenged by their presence in relatively low abundance and ability to persist in a viable but nonculturable state. In the study reported here, hybridization capture sequencing (HCS) was employed to profile low-abundance Vibrio spp. in environmental samples. The HCS panel targeted a family of molecular chaperones (CPN60) specific to 69 Vibrio spp. and 162 Vibrio-specific virulence factors. This approach was evaluated in parallel with traditional whole-community shotgun sequencing in a metagenomic analysis of water and oyster samples collected from the Chesapeake Bay. In addition, Vibrio parahaemolyticus and Vibrio vulnificus strains isolated from the samples were subjected to whole-genome sequencing to determine the genetic characteristics of pathogenic Vibrio spp. circulating in an aquatic environment. HCS, employed to determine the incidence and characterization of specific Vibrio spp., yielded significantly greater metagenomic insight, notably a variety of other Vibrio spp., including detection of Vibrio cholerae, Vibrio fluvialis, and Vibrio aestuarianus, in addition to Vibrio parahaemolyticus and Vibrio vulnificus, and also important virulence factors not detectable using traditional molecular methods. Thus, pathogenic Vibrio spp. in aquatic ecosystems may be far more common than currently understood. It is concluded that environmental surveillance should include HCS, a valuable tool for the detection and characterization of pathogenic agents in aquatic ecosystems, notably vibrios.IMPORTANCEThe increasing prevalence of pathogenic Vibrio spp. in aquatic ecosystems, driven by climate change, is closely linked to a rise in cholera and vibriosis cases, emphasizing the need for improved environmental surveillance. Vibrios are naturally occurring in aquatic environments globally, but traditional metagenomic methods for detecting and typing pathogenic Vibrio spp. are challenged by their presence in relatively low abundance and ability to persist in a viable but nonculturable state. In the study reported here, hybridization capture sequencing was employed to profile low-abundance Vibrio spp. in metagenomic samples, namely water and oysters collected from the Chesapeake Bay. This approach was evaluated in parallel with traditional whole-community shotgun sequencing and whole-genome sequencing of Vibrio parahaemolyticus and Vibrio vulnificus strains isolated from the samples. Results suggest pathogenic Vibrio spp. in aquatic ecosystems may be far more common than currently understood, when multiple methods are considered for environmental surveillance.},
}
@article {pmid40558055,
year = {2025},
author = {Huang, F and Zhou, Y and Chen, D and Lin, H},
title = {Anti-cariogenic activity of mutanocyclin, a secondary metabolite of Streptococcus mutans, in mono- and multispecies biofilms.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0018325},
doi = {10.1128/spectrum.00183-25},
pmid = {40558055},
issn = {2165-0497},
abstract = {UNLABELLED: Streptococcus mutans (S. mutans), a principal cariogenic pathogen responsible for dental caries, alters the oral biofilm ecology through the production of various metabolites. One such metabolite, mutanocyclin (MUC), a recently identified secondary metabolite, may have implications for both caries development and oral microbiome interactions. This study aimed to investigate the properties of MUC and its effects on S. mutans, as well as other oral commensal streptococci in mono- and multispecies biofilms. Our findings revealed that MUC significantly inhibited S. mutans planktonic growth, biofilm formation, lactic acid production, water-insoluble glucan synthesis, and extracellular polysaccharide production. In contrast, at lower concentrations, MUC stimulated the growth of Streptococcus gordonii (S. gordonii) and Streptococcus sanguinis (S. sanguinis). Additionally, MUC reduced the abundance of S. mutans and enhanced the antagonistic activity of S. gordonii and S. sanguinis against S. mutans in multispecies biofilms by upregulating the expression of the H2O2-related gene spxB and stimulating H2O2 production. These results suggest that MUC has potential for anti-cariogenic activity against S. mutans and for modulating oral microbial communities within the cariogenic microenvironment, providing new therapeutic strategies for preventing dental caries.<br><br>IMPORTANCE: Dental caries is a major global health concern, affecting millions and contributing to reduced quality of life and economic burdens. Our study investigated the properties of mutanocyclin (MUC), a recently discovered secondary metabolite produced by S. mutans. Our work sheds light on the role of MUC in modulating microbial communities in the oral cavity. We demonstrated that MUC influences the formation and cariogenicity of S. mutans biofilms and its interactions with other beneficial oral bacteria. This research enhances our understanding of newly discovered secondary metabolites of S. mutans and offers a potential novel strategy for managing the microbial imbalances that lead to caries.},
}
@article {pmid40558050,
year = {2025},
author = {Phan, J and Jain, S and Nijkamp, JF and Sasidharan, R and Agarwal, A and Bird, JK and Spooren, A and Wittwer Schegg, J and Ver Loren van Themaat, E and Mak, TN},
title = {Gut health predictive indices linking gut microbiota dysbiosis with healthy state, mild gut discomfort, and inflammatory bowel disease phenotypes using gut microbiome profiling.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0027125},
doi = {10.1128/spectrum.00271-25},
pmid = {40558050},
issn = {2165-0497},
abstract = {Despite the complexity of the gut microbiome, several scores that use taxonomic characteristics exist that attempt to identify a healthy gut or gastrointestinal disease. Two systems in use are the metagenomic aerotolerant predominance index (MAPI) and keystone scores. The aim of this analysis was to compare different gut microbiome scores, specifically MAPI and a keystone species score, on two cross-sectional data sets and to investigate correlations of these scores with self-reported gut discomfort and gastrointestinal disease. The first data set is a commercial data set (Sun Genomics data set) with whole-genome shotgun sequencing samples from 5,372 customers. The second data set is curated from publicly available data (public data set) with 2,415 samples from participants in human studies with gut-related taxonomic profiles. MAPI scores and keystone species scores were calculated using standard methodology. The MAPI score was significantly lower in men for the public data set. There was a graded response for both the MAPI and keystone scores between healthy subjects, subjects with mild gastrointestinal discomfort, and patients with gastrointestinal disease: the MAPI score was higher, and the keystone score was lower in subjects with gastrointestinal discomfort or with inflammatory bowel disease patients. The keystone and MAPI scores have the potential to help identify factors associated with gut microbial dysbiosis and gastrointestinal discomfort or disease. Furthermore, given the functional link of the MAPI score to oxidative stress in the microbiome, the scores can help to identify conditions where oxidative stress is one of the hallmarks of dysbiosis.IMPORTANCEGut bacteria play a role in both mild gastrointestinal discomfort, which includes bloating and constipation, and inflammatory bowel disease. There are many different types of bacteria in the gut, and gut microbiome composition differs greatly between different people. Therefore, it is difficult to predict who has a gut microbiome associated with a healthy gut and who might develop disease or experience gut discomfort. Several scoring systems have been developed to categorize gut health states. This analysis compared two different scoring systems using data from two different sources to see how well they could identify people with gastrointestinal disease, gastrointestinal complaints, or a healthy gut. The scoring systems showed similar trends according to gut health status: groups of people with gut bacteria imbalance or gut disease had a different score than groups of people with healthy gut bacteria.},
}
@article {pmid40558046,
year = {2025},
author = {Wu, S and Luo, G and Jiang, F and Jia, W and Li, J and Huang, T and Zhang, X and Mao, Y and Su, S and Han, W and He, F and Cheng, R},
title = {Early life bifidobacterial mother-infant transmission: greater contribution from the infant gut to human milk revealed by microbiomic and culture-based methods.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0048025},
doi = {10.1128/msystems.00480-25},
pmid = {40558046},
issn = {2379-5077},
abstract = {UNLABELLED: The colonization and development of the gut microbiota during early life, especially Bifidobacterium, may be influenced by maternal bacterial communities, including those of human milk. However, the interaction of bacteria in mother-infant dyads during breastfeeding remains unclear. This study focused primarily on the characteristics and dynamics of the infant gut and human milk microbiota within the first month of life on the basis of a birth cohort and explored the interaction of the microbiota derived from the two niches by sequencing and culture-based methods, especially Bifidobacterium, as the representative dominator in the infant gut. Infant feces and human milk samples from 21 mother-infant dyads were collected on days 0, 7, and 30 postpartum. The bacterial composition was identified by sequencing the 16S rRNA gene, and the contributions of the bacterial communities were estimated via SourceTracker2. Bifidobacterial strains were isolated from infant feces and human milk via culture-based methods. The suspected strains were identified through Sanger sequencing and genotyped via multilocus sequence typing (MLST). The bacterial communities were distinct between infant feces and human milk. Human milk microbes contribute 63.89%-77.61% to the infant's gut within the first month of life, whereas Bifidobacterium in the infant's gut contributes more (80.18%-84.30%) to human milk. A total of 60 bifidobacterial isolates were obtained from 10 pairs of mother-infant samples, 48 isolates from 10 out of 27 infant feces samples, and 12 isolates from 4 out of 27 human milk samples. Among these, 30 isolates were identified as Bifidobacterium breve, and 18 were identified as B. longum subsp. longum. Strains belonging to B. breve from a single mother-infant pair were found to be monophyletic (ST: BRE-1), whereas this strain was found much earlier in infant feces across the three time points (collected on days 0, 7, and 30) than in human milk (collected on day 30). Our data suggest that during very early breastfeeding, human milk contributes a significant proportion of the overall bacterial population to the infant's gut, whereas the infant's gut selectively contributes a greater proportion of Bifidobacterium to human milk. Certain bifidobacterial strains, such as B. breve, are retrogradely transmitted from the infant's gut to the mother's human milk during breastfeeding, implying a potential challenge regarding the reliability of the source when potential probiotics are isolated from human milk.<br><br>IMPORTANCE: Understanding how microbes, especially beneficial bacteria such as Bifidobacterium, are shared between mothers and infants during breastfeeding is crucial for promoting infant health. Although most research has focused on transmission from mother to child, our study reveals a novel and significant reverse route: from the infant gut to breast milk. By combining microbiome sequencing with culture-based techniques, we provide evidence that specific strains of Bifidobacterium, especially B. breve, may transmit back to the mother during breastfeeding. This insight reshapes our understanding of microbial exchange within the mother-infant dyad and highlights breastfeeding as a bidirectional process that influences both maternal and infant microbiota. These findings may have important implications for designing probiotics and supporting early-life microbial development through maternal health interventions.},
}
@article {pmid40558044,
year = {2025},
author = {Li, K and Liu, X and Zhong, X and Zeng, H and Liu, T and Lin, B and Chen, P and Xie, B and Zhong, X},
title = {Significant associations between high-risk sexual behaviors and enterotypes of gut microbiome in HIV-negative men who have sex with men.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0023225},
doi = {10.1128/msphere.00232-25},
pmid = {40558044},
issn = {2379-5042},
abstract = {UNLABELLED: Gut microbiome of men who have sex with men (MSM) exhibits distinctive characteristics compared with general populations. The dysbiosis of the gut microbiome in MSM is also associated with the onset and evolution of HIV infection. Enterotype is an important feature of the gut microbiome and remains unaffected by demographic factors. However, the enterotypes of gut microbiome in MSM are unclear. The associations between enterotypes and high-risk sexual behaviors in this population also remain to be elucidated. HIV-negative MSM were recruited in this study. Fecal samples of the participants were collected and subjected to 16S rRNA gene sequencing. Enterotype clusters were determined by Jensen-Shannon divergence based on genus-level relative abundance. Microbial function predictions were conducted by PICRUSt2 software. Univariate and multivariate logistic regression approaches were utilized to analyze the associations of enterotypes with sexual behaviors. A three-category random forest machine learning model was performed to further examine the correlation between abundant microbiome in each enterotype cluster and anal sex roles. Two enterotype clusters were identified in our data sets, primarily driven by genera Phocaeicola and Segatella. The alpha diversity was comparable between the two enterotype clusters. Microbial metabolic functions significantly differed, and multivariate logistic regression indicated a significant association between anal sex role and enterotype. The results of the three-category random forest model indicate that the dominant bacterial communities in gut enterotypes can effectively differentiate MSM who engage exclusively in receptive anal intercourse from those who engage in insertive or versatile anal intercourse (AUC: 0.6400, 0.6929, respectively). We identified two enterotype clusters of gut microbiome in HIV-negative MSM. Enterotypes of MSM were significantly associated with anal sex roles. These findings further highlight the close correlation between the gut microbiome and anal intercourse roles.<br><br>IMPORTANCE: Our study's discovery that gut microbiome enterotypes are significantly associated with anal sex roles in HIV-negative MSM opens a new frontier in understanding the complex interplay between microbiology and sexual health. This finding underscores the urgency of delving into the mechanistic connections between the gut microbiome, sexual behaviors, and HIV infection. By identifying modifiable factors influencing gut microbiome composition, we have paved the way for developing personalized preventive strategies that could disrupt the transmission dynamics of HIV within this high-risk population. This research contributes to the fundamental understanding of the gut microbiome's role in the sexual health of MSM, making it a pivotal advancement in the fields of gut microbiome research and sexual health.},
}
@article {pmid40558028,
year = {2025},
author = {Gao, Y and Zhang, H and Chu, D and Ning, K},
title = {Intra-tumor microbiome-based tumor survival indices predict immune interaction and drug sensitivity on pan-cancer scale.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0031225},
doi = {10.1128/msystems.00312-25},
pmid = {40558028},
issn = {2379-5077},
abstract = {UNLABELLED: Growing research evidence indicates a substantial influence of the intra-tumor microbiome on tumor outcome. However, there is currently no consistent criterion for identifying the association of microbes with tumor progression and response to treatment across various types of cancer. In this study, we concentrate on the intra-tumor microbiome and develop the Tumor Microbiome Survival Index (TMSI), a measure indicative of cancer patient survival risk. Our indices revealed notable distinctions between two stratified risk groups for each of the 10 cancer types and could precisely predict patients' overall survival. For each type of cancer, our findings unveiled two distinct gene expression profiles and shed light on the varying patterns of immune and stromal cell enrichment between the two risk groups. Additionally, we noted that the high-TMSI group exhibited substantially elevated IC50 values for a number of drugs, indicating that individuals in the low-TMSI group might experience superior therapeutic effects from chemotherapy. These findings illuminate the complex dynamics between the tumor microbiome, the patient's immune reaction, and medical outcomes, thus shedding light on microbiome-based personalized therapeutic interventions.<br><br>IMPORTANCE: This work presents the Tumor Microbiome Survival Index (TMSI), a crucial innovation. It stratifies cancer patients into risk groups across 10 cancer types, accurately predicting survival. By uncovering distinct gene expression and immune/stromal cell patterns, it deepens understanding of tumor complexity. The finding of altered drug sensitivity in different TMSI groups offers insights for personalized chemotherapy. Overall, it paves the way for microbiome-targeted cancer therapies and enhanced patient prognostication.},
}
@article {pmid40557875,
year = {2025},
author = {Ikeda, SI and Lee, D and Chen, J and Fukuda, S and Negishi, K and Tsubota, K and Kurihara, T},
title = {Antibiotics-Induced Gut Microbiome Dysbiosis Affects Susceptibility to Minus Lens-Induced Myopia in Mice.},
journal = {Investigative ophthalmology &amp; visual science},
volume = {66},
number = {6},
pages = {76},
doi = {10.1167/iovs.66.6.76},
pmid = {40557875},
issn = {1552-5783},
mesh = {Animals ; Mice, Inbred C57BL ; *Dysbiosis/chemically induced/microbiology/complications ; *Anti-Bacterial Agents/pharmacology ; Mice ; Male ; *Myopia/etiology/microbiology ; *Gastrointestinal Microbiome/drug effects ; Disease Models, Animal ; Disease Susceptibility ; RNA, Ribosomal, 16S/genetics ; Vancomycin ; },
abstract = {PURPOSE: The prevalence of myopia has increased worldwide in recent decades, shifting the focus in research from genetic to environmental factors. The roles of diet in the development of myopia may be directly associated with gut microbiota composition. Therefore this study evaluated the effects of antibiotic-induced gut dysbiosis on the development of negative lens-induced myopia.<br><br>METHODS: We administered several antibiotics (ampicillin, vancomycin, neomycin, or a mixture) to induce gut dysbiosis in male C57BL/6J mice with negative lens-induced myopia. Gut microbiome profiles were analyzed by 16 S rRNA gene sequencing.<br><br>RESULTS: Mice administered vancomycin, neomycin, and a mixture of three antibiotics exhibited resistance to lens-induced myopia, unlike control or ampicillin-administered mice. Further analyses revealed no specific trend in the gut microbiota composition and diversity related to myopia resistance, except for an increase in the abundance of Clostridiaceae.<br><br>CONCLUSIONS: These findings demonstrate the potential role of the gut microbiome, particularly Clostridiaceae family, in myopia susceptibility. This study offers new insights into the preventive strategies and therapeutic interventions to mitigate myopia development.},
}
@article {pmid40557534,
year = {2025},
author = {Dong, H and Yang, X and Zhou, Y and Yang, M and Zhang, H and Liu, X and Zhu, W},
title = {Kudzu resistant starch effectively ameliorates non-alcoholic fatty liver disease by protecting the gut microbiota intestinal barrier and suppressing inflammatory responses.},
journal = {Journal of the science of food and agriculture},
volume = {},
number = {},
pages = {},
doi = {10.1002/jsfa.14371},
pmid = {40557534},
issn = {1097-0010},
support = {82260765//National Natural Science Foundation of China/ ; 2017YFC1702905//National Key R&amp;D Program Key Special Project, China/ ; CXTD-22004//Jiangxi University of Chinese Medicine Science and Technology Innovation Team Development Program/ ; },
abstract = {BACKGROUND: Non-alcoholic fatty liver disease (NAFLD), including non-alcoholic steatohepatitis, may lead to a cocktail of disease consequences, for instance, type II diabetes, liver fibrosis, and even hepatocarcinogenesis. The complex pathogenesis of NAFLD results in a shortage of an effective drug for its treatment. Currently, a healthy diet and regular exercise are considered one of the most effective and safe ways to mitigate NAFLD as well as other types of metabolic disorders. Kudzu-resistant starch (KRS) has developed as a potential dietary supplement attributed to its prebiotic properties, particularly its ability to regulate gut microbiota and intestinal barrier function. This study discusses the alleviative effects of KRS on high-fat diet and dextran sulfate sodium induced intestinal barrier dysfunction, inflammation, gut microbial dysbiosis, and liver steatosis.<br><br>RESULTS: The results identified KRS has ameliorated intestinal barrier dysfunction by increasing the expression of zonula occludens-1 (ZO-1) and mucin 2 (Muc2). Furthermore, it also down-regulated the gut-derived LPS/TLR4 signaling pathway, dramatically alleviating inflammatory responses, including serum, colon, and liver tumor necrosis factor-&#x3b1; (TNF-&#x3b1;), interleukin-6 (IL-6), and monocyte chemotactic protein-1 (MCP-1) levels. KRS also had attenuating effects on gut microbiota dysbiosis, restored the gut microbiota abundance and diversity, and increased the butyric acid-producing bacteria, such as Coprococcus, Bifidobacterium, and Lactobacillus, and it exhibited positive effects in short-chain fatty acids (SCFAs). KRS attenuated fatty acid-induced lipid accumulation and regulates lipid metabolism via the sterol regulatory element-binding protein 1-c (SREBP-1c), G-protein coupled receptors 43 (GPR43), peroxisome proliferator-activated receptor-&#x3b3; (PPAR-&#x3b3;), and CCAAT/enhancer-binding proteins-&#x3b1; (C/EBP-&#x3b1;).<br><br>CONCLUSION: The findings reveal that kudzu resistant starch could be a potential supplement for metabolic syndromes, and the efficacy and effectiveness might facilitate the multi-targeting strategy required to mitigate NAFLD. &#xa9; 2025 Society of Chemical Industry.},
}
@article {pmid40557325,
year = {2025},
author = {Sellers-Porter, C and Lueschow-Guijosa, SR and Santana, JM and Cera, AJ and Bautista, GM and Persiani, M and Good, M and McElroy, SJ},
title = {Modeling pathogen-driven neonatal late-onset sepsis: a modification to the murine cecal slurry.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1589712},
pmid = {40557325},
issn = {2235-2988},
mesh = {Animals ; *Disease Models, Animal ; *Cecum/microbiology/pathology ; Mice ; Animals, Newborn ; *Neonatal Sepsis/microbiology/pathology ; Gastrointestinal Microbiome ; Enterocolitis, Necrotizing/microbiology ; Humans ; Cytokines/blood ; Infant, Newborn ; Mice, Inbred C57BL ; *Sepsis/microbiology ; Female ; },
abstract = {INTRODUCTION: Neonatal sepsis is a major cause of neonatal morbidity and mortality. Reliable animal models are essential to our understanding of late-onset sepsis, but notable limitations exist in the current standard murine cecal slurry model. We sought to refine the existing model by using an injection of known stock slurry ("NEC'teria") cultured from an infant who died of necrotizing enterocolitis to better mimic sepsis following the translocation of neonatal specific bacterial pathogens from the intestine into the peritoneum.<br><br>METHODS: To induce sepsis, neonatal mice (P7 and P14 - P16) were given an intraperitoneal injection of varying concentrations of NEC'teria, while sham controls received an injection of PBS. Mice were monitored for survival and tissue samples, serum, and peritoneal washes were collected for further assessment of inflammation, immune response, and intestinal injury. Ceca were collected for microbiome analysis.<br><br>RESULTS: While the polymicrobial cecal slurry from adult mice contained common healthy gut microbes, NEC'teria is composed of bacteria, primarily from the Enterobacteriaceae and Enterococcaceae families, that are common causes of late-onset sepsis. NEC'teria exposure significantly increased serum inflammatory cytokines, resulted in intestinal injury, altered the microbiome composition, and induced significant changes in local and systemic immune cell expression. Sepsis-induced mortality, inflammation, and intestinal injury were live-bacteria dependent and could be attenuated by administration of an antibiotic one hour after bacterial injection.<br><br>DISCUSSION: Our modification to the cecal slurry neonatal sepsis model resulted in a consistent sepsis-related mortality and phenotypic changes in neonatal mouse pups that resembled the changes that occur in human preterm infants who develop late-onset sepsis. Our pathogenic slurry is highly relevant to neonatal sepsis, as it is comprised of bacterial families found commonly in septic neonates. We expect our model to be highly reproducible between institutions, due to the standardized bacterial dose and characterized stock solution.},
}
@article {pmid40557322,
year = {2025},
author = {Melvan, E and Allen, AP and Vuckovic, T and Soljic, I and Starcevic, A},
title = {Predicting gut microbiota dynamics in obese individuals from cross-sectional data.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1485791},
pmid = {40557322},
issn = {2235-2988},
mesh = {Humans ; *Obesity/microbiology ; *Gastrointestinal Microbiome ; Cross-Sectional Studies ; RNA, Ribosomal, 16S/genetics ; *Dysbiosis/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; *Microbial Interactions ; Adult ; Firmicutes/isolation &amp; purification/genetics ; Male ; Bacteroidetes ; Female ; },
abstract = {INTRODUCTION: Obesity affects approximately 39% of adults worldwide. While gut microbiota has been linked to obesity, most research has focused on static taxonomic composition rather than the dynamic interactions between microbial taxa.<br><br>METHODS: We applied BEEM-Static, a generalized Lotka-Volterra model, to cross-sectional 16S rRNA gut microbiome data from six public datasets, comprising 2,435 profiles from lean and obese individuals.<br><br>RESULTS: A total of 57 significant microbial interactions were identified in obese individuals (79% negative), compared to 37 in lean individuals (92% negative). For example, Bacteroidetes showed a stronger inhibitory effect on Firmicutes in obese individuals (-0.41) than in lean ones (-0.26). Firmicutes and Proteobacteria exhibited consistently higher carrying capacities in obese populations.<br><br>DISCUSSION: These findings suggest that microbial interaction networks-not just taxonomic abundance-play a key role in obesity-related dysbiosis. Our approach enables the inference of microbiota dynamics from a single time point, paving the way for tailored dietary interventions, which we refer to as Optibiomics.},
}
@article {pmid40557264,
year = {2025},
author = {Radulovic, E and Mehinagic, K and Wüthrich, TM and Hilty, M and Summerfield, A and Ruggli, N and Benarafa, C},
title = {Development of protective immunity against African swine fever depends on host-environment interactions.},
journal = {Frontiers in veterinary science},
volume = {12},
number = {},
pages = {1553310},
pmid = {40557264},
issn = {2297-1769},
abstract = {African swine fever virus (ASFV) is a major threat for pig health and meat production in many countries. The development and commercialization of vaccine candidates are complicated by efficacy and safety concerns. Improved vaccine design requires further studies to identify factors that regulate immune responses to vaccines leading to protective immunity against a virulent challenge. In a previous study, we reported that infection with the moderately virulent ASFV field strain Estonia 2014 was less severe in specific pathogen-free (SPF) pigs than in conventional farm pigs, which differ in their gut microbiome and their basal immune activation status. As shown previously using intramuscular infection, SPF pigs were more resilient to oronasal infection with the ASFV Estonia 2014 strain compared to farm pigs, which showed increased fever and clinical signs. All SPF and farm pigs nevertheless survived the infection and remained viremic for approximately 4 months. When all animals had no detectable viremia, both groups were rechallenged with the virulent ASFV Armenia 2008 strain. SPF pigs were fully protected against disease and showed little or no viremia upon re-challenge. In contrast, farm pigs developed high viremia, high proinflammatory cytokine responses, severe clinical signs, and 40% (2 of 5 pigs) reached humane endpoints. Our findings suggest that limited prior immune exposure to other pathogens and/or the microbiome composition of SPF pigs promotes resilience to infection with a moderately virulent strain such as Estonia 2014, and importantly promotes the development of a strong protective immune response against a second challenge with a virulent ASFV strain. In conclusion, testing safety and efficacy of live attenuated vaccine candidates should take into account the specific hygiene conditions and the associated changes of general immune status of pigs in clinical trials.},
}
@article {pmid40557239,
year = {2025},
author = {Hamari, N and Blaak, EE and Canfora, EE},
title = {The impact of butyrate on glycemic control in animals and humans: a comprehensive semi-systemic review.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1603490},
pmid = {40557239},
issn = {2296-861X},
abstract = {The gut microbiome has been identified as a significant factor in host metabolism, playing a key role in the etiology of obesity, type 2 diabetes and cardiometabolic risk. Butyrate, produced by the gut microbiome from indigestible carbohydrates, has been shown to have beneficial effects on body weight control, inflammation, and insulin resistance, primarily evidenced by animal studies and in vitro experiments. However, translating these benefits to humans remains challenging due to variability in mode of butyrate administration or production upon fermentation of dietary fibers, as well as in butyrate absorption, and its metabolism. For instance, oral butyrate supplementation can directly increase circulating butyrate levels, thereby targeting peripheral tissues. In contrast, butyrate produced by the gut microbiome may also influence metabolism through local signaling mechanisms affecting peripheral tissues. Additionally, there may be large heterogeneity in the response of the individuals to butyrate interventions. Future research should aim to better understand butyrate kinetics and dynamics and its mechanisms in regulating intestinal and metabolic health. In human studies, longer-term, placebo-controlled trials are needed to establish the efficacy of either targeting butyrate production or supplementation in individuals with obesity and/or metabolic disturbances. Personalized dietary interventions based on individual microbiota composition and/or function and metabolic profiles may optimize butyrate production and its metabolic benefits. This could pave the way for effective butyrate-based interventions to improve metabolic health and prevent obesity-related complications.},
}
@article {pmid40557154,
year = {2025},
author = {Bai, X and Raju, SC and Knudsen, AD and Thudium, RF and Arentoft, NS and Gelpi, M and Heidari, SL and Kunisaki, KM and Kristiansen, K and Hov, JR and Nielsen, SD and Trøseid, M},
title = {Microbiome profiling reveals gut bacterial species associated with rapid lung function decline in people with HIV.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1555441},
pmid = {40557154},
issn = {1664-3224},
mesh = {Humans ; *Gastrointestinal Microbiome ; Male ; Female ; *HIV Infections/microbiology/complications/physiopathology ; Middle Aged ; Dysbiosis ; *Lung/physiopathology ; *Bacteria/genetics/classification ; Adult ; *Lung Diseases/microbiology ; Respiratory Function Tests ; Aged ; },
abstract = {BACKGROUND: People with HIV (PWH) have an increased risk of pulmonary comorbidities compared to people without HIV. The gut microbiome regulates host immunity and is altered in PWH. This study aims to determine potential associations between gut microbiome, lung function decline, and airflow limitation in PWH.<br><br>METHODS: PWH from the Copenhagen Comorbidity in HIV Infection (COCOMO) Study with available lung function testing and microbiome data were included (n=385). The gut microbiome was characterized using shotgun metagenomic sequencing. Associations between gut microbiome, rapid lung function decline, and airflow limitation were analysed in multivariable logistic regressions adjusted for traditional and HIV-associated risk factors for lung disease.<br><br>RESULTS: Several bacterial species were significantly enriched in PWH with rapid lung function decline, including opportunistic pathogenic bacterial species Bacteroides coprophilus, Klebsiella michiganensis, and Clostridium perfringens. A gut microbial dysbiosis index based on compositional changes was associated with rapid lung function decline (adjusted odds ratio (aOR) 1.18, 95% confidence interval (CI) [1.11-1.27], p<0.001), and airflow limitation (aOR 1.16, 95% CI [1.04-1.29], p=0.007) in adjusted multivariable logistic regression analyses.<br><br>CONCLUSION: Associations between the gut dysbiosis index and rapid lung function decline and airflow limitation suggest a potential role of certain gut bacterial species in the pathogenesis of pulmonary comorbidities in PWH.},
}
@article {pmid40556945,
year = {2025},
author = {Wang, S and Li, S and Zhang, M and Liu, R and Ye, X and Mao, S and Yu, J and Xie, X and Tan, W},
title = {Unraveling the Role of the Microbiota in Cancer Immunotherapy: A New Frontier.},
journal = {Research (Washington, D.C.)},
volume = {8},
number = {},
pages = {0744},
pmid = {40556945},
issn = {2639-5274},
abstract = {Cancer immunotherapy has greatly changed the therapeutic landscape for metastatic malignancies. Nevertheless, due to immune-related adverse events, drug resistance, and other factors, cancer immunotherapy remains largely untapped. Recent research has shown that the microbiota is crucial in shaping immune function and that its modulation can influence antitumor immunity. However, because of the intricate nature of the microbiome and immune system, a comprehensive mechanistic framework for understanding how the microbiota influences antitumor immune responses is still lacking. In this review, we summarize the mechanisms of the microbiota in antitumor immunity. We also comprehensively outline the methods for measuring the microbiota and their limitations. Additionally, we discuss the key challenges facing the targeting of the microbiota as a regulatory strategy for cancer immunotherapy.},
}
@article {pmid40556896,
year = {2025},
author = {Viquez-Umana, FL and Erickson, MG and Young, JD and Zanton, GI and Wattiaux, MA and Suen, G and Mantovani, HC},
title = {Assessing the impact of oscillating dietary crude protein on the stability of the rumen microbiome in dairy cattle.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1568112},
pmid = {40556896},
issn = {1664-302X},
abstract = {INTRODUCTION: Understanding how the rumen microbiota responds to varying protein levels and feeding patterns is critical for optimizing dairy cattle nutrition. This study investigated the influence of dietary crude protein (CP) levels (13.8% or 15.5% CP of ration dry matter) and CP feeding patterns (constant over time (static) or oscillating by 1.8 percentage units above and below the mean every 48 h) on the composition, diversity, and function of the rumen microbiome.<br><br>METHODS: Using a replicated Latin Square design, eight rumen-cannulated Holstein cows were assigned each of the four dietary treatments (structured as a 2 &#xd7; 2 factorial) in four consecutive 28-day periods (with 24 days of adaptation and 4 days of sampling). Rumen samples were collected 4 h post-feeding, and amplicon libraries of the V4 region of the 16S rRNA gene were sequenced and analyzed to assess changes in microbiome composition. Additionally, volatile fatty acids (VFAs) were measured to evaluate rumen microbial function.<br><br>RESULTS: Results indicated that dietary CP level did not alter microbial diversity (p&#x202f;=&#x202f;0.30), but oscillating diets increased rumen microbial diversity (Shannon index, p&#x202f;=&#x202f;0.04). The rumen microbiome richness was also affected by CP feeding pattern (p&#x202f;=&#x202f;0.05), but not dietary CP level (p&#x202f;=&#x202f;0.27). Furthermore, differential abundance analysis using ANCOM-BC identified CAG- 352 (p&#x202f;=&#x202f;0.0001) and an unclassified member of the family Acholeplasmataceae (p&#x202f;=&#x202f;0.0002) as taxa significantly impacted by protein level and feeding pattern, even though their relative abundance was low (below 0.02%). The functional profile of the rumen bacterial communities was not affected by CP level or feeding pattern, and VFA profiles also remained consistent across treatments, with no observable changes in concentration.<br><br>DISCUSSION: These findings support the hypothesis that the rumen microbiome remains stable despite variations in the ruminal supply of dietary CP, suggesting that compensatory mechanisms may be involved. Although oscillating dietary CP concentration might alter the rumen microbiome, further research into rumen metabolic processes and host-microbiome interactions is needed to evaluate if the changes observed in our study are biologically relevant for developing new opportunities to enhance protein nutrition in dairy cattle.},
}
@article {pmid40556886,
year = {2025},
author = {Klein, ML and Erikson, CB and McCabe, CJ and Huang, L and Rodrigues, JLM and Mitloehner, FM},
title = {Limited effects of tannin supplementation on the dairy cattle fecal microbiome with modulation of metabolites.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1570127},
pmid = {40556886},
issn = {1664-302X},
abstract = {Tannins are plant secondary metabolites that bind organic carbon (C) and nitrogen (N), potentially altering substrate bioavailability for enteric fermentation in ruminants. This interaction may reduce greenhouse gas (GHG) emissions and influence nitrogen partitioning. Given tannins' resistance to ruminal degradation and persistence through the gastrointestinal tract, this study investigated the effects of a tannin-based feed additive on fecal microbial diversity, fecal chemical composition, and GHG emissions. Twenty-four early- to mid-lactation dairy cows were randomized to receive either a tannin-based feed additive (TRT; containing condensed and hydrolyzable tannins from Schinopsis quebracho-colorado [Schltdl.]) or a control diet (CON) for 64 days. Cows were blocked by parity, dry matter intake, milk yield, body weight, and days in milk. Fecal samples were collected on days 0, 16, 32, and 64 and analyzed using 16S rRNA gene amplicon sequencing. Fecal C, N, and indole-3-lactate were measured, and GHG emissions (N2O, CH4, CO2) were assessed via 14-day laboratory incubation. A total of 1,538 amplicon sequence variants were identified, with Firmicutes as the dominant phylum. Fecal phylogenetic diversity showed a significant treatment × day interaction (p < 0.01), with TRT cows exhibiting reduced microbial diversity from day 16 to 64. Fecal C and N concentrations were significantly lower (p < 0.01) in TRT cows on day 16, while indole-3-lactate levels were higher on day 64 (p = 0.02). GHG emissions did not differ significantly between treatments. The tannin-based feed additive influenced fecal microbial community structure and select chemical parameters but did not significantly affect GHG emissions from feces. These findings suggest that dietary tannins may modulate gut microbial ecology with minimal impact on downstream manure-related emissions.},
}
@article {pmid40556746,
year = {2025},
author = {Urquhart, SA and Christof, M and Coelho-Prabhu, N},
title = {The impact of artificial intelligence on the endoscopic assessment of inflammatory bowel disease-related neoplasia.},
journal = {Therapeutic advances in gastroenterology},
volume = {18},
number = {},
pages = {17562848251348574},
pmid = {40556746},
issn = {1756-283X},
abstract = {Inflammatory bowel disease (IBD) is a group of chronic inflammatory conditions of the gastrointestinal tract resulting from an inappropriate immune response to an altered gut microbiome in genetically predisposed individuals. Endoscopy plays a central role in IBD management, aiding in diagnosis, disease staging, monitoring, and therapeutic guidance. Patients with IBD face an increased risk of colorectal neoplasia due to chronic inflammation. Artificial intelligence (AI)-based systems show promise in detecting and classifying dysplasia and neoplasia during endoscopic evaluation. While there have been several studies on the application of AI to detect and diagnose various types of neoplasia in the non-IBD population, the literature in patients with IBD is limited. We aim to summarize the current evidence on the application of AI technologies to detect IBD-associated neoplasia, highlighting potential benefits, limitations, and future directions. A comprehensive literature search was performed using the PubMed database to identify relevant studies from January 2010 to February 2025. Additional references were identified from the relevant articles' bibliographies. AI-assisted endoscopy, particularly using machine learning and deep learning techniques, has shown promise in improving lesion detection rates and supporting real-time decision-making. Computer-aided detection systems may increase the sensitivity of dysplasia identification, while computer-aided diagnosis tools can aid in lesion characterization. Early studies suggest that AI can reduce interobserver variability, improve targeting of biopsies, and potentially lead to more personalized surveillance strategies. Although clinical data specific to IBD-related neoplasia remain limited compared to sporadic colorectal neoplasia, the integration of AI into endoscopic practice holds significant potential to enhance dysplasia detection and improve patient outcomes. Continued research, validation in IBD-specific cohorts, and integration with clinical workflows are essential to realize the full impact of AI in this setting.},
}
@article {pmid40556628,
year = {2025},
author = {Stoll, ML and Appah, M and Tiwari, HK},
title = {The microbiota in axial spondyloarthritis: what have we learned from Mendelian randomisation studies?.},
journal = {Clinical and experimental rheumatology},
volume = {},
number = {},
pages = {},
doi = {10.55563/clinexprheumatol/rvb37m},
pmid = {40556628},
issn = {0392-856X},
abstract = {OBJECTIVES: It has been postulated that the gut microbiota plays an important role in the pathogenesis of spondyloarthritis (SpA). However, cross-sectional studies are limited in their ability to differentiate disease-driven microbial alterations from causative changes. Mendelian randomisation (MR) studies leverage existing genetic associations to investigate causality, offering insights into microbiota-disease associations.<br><br>METHODS: We conducted a systematic review of all MR studies that evaluated the relationship between the microbiota and axial SpA. Eight studies were identified and reviewed. To look for genetic associations with the microbiota, all of them used the MiBioGen microbiota genome-wide association study (GWAS), with one also using the Dutch Microbiome Project. To find associations between the human genome and disease, various data sources were used, including the published GWAS in ankylosing spondylitis (AS), FinnGen, the UK Biobank, and the Integrative Epidemiology Unit (IEU) Open GWAS project.<br><br>RESULTS: MR findings revealed predicted increased abundances of Ruminococcaceae NK4A214 and Verrucomicrobia among others, alongside decreased abundances of Lactobacillaceae, and Rikenellaceae families, as well as the Bacteroides genus. These findings largely support the results from cross-sectional studies of the microbiota in patients with SpA. They suggest that bacteria that disrupt gut barrier function may result in an increased risk of SpA, while the opposite may be true with bacteria such as Alistipes and Bacteroides that may have a protective role.<br><br>CONCLUSIONS: These results underscore the interplay of genetics, microbiota, and disease. Further research is needed to refine these findings and optimise therapeutic approaches.},
}
@article {pmid40556581,
year = {2025},
author = {Guo, M and Li, B and Li, H and Chen, Y and Yuan, Q and Shui, M and Zhou, H and Hao, W and Wang, S},
title = {Colon-Targeted Natural Polysaccharide-Berberine Armored Hydrogel for the Treatment of Colitis.},
journal = {Advanced healthcare materials},
volume = {},
number = {},
pages = {e2404908},
doi = {10.1002/adhm.202404908},
pmid = {40556581},
issn = {2192-2659},
abstract = {The maintenance of gut immune homeostasis and microbial balance is pivotal in the pathogenesis and progression of ulcerative colitis (UC). Despite advances in therapy, effective UC management remains challenging due to the limited efficacy and significant side effects of conventional treatments. Inspired by the synergistic mechanisms of bioactive compounds in traditional Chinese medicine, a colon-targeted hydrogel integrating rhubarb-derived polysaccharides and berberine-loaded dendrimers is engineered. This hydrogel self-assembles via intermolecular hydrogen bonding and electrostatic interactions, enabling localized accumulation in colonic tissues to suppress aberrant immune activation and remodel the dysbiotic microbiome. Mechanistic studies reveal that the hydrogel potently promotes the polarization of anti-inflammatory M2 macrophages while suppressing pro-inflammatory cytokine secretion, resulting in significant amelioration of colitis symptoms in murine models. Importantly, the therapeutic intervention not only restored gut microbiota composition but also corrected metabolic disturbances, collectively contributing to the re-establishment of intestinal homeostasis. The findings underscore the potential of this polysaccharide-based hydrogel as an effective oral therapeutic strategy for UC while demonstrating the translational value of combining natural bioactive constituents for targeted drug delivery.},
}
@article {pmid40556523,
year = {2025},
author = {Huang, J and Liang, W and Zhang, R and Zhao, Y and Shi, R and Chen, X and Zheng, Y and Li, X and Liu, D and Wang, H and Liu, J and Liao, Y and Zhang, X and Jiang, Z and Fu, C and Huang, T and Shan, X and Wang, W and Bu, J and Peng, T and Shen, E},
title = {Pou2af1 Deficiency Aggravates DSS-Induced Colitis via Impaired Germinal Center Responses and Altered Gut Microbiota.},
journal = {Inflammatory bowel diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/ibd/izaf089},
pmid = {40556523},
issn = {1536-4844},
support = {//The Affiliated Qingyuan Hospital/ ; 202301-316//Guangzhou Medical University/ ; JCXKJS2021C11//Discipline from School of Basic Medicine of Guangzhou Medical University/ ; 2021KTSCX090//Department of Education of Guangdong Province/ ; //Guangzhou Medical University 2022 Student Innovation Ability Improvement Program/ ; },
abstract = {BACKGROUND: Bob1 plays a critical role in immune system regulation, particularly in the function of B cells. Its deficiency in the context of colitis remains underexplored. This study investigates the effects of Bob1 (Pou2af1) deficiency on colitis, particularly focusing on immune responses and gut microbiota alterations in a murine model.<br><br>METHODS: In this study, we employed Pou2af1 knockout (KO) and wild-type (WT) mice to investigate the role of Bob1 in dextran sodium sulfate (DSS)-induced colitis. Colitis was induced by administering 2.5% DSS in drinking water for 7 days. Mice were monitored daily for weight loss, stool consistency, and rectal bleeding to calculate the disease activity index (DAI). Colon length was measured, and colon tissues were collected for histological analysis using hematoxylin and eosin (H&amp;E) staining. Flow cytometry was performed to assess germinal center responses as well as the proportion of T helper (Th)1 and Th17 cells in the colonic lamina propria. Metagenomic sequencing was conducted on fecal samples to evaluate gut microbiota composition.<br><br>RESULTS: Pou2af1-deficient mice exhibited significantly exacerbated colitis compared to WT mice. This was evidenced by greater weight loss, elevated disease activity index, reduced colon length, and more severe pathological changes. Immune analysis revealed an impaired germinal center response, diminished generation of IgA&#x207a; plasma cells, and decreased Th17 cells in the colonic lamina propria in Pou2af1-deficient mice. Additionally, microbiota analysis indicated dysbiosis in the Pou2af1-deficient group, with a notable decrease in Bacteroides species and an increase in pro-inflammatory microbes.<br><br>DISCUSSION: The findings suggest that Pou2af1 deficiency exacerbates DSS-induced colitis by impairing immune responses, particularly the germinal center reaction, and altering gut microbiota composition. These alterations contribute to increased disease severity, highlighting the importance of Pou2af1 in maintaining intestinal immune homeostasis.},
}
@article {pmid40556416,
year = {2025},
author = {Zeng, Q and Wang, S and Nurxat, N and Min, X and Guo, Y and Chen, F and Tang, W and Yang, Y and Liu, Q and Li, M},
title = {Staphylococcus aureus Promotes Cutaneous Lesions in Patients With Epidermolysis Bullosa.},
journal = {Experimental dermatology},
volume = {34},
number = {6},
pages = {e70129},
doi = {10.1111/exd.70129},
pmid = {40556416},
issn = {1600-0625},
support = {//the Natural Science Foundation of China/ ; //National Key Research and Development Program of China/ ; },
mesh = {Humans ; *Staphylococcus aureus/pathogenicity/genetics/isolation &amp; purification ; *Epidermolysis Bullosa/microbiology/pathology ; Male ; Female ; *Skin/microbiology/pathology ; Child ; Animals ; Microbiota ; Adolescent ; Adult ; Child, Preschool ; Young Adult ; RNA, Ribosomal, 16S ; Dysbiosis/microbiology ; China ; Mice ; },
abstract = {Epidermolysis bullosa (EB) is a group of rare, heterogeneous congenital conditions characterised by epidermal fragility, resulting in blister formation and lesions. Patients with EB are prone to developing cutaneous wounds. However, the composition of the EB skin microbiome in Chinese individuals remains poorly understood. The objective was to investigate the EB skin microbiome in Chinese individuals. The clinical symptoms and laboratory tests were collected for a total of 29 EB patients (23 Recessive Dystrophic EB, 3 EB simplex, 2 Kindler syndrome, and 1 Dominant Dystrophic EB). A total of 120 swabs were collected from 62 lesion sites, 29 non-lesion skin areas, and 29 nostrils. These samples underwent 16S rRNA amplicon sequencing and bacterial culture. The epidemiology of S. aureus was characterised, and its features were analysed using an animal model. Patients with EB exhibited a characteristic inflammatory response, marked by cutaneous lesions and elevated levels of C-reactive protein (CRP) and serum amyloid (SAA). Consistently, skin dysbiosis in EB patients was characterised by a predominance of S. aureus, particularly sequence type (ST) 7. Specifically, the abundance of S. aureus showed a positive correlation with EB severity and activity. Mechanistically, S. aureus isolated from lesional skin exhibited higher virulence due to increased accessory gene regulator (Agr) activity. Our study reported altered bacterial diversity and increased carriage of higher-virulence S. aureus in Chinese EB patients, which may potentially influence disease severity through microbiome alterations. Our findings suggested that maintaining the balance of the microbiome is crucial for optimising patient care.},
}
@article {pmid40556262,
year = {2025},
author = {Zhang, P and Garg, PP and Liu, L and Zhang, W and Kavanagh, K and Shetty, A and Howard, T and Varshney, N and Sawaya, D and Hawkins, G and Schwartz, DJ and Garg, PM},
title = {Distinct microbiota profiles in non-survivors in preterm infants with surgical necrotizing enterocolitis: Insights from FFPE intestinal tissue analysis.},
journal = {Journal of neonatal-perinatal medicine},
volume = {},
number = {},
pages = {19345798251353777},
doi = {10.1177/19345798251353777},
pmid = {40556262},
issn = {1878-4429},
abstract = {BackgroundThe variant microbiome is associated with necrotizing enterocolitis (NEC). We aimed to analyze remnant formalin fixed paraffin-embedded (FFPE) intestine tissue for microbiome profiling in preterm infants with surgical NEC.MethodsWe analyzed FFPE small intestine tissues from 16 infants with NEC (8 survivors and 8 non-survivors). Extracted DNA from FFPE tissue blocks underwent 16S rRNA sequencing. We compared the microbiota profiles in survivors and non-survivors. Alpha- and beta diversity metrics were calculated using QIIME2. To assess differences in overall microbial community structure, we performed a Permutational Multivariate Analysis of Variance (PERMANOVA). The analysis was performed in MaAsLin2 R package to determine the specific microbial taxa whose relative abundances were significantly associated with survival status in a multivariable linear model.ResultsSequencing of FFPE extracted DNA resulted in high-quality sequence reads in 16 cases.AnalysisAnalysis of microbial communities from 16 cases revealed a significant association between microbiome structure and survival status. Beta diversity analysis demonstrated distinct clustering of microbiome profiles between survivor and non-survivor groups. Alpha diversity metrics further characterized these differences: the non-survivor group exhibited a more complex and even microbiota (Shannon entropy, p = 0.02; Pielou's evenness, p = 0.017), whereas the survivor group's microbiome was significantly richer in observed features (p = 0.004). Notably, this association was specific to survival outcome, as overall community structure did not significantly differ when grouped by histological features of disease severity such as necrosis, inflammation, or hemorrhage. Linear mixed effect models and direct comparisons further identified numerous taxa potentially associated with survival status.ConclusionFFPE intestinal tissue enabled retrospective and spatially relevant microbiota assessment at the disease site. The non-survivors had complex microbiota and had distinct bacterial communities compared to survivors. Our findings suggest that the gut microbiome is a key factor related to prognosis, independent of other measures of NEC severity.},
}
@article {pmid40556049,
year = {2025},
author = {Kuo, CH and El-Omar, E and Kao, CY and Lin, JT and Wu, CY},
title = {Compositional and Metabolomic Shifts of the Gut Microbiome in Alcohol-Related Liver Disease.},
journal = {Journal of gastroenterology and hepatology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jgh.17038},
pmid = {40556049},
issn = {1440-1746},
abstract = {Alcohol-related liver disease (ALD) is a major global health concern characterized by steatosis and liver inflammation due to chronic alcohol consumption. Emerging evidence suggests that ALD is not solely a liver pathology but also involves dysfunction of the gut-liver axis, where alterations in the gut microbiota play a significant role. Although alcohol-associated dysbiosis has been extensively studied, whether these microbial changes contribute to ALD development or are merely a consequence of alcohol exposure remains unclear. To prove causation, it is essential to decipher which specific taxa and their metabolites drive the maladaptation of host-microbiota interactions upon alcohol exposure. In this review, we summarize the compositional changes in the gut microbiome after alcohol exposure, identifying traits of alcohol-induced dysbiosis and distinguishing them from those associated with liver disease. The effects of alcohol-induced dysbiosis on microbial metabolism and host responses are reviewed, focusing on the key classes of microbiota-derived metabolites, notably free fatty acids, tryptophan and its indole derivatives, and secondary bile acids. We discuss how alterations in these metabolites disrupt intestinal barrier function, immune responses, and metabolic signaling pathways, thereby exacerbating alcohol-induced injury. Advanced omics technologies and microbiome modulation strategies will help further investigation into these mechanisms. Detailed mechanistic insights into host-microbiota interactions could unveil novel therapeutic targets, offering potential strategies to prevent or mitigate ALD by modulating the gut microbiome and its metabolites.},
}
@article {pmid40555888,
year = {2025},
author = {Tyagi, A and Kumar, V},
title = {The gut microbiota-bile acid axis: a crucial regulator of immune function and metabolic health.},
journal = {World journal of microbiology &amp; biotechnology},
volume = {41},
number = {7},
pages = {215},
pmid = {40555888},
issn = {1573-0972},
mesh = {Humans ; *Gastrointestinal Microbiome/immunology/physiology ; *Bile Acids and Salts/metabolism/immunology ; Animals ; Dysbiosis/immunology/microbiology ; Signal Transduction ; Metabolic Diseases/microbiology/immunology ; Liver/metabolism ; Receptors, G-Protein-Coupled/metabolism ; Bacteria/metabolism/classification ; Inflammatory Bowel Diseases/microbiology ; },
abstract = {The gut microbiota and bile acid metabolism are intricately linked, playing a crucial role in immune regulation, metabolic processes, and overall health. The gut microbiome, consisting of diverse bacterial genera such as Bacteroides, Clostridium, Lactobacillus, Bifidobacterium, and Eubacterium, facilitates the conversion of primary bile acids into secondary bile acids through enzymatic modifications. Bile acids, synthesized in the liver and modified by gut microbiota, act as signaling molecules that regulate immune responses via bile acid receptors, including the farnesoid X receptor (FXR), G protein-coupled bile acid receptor 1 (GPBAR1), pregnane X receptor (PXR), vitamin D receptor (VDR), and sphingosine-1-phosphate receptor 2 (S1PR2). Dysbiosis-an imbalance in gut microbial composition-disrupts bile acid metabolism, leading to impaired activation of bile acid receptors and contributing to various diseases. These include inflammatory bowel disease, metabolic disorders such as obesity and type 2 diabetes, autoimmune diseases like multiple sclerosis, and liver conditions such as cholestasis and non-alcoholic fatty liver disease. Dysfunctional bile acid receptor signaling further promotes chronic inflammation, metabolic dysregulation, and disturbances in gut-liver-immune homeostasis. Emerging therapeutic strategies targeting bile acid receptors, restoring microbiota balance, and implementing dietary interventions offer promising avenues for disease prevention and management. This review explores the pivotal role of gut microbiota in modulating immune responses through bile acid receptors and highlights their therapeutic potential in improving treatment outcomes.},
}
@article {pmid40555747,
year = {2025},
author = {Jarman, JB and Torres, PJ and Stromberg, S and Sato, H and Stack, C and Ladrillono, A and Pace, S and Jimenez, NL and Haselbeck, RJ and Insel, R and Van Dien, S and Culler, SJ},
title = {Bifidobacterium deficit in United States infants drives prevalent gut dysbiosis.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {867},
pmid = {40555747},
issn = {2399-3642},
mesh = {Humans ; *Bifidobacterium/isolation &amp; purification/genetics ; *Gastrointestinal Microbiome ; *Dysbiosis/epidemiology/microbiology ; Infant ; United States/epidemiology ; Female ; Male ; Infant, Newborn ; Metagenomics ; },
abstract = {The composition of the infant gut microbiome is critical to immune development and noncommunicable disease (NCD) trajectory. However, a comprehensive evaluation of the infant gut microbiome in the United States is lacking. The My Baby Biome study, designed to address this knowledge gap, evaluated the gut microbiomes of 412 infants (representative of U.S. demographic diversity) using metagenomics and metabolomics. Regardless of birth mode and/or feeding method, widespread Bifidobacterium deficit was observed, with approximately 25% of U.S. infants lacking detectable Bifidobacterium. Bifidobacterium-dominant microbiomes exhibit distinct features when compared to microbiomes with other dominant microbial compositions including reduced antimicrobial resistance and virulence factor genes, altered carbohydrate utilization pathways, and altered metabolic signatures. In C-section birth infants, Bifidobacterium tended to be replaced in the human milk oligosaccharide utilization niche with potentially pathogenic species. Longitudinal health outcomes from these infants suggest that the disappearance of key Bifidobacterium may contribute to the development of atopy.},
}
@article {pmid40555497,
year = {2025},
author = {Nei, J and Wu, Y and DU, Y},
title = {[The role of Staphylococcus aureus in the occurrence and development of chronic rhinosinusitis with nasal polyps].},
journal = {Lin chuang er bi yan hou tou jing wai ke za zhi = Journal of clinical otorhinolaryngology head and neck surgery},
volume = {39},
number = {7},
pages = {679-685},
doi = {10.13201/j.issn.2096-7993.2025.07.015},
pmid = {40555497},
issn = {2096-7993},
mesh = {Humans ; *Sinusitis/microbiology ; *Nasal Polyps/microbiology ; *Staphylococcus aureus ; Chronic Disease ; *Rhinitis/microbiology ; *Staphylococcal Infections/microbiology ; Quorum Sensing ; Biofilms ; Rhinosinusitis ; },
abstract = {Chronic rhinosinusitis with nasal polyps（CRSwNP） represents a prevalent inflammatory disorder, which is often accompanied by nasal congestion, mucopurulent discharge, olfactory dysfunction, dizziness, and headache. Staphylococcus aureus（SA）, a predominant opportunistic pathogen within the sinonasal microenvironment, has been implicated in modulating the pathogenesis and progression of CRSwNP through multifaceted mechanisms. The physiological activities of SA-dependent quorum-sensing system and biofilm in the nasal microenvironment, including interactions with host, fungi, viruses, and other bacteria, as well as the effects of important superantigens secreted by SA on the microenvironment and immune barrier, are briefly reviewed in this article. These insights provide theoretical foundations for elucidating CRSwNP mechanisms and advancing clinical therapeutic strategies.},
}
@article {pmid40555474,
year = {2025},
author = {Akatsu, T and Souno, H and Fujii, A and Minegishi, Y and Ota, N and Yamashita, Y},
title = {Characteristics of Subgingival Plaque Microbiome in Japanese Older Adults With Healthy Gingiva.},
journal = {Journal of clinical periodontology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jcpe.14192},
pmid = {40555474},
issn = {1600-051X},
support = {//Kao Corporation/ ; },
abstract = {AIM: To elucidate the characteristics of the subgingival plaque microbiome in older adults without gingival inflammation.<br><br>MATERIALS AND METHODS: Subgingival plaque from 180 participants was collected and analysed using 16S rRNA sequencing. Based on the clinical parameters at the sampling sites, participants were categorised as healthy (gingival index [GI] =&#x2009;0, maximum probing pocket depth [PPDmax] &#x2264;&#x2009;2.0 and gingival recession [GR] =&#x2009;0) or non-healthy (GI >&#x2009;0, or PPDmax >&#x2009;2.0 or GR >&#x2009;0). Each group was further stratified by age into younger (<&#x2009;65&#x2009;years) and older (&#x2265;&#x2009;65&#x2009;years) subgroups. We performed diversity and linear discriminant effect size (LEfSe) analyses to elucidate microbiome characteristics of healthy older adults.<br><br>RESULTS: We observed differences in &#x3b1;-diversity and &#x3b2;-diversity between younger and older individuals only in the healthy group. Healthy older individuals showed a lower &#x3b1;-diversity index, indicating a healthy-like profile shift and also a significantly greater difference in &#x3b2;-diversity from the non-healthy group than the healthy younger subgroup. LEfSe analysis indicated that six amplicon sequence variants (ASVs), such as Rothia dentocariosa, Neisseria perflava and Actinomyces sp. HMT-448, were predominant in the healthy older subgroup.<br><br>CONCLUSION: Maintaining lower &#x3b1;-diversity, with an abundance of R. dentocariosa and N. perflava, which are possible nitrate-reducing bacteria, may contribute to lifelong healthy gingiva by preventing microbial dysbiosis.},
}
@article {pmid40555367,
year = {2025},
author = {McGrath, AH and Steinberg, PD and Egan, S and Kjelleberg, S and Marzinelli, EM},
title = {Disruption of host-associated and benthic microbiota affects reproductive output and settlement of a habitat-forming macroalga.},
journal = {Proceedings. Biological sciences},
volume = {292},
number = {2049},
pages = {20250729},
doi = {10.1098/rspb.2025.0729},
pmid = {40555367},
issn = {1471-2954},
support = {//University of Sydney/ ; //Australian Research Council/ ; //Ecological Society of Australia/ ; },
mesh = {*Microbiota/drug effects ; Reproduction ; Ecosystem ; *Rhodophyta/microbiology/physiology ; Anti-Bacterial Agents/pharmacology ; },
abstract = {The reproduction and establishment of habitat-forming species are key processes affecting their persistence and associated biodiversity. In marine systems, microbial communities associated with habitat-forming macroalgae can influence various aspects of host performance; however, the role of these microorganisms in influencing macroalgal reproduction and settlement is poorly understood. Using a dominant habitat-forming macroalga on Australian rocky shores, Hormosira banksii, we manipulated host- and benthic-associated microbiota to determine the relative importance of microorganisms to reproductive output (number of viable eggs released) and settlement (settlement and morphogenesis of algal zygotes). Disruption of the host microbiota using antibiotics decreased reproductive output after 2 weeks, with the effect dependent on the type of antibiotic used. Disruption of host- and benthic-associated microbiota, in combination, caused a significant decrease in settlement of H. banksii zygotes, with the combined disruption having the greatest impact on settlement success. Our results demonstrate the importance of host-associated microbiota in macroalgal reproduction and an interactive effect of host- and benthic-associated microbiota on settlement-a key ecological process with important implications for host fitness and potentially ecosystem persistence.},
}
@article {pmid40555128,
year = {2025},
author = {Amsalu, A and Alvaro, A and Huang, S and May, A and Antipov, A and Quinn, L and Carney, B and Kopecki, Z},
title = {Risk factors for antimicrobial resistance in paediatric burn infections: Insights from a retrospective cohort study.},
journal = {Burns : journal of the International Society for Burn Injuries},
volume = {51},
number = {6},
pages = {107584},
doi = {10.1016/j.burns.2025.107584},
pmid = {40555128},
issn = {1879-1409},
abstract = {AIM: To define the microbiome, antimicrobial resistance profiles and associated risk factors among paediatric patients with infected burns.<br><br>METHODS: A retrospective cohort study was conducted among paediatric patients with infected burns admitted to a tertiary burns service between January 2011 to December 2023. Basic demographic data and burn-related clinical information were extracted from the Burns Unit database and linked with microbiological data.<br><br>RESULT: Among a total of 3679 paediatric burn patients admitted, 183 (5&#x202f;% of overall admitted) were identified as clinically having infected burns. Of the 173 (4.7&#x202f;% of overall admitted) patients with documented cultures, 152 (87.9&#x202f;% of suspected clinical infections) had culture-positive burn wound infections (BWIs) and 15 (8.7&#x202f;% of overall admitted) had developed blood stream infections. The most common microorganisms identified in BWI were Gram-positive bacteria (245 isolates, 63.1&#x202f;%), with Staphylococcus aureus being the most prevalent (32&#x202f;%) followed by Streptococcus species (11.9&#x202f;%). Gram-negative bacteria were identified in 32.5&#x202f;% of cases, with Pseudomonas aeruginosa being the most common organism (5.7&#x202f;%). Nineteen (5&#x202f;%) methicillin-resistant Staphylococcus aureus isolates were detected from 17&#xa0;(9.8&#x202f;%) paediatric patients with burns. The highest resistance was reported against ampicillin (100&#x202f;%) followed by penicillin (91.7&#x202f;%), and amoxicillin (88.6&#x202f;%) against S. aureus isolates. P. aeruginosa isolates showed resistance in 58.8&#x202f;% of cases to ceftazidime, followed by 47&#x202f;% to piperacillin-tazobactam, and 2 isolates were resistant to imipenem, a carbapenem antibiotic considered a last-resort option. Multivariate logistic regression analysis revealed that burns to the head and neck regions (AOR = 5.2, 95&#x202f;%CI: 2.20-12.31; p&#x202f;<&#x202f;0.001), admission to the paediatric intensive care unit (PICU) (AOR = 8.2, 95&#x202f;%CI: 1.03-64.86; p&#x202f;=&#x202f;0.047) and previous medical history (AOR = 2.4, 95&#x202f;%CI: 1.07-5.55; p&#x202f;=&#x202f;0.033) were independent risk factors associated with antimicrobial-resistant (AMR) burn infections CONCLUSIONS: AMR in paediatric patients with infected burns is common and therefore early culture confirmation could improve treatment outcomes especially for patients with high risk factors.},
}
@article {pmid40555059,
year = {2025},
author = {Faysal, M and Zehravi, M and Amin, MA and Rab, SO and Jahnavi, P and Arjun, UVNV and Gupta, JK and Billah, AAM and Vodeti, R and Prasad, PD and Aseri, SSS and Siddiqui, FA and Bin Emran, T},
title = {Clinical insights into the mechanisms of infectious microbes and microbiota in chronic neurologic and psychiatric diseases.},
journal = {Pathology, research and practice},
volume = {272},
number = {},
pages = {156090},
doi = {10.1016/j.prp.2025.156090},
pmid = {40555059},
issn = {1618-0631},
abstract = {Chronic neurologic and psychiatric diseases such as schizophrenia, depression, Parkinson's, and Alzheimer's are increasingly linked to infectious microorganisms and gut microbiota. This review explores how pathogenic microorganisms and microbial communities impact neuropsychiatric, neurodegenerative, and neuroinflammatory processes, highlighting the gut-brain axis' crucial communication network in influencing behavior and brain function. Infectious agents like bacteria, viruses, and fungi cause disease by causing neurotoxic reactions, disrupting the blood-brain barrier, and activating neuroinflammatory cascades. Gut dysbiosis impacts immunological homeostasis and neural transmission by altering the synthesis of metabolites from microorganisms, such as short-chain fatty acids and neurotransmitter precursors. Neurodegeneration and psychiatric diseases are influenced by molecular mechanisms such as toll-like receptor signaling, microglial activation, and mitochondrial dysfunction. This review highlights the potential of microbiota-targeted treatments such as probiotics, prebiotics, and microbiome transplantation as novel treatments for chronic diseases. Understanding the intricate interactions between infectious microorganisms, microbiota, and the central nervous system enables the formation of precision medicine strategies to challenge the rising incidence of neurologic and psychiatric diseases. Future research should explore causal relationships and identify specific microbial biomarkers to enhance early diagnosis, prevention, and personalized treatment plans.},
}
@article {pmid40554434,
year = {2025},
author = {Chen, H and Gao, Y and Huang, H},
title = {Exploration of the GM-IC-DLBCL Axis: A Mendelian Randomization Analysis of the Gut Microbiota, Immune Cells, and Diffuse Large B-Cell Lymphoma.},
journal = {British journal of hospital medicine (London, England : 2005)},
volume = {86},
number = {6},
pages = {1-17},
doi = {10.12968/hmed.2025.0068},
pmid = {40554434},
issn = {1750-8460},
mesh = {*Lymphoma, Large B-Cell, Diffuse/immunology/genetics/microbiology ; Humans ; *Gastrointestinal Microbiome/immunology/genetics ; Mendelian Randomization Analysis ; Genome-Wide Association Study ; },
abstract = {Aims/Background This study aims to investigate the causal relationship among gut microbiome (GM), immune cells (IC), and diffuse large B-cell lymphoma (DLBCL) using the Mendelian randomization (MR) approach. Methods This analysis included GM data (471 taxa; n = 5959), genome-wide association study (GWAS) data on 731 IC phenotypes, and DLBCL data (1373 cases and 345,118 controls) from the FinnGen Consortium. A two-sample bidirectional MR analysis established causal links between GM, IC phenotypes, and DLBCL, followed by a two-step mediation analysis to assess immune cell mediation. Results Potential causal links were observed among 15 GM taxa, 38 IC phenotypes, and DLBCL. Mediation analysis revealed 14 possible gut microbiota-immune cell-diffuse large B-cell lymphoma (GM-IC-DLBCL) axes, with quantifiable effects in five. The maximum and minimum mediating effects included g__Roseibacillus (odds ratio [OR] = 3.30, 95% confidence interval [CI]: 1.22-8.91, p < 0.05; 10.4% via "CD45RA on naive CD8br cells") and s__Lachnospira rogosae (OR = 1.14, 95% CI: 1.01-1.28, p < 0.05; 5.8% via "CD127 on CD28- CD8br cells"), respectively. Conclusion This study suggests that GM may contribute to DLBCL pathogenesis through IC mechanisms, supporting the potential existence of a GM-IC-DLBCL axis.},
}
@article {pmid40554345,
year = {2025},
author = {Qi, X and Xu, X and Xu, C and Lv, G and Cai, J and Cheng, Z and Yang, Z and Yin, H},
title = {Pseudomonas plecoglossicida inoculation reshapes rhizosphere microbiome for BDE-47 dissipation in the alfalfa rhizosphere.},
journal = {Journal of hazardous materials},
volume = {495},
number = {},
pages = {138959},
doi = {10.1016/j.jhazmat.2025.138959},
pmid = {40554345},
issn = {1873-3336},
abstract = {Microbe-assisted phytoremediation emerges as a promising strategy for the removal of organic pollutants. In addition to the direct effects on plants and pollutants, the inoculant can induce changes in the rhizosphere microbiome; but its association with the dissipation of organic pollutants and the mechanisms underlying the rebuilding of rhizosphere microbiome remain unclear. Here, we study the effects of Pseudomonas plecoglossicida inoculation on BDE-47 elimination in the alfalfa rhizosphere, as well as the corresponding microbial response mechanisms. Microbial degradation in the rhizosphere, rather than plant extraction, was identified as the primary mechanism responsible for BDE-47 dissipation. Compared to the control without strain inoculation, BDE-47 concentration significantly decreased by 40.8 % with the strain inoculation in rhizosphere soil. The inoculate enriched populations of beneficial bacteria (e.g., Pseudomonas, Sphingomonas, Bacillus, and Lysobacter) known for their roles in promoting plant growth and degrading BDE-47. Furthermore, the inoculate markedly induced the production of root metabolites such as amino acids, carbohydrates, lipids, and terpenoids, which played a pivotal role in recruiting beneficial bacterial communities and enhancing the bioavailability of BDE-47. In conclusion, root metabolites and microbial inoculants collaboratively reshaped the rhizosphere microbiome, thereby supporting plant growth and enhancing the degradation of organic pollutants in the rhizosphere soils.},
}
@article {pmid40554292,
year = {2025},
author = {Li, J and Hu, J and Zhuo, D and Yang, L and Wang, L and Yang, B},
title = {Ginger-processed Magnoliae Officinalis Cortex ameliorates ovalbumin-induced asthma by alleviating inflammation via the gut-lung axis.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {145},
number = {},
pages = {156971},
doi = {10.1016/j.phymed.2025.156971},
pmid = {40554292},
issn = {1618-095X},
abstract = {BACKGROUND: The complex pathophysiology of asthma and the lack of effective therapies have driven research into natural product remedies. Ginger-processed Magnoliae Officinalis Cortex (GMOC), a traditional Chinese medicine, has been used for asthma treatment, but the lack of its potential mechanism of action limits the clinical application of GMOC.<br><br>PURPOSE: To investigate the mechanism of action of GMOC in asthmatic mice based on the gut-lung axis.<br><br>METHODS: The anti-asthma effects of GMOC were evaluated in an ovalbumin (OVA)-induced mouse model of asthma. The lung and gut microbiota were analysed via 16S rRNA gene sequencing and short-chain fatty acids (SCFAs) were determined using GC/MS. Protein expression was evaluated by western blotting. Additionally, the chemical profile of GMOC was elucidated using LC/MS. Candidate compounds targeting target proteins were screened using in silico analysis, and an in vitro experiment was used to preliminarily verify the results.<br><br>RESULTS: GMOC mitigated lung inflammation, mucus hypersecretion, and airway hyperresponsiveness (AHR) in asthmatic mice. It modulated the lung and gut microbiota and increased the levels of SCFAs in the colon, resulting in a reduction in inflammatory responses. In addition, GMOC downregulated transient receptor potential (TRP) channels and key proteins in the PI3K/AKT pathway in the lung and colon. The communication between TRPs and the PI3K/AKT pathway was further investigated in vitro using honokiol, the main compound in GMOC. Further, GMOC upregulated the expression of junction proteins in the lungs and colon to protect the epithelial barrier.<br><br>CONCLUSION: Crosstalk between organs (lung-gut-microbiota) and proteins (TRPs, junction proteins, and proteins in the PI3K/AKT pathway) contributes to the anti-inflammatory activities of GMOC in asthmatic mice.},
}
@article {pmid40554148,
year = {2025},
author = {Xiang, J and Zhou, Z and Liu, Z and Ren, C and Xu, Y},
title = {Constructing simplified microbial consortia that couple lactic acid and ethanol utilization to highly produce caproic acid from liquor-making wastewater.},
journal = {Water research},
volume = {284},
number = {},
pages = {123973},
doi = {10.1016/j.watres.2025.123973},
pmid = {40554148},
issn = {1879-2448},
abstract = {Converting biodegradable carbon in wastewater into medium-chain fatty acids (MCFAs) through stable microbiota is highly attractive. In this study, we utilized a top-down approach for constructing MCFA-producing microbial consortia. Specifically, an enrichment and plating-screening strategy employing lactic acid and ethanol as selective carbon sources was applied to isolate simplified caproic acid-producing microbial consortia from liquor-making pit mud. The representative microbial consortium SimpCom3 demonstrated high level of caproic acid production (14.62 ± 0.48 g/L) in a semi-synthetic medium, significantly outperforming consortium SimpCom1 (5.96 ± 0.11 g/L) and consortium SimpCom2 (9.63 ± 0.16 g/L). This performance of microbial consortium SimpCom3 was attributed to its ability to co-utilize lactic acid and ethanol, produce fewer odd-chain fatty acids byproducts, and maintain pH self-regulation between 6.45 and 8.29. Metagenomic analyses revealed the dominance of Clostridium kluyveri (30.69 %-50.46 %), C. butyricum (6.71 %-13.98 %) and C. tyrobutyricum (37.11 %-58.07 %) in consortium SimpCom3, which synergistically converted lactic acid and ethanol to caproic acid via reverse β-oxidation. Stable performance over 56 days of cyclic-batch fermentation processes confirmed the robustness of consortium SimpCom3. When applying consortium SimpCom3 to unsterilized liquor-making wastewater in a fermenter with a fed-batch approach, 22.13 g/L caproic acid was produced with 66.38 % selectivity, and microbial dynamics analysis demonstrated the consortium's high adaptability to real wastewater. Metabolic analysis based on high-quality assembly metagenomes (HQ-MAGs) revealed a novel cooperative metabolism: cross-feeding between Clostridium kluyveri (which utilizes ethanol and produces caproic acid) and lactate-utilizing butyrate producers maintained consortium stability and enhanced caproic acid production. Crucially, the decarboxylation of lactic acid counteracted acidification caused by ethanol-driven caproic acid synthesis, enabling self-regulated pH stability within the simplified microbiome system. Together, this study presents a simplified microbial consortium construction method for caproic acid production from liquor-making wastewater, overcoming the limitations of synthetic co-cultures and enhancing the viability of chain-elongation biorefineries in wastewater treatment.},
}
@article {pmid40554105,
year = {2025},
author = {Yang, SI and Im, H and Kim, Y and Kim, HB and Kim, JH and Yeom, J and Yoo, HJ and Kim, MJ and Seong, HJ and Oh, HY and Park, YJ and Kang, MJ and Lee, SH and Kim, HC and Kwon, SO and Lee, KS and Shin, YJ and Yoon, J and Choi, EJ and Shin, YH and Suh, DI and Park, JS and Kim, KW and Ahn, K and Kim, J and Hong, SJ},
title = {Exposome study for allergic diseases in children: Rationale and design of ECHO-COCOA study.},
journal = {Ecotoxicology and environmental safety},
volume = {302},
number = {},
pages = {118533},
doi = {10.1016/j.ecoenv.2025.118533},
pmid = {40554105},
issn = {1090-2414},
abstract = {BACKGROUND: Comprehensive consideration of the totality of environmental exposures and the resulting endogenous responses plays a crucial role in assessing the effect of early-life exposure on child health.<br><br>OBJECTIVES: The Exposome and Child Health with Omics-COhort for Childhood Origin of Asthma and allergic diseases (ECHO-COCOA) study was conducted based on the COCOA birth cohort, a general population-based cohort study that aimed to evaluate multi-omics signatures of environmental exposures and their effect on childhood allergic diseases, obesity and neurodevelopment in Korea.<br><br>METHODS: In total, 156 chemical pollutants and multi-omics profiles (methylome, genome, gut microbiome, transcriptome, metabolome, proteome, and multiplex cytokine assay) were investigated in 481 mother-child pairs. Our previous studies using omics analysis revealed the mechanisms of childhood allergic diseases. Studies on the complex interactions between early-life environmental exposures, omics, and various endotypes of childhood allergic diseases using an integrative multi-omics approach are underway. The ECHO-COCOA study will evolve further in the future by increasing its sample size, using advanced exposure measurement methods, integrating different omics technologies, and developing new statistical methods. Collaboration and integration with other birth cohort studies or external validation will aid in advancing the ECHO-COCOA study.<br><br>CONCLUSIONS: The findings of this study may enable the development of precision medicine and prevention of allergic diseases, obesity, and neurodevelopment based on harmful exposures, especially during critical periods of life.},
}
@article {pmid40553934,
year = {2025},
author = {Hazani, R and Weller, A and Turjeman, S and Sharon, E and Saleev, N and Moadi, L and Elliott, E and Bartal, IB and Koren, O},
title = {The social microbiome: Eubacterium links gut microbiota to prosocial behavior in stressed and naïve rats, a gut-brain axis study.},
journal = {Brain, behavior, and immunity},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.bbi.2025.06.023},
pmid = {40553934},
issn = {1090-2139},
abstract = {BACKGROUND: Prosocial behavior is associated with positive health outcomes, but the underlying biological mechanisms remain unclear, especially regarding the role of the gut microbiome.<br><br>RESULTS: We used the Helping Behavior Test to assess prosocial tendencies in rats and compared gut microbiome profiles between prosocial and non-social individuals across two experiments. In the first, we linked nucleus accumbens mRNA expression to microbiome composition in na&#xef;ve rats. Prosocial behavior was associated with enriched Eubacterium species and genes tied to immune and neurotransmitter functions. An in vitro follow-up tested effects of additives on Eubacterium ventriosum. In the second experiment, we studied how early life stress (maternal separation) influenced prosocial behavior and the microbiome. Microbiome differences aligned with social behavior. Different stressors led to distinct microbiome profiles, especially among non-social rats, with variations in Bacillota and Bacteroidota abundance.<br><br>CONCLUSIONS: Overall, these detailed analyses provide insights into the behavioral, molecular, and microbial bases of prosocial behavior, highlighting the complex relationships between prosocial behavior, the gut-brain-microbiota axis, and early life experiences.},
}
@article {pmid40553933,
year = {2025},
author = {Kaufhold, CJ and Mani, KK and Akbari, Z and Sohrabji, F},
title = {Sex differences in neurological disorders: Insights from ischemic stroke, Parkinson's disease, and multiple sclerosis.},
journal = {Brain, behavior, and immunity},
volume = {129},
number = {},
pages = {335-347},
doi = {10.1016/j.bbi.2025.06.026},
pmid = {40553933},
issn = {1090-2139},
abstract = {Ischemic stroke, Parkinson's disease (PD), and multiple sclerosis (MS), are neurodegenerative disorders that exhibit significant sex differences in pathophysiology, clinical manifestations, and outcomes. Women are more likely to experience strokes in older age, with estrogen playing dual protective/detrimental roles depending on reproductive age. In PD, men show earlier onset and steadier decline, while women exhibit a protective estrogen-driven advantage and distinct gut-brain axis interactions. MS disproportionately affects women (3:1 ratio), particularly during reproductive years, with sex hormones and X-linked genes modulating autoimmune demyelination. This review synthesizes sex-specific mechanisms across these diseases, emphasizing immune dysregulation, hormonal influences, and emerging roles of the gut microbiome. Key modifiers such as epigenetic factors, microbiome composition, and sex chromosome interactions are discussed to inform personalized therapeutic strategies.},
}
@article {pmid40553921,
year = {2025},
author = {Liu, C and Yin, Z and Liu, X and Wang, X and Luo, J and Zhang, Z and Zhou, Y},
title = {Integrative transcriptomics and microbiomicsto exploring the mechanism of Lonicerae japonicae Flos-alleviated alcoholic liver disease.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {107817},
doi = {10.1016/j.micpath.2025.107817},
pmid = {40553921},
issn = {1096-1208},
abstract = {Lonicerae japonicae Flos (LJF) is a well-known medicinal and food homologous (MFH) plant used for the prevention and treatment of liver diseases. Our preliminary study indicated that LJF can intervene in alcoholic liver injury (ALI); however, the relationship between genes and gut microbiota in preventing ALI is less clear in the context of LJF. Therefore, we aimed to elucidate the effects of LJF on inflammation and gut microbiota to prevent ALI using multi-omics analysis. Based on the RNA-Seq, we find that 1689 genes showed differential expression in the LJF group compared to model group. These genes are enriched with functions related to immune response, inflammation, and lipometabolism, such as PPAR signaling pathway, NF-κB signaling pathway, and so on. RNA-seq results showed that LJF may protect the liver from injuries through the PPAR/NF-κB pathway. Interestingly, LJF changed the gut microbiota and composition in ALI rat based on α-diversity and β-diversity, and enriched the Akkermansia, Bifidobacteriaceae, Bacteroides, Blautia, Romboutsia by using 16S rRNA gene sequencing. An integrative analysis revealed that the function of the gut microbiome in ALI is significantly associated with the PPAR signaling pathway and the NF-κB signaling pathway. These findings suggest that LJF exerts a hepatoprotective effect by alleviating inflammation, enhancing antioxidant capacity, and restoring the balance of the gut microbiota.},
}
@article {pmid40553881,
year = {2025},
author = {Paillé, V},
title = {Boosting Fertility Through Tryptophan: Linking Diet, Hormones, and the Gut Microbiome.},
journal = {The Journal of nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tjnut.2025.06.005},
pmid = {40553881},
issn = {1541-6100},
}
@article {pmid40553766,
year = {2025},
author = {Carrillo, MP and Vila-Costa, M and Barata, C},
title = {Micro-Bioplastic Impact on Gut Microbiome, Cephalic transcription and Cognitive Function in the aquatic invertebrate Daphnia magna.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {126690},
doi = {10.1016/j.envpol.2025.126690},
pmid = {40553766},
issn = {1873-6424},
abstract = {The role of the gut microbiome-brain axis on contaminant effects in invertebrates is limited by our poor knowledge of gut microbiome neurological regulatory pathways. This study investigates the influence of microplastics on the gut microbiome composition and assess subsequent alterations in the cephalic transcriptome, feeding patterns, and overall behaviour of the organism. D. magna individuals were exposed to low and high levels of bioplastic particles and kaolin natural particles and under starving conditions. Feeding and behavioral effects were assessed using previously well-established assays. Changes in gut microbiome composition, cephalic transcription and their functional interpretation were studied by 16S rRNA gene sequencing and cephalic D magna RNA high-throughput sequencing, respectively, and using appropriate bioinformatic pipelines. Only exposures to high concentrations of bioplastic microparticles inhibited feeding and impacted behavioural responses in D. magna, resembling effects observed under starvation. Microbiome analysis revealed shifts in taxonomic composition and functional profiles across the tested microplastic concentrations, which become more notable at higher ones. Functional changes in the gut microbiome indicated that bioplastics at high concentrations altered to a greater extent short-chain fatty acid biosynthesis and tryptophan and L-glutamate metabolism pathways than at low concentrations. Transcriptomic analyses revealed that microplastics up-regulated neurological pathways, cell turnover, and differentiation. In summary exposure to microplastics resulted in gut dysbiosis and increased biosynthesis of short-chain fatty acid signalling pathways in the gut, altered neurological pathways in the cephalic transcriptome and disrupted behavioural responses, altogether supporting the role of the microbiota-gut-brain crosstalk on neurological disorders.},
}
@article {pmid40553763,
year = {2025},
author = {Villegas, V and Rajarajan, A and Funke, E and Susan, M and Sparmann, S and Perez, JPH and Schupp, B and Wolinska, J},
title = {Nanoplastics diversify and reshape Daphnia microbiomes in parasite-infected and uninfected hosts.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {126698},
doi = {10.1016/j.envpol.2025.126698},
pmid = {40553763},
issn = {1873-6424},
abstract = {Nanoplastics (NPs) are emerging contaminants of concern that may interact with natural biotic stressors (such as parasites) to disrupt host-associated microbiomes, which play a crucial role in the health and ecological dynamics of aquatic animals. Here, we investigate the effects of polystyrene NP beads and parasite infection on the microbiome diversity and composition of the model plankton organism Daphnia magna. We exposed D. magna to two NP sizes (50 nm and 100 nm) at two concentrations (1 mg L[-1] and 5 mg L[-1]), both with and without infection by the yeast parasite Metschnikowia bicuspidata and sequenced the microbiomes of gut and body tissues using 16S rRNA gene sequencing. High concentrations of 50 nm NPs significantly increased bacterial richness in both gut and body tissue, with shifts exceeding those induced by parasite infection. In the gut, the relative abundances of Burkholderiales and Chitinophagales decreased, while Caulobacterales, Rhizobiales, and Salinisphaerales increased. In body tissues, Chitinophagales declined, whereas Burkholderiales, Caulobacterales, Rhizobiales, and Salinisphaerales were enriched. NP size, concentration and interaction with infection, significantly influenced gut and body microbiome alpha diversity. Bray-Curtis dissimilarity analysis confirmed that 50 nm NPs drove distinct shifts in bacterial community composition, independent of parasite infection. Overall, NP-size and concentration had a stronger influence on the Daphnia microbiome than parasite infection. Given the critical roles of the Daphnia microbiome in nutritional support and stress tolerance, our findings highlight the potential ecological impacts of NPs on aquatic ecosystems.},
}
@article {pmid40553754,
year = {2025},
author = {Karska, J and Skonieczna-Żydecka, K and Jakubiak, N and Czarnecka, W and Misiak, B},
title = {Short-chain fatty acids in mood and schizophrenia spectrum disorders: Evidence in the field and translational perspectives.},
journal = {Progress in neuro-psychopharmacology &amp; biological psychiatry},
volume = {140},
number = {},
pages = {111430},
doi = {10.1016/j.pnpbp.2025.111430},
pmid = {40553754},
issn = {1878-4216},
abstract = {The etiology of mood and schizophrenia spectrum disorders remains largely unknown. In recent years, several studies have focused on the role of the microbiome-gut-brain-axis (MGBA) in its etiology, providing several novel insights. The communication within MGBA involves various pathways leading through the vagus nerve and the bloodstream mediators. The latter are represented by short-chain fatty acids (SCFAs), produced by gut microbiota from dietary fiber. To date, several physiological and pathophysiological roles in the periphery and the central nervous system for SCFAs have been suggested. Studies investigating gut microbiota have consistently reported a decreased abundance of bacteria-producing SCFAs in people with mood and schizophrenia spectrum disorders. Yet, studies investigating faecal and blood levels of SCFAs have provided mixed findings. The present article provides a narrative review of studies examining the physiological roles of SCFAs, along with animal model and human studies addressing the involvement of SCFAs in mood and schizophrenia spectrum disorders, formulates future directions and provides translational perspectives.},
}
@article {pmid40553742,
year = {2025},
author = {Frutkoff, YA and Plotkin, L and Pollak, D and Livovsky, J and Focht, G and Lev-Tzion, R and Ledder, O and Assa, A and Yogev, D and Orlanski-Meyer, E and Broide, E and Kierkuś, J and Kang, B and Weiss, B and Aloi, M and Schwerd, T and Shouval, DS and Bramuzzo, M and Griffiths, AM and Yassour, M and Turner, D},
title = {Whole food diet induces remission in children and young adults with mild-moderate Crohn's disease and is more tolerable than exclusive enteral nutrition: a randomized controlled trial.},
journal = {Gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1053/j.gastro.2025.06.011},
pmid = {40553742},
issn = {1528-0012},
abstract = {BACKGROUND: Tasty&amp;Healthy (T&amp;H) is a whole-food diet for Crohn's disease (CD), which excludes processed food, gluten, red meat, and dairy, without requiring formula or mandatory ingredients. TASTI-MM was a clinician-blinded, randomized-controlled trial comparing tolerability and effectiveness of T&amp;H vs. exclusive enteral nutrition (EEN).<br><br>METHODS: Patients with biologic-naive mild-moderate CD aged 6-25 years were randomized to either T&amp;H or EEN for 8 weeks, receiving weekly dietary support. Tolerability was evaluated by weekly interviews, questionnaires and intake diaries. Other outcomes included symptomatic remission, Mucosal-Inflammation Non-Invasive (MINI) index, calprotectin, C-reactive protein (CRP) and erythrocyte sedimentation rate (ESR). Fecal microbiome was analyzed by metagenomics at baseline, week-4 and week-8. Data were analyzed by the intention-to-treat approach unless specified otherwise.<br><br>RESULTS: Among 83 included patients (41 T&amp;H, 42 EEN; mean age 14.5&#xb1;3.7 years), 88% tolerated T&amp;H vs. 52% for EEN (aOR 7.7 [95%CI 2.4-25]; p<0.001). Calprotectin, CRP and ESR decreased significantly in both groups, with no between-group differences. Symptomatic remission was achieved in 56% of T&amp;H group vs. 38% of the EEN group (aOR 2.5 [0.98-6.3], p=0.1; per-protocol: 67% vs. 76%; p=0.47). Calprotectin <250&#x3bc;g/g was achieved in 34% vs. 33% (aOR 0.97 [0.37-2.6], p=0.84) and MINI<8 in 44% vs. 31% (aOR 1.8 [0.7-4.5]; p=0.33). Microbiome &#x3b1;-diversity improved in the T&amp;H arm and declined in the EEN arm, showing superior species richness at both week-4 and week-8. Species associated with bowel inflammation, such as Ruminococcus gnavus, decreased in T&amp;H and increased in EEN (q<0.001).<br><br>CONCLUSIONS: T&amp;H demonstrated better tolerability than EEN for inducing remission in mild-to-moderate CD, while positively affecting the microbiome (TASTI-MM, NCT#04239248).},
}
@article {pmid40553443,
year = {2025},
author = {Wang, T and Xu, Y and Li, S and Du, R and Shi, J and Jiang, C and Wang, R and Zhu, Y},
title = {Novel Small-Molecule miR-124 Inducer Acts as "a Physiological Brake" of Inflammation in Ulcerative Colitis by Targeting the PIK3R2/PI3K/Akt Axis.},
journal = {Journal of medicinal chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jmedchem.5c01398},
pmid = {40553443},
issn = {1520-4804},
abstract = {Ulcerative colitis (UC), a chronic inflammatory bowel disease with limited therapeutic options, necessitates novel treatments targeting its complex pathophysiology. This study identified FHND5032, a novel small-molecule miR-124 inducer, as a potent therapeutic candidate for UC. We found that FHND5032 significantly upregulated miR-124 expression in macrophages, surpassing the clinical-stage comparator ABX464 in vitro and in vivo. Mechanistically, miR-124-5p directly targeted PIK3R2, suppressing the PI3K/Akt pathway and decreasing proinflammatory cytokines while promoting M2 macrophage polarization. In dextran sodium sulfate-induced mouse colitis, FHND5032 markedly reduced the disease activity index, restored colon length, preserved mucosal architecture, and repaired intestinal barrier integrity. Additionally, FHND5032 reversed gut dysbiosis by reducing Proteobacteria and enriching beneficial Firmicutes, outperforming ABX464 in microbiome modulation. Safety assessments confirmed no organ toxicity or biochemical abnormalities. Collectively, FHND5032 exerted multifaceted anticolitis effects by targeting the PIK3R2/PI3K/Akt axis, restoring immune homeostasis, and modulating gut microbiota, positioning it as a promising therapeutic agent for UC.},
}
@article {pmid40553348,
year = {2025},
author = {Ramakrishnan, R and Washington, A and Suveena, S and Rani, JR and Oommen, OV},
title = {From DNA to Big Data: NGS Technologies and Their Applications.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2952},
number = {},
pages = {459-482},
pmid = {40553348},
issn = {1940-6029},
mesh = {*High-Throughput Nucleotide Sequencing/methods ; *Big Data ; Humans ; *COVID-19/virology/epidemiology/genetics ; Genomics/methods ; SARS-CoV-2 ; Computational Biology/methods ; Sequence Analysis, DNA/methods ; *DNA/genetics ; },
abstract = {The last decade has witnessed an explosion in NGS data, which was the gift of advances in NGS technology as well as computing power. Along with AI, NGS is revolutionizing healthcare research. In this chapter, we briefly discuss the contribution of NGS in dealing with the COVID-19 pandemic and mention its application across various fields like oncology, agriculture, archaeogenetics, and space biology, followed by a historical perspective on sequencing, the evolution of NGS technologies and those currently in use. The chapter further outlines various NGS methods and workflows, detailing the key stages and the tools commonly employed for efficient analysis. Additionally, we highlight the surge and complexity of NGS data generated by genomics, transcriptomics, and microbiome studies, challenges and discusses their clinical applications. Toward the end, we explore the future directions of NGS. Given the rapid increase in data volume and complexity, there is an urgent need for efficient big data technologies, state-of-the-art tools, and techniques to manage, analyze, and derive actionable insights from these vast datasets, addressing the demands of the present-day scientific landscape.},
}
@article {pmid40553325,
year = {2025},
author = {Mukhopadhyay, S and Ulaganathan, N and Dumpuri, P and Aich, P},
title = {Integrative AI-Based Approaches to Connect the Multiome to Use Microbiome-Metabolome Interactive Outcome as Precision Medicine.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2952},
number = {},
pages = {15-37},
pmid = {40553325},
issn = {1940-6029},
mesh = {Humans ; *Precision Medicine/methods ; *Metabolomics/methods ; *Metabolome ; Metagenomics/methods ; *Microbiota ; *Artificial Intelligence ; Computational Biology/methods ; Gastrointestinal Microbiome ; },
abstract = {In the era of Genome-Wide Association Studies (GWAS), biologists have unprecedented access to vast datasets, mirrored in the wealth of information from various omics studies, including genomics, transcriptomics, proteomics, metabolomics, and metagenomics. Integrating diverse data sources has emerged as crucial in unravelling the intricacies of biological processes. This chapter delves into our method for merging various omics methodologies, emphasizing metabolomics and metagenomics data. A powerful strategy addresses data processing challenges and opens new avenues for personalized microbiome-based interventions. The combined analysis of host and microbial metabolomics and metagenomics data has significantly advanced our understanding in diagnosing and treating conditions such as inflammatory bowel disease and irritable bowel syndrome. Metabolic signatures in biological fluids and their microbial counterparts serve as indicators, differentiating health from disease. The sheer volume of data demands sophisticated automated tools for processing and interpretation. Recognizing this need, integrating artificial intelligence (AI) and data science has become increasingly prominent. In this chapter, we combine microbiome and metabolome analyses through publicly available models to elucidate the correlations between microbial and metabolic profiles. By harnessing AI models across various omics data sources, this chapter bridges the gap between data acquisition and clinical applications, paving the way for personalized interventions and optimizing individual health.},
}
@article {pmid40552988,
year = {2025},
author = {Park, JM and Beckman, I and Delaney, CL},
title = {Narrative review of the association between gut microbiota and peripheral artery disease.},
journal = {Vascular medicine (London, England)},
volume = {},
number = {},
pages = {1358863X251346062},
doi = {10.1177/1358863X251346062},
pmid = {40552988},
issn = {1477-0377},
abstract = {It has been posited that the inflammatory process seen in atherosclerosis is underpinned by gut dysbiosis. Dysbiosis refers to alterations in the function, composition, and diversity of the human gut microbiota, all of which are influenced by endogenous and exogenous stimuli. Currently there is limited literature describing the association between gut microbiota and peripheral artery disease (PAD). This review summarizes the evidence surrounding the role of gut microbiota in the initiation of atherosclerosis (through direct infection of atherosclerotic plaque or systemic immune response to bacterial products and metabolites) and how dysbiosis may influence the various treatment modalities for PAD, including medical therapy (pharmacotherapy, lifestyle changes, and supervised exercise training) and surgery (endovascular and open revascularization). In particular, the role of short chain fatty acids (SCFAs), the effects of exercise on SCFA-producing and lactic acid bacteria (LAB) and, consequently, the lack of targeted research into dietary interventions and supplementation are highlighted in this review. This review highlights the potential for gut microbiota as not only a therapeutic target in patients with PAD, but also as a diagnostic and screening tool. It is imperative that the focus of future research is on the potential for personalized treatment which targets the gut microbiota (such as synbiotics, postbiotics, nicotinamide adenine dinucleotide (NAD) supplementation, selective antibiotics, resistance exercise, senolytics, and fecal microbial transplantation [FMT]) to be utilized as adjuncts to already existing treatment options for PAD. This review also highlights the potential role of biobanks and analysis of atherosclerotic plaques in further advancing knowledge and research in this area.},
}
@article {pmid40552978,
year = {2025},
author = {Oncu, AD and Ozgur, A and Ulgen, KO},
title = {Alterations in Gut Microbiota-Brain Axis in Major Depressive Disorder as Identified by Machine Learning.},
journal = {Omics : a journal of integrative biology},
volume = {},
number = {},
pages = {},
doi = {10.1089/omi.2025.0084},
pmid = {40552978},
issn = {1557-8100},
abstract = {Major depressive disorder (MDD) is a complex mental health condition whose causes may extend beyond purely biological explanations and are increasingly understood within wider ecological and social frameworks. Emerging research on the human gut-brain axis with the help of statistical and artificial intelligence tools aims to elucidate the links between the gut microbiota, diet, environment, and MDD. In this study, we analyzed data from the American Gut Project (AGP), including 361 control and 23 MDD samples, to find potential biomarkers associated with MDD. While alpha and beta diversity analyses revealed no significant differences except for age, multiple differential abundance tools and machine learning (ML) models (Random Forest and XGBoost), whose results were analyzed using Shapley Additive Explanations values, consistently detected a decrease in Bifidobacterium adolescentis and increases in Odoribacter, Ruminococcus, and Adlercreutzia among MDD samples. These four organisms influence inflammation, neurotransmitter balance, gut permeability, and other pathways associated with depression and thus can be recognized as potential biomarkers for MDD. This study highlights the promise of ML to decode the gut-brain axis as a first step in biomarker discovery, thus providing new possibilities for a personalized treatment approach and an improvement in diagnostic tools for MDD.},
}
@article {pmid40552763,
year = {2025},
author = {Claypool, J and Lindved, G and Myers, PN and Ward, T and Nielsen, HB and Blount, KF},
title = {Microbiome compositional changes and clonal engraftment in a phase 3 trial of fecal microbiota, live-jslm for recurrent Clostridioides difficile infection.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2520412},
doi = {10.1080/19490976.2025.2520412},
pmid = {40552763},
issn = {1949-0984},
mesh = {Humans ; *Clostridium Infections/therapy/microbiology ; *Fecal Microbiota Transplantation ; *Gastrointestinal Microbiome ; *Feces/microbiology ; Male ; *Clostridioides difficile/physiology ; Female ; Middle Aged ; *Bacteria/classification/genetics/isolation &amp; purification ; Adult ; Recurrence ; Aged ; },
abstract = {Live microbiota therapies have shown promise in many gastrointestinal diseases, including in the prevention of recurrent Clostridioides difficile infections (rCDI); however, frameworks for their pharmacokinetic and pharmacodynamic analysis are not fully established. Fecal microbiota, live-jslm (RBL) is the first microbiota-based product approved by the US Food and Drug Administration for the prevention of rCDI and was superior to placebo in the PUNCH™ CD3 phase 3 clinical trial (NCT03244644). In this analysis, deep shotgun metagenomic sequencing was used to assess changes in gut microbiome compositions of participants and engraftment of bacterial clonal populations (i.e. strains) from RBL to recipients. Among RBL responders, gut microbiota shifted toward compositions that resembled healthy donors as early as 1 week after RBL administration; the resulting microbiota compositions included clonal populations that engrafted from RBL to recipients. Engraftment was higher in RBL responders compared with non-responders, and many clonally engrafted populations persisted for ≥ 6 months. Bacteroidia species were among the most effectively engrafted species from RBL. This study utilizes data from a large clinical trial to establish a method with high specificity for exploring clonal engraftment from microbiota-based treatments to facilitate future pharmacokinetic and pharmacodynamic analyses.Clinicaltrials Registration: NCT03244644.},
}
@article {pmid40552387,
year = {2025},
author = {Ozbek, DA and Koc, NS and İnal, N and Kablan, SE and Kaygusuz, Y and Karahan, S and Uyaroğlu, OA and Yildirim, T and Ergunay, K and Nemutlu, E and Akyon, Y and Altun, B},
title = {Interplay of gut microbiome and metabolome in various blood pressure phenotypes based on ambulatory BP monitoring reveal new insights in nondipper patients.},
journal = {Journal of hypertension},
volume = {},
number = {},
pages = {},
doi = {10.1097/HJH.0000000000004086},
pmid = {40552387},
issn = {1473-5598},
abstract = {OBJECTIVE: Accumulating evidence has shown an association between stool microbiome and hypertension. However, gut microbiome and metabolome of nondipping blood pressure (BP), high BP variability and morning BP surge have not been extensively studied. Here, we aimed to investigate the interplay between the gut microbiome, metabolome and 24-h urine sodium (Na) levels in different BP phenotypes.<br><br>METHODS: This study included 45 newly diagnosed hypertensive, and healthy participants. Ambulatory BP monitoring was performed in all patients to confirm the diagnosis and determine corresponding BP phenotypes. Gut microbiome and metabolome were determined using 16S ribosomal RNA sequencing and gas chromatography-mass spectrometry, respectively.<br><br>RESULTS: Firmicutes/Bacteroides ratio was higher in nondipper than dipper group (P&#x200a;=&#x200a;0.01). Comparative analyses showed that 23 species, 21 genera and 9 families were significantly differentiated in different BP phenotype subgroups. Functional metabolomic enrichment analysis of nondipper patients showed enrichment of catecholamine biosynthesis and tyrosine metabolism due to noradrenaline, dopamine, 3,4-dihydroxyphenylglycol and 3,4-dihydroxyphenylacetic acid. Spearman analyses between significantly enriched metabolites and organized taxonomic units (OTUs) in nondipper patients showed correlations between 3,4-dihydroxyphenylglycol and Parabacteroides diastonis (rho&#x200a;=&#x200a;-0.33, P&#x200a;=&#x200a;0.03) and dopamine with Chryseobacterium genus (rho&#x200a;=&#x200a;0.71, P&#x200a;=&#x200a;0.02). Enterococcus, Lachnobacterium, Odoribacter and Pseudomonas were positively, whereas Lactobacillus and Clostridium were negatively correlated with urine Na levels.<br><br>CONCLUSION: We revealed novel relationships among gut microbiome, metabolome and sodium intake in different BP phenotypes. Enrichment of catecholamine synthesis and correlations between OTUs and metabolites in nondipper patients indicated that sympathetic system activation via gut-brain axis could play a role in the nondipping BP profile.},
}
@article {pmid40552317,
year = {2025},
author = {Jafari, E and Azizian, R and Tabasi, M and Banakar, M and Bagheri Lankarani, K},
title = {Human Gut Bacteriophageome: Insights Into Drug Resistance Mechanisms in Tuberculosis.},
journal = {Interdisciplinary perspectives on infectious diseases},
volume = {2025},
number = {},
pages = {8811027},
pmid = {40552317},
issn = {1687-708X},
abstract = {Tuberculosis (TB), caused by Mycobacterium tuberculosis, remains a major global health burden. The emergence of drug-resistant strains presents a critical challenge in TB management. The recent research has explored the interaction between TB and the human gut bacteriophage community (phageome). The gut phageome plays a crucial role in regulating microbial diversity and functionality, and its composition and function have been linked to various health conditions. Examining the gut phageome through metagenomic analysis provides insights into its composition, role in health, and interactions with the host immune system. Exploring the interaction between the gut phageome and M. tuberculosis may reveal how phages affect the bacterium's pathogenicity, survival, and mechanisms of drug resistance. Understanding the gut phageome's impact on TB drug resistance could inform novel therapeutic strategies, such as phage therapy, and highlight the importance of microbiome-based interventions in combating drug-resistant TB strains. This review explores the role of the gut phageome in influencing drug resistance in TB, focusing on interaction mechanisms and potential therapeutic implications, synthesizing current research findings, and identifying knowledge gaps in this emerging field. This review also synthesizes the current evidence on the gut phageome's role in TB drug resistance, focusing on phage-mediated horizontal gene transfer (e.g., rpoB, katG), immune modulation, and preclinical efficacy of mycobacteriophage therapies. Key findings highlight phage cocktails (e.g., DS6A, D29 LysB) as promising adjuncts to antibiotics, reducing M. tuberculosis burden in murine models. These insights advocate for phage therapy as a complementary strategy against drug-resistant TB, urging clinical validation to bridge the existing knowledge gaps.},
}
@article {pmid40552289,
year = {2025},
author = {Xu, DT and Chen, Q and Yang, JY and Yan, GR and Zhang, LL and Liu, XJ and Wang, PR and Liu, J and Wang, XL},
title = {A noteworthy issue: microbiome data variation depending on sampling methods in skin microecology studies in acne vulgaris patients.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1566786},
pmid = {40552289},
issn = {1664-3224},
mesh = {Humans ; *Acne Vulgaris/microbiology/diagnosis ; *Skin/microbiology/pathology ; *Microbiota ; Female ; Male ; *Specimen Handling/methods ; Young Adult ; Adult ; *Bacteria/genetics/classification/isolation &amp; purification ; Biopsy/methods ; },
abstract = {INTRODUCTION: Skin microecology significantly affects health, with the microbiome being a complex community of microorganisms. Different niche preferences of microorganisms raise concerns about the adequacy of common sampling methods like swabbing and cyanoacrylate biopsy. In this study, we aim to contribute to a more suitable sampling strategy in acne microbiome studies.<br><br>METHODS: This study involved ten mild to moderate acne patients. Three sampling methods were used: swab sampling (S1), modified standardized skin surface biopsy (S2), and individual comedo extraction (S3). DNA was extracted and sequenced to analyze the microbiome data.<br><br>RESULTS: There were significant differences in the bacterial and fungal microbiome data obtained by the three different sampling methods. Staphylococcus spp. (significantly higher in S3, P<0.05) and Malassezia spp. (higher in S3, P<0.05) were most affected by sampling methods. Bacterial phyla Proteobacteria (abundant in S1) and Bacteroidota (dominant in S2) also showed method-dependent variations.<br><br>CONCLUSION: The choice of sampling method significantly impacts microbiome data, highlighting the need for accurate sampling to understand the relationship between the skin microbiome and acne. Standardizing sampling methods in future studies is essential for advancing skin microecology research.<br><br>CLINICAL TRIAL REGISTRATION: http://www.chictr.org.cn, identifier ChiCTR-CPC-17012398.},
}
@article {pmid40552287,
year = {2025},
author = {Dong, J and Lv, Y and Zhao, C and Shi, Y and Tang, R and He, L and Fan, R and Jia, X},
title = {Extraction of anthocyanins from purple sweet potato: evaluation of anti-inflammatory effects in a rheumatoid arthritis animal model, mechanistic studies on inflammatory cells, and development of exosome-based delivery for enhanced targeting.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1559874},
pmid = {40552287},
issn = {1664-3224},
mesh = {Animals ; *Anthocyanins/pharmacology/isolation &amp; purification ; *Arthritis, Rheumatoid/drug therapy/immunology/pathology/metabolism ; *Ipomoea batatas/chemistry ; *Exosomes/metabolism ; Rats ; Humans ; *Anti-Inflammatory Agents/pharmacology/isolation &amp; purification ; Disease Models, Animal ; *Arthritis, Experimental/drug therapy/pathology/immunology ; Apoptosis/drug effects ; Male ; Cell Line ; Cytokines/metabolism ; Gastrointestinal Microbiome/drug effects ; },
abstract = {OBJECTIVE: Rheumatoid arthritis (RA) is a chronic autoimmune disease marked by inflammation and joint damage. Anthocyanins, such as those from purple sweet potato are known for their anti-inflammatory effects.<br><br>METHODS: This study evaluated purple sweet potato anthocyanins (PSPA) therapeutic potential in RA using Human RA cells (MH7A) and collagen-induced arthritis (CIA) rat models. Rats were divided into control, CIA model, and three PSPA treatment groups (10, 20, 40 mg/kg) for 14 days. Meanwhile, exosomes were extracted from MH7A cells and loaded with PSPA, then co-incubated with inflammatory cells to observe the targeting capability of the drug-loaded exosomes.<br><br>RESULTS: PSPA significantly reduced joint swelling and structural damage in CIA rats, with the highest dose (40 mg/kg) reducing tissue hyperplasia and inflammatory infiltration. PSPA also altered the gut microbiota, increasing beneficial bacteria like Akkermansia and Lactobacillus. Molecular analysis showed reduced serum levels of inflammatory cytokines TNF-&#x3b1;, IL-1&#x3b2;, and rheumatoid factor (RF). In MH7A cells, PSPA decreased inflammatory cytokines (IL-1&#x3b1;, IL-6, IL-18), inhibited cell proliferation (IC50 = 1.43 &#x3bc;g/mL), and induced apoptosis by modulating Bcl-2, Bax, Caspase-3, and Caspase-9. PSPA also restored the PI3K/AKT signaling pathway, reversing the suppression seen in CIA models, particularly at 40 mg/kg. Flow cytometry and microscopy confirmed dose-dependent apoptosis and cell cycle modulation. Meanwhile the PSPA-loaded exosomes demonstrated a high targeting capability toward inflammatory cells.<br><br>CONCLUSION: These findings indicate that PSPA can alleviate RA symptoms by reducing inflammation, modulating gut microbiota, and promoting apoptosis in synovial fibroblasts, with exosome-encapsulated anthocyanins enhancing its targeting efficiency.},
}
@article {pmid40552147,
year = {2025},
author = {Tang, L and Dong, W and Liu, D and Zhao, C and Chen, J and Wen, Y and Zeng, J and Dong, T and Yang, W},
title = {Gandouling ameliorates Wilson's disease-associated liver fibrosis in mice with associated faecal microbiome and metabolome remodeling.},
journal = {Frontiers in pharmacology},
volume = {16},
number = {},
pages = {1586171},
pmid = {40552147},
issn = {1663-9812},
abstract = {INTRODUCTION: Individuals with Wilson's disease (WD) exhibit liver fibrosis, a basic pathological change that was recently demonstrated to be dynamic and reversible. The gut microbiota markedly influences the occurrence of WD. Gandouling (GDL), a standardized Chinese herbal formula, has demonstrated an anti-fibrotic effect against WD-associated liver fibrosis. We sought to determine whether GDL may prevent liver fibrosis in toxic milk (TX) mice by assessing its ability to regulate gut microbiota, metabolites, and barrier function.<br><br>METHODS: TX male mice aged 6 months were analysed. GDL was administered at varying doses over a 6-week period. The biochemical indexes related to liver function, fibrosis, and inflammation were determined using commercial assay kits. Histological analyses and immunohistochemistry staining, were performed to evaluate the histopathological changes and collagen deposition in mouse liver tissues. Additionally, to detect alterations in the intestinal bacterial composition and metabolites, faecal samples were examined using non-targeted metabolomics and 16S rRNA sequencing.<br><br>RESULTS: The administration of GDL demonstrated anti-fibrotic effects on the liver, decreased serum inflammatory markers, ameliorated liver histopathology, and restored ileal permeability in the model group, as compared to the control group. Furthermore, a medium dosage of GDL treatment significantly rebalance microbiota composition and function and modulated lipid and lipid-like molecule levels.<br><br>DISCUSSION: Modulating intestinal homeostasis is a promising approach for treating liver fibrosis in patients with WD. Therefore, GDL may serve as a useful agent for treating WD-associated liver fibrosis.},
}
@article {pmid40552117,
year = {2025},
author = {Tong, X and Chen, X and Shen, C and Pan, J and Wang, X and Xu, X and Liu, S},
title = {Integrated analysis of microbiome and host transcriptome revealed correlations between tissue microbiota and tumor progression in early-stage papillary thyroid carcinoma.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1571341},
pmid = {40552117},
issn = {2235-2988},
mesh = {Humans ; *Thyroid Cancer, Papillary/microbiology/pathology/genetics ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; Disease Progression ; *Thyroid Neoplasms/microbiology/pathology/genetics ; *Transcriptome ; Tumor Microenvironment/genetics ; Female ; Male ; Bacteria/classification/genetics/isolation &amp; purification ; Middle Aged ; Adult ; },
abstract = {INTRODUCTION: Emerging evidences suggest that microorganisms in the tumor microenvironment play important roles in tumor occurrence and progression. However, the microbial distribution in the papillary thyroid carcinoma (PTC) tissue and its relationship with PTC are unclear.<br><br>METHODS: We performed 16S rRNA amplicon sequencing and RNA-Seq to characterize the tissue microbiome and transcriptome between the tumor and paracancerous tissue, respectively. The association analysis between microbes and host gene expression were conducted to screen the potential microbe-gene/cell interactions.<br><br>RESULTS: We found that the tumor tissues indeed harbored complex microbial communities, which showed significant differences in microbial and functional composition between the tumor and para-cancerous tissues. A set of differential microbial genera were identified to be significantly associated with the clinical factors, such as Planococcus enriched in tumor tissue, Limnobacter in T1a stage and Cutibacterium in N1b stage. 793 differential expressed genes were also identified, which are mainly enriched with functions related to cell-cell communication and extracellular matrix. In terms of the immune cell composition, 8 differential immune cell types were further identified, suggesting a significant immune response in PTC. Finally, association analysis identified 5 pairs of microbe-gene association and 1 pair of microbe-cell with significance, which were all involved in the tumorigenesis and tumor progression via inflammation-related pathways.<br><br>CONCLUSIONS: In addition to characterizing the tissue microbiome and host gene expression in PTC patients, we further explored the roles of microbe-gene/cell interactions in PTC. The results provide candidate biomarkers for exploring the molecular mechanisms of tissue microbiome in tumorigenesis and tumor progression of PTC.},
}
@article {pmid40552099,
year = {2025},
author = {Shah, SAUR and Tang, B and He, D and Ahmad, M and Nabi, G and Wang, C and Kou, Z and Wang, K and Hao, Y},
title = {Seasonal Breeding Alters Fecal Microbiota and Metabolome in the Male Captive Yangtze Finless Porpoise (Neophocaena asiaeorientalis asiaeorientalis).},
journal = {Ecology and evolution},
volume = {15},
number = {6},
pages = {e71611},
pmid = {40552099},
issn = {2045-7758},
abstract = {The Yangtze finless porpoise (YFP) is a critically endangered freshwater cetacean endemic to China. Understanding seasonal breeding patterns is critical for the effective conservation of critically endangered species. The current study was designed to examine the function and taxonomic characteristics of fecal microbiota and their metabolites in male captive YFPs during both nonbreeding (NB) and breeding (B) seasons, analyzing 20 fecal samples using both UHPLC-MS/MS and 16S rRNA gene sequencing approaches. The present study revealed that Firmicutes were increased in the NB season, while Actinobacteria, Proteobacteria, and Fusobacteriota were increased in the B season at the phylum level. At the genus level, Paeniclostridium, Clostridium_sensu_stricto_13, and Mycobacterium were increased in the NB season, while Romboutsia, Plesiomonas, and Cetobacterium were increased in the B season. LEfSe analysis revealed that Staphylococcus, Comamonas, and Tetrasphaera were significantly increased in the B season, while the genus Terrisporobacter was substantially increased in the NB season. The fecal metabolome undergoes significant changes during the B and NB seasons, altering metabolic pathways such as phenylalanine metabolism, protein digestion, taurine and hypotaurine metabolism, lysine degradation, tryptophan biosynthesis, tyrosine metabolism, and bile secretion. Moreover, there was a significant correlation between the fecal metabolome and microbiome in the captive YFPs in the B and NB seasons. This study explores the impact of seasonal reproduction on gut microbes and their metabolites, providing insights into animal seasonal reproductive behavior and providing a theoretical basis for studying gut microbiota and metabolites in cetaceans, both in captivity and in the wild.},
}
@article {pmid40552080,
year = {2025},
author = {Curso-Almeida, P and Subramaniam, M and Costa, MO and Adolphe, JL and Drew, MD and Loewen, ME and Weber, LP},
title = {Effects of feeding Candida utilis-fermented pea starch on overall, metabolic and intestinal health of dogs and cats.},
journal = {Frontiers in veterinary science},
volume = {12},
number = {},
pages = {1542484},
pmid = {40552080},
issn = {2297-1769},
abstract = {Pulse-based pet foods often contain peas or pea starch, which tend to impart a bitter taste. Fermentation increases feed palatability, but also has the potential to improve overall health. Therefore, the current study used the yeast, Candida utilis, to ferment pea starch for use in pet food and assessed health effects, focusing on metabolic and intestinal health in dogs and cats. Whole diets had ~30% starch inclusion of either C. utilis-fermented pea starch, unfermented pea starch, or a control corn diet fed over a 20-day period to beagle dogs and domestic cats. Complete blood count, biochemistry, adipokines, and triglyceride levels were assessed, along with fecal short chain fatty acids, microbial diversity and abundance to measure intestinal health. It was found that pea-based diets (regardless of fermentation) generally resulted in improved metabolic health by both species, indicated by lower plasma triglycerides, cholesterol, and leptin levels compared to the control corn diet. Additionally, the C. utilis-fermented pea starch diet improved dog fecal microbial diversity, while both pea diets increased richness and evenness in the microbial population and a larger Faecalibacterium population compared to dogs fed the corn-based diet. In contrast, cat microbiome could not be quantitatively evaluated due to poor fecal quality. Taken together, inclusion of pea starch improves metabolic and intestinal health after 20 days consumption in dogs, while fermentation of pea starch with C. utilis may provide additional benefit.},
}
@article {pmid40552053,
year = {2025},
author = {Menéndez, E and Brígido, C},
title = {Editorial: Deciphering the root nodule microbiome: implications for legume fitness and stress resilience.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1634838},
pmid = {40552053},
issn = {1664-302X},
}
@article {pmid40552042,
year = {2025},
author = {Mu, YQ and Song, JB and Zhao, M and Ren, P and Liu, HY and Huang, X},
title = {Integrative omics analysis of plant-microbe synergies in petroleum pollution remediation.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e19396},
pmid = {40552042},
issn = {2167-8359},
mesh = {Biodegradation, Environmental ; *Medicago sativa/microbiology/metabolism/genetics ; Metabolomics ; *Petroleum Pollution ; *Petroleum/metabolism ; *Soil Pollutants/metabolism ; Rhizosphere ; RNA, Ribosomal, 16S/genetics ; Soil Microbiology ; Hydrocarbons/metabolism ; Plant Roots/microbiology/metabolism ; Transcriptome ; Multiomics ; },
abstract = {As the petrochemical industry continues to advance, the exacerbation of ecological imbalance and environmental degradation due to petroleum pollution is increasingly pronounced. The synergistic interaction between plants and microorganisms are pivotal in the degradation of petroleum hydrocarbons; however, the underlying degradation mechanisms are not yet fully understood. This study aims to contribute to understanding these mechanisms by employing a multi-omics approach, integrating transcriptomics, 16S rRNA gene sequencing, and metabolomics, to analyze key differential genes, dominant microbial strains, and root-secreted metabolites involved in petroleum hydrocarbon degradation in alfalfa. Our findings revealed that several stress-related genes are upregulated in alfalfa contaminated with petroleum hydrocarbon. Moreover, Pseudomonas, Rhodococcus, and Brevundimonas were identified as dominant species in the rhizosphere microbiome. Metabolomics analysis identified pantothenic acid, malic acid, and ascorbic acid as critical metabolites that enhance hydrocarbon degradation. Application of pantothenic acid in oil-contaminated soil increased the degradation rate by approximately 10% compared to other treatments. These results highlight the potential of alfalfa-based phytoremediation strategies and offer a novel perspective for improving the efficiency of soil decontamination. Further research is needed to validate the scalability of these strategies for practical applications.},
}
@article {pmid40551757,
year = {2025},
author = {Goel, R and Singh, G and Pepine, CJ},
title = {Potential role of gut microbiota in cardiac arrhythmias.},
journal = {American heart journal plus : cardiology research and practice},
volume = {55},
number = {},
pages = {100557},
pmid = {40551757},
issn = {2666-6022},
}
@article {pmid40551742,
year = {2025},
author = {Jiang, Y and Li, Y},
title = {The role of nutrition and gut microbiome in childhood brain development and behavior.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1590172},
pmid = {40551742},
issn = {2296-861X},
abstract = {The intricate relationship between nutrition, the gut microbiome, and brain development has garnered significant attention in recent years, concerning its implications for child behavior and cognitive function. The gut-brain axis mediates this relationship through microbial modulation of inflammation, neuroactive compounds, and blood-brain barrier integrity, particularly during prenatal and early postnatal periods. Healthy dietary patterns such as whole foods, high-fiber foods, and minimally processed foods play a crucial role in shaping the gut microbiota, promoting microbial diversity and overall gut health. As a result, a balanced and diverse microbiome supports healthy brain function and development. Furthermore, disruptions in gut microbiota composition have been linked to various neurodevelopmental disorders in children, including autism spectrum disorder, attention deficit hyperactivity disorder, and anxiety. By integrating findings from animal models, clinical trials, and epidemiological studies, this review summarizes current advances on how early-life nutrition and gut microbiota interaction influence brain development and childhood behaviors. Ultimately, this paper underscores the potential for dietary interventions to promote optimal neurodevelopmental health and address behavioral issues in children.},
}
@article {pmid40551741,
year = {2025},
author = {Gaskell, C and MacDonald, R and Aleem, E and Bendriss, G},
title = {Obesity and cancer: unravelling the microbiome's hidden role.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1602603},
pmid = {40551741},
issn = {2296-861X},
abstract = {Obesity has been implicated as the driving force of many diseases including cancer through multiple biological mechanisms, including gut microbial imbalances, compromised intestinal barrier integrity, persistent low-grade inflammation, and alterations in energy uptake. As lifestyle factors such as diet, physical activity, and sleep are known to influence disease susceptibility, understanding the role of the gut microbiome in these interactions is critical. A deeper understanding of the intricate connections between gut microbiota, obesity, and various cancers could be used to better inform effective strategies for disease prevention and treatment. Investigating the microbiome's influence on tumor progression and systemic metabolic health may be the way forward for novel diagnostic and therapeutic approaches. It is essential to investigate how lifestyle factors are linked to both obesity and cancer, and what role the microbiome is playing. This review synthesizes current research on the mechanistic role of the gut microbiome in obesity and cancer, highlighting its potential role in early detection, prognosis, and its use as a targeted intervention to restore gut eubiosis.},
}
@article {pmid40551738,
year = {2025},
author = {Singh, R and Toumi, M and Salathé, M},
title = {Personalized glucose prediction using in situ data only.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1539118},
pmid = {40551738},
issn = {2296-861X},
abstract = {The worldwide rise in blood glucose levels is a major health concern, as various metabolic diseases become increasingly common. Diet, a modifiable health behaviour, is a primary target for the preventive management of glucose levels. Recent studies have shown that blood glucose responses after meals (post-prandial glucose responses, PPGR) can vary greatly among individuals, even with identical food consumption, and demonstrated accurate PPGR prediction using various features like microbiome data and blood parameters. Our study addresses whether accurate PPGR prediction can be achieved with a limited and easily obtainable set of data collected in real-world, everyday settings. Here, we show that a machine learning algorithm with such real-world data (RWD) collected from a digital cohort with over 1,000 participants can achieve high accuracy in PPGR prediction. Interestingly, we find that the best PPGR prediction model only required glycemic and temporally resolved diet data. This ability to predict PPGR accurately without the need for biological lab analysis offers a path toward highly scalable personalized nutrition and glucose management strategies.},
}
@article {pmid40551557,
year = {2025},
author = {Han, F and Li, W and Duan, N and Hu, X and Yao, N and Yu, G and Qu, J},
title = {Relationship Between Salt Intake and Cardiovascular Disease.},
journal = {Journal of clinical hypertension (Greenwich, Conn.)},
volume = {27},
number = {6},
pages = {e70078},
doi = {10.1111/jch.70078},
pmid = {40551557},
issn = {1751-7176},
mesh = {Humans ; *Cardiovascular Diseases/epidemiology/etiology/prevention &amp; control ; *Sodium Chloride, Dietary/adverse effects ; Blood Pressure/drug effects/physiology ; Gastrointestinal Microbiome ; Risk Factors ; Hypertension/epidemiology ; Heart Disease Risk Factors ; Feeding Behavior/physiology ; },
abstract = {Cardiovascular disease (CVD) is a predominant global health issue, with dietary salt intake recognized as a crucial modifiable risk factor. This review elucidates the multifaceted relationship between salt consumption and CVD, exploring both its direct and indirect effects. While early research emphasized salt's influence on blood pressure, contemporary studies highlight the combined effects of dietary habits and genetic factors on CVD risk. The paper underscores the complex biological mechanisms linking high salt intake to CVD, including its impact on blood pressure, direct cardiovascular effects, immune responses, the role of prostanoids, epigenetic changes, and gut microbiome. Additionally, the review delves into the concept of salt sensitivity and its genetic underpinnings, emphasizing the heightened CVD risk in salt-sensitive individuals. The potential benefits and challenges of salt substitutes are also discussed. Drawing from various study designs, including epidemiological studies and randomized controlled trials, the review provides a comprehensive understanding of the detrimental effects of excessive salt intake on cardiovascular health, emphasizing the need for refined dietary guidelines and targeted interventions.},
}
@article {pmid40551374,
year = {2025},
author = {Gould, AAM and Walsh, NP and Tipton, MJ and Zurawlew, MJ and Tayari, O and House, C and Delves, SK and Robson, SC and Shute, JJ and Watts, JEM and Roberts, AJ and Rawcliffe, AJ and Robinson, MR and Corbett, J},
title = {Faecal microbiome, gastrointestinal integrity, inflammation and thermoregulation in recent exertional heat illness patients and matched controls.},
journal = {Experimental physiology},
volume = {},
number = {},
pages = {},
doi = {10.1113/EP092849},
pmid = {40551374},
issn = {1469-445X},
support = {//Army Recruiting and Initial Training Command/ ; },
abstract = {The gastrointestinal (GI) microbiota and GI barrier integrity are hypothesised to contribute to exertional heat illness (EHI) aetiology. We compared the faecal microbiome, GI barrier integrity, inflammation and thermoregulation of 29 recent (∼4 months) EHI patients (a group with elevated EHI risk) and 29 control individuals without prior EHI history, matched for variables influencing thermoregulation and GI microbiota. Participants completed an exercise heat tolerance assessment (HTA), with faecal microbiome assessed by 16S rRNA gene amplicon sequencing of stool samples and blood biomarkers of GI barrier integrity and inflammation measured pre- and post-HTA. With the exception of the Simpson index (patient = 0.97 ± 0.01 vs. control = 0.98 ± 0.00, P = 0.030), there were no between-groups differences in faecal microbiome composition (α-diversity, β-diversity, relative abundance, differential abundance), GI barrier integrity, inflammation or terminal thermoregulatory indices. Individuals were subsequently classified as heat tolerant (n = 46) or intolerant (n = 12) on the basis of the HTA. Heat intolerant individuals demonstrated lower sudomotor response (intolerant = 0.53 (0.17) vs. tolerant = 0.62 (0.20) L m[-2] h[-1], P = 0.011) despite greater thermoregulatory strain (e.g., terminal Trec: intolerant = 39.20 ± 0.31 vs. tolerant = 38.80 ± 0.31°C, P < 0.001), lower Firmicutes:Bacteroidota ratio (intolerant = 3.7 (0.6) vs. tolerant = 4.5 (2.0), P = 0.019) and higher plasma [sCD14] (P = 0.014), but other aspects of faecal microbiome, GI integrity or inflammation did not differ from heat tolerant individuals. In conclusion, the faecal microbiome composition and the GI barrier integrity and inflammatory responses to exercise heat-stress showed limited differences between recent EHI patients and matched controls, or between individuals classified as heat intolerant or heat tolerant and are unlikely to explain elevated EHI risk in recent EHI patients, or heat intolerance.},
}
@article {pmid40551275,
year = {2025},
author = {Zhang, Q and Du, M and Shen, Y and Lu, X and Jin, M and Wang, Y},
title = {Prevotella stercorea increases fat deposition in Jinhua pigs fed alfalfa grass-based diets.},
journal = {Journal of animal science and biotechnology},
volume = {16},
number = {1},
pages = {88},
pmid = {40551275},
issn = {1674-9782},
support = {U21A20249//National Natural Science Foundation of China/ ; CARS-35//National Center of Technology Innovation for Pigs/ ; YFD1300702//National Key R&amp;D Program of China/ ; },
abstract = {BACKGROUND: Fat is a key component of body composition in both humans and animals, with intramuscular fat (IMF) being a critical determinant of pork quality. Higher IMF level enhances meat qualities such as flavor, tenderness, and juiciness, directly influencing consumer preference and market demand. Therefore, identifying microbial biomarkers associated with fat deposition is essential for improving meat quality in livestock and understanding how gut microbiota regulates host metabolism.<br><br>RESULTS: In this study, we examined changes in meat quality, fat metabolism, and gut microbiota during the pig life cycle, from weaning to marketing. We found that Jinhua pig exhibited higher IMF content and marbling score, and higher &#x3b1; diversity of colonic microbial communities. Microbiome Multivariate Association with Linear Models was used to identify the core genera associated with age, breed, and feed, and Prevotella was found to respond to both age and breed factors. The correlation analysis of fat deposition indicators with microbial genera revealed that Prevotella was a potential biomarker in response to IMF. In addition, the P. stercorea DSM 18206 (P. stercorea) was identified in porcine sample and administered to pseudo sterile mouse to examine the effect on IMF deposition. We found that the gavage of P. stercorea with alfalfa-enriched diet led to a significant increase in triglyceride (TG) and IMF contents in muscle. Metabolomic analysis further confirmed P. stercorea may potentially regulate fat deposition through the sphingolipid signaling pathway.<br><br>CONCLUSIONS: We identified P. stercorea as a potential biomarker linked to higher IMF deposition and validated their role in shaping the gut microbiota and promoting fat accumulation in a mouse model, which correlated with the sphingolipid signaling pathway. These findings provide valuable insights into the role of P. stercorea in regulating fat deposition and metabolic health, offering implications for improving both livestock meat quality and lipid metabolism in humans.},
}
@article {pmid40550997,
year = {2025},
author = {Zhang, Y and Ke, S and Wang, XW and Sun, Y and Weiss, ST and Liu, YY},
title = {Association rule mining of the human gut microbiome.},
journal = {Science China. Life sciences},
volume = {},
number = {},
pages = {},
pmid = {40550997},
issn = {1869-1889},
abstract = {The human gut carries a vast and diverse microbial community that is essential for human health. Understanding the structure of this complex community is a crucial step toward comprehending human-microbiome interactions. Traditional co-occurrence and correlation analyses typically focus on pairwise relationships and ignore higher-order relationships. Association rule mining (ARM) is a well-developed technique in data mining and has been applied to human microbiome data to identify higher-order relationships. Yet, existing attempts suffer from small sample sizes and low taxonomic resolution. We developed an advanced ARM framework and systematically investigated the interactions between microbial species using a public large-scale uniformly processed human microbiome data from the curatedMetagenomicData (CMD) together with ARM. First, we inferred association rules in the gut microbiome samples of healthy individuals (n=2,815) in CMD. Then we compared those rules with those inferred from the individuals with different diseases: inflammatory bowel disease (IBD, n=768), colorectal cancer (CRC, n=368), impaired glucose tolerance (IGT, n=199), and type 2 diabetes (T2D, n=164). Finally, we demonstrated that ARM is an efficient feature selection tool that can improve the performance of microbiome-based disease classification. Together, this study illustrates the higher-order microbial relationships in the human gut microbiome and highlights the critical importance of incorporating association rules in microbiome-based disease classification.},
}
@article {pmid40550754,
year = {2025},
author = {Dubey, VP and Kansagra, JJ and Sureja, VP and Kheni, DB},
title = {Efficacy of a Probiotic Combination on Glycemic Index and Insulin Resistance in Adults: A Systematic Review and Meta-Analysis.},
journal = {Journal of dietary supplements},
volume = {},
number = {},
pages = {1-23},
doi = {10.1080/19390211.2025.2522463},
pmid = {40550754},
issn = {1939-022X},
abstract = {Insulin resistance leads to increased glucose and insulin levels. Probiotics can reduce insulin resistance, but the presence of different probiotic strains and doses prevents the generalization to real-world scenario. The current systematic review and meta-analysis study investigated the efficacy of a triple probiotic combination (Lactobacillus acidophilus, Lactobacillus casei, and Bifidobacterium bifidum) on glycemic index and insulin resistance parameters in adults. Randomized controlled trials evaluating the efficacy of the probiotics combination on glycemic index and insulin resistance parameters were identified. Physiotherapy Evidence Database scale and the Cochrane Risk of Bias tool were used for risk of bias assessment and RevMan for meta-analysis. Fourteen good-quality clinical trials were included in the current study. Low-to-moderate risk of bias was observed. Data from 823 participants were included. Probiotics supplementation significantly reduced insulin resistance (MD: -1.05 HOMA-IR score, p < 0.00001), serum glucose (MD: -3.99 mg/dl, p = 0.0003) and insulin levels (MD: -3.79 µIU/ml, p < 0.00001), while significantly improved insulin sensitivity (MD: +0.02 QUICKI score, p < 0.00001) and pancreatic β-cell functioning (MD: -14.71 HOMA-B score, p < 0.00001) compared to the control group. Significant heterogeneity was observed for all evaluation parameters (except the HOMA-B score) while no significant publication bias was observed. The current study suggests that the probiotic combination of Lactobacillus acidophilus, Lactobacillus casei, and Bifidobacterium bifidum is effective in reducing insulin resistance, improving glycemic index parameters, and improving pancreatic β-cell functioning in adults by improving the gastrointestinal microbiome.},
}
@article {pmid40550680,
year = {2025},
author = {Lin, M and Hu, L and Hao, L and Wang, Z},
title = {[Microbiome and its genetic potential for carbon fixation in small urban wetlands].},
journal = {Sheng wu gong cheng xue bao = Chinese journal of biotechnology},
volume = {41},
number = {6},
pages = {2415-2431},
doi = {10.13345/j.cjb.240399},
pmid = {40550680},
issn = {1872-2075},
mesh = {*Wetlands ; *Microbiota/genetics ; *Carbon Cycle/genetics ; *Bacteria/genetics/metabolism/classification ; RNA, Ribosomal, 16S/genetics ; China ; Cities ; Geologic Sediments/microbiology ; Archaea/genetics/metabolism/classification ; Metagenomics ; Metagenome ; },
abstract = {Small urban wetlands are widely distributed and susceptible to human activities, serving as important sources and sinks of carbon. Microorganisms play a crucial role in carbon cycle, while limited studies have been conducted on the microbial diversity in small urban wetlands and the functions of microbiome in carbon fixation and metabolism. To probe into the microbiome-driven carbon cycling in small urban wetlands and dissect the composition and functional groups of microbiome, we analyzed the relationships between the microbiome structure, element metabolism pathways, and habitat physicochemical properties in sediment samples across three small wetlands in Huzhou City, and compared them with natural wetlands in the Zoige wetland. High-throughput sequencing of 16S rRNA gene amplicons and metagenomics was employed to determine the species and functional groups. Sixty medium to high-quality metagenome-assembled genomes (MAGs) were constructed, including 55 bacterial and 5 archaeal taxa, and their potential in driving elemental cycles were analyzed, with a focus on carbon fixation. Several bacterial species were found to encode a nearly complete carbon fixation pathway, including the Calvin cycle, the reductive tricarboxylic acid cycle, the Wood-Ljungdahl pathway, and the reductive glycine pathway. There were several potential novel carbon-fixing bacterial members, such as those belonging to Syntrophorhabdus (Desulfobacterota) and UBA4417 (Bacteroidetes), which had high relative abundance in the wetland microbiome. Unveiling the genetic potential of these functional groups to facilitate element cycling is of great scientific importance for enhancing the carbon sequestration capacity of small urban wetlands.},
}
@article {pmid40550667,
year = {2025},
author = {Zhao, X and Jiang, C and Liu, S},
title = {[Synthetic microbiomes: rational design, engineering strategies, and application prospects].},
journal = {Sheng wu gong cheng xue bao = Chinese journal of biotechnology},
volume = {41},
number = {6},
pages = {2221-2235},
doi = {10.13345/j.cjb.250201},
pmid = {40550667},
issn = {1872-2075},
mesh = {*Microbiota/genetics ; *Synthetic Biology/methods ; Biotechnology/methods ; Biodegradation, Environmental ; Humans ; },
abstract = {Microbiomes in natural environments have diverse functions and harbor vast exploitable potential of modifying the nature and hosts, being significant resources for development. The inherent high complexity and uncontrollability of natural microbiomes, as well as the selection by the nature and hosts, impose significant constraints on practical applications. Synthetic microbiomes, serving as precisely defined engineered microbiomes, demonstrate enhanced functionality, stability, and controllability compared with natural microbiomes. These engineered microbiomes emerge as a prominent research focus and are potentially having applications across various fields including environmental bioremediation and host health management. Nevertheless, substantial challenges persist in both fundamental research and practical application of synthetic microbiomes. This review systematically summarizes three core design principles for synthetic microbiomes, introduces current construction strategies including top-down, bottom-up, and integrated approaches, and comprehensively lists their applications in environmental remediation, agricultural innovation, industrial biotechnology, and healthcare. Furthermore, it critically examines existing technical and conceptual challenges while proposing strategic recommendations, thereby providing theoretical guidance for future advancements in the design, engineering, and application of synthetic microbiomes.},
}
@article {pmid40550666,
year = {2025},
author = {Liu, S},
title = {[Preface for special issue on microbiome engineering].},
journal = {Sheng wu gong cheng xue bao = Chinese journal of biotechnology},
volume = {41},
number = {6},
pages = {1-6},
doi = {10.13345/j.cjb.250476},
pmid = {40550666},
issn = {1872-2075},
mesh = {*Microbiota ; Humans ; *Biotechnology ; *Bioengineering ; },
abstract = {Microbiome engineering is an emerging interdisciplinary field that systematically investigates and applies engineering methods to uncover the functions, structures, and interaction mechanisms of microbial communities with their environments, offering critical insights into global challenges. To showcase the latest advancements and achievements in this field, Chinese Journal of biotechnology has specially organized a special issue, inviting experts and scholars from multiple domestic institutions to elaborate on the practical applications and potential of microbiome engineering in agriculture and industrial production, environmental and ecological restoration, and health and medical treatment, from perspectives of fundamental research, technological innovation, and engineering applications. Additionally, this issue explores future trends in the field, providing valuable references to promote innovation and contribute to the sustainable development of human society.},
}
@article {pmid40550651,
year = {2025},
author = {Liu, F and Ye, YJ},
title = {[Preoperative anal function assessment in sphincter-preserving surgery for rectal cancer: clinical significance and strategies].},
journal = {Zhonghua wei chang wai ke za zhi = Chinese journal of gastrointestinal surgery},
volume = {28},
number = {6},
pages = {609-614},
doi = {10.3760/cma.j.cn441530-20250410-00152},
pmid = {40550651},
issn = {1671-0274},
mesh = {Humans ; *Anal Canal/surgery/physiopathology ; *Rectal Neoplasms/surgery/physiopathology ; Quality of Life ; Postoperative Complications/prevention &amp; control ; Organ Sparing Treatments ; Clinical Relevance ; },
abstract = {Sphincter-preserving surgery has become the mainstream approach for mid-to-low rectal cancer, yet postoperative anal dysfunction (low anterior resection syndrome, LARS) occurs in 30%-50% of patients, significantly impacting quality of life. This review systematically elaborates the clinical value of preoperative anal function assessment (mainly digital rectal examination), proposing a multidimensional evaluation system integrating anatomical (including high-resolution anorectal MRI, 3D transrectal ultrasound and dynamic contrast-enhanced ultrasound), physiological (anorectal amnometry and anal electromyography), and neurological assessments (including Parks scale, Wexner score, MSK-BFI scale and LARS score), alongside innovative strategies such as artificial intelligence and gut microbiome analysis. We advocate incorporating preoperative functional assessment into quality control standards for sphincter preservation, promoting a paradigm shift from "anatomical preservation" to "functional preservation".},
}
@article {pmid40550271,
year = {2025},
author = {Ali, B and Franck, B and Rusch, E},
title = {Microbiome And Immunotherapy In Bladder Cancer: The Missing Link.},
journal = {The French journal of urology},
volume = {},
number = {},
pages = {102922},
doi = {10.1016/j.fjurol.2025.102922},
pmid = {40550271},
issn = {2950-3930},
abstract = {BACKGROUND: Bladder cancer remains a significant global health concern, with immunotherapies such as Bacillus Calmette-Guérin (BCG) and immune checkpoint inhibitors (ICIs) playing pivotal roles in treatment. Emerging evidence suggests that the microbiome, encompassing both gut and urinary tract microorganisms, may influence the efficacy and outcomes of these immunotherapies.<br><br>OBJECTIVE: This review aims to explore the intricate relationship between the microbiome and immunotherapy in bladder cancer, highlighting current research findings, potential mechanisms, and future therapeutic implications.<br><br>METHODS: A comprehensive literature search was conducted across databases including PubMed and Scopus, focusing on studies published up to [insert date]. Keywords utilized encompassed "bladder cancer," "microbiome," "immunotherapy," "BCG therapy," and "immune checkpoint inhibitors.".<br><br>RESULTS: The analysis indicates that specific microbial compositions are associated with varied responses to bladder cancer immunotherapies. Notably, certain gut microbiota profiles correlate with enhanced ICI efficacy, while alterations in the urinary microbiome may impact BCG treatment outcomes. Potential mechanisms involve microbial modulation of systemic and local immune responses, influencing tumor microenvironments and therapeutic effectiveness.<br><br>CONCLUSION: Understanding the microbiome's role in bladder cancer immunotherapy presents a promising avenue for optimizing treatment strategies. Further research is imperative to elucidate these relationships and translate findings into clinical practice, potentially leading to microbiome-targeted interventions to improve patient outcomes.},
}
@article {pmid40550033,
year = {2025},
author = {Chao, H and Shan, J and Che, LQ and Cheng, Y and Li, HJ and Qian, XY},
title = {Correlations between serum cytokines and gut microbiota in patients with Graves' disease: A case-control study.},
journal = {Medicine},
volume = {104},
number = {25},
pages = {e43000},
doi = {10.1097/MD.0000000000043000},
pmid = {40550033},
issn = {1536-5964},
support = {LSFGG-2022062//Qiqihar Science and Technology Bureau/ ; QMSI2021L-22//Qiqihar Academy of Medical Sciences/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; *Graves Disease/microbiology/blood/immunology ; Case-Control Studies ; Female ; Male ; Adult ; *Cytokines/blood ; Middle Aged ; RNA, Ribosomal, 16S ; Feces/microbiology ; },
abstract = {Graves' disease (GD) is the most prevalent autoimmune thyroid disorder. Gut microbiome as a critical modulator of autoimmune pathogenesis through its bidirectional communication with host immunity. To elucidate the pathophysiological interplay between cellular immunity and gut microbiome composition in GD through systematic analysis of associations between peripheral blood cytokine profiles and microbial community dynamics. This case-control study enrolled 30 untreated GD patients consecutively admitted to the Department of Endocrinology at the Third Affiliated Hospital of Qiqihar Medical University between January and July 2023, along with 30 age/sex-matched healthy controls (HC). Comprehensive evaluations included: electrochemiluminescence immunoassay quantification of thyroid function parameters, high-resolution Illumina HiSeq 2000 platform-based 16S rRNA gene sequencing for fecal microbial community profiling, multiplex cytokine array analysis of peripheral blood immune markers. Spearman correlation analyses were conducted to delineate relationships among cytokines, thyroid function index and gut microbial taxa alterations in GD pathogenesis. Alpha diversity analysis revealed that the abundance and diversity of certain microbiota in the GD group decreased. Beta diversity analysis revealed that the intestinal microbiome composition of GD patients was significantly different from that of HC. The proportion of Firmicutes in patients with GD was lower than that in HC, while the proportion of Bacteroidetes in patients with GD was greater than that in HC. Immunoregulatory cytokine interleukin-10 exhibited positive correlations with commensal genera Bifidobacterium (R = 0.28) and Parasutterella (R = 0.30), while showing negative correlations with the pathobionts Prevotella_9 (r = -0.51) and Megamonas (r = -0.31). Transforming growth factor β demonstrated similar positive correlations with Bifidobacterium (R = 0.31) and negative correlations with Prevotella_9 (r = -0.45) and Megamonas (r = -0.38). Interleukin-17A displayed positive correlated with Prevotella_9 (R = 0.43) and Megamonas (R = 0.32), but negative correlations with Bifidobacterium (r = -0.27), Veillonella (r = -0.47), Prevotella_9 (r = -0.51) and Megamonas (r = -0.31). Clinically, key microbial taxa showed significant associations with thyroid dysfunction parameters. Our findings identify that GD gut ecosystem demonstrates profound microbial dysbiosis characterized by depleted commensal symbionts and expansion of immunomodulatory pathobionts. Specific bacterial taxa correlate with both cytokine and clinical thyroid dysfunction markers.},
}
@article {pmid40549867,
year = {2025},
author = {Qiu, X and Ma, S and Liu, Z and Pan, J and Ding, L and Zhang, B and Liang, X and Wang, P and Chen, T and Guo, X},
title = {Microplastics Influence Dissolved Organic Matter Transformation Mediated by Microbiomes in Soil Aggregates.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c00875},
pmid = {40549867},
issn = {1520-5851},
abstract = {Soil aggregate stability is vital for soil structure, erosion control, fertility, and crop productivity. Dissolved organic matter (DOM) turnover plays an important role in controlling the stability of soil aggregates, affecting aggregate formation and microbial activity. Microplastics (MPs) are known to impact soil DOM composition and structure, but their effects on DOM transformation in different soil aggregates remain unclear. Herein, we conducted 450 day incubation assays to study the effects of nondegradable and biodegradable MPs with varying aging levels on DOM transformations in agricultural soil aggregates. MPs were found to increase DOM transformation in soil aggregates, leading to changes in soil aggregate stability, including a reduction in geometric mean diameter and mass-weighted diameter. The addition of MPs resulted in a decrease in the stability of DOM in large-sized aggregates but an increase in the aromaticity and unsaturation of DOM in small-sized aggregates, which were more pronounced in the PLAMPs-treated group. This phenomenon is primarily attributed to the transformation of unsaturated aliphatic compounds and highly unsaturated and phenolic compounds, which play a major role in the intra- and intergroup transformation of DOM. In this process, microbial communities play a significant role. They tend to consume DOM in larger aggregates and produce DOM in smaller aggregates, leading to an accumulation of DOM in smaller aggregates, thereby promoting the formation of smaller aggregates and reducing the aggregate stability. This study uncovers the mechanisms of DOM transformation in response to MPs in soil aggregates, providing a scientific basis for soil management and sustainable agricultural development.},
}
@article {pmid40549551,
year = {2025},
author = {Huo, L and Chen, Q and Jia, S and Zhang, Y and Wang, L and Li, X and Li, Z and Sun, B and Shan, J and Lin, J and Yang, L and Sui, H},
title = {Gut microbiome promotes succinate-induced ulcerative colitis by enhancing glycolysis through SUCNR1/NF-κB signaling pathway.},
journal = {American journal of physiology. Cell physiology},
volume = {},
number = {},
pages = {},
doi = {10.1152/ajpcell.00411.2025},
pmid = {40549551},
issn = {1522-1563},
support = {82204887//MOST | National Natural Science Foundation of China (NSFC)/ ; ZY(2021-2023)-0207-01//Shanghai Municipal Health Commission ()/ ; ZB202406//JiaDing District Health Commission/ ; 2023ZY1012//Henan Provincial Health Commission/ ; GZY-KJS-2022-047-3//National Administration of Traditional Chinese Medicine/ ; YC-2023-0901//Ministry of Finance of China/ ; },
abstract = {Ulcerative colitis (UC) is a chronic recurrent inflammatory disease. Previous studies demonstrate that excessive accumulation of gut microbial metabolites, especially succinate increases the risk of disease progression. However, the role of succinate and its molecular mechanism has not been explored. We investigated the effects of succinate on colonic inflammation and intestinal microbiota, and their association with succinate receptor (SUCNR1) signaling in 3% dextran sodium sulfate (DSS) induced-acute UC in C57BL/6J mice. After treatment, fecal bacteria from UC mice were evaluated by 16S rRNA sequencing. Colon tissues and cell lysates were collected and prepared for histological evaluation, immunohistochemistry, Western blotting, and inflammatory activity cytokine analysis. It was found that Phascolarctobacterium spp. (P.bacterium), which consumed succinate, significantly decreased SUCNR1 expression, relieved colonic damage, reduced cytokine levels, and restored the integrity of the intestinal epithelial barrier in UC mice. In addition, the results of flow cytometry, quantitative real-time polymerase chain reaction, and enzyme-linked immunosorbent assay indicated that succinate deficiency markedly suppressed secretion of proinflammatory cytokines (e.g, interleukin-1β, interleukin-6, interleukin-10, and tumor necrosis factor-α). Moreover, SUCNR1 inhibitor (NF-56-EJ40) inhibited glycolysis of intestinal epithelial cells (IECs) in the co-culture system with Th17 cells, including downregulation of oxygen consumption rate (OCR) and increased extracellular acidification rate (ECAR) reflecting overall glycolytic flux, and regulated the expression of glycolysis-related proteins, such as GLUT1, HK-II, and LDHA. Collectively, our findings indicate that microbiota consumption of succinate can ameliorate DSS-induced UC through suppressing Th17, reducing IECs glycolysis, lowing the secretion of proinflammatory cytokines, maintaining epithelial barrier function, and improving dysbiosis.},
}
@article {pmid40549543,
year = {2025},
author = {Barbosa, MC and Marques da Silva, JF and Alves, LC and Finn, RD and Paschoal, AR},
title = {CODARFE: Unlocking the prediction of continuous environmental variables based on microbiome.},
journal = {GigaScience},
volume = {14},
number = {},
pages = {},
doi = {10.1093/gigascience/giaf055},
pmid = {40549543},
issn = {2047-217X},
mesh = {*Microbiota ; Humans ; *Software ; *Computational Biology/methods ; Environment ; Bacteria/classification/genetics ; },
abstract = {BACKGROUND: Despite the surge in microbiome data acquisition, there is a limited availability of tools capable of effectively analyzing it and identifying correlations between taxonomic compositions and continuous environmental factors. Furthermore, existing tools also do not predict the environmental factors in new samples, underscoring the pressing need for innovative solutions to enhance our understanding of microbiome dynamics and fulfill the prediction gap. Here we introduce CODARFE, a novel tool for sparse compositional microbiome predictor selection and prediction of continuous environmental factors.<br><br>RESULTS: We tested CODARFE against 4 state-of-the-art tools in 2 experiments. First, CODARFE outperformed predictor selection in 21 of 24 databases in terms of correlation. Second, among all the tools, CODARFE achieved the highest number of previously identified bacteria linked to environmental factors for human data-that is, at least 7% more. We also tested CODARFE in a cross-study, using the same biome but under different external effects, using a model trained on 1 dataset to predict environmental factors on another dataset, achieving 11% of mean absolute percentage error. Finally, CODARFE is available in 5 formats, including a Windows version with a graphical interface, to installable source code for Linux servers and an embedded Jupyter notebook available at MGnify.<br><br>CONCLUSIONS: Our findings underscore the robustness and broad applicability of CODARFE across diverse fields, even under varying experimental conditions. Additionally, the ability to predict outcomes in new samples allows for the generation of new insights in previously unexplored contexts, providing researchers with a versatile tool.},
}
@article {pmid40549455,
year = {2025},
author = {Goryanin, I and Sorokin, A and Seitov, M and Emilov, B and Iskakov, M and Goryanin, I and Osmonov, B},
title = {Metagenome and metabolome study on inhaled corticosteroids in asthma patients with side effects.},
journal = {Journal of integrative bioinformatics},
volume = {},
number = {},
pages = {},
pmid = {40549455},
issn = {1613-4516},
abstract = {This study investigates the gut microbiome and metabolome of asthma patients treated with inhaled corticosteroids (ICS), some of whom experience adverse side effects. We analyzed stool samples from 24 participants, divided into three cohorts: asthma patients with side effects, those without, and healthy controls. Using next-generation sequencing and LC-MS/MS metabolomics, we identified significant differences in bacterial species and metabolites. Multi-Omics Factor Analysis (MOFA) and Global Sensitivity Analysis-Partial Rank Correlation Coefficient (GSA-PRCC) provided insights into key contributors to side effects, such as tryptophan depletion and altered linolenate and glucose-1-phosphate levels. The study proposes dietary or probiotic interventions to mitigate side effects. Despite the limited sample size, these findings provide a basis for personalized asthma management approaches. Further studies are required to confirm initial fundings.},
}
@article {pmid40549050,
year = {2025},
author = {Song, Y and Chen, J and Chen, N and Xu, T},
title = {Unveiling urinary microbiota dysbiosis in urolithiasis: beyond gut microbiome.},
journal = {Urolithiasis},
volume = {53},
number = {1},
pages = {125},
pmid = {40549050},
issn = {2194-7236},
}
@article {pmid40548945,
year = {2025},
author = {},
title = {Correction to 'Enhancing insights into diseases through horizontal gene transfer event detection from gut microbiome'.},
journal = {Nucleic acids research},
volume = {53},
number = {12},
pages = {},
doi = {10.1093/nar/gkaf631},
pmid = {40548945},
issn = {1362-4962},
}
@article {pmid40548738,
year = {2025},
author = {Mattelin, V and Van Landuyt, J and Kerkhof, F-M and Minnebo, Y and Boon, N},
title = {Integrating taxonomic and phenotypic information through FISH-enhanced flow cytometry for microbial community dynamics analysis.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0197324},
doi = {10.1128/spectrum.01973-24},
pmid = {40548738},
issn = {2165-0497},
abstract = {UNLABELLED: Flow cytometry is a powerful tool to monitor microbial communities, as it allows tracking both changes in the subpopulations and cell numbers at high throughput and a low sample cost. This information can be combined in a phenotypic fingerprint that can be leveraged for diversity analysis. However, as isogenic individuals can manifest phenotypic diversity, for example, due to differing physiological state and phenotypic plasticity, combining the phenotypic information with taxonomic information adds an extra dimension for describing the dynamics of a microbial community. In this research, taxonomic information was incorporated in the microbial fingerprint through fluorescent in situ hybridization (FISH) at a single-cell level. To validate this concept and explore its versatility, two ecosystems with different micro-biodiversity were considered. In the first environment, marine bacteria were monitored for plastic biodegradation in a trickling filter, and in the second, an in vitro simulated human gut microbiome was followed over time. Samples were prepared using different (staining) methods, including FISH, and beta diversity analysis was used to evaluate the level of distinction between differently treated groups in both environments. As a reference to correlate increased distinction with the incorporation of taxonomic information, 16S rRNA gene sequencing was used. Finally, a predictive algorithm was trained to correctly classify samples in the differently treated groups. The results showed that the implementation of FISH in flow cytometry provides more information on a single-cell level to answer specific scientific questions, like distinguishing between phenotypically similar communities or following a specific taxonomic group over time.<br><br>IMPORTANCE: Understanding microbial communities is crucial for elucidating their role in maintaining ecosystem health and stability. Researchers are increasingly interested in studying microbial communities by looking at not just their genetic makeup but also their physical traits and functions. In our study, we used common techniques like fluorescence in situ hybridization and flow cytometry, along with advanced data analysis, to better understand these communities. This combination allowed us to gather and use data more effectively, demonstrating that these easy-to-use methods, when paired with proper analysis, can enhance our understanding of changing microbial ecosystems.},
}
@article {pmid40548729,
year = {2025},
author = {Abbas, N and Willmott, T and Campbell, PM and Singh, G and Basu, M and Reid, F and McBain, AJ},
title = {Distinct microbiome profiles on vaginally inserted polypropylene midurethral mesh slings compared to vaginal, urinary, and skin microbiomes.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0246324},
doi = {10.1128/aem.02463-24},
pmid = {40548729},
issn = {1098-5336},
abstract = {Midurethral slings are widely used in the treatment of stress urinary incontinence in women. However, little is known about the microbiomes that develop on these implants, their relationship to the urinary and vaginal microbiomes, or their potential role in mesh-related complications. In this study, we characterized the microbiomes of explanted midurethral slings and examined associations with clinical complications. Seventy-four women provided a total of 397 samples, including explanted mesh, urine, and swabs from the vagina and groin or suprapubic skin. Participants were categorized into clinical groups: chronic pain, vaginal mesh exposure, lower urinary tract perforation, or recurrent incontinence (control group). Samples underwent 16S rRNA gene sequencing. The mesh microbiome was dominated by Firmicutes, Proteobacteria, and Actinobacteria, with Enterococcus particularly abundant. Microbial diversity was significantly higher in mesh samples compared to vaginal and skin swabs, but not urine. The mesh microbiome was compositionally distinct from the urinary, vaginal, and skin microbiomes, potentially reflecting vaginal microbiome alterations due to urinary incontinence at the time of implantation. Differences in microbial diversity in mesh and skin samples among women with pain suggest a possible microbial contribution to mesh complications. These findings demonstrate the presence of distinct, site-specific microbial communities on explanted midurethral slings, with potential implications for understanding mesh-related complications.IMPORTANCEStress urinary incontinence commonly affects women, and effective treatment is essential. Midurethral mesh slings have provided effective relief; however, long-term complications such as chronic pain, vaginal mesh exposure, and lower urinary tract perforation have emerged. The pathophysiology of these complications is not well understood but is thought to involve a heightened inflammatory response to mesh implants. The local microbiome may contribute to this inflammation. We have shown that the mesh samples harbored a distinct microbiome and that differences in microbial composition may be associated with mesh complications. Understanding the role of specific bacteria in modulating host responses may offer new insights into the pathogenesis of mesh complications and inform future clinical approaches.},
}
@article {pmid40548719,
year = {2025},
author = {Zhou, M and Wang, Q and Yang, R and Zong, Z and Huang, B and Chen, J and Bao, X and Li, S and Shen, L and Dong, J and Zhao, X and Chen, Y and Chen, D},
title = {Microbial diagnostic features identified across populations possess potential antitumor properties in breast cancer.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0027125},
doi = {10.1128/msystems.00271-25},
pmid = {40548719},
issn = {2379-5077},
abstract = {The consistency of the associations between the breast microbiome and breast cancer (BC) across various studies remains uncertain. Publicly accessible data sets from five BC studies, comprising 16S rRNA gene sequencing data from 161 BC tissues (BC_tissue), 195 BC adjacent non-cancerous tissues (BC_adjacent), and 451 normal breast tissues (normal_tissue), were retrieved from the European Nucleotide Archive. Overall, the microbial composition across the three breast tissue statuses was predominantly characterized by the phyla Proteobacteria and Firmicutes, a distribution likely attributable to the fatty acid-rich environment of the breast tissue. Comparative analysis revealed that the relative abundances of the genera Cutibacterium and Burkholderia were significantly increased in both BC_adjacent and normal_tissue compared to BC_tissue. This observation suggested a potential anticancer effect associated with these genera. Our analysis revealed a significant reduction in the abundance of Cutibacterium and Cutibacterium acnes in BC tissues, which served as specific diagnostic features for BC. This finding was corroborated by our in-house data set (n = 28), which yielded similar conclusions. Subsequent in vitro and in vivo experiments verified the potential antitumor effects of C. acnes supernatant in BC. In conclusion, our study highlighted the predictive capacity of microbial biomarkers in the onset of BC. Notably, specific bacterial species within the breast microbiome, such as Cutibacterium and C. acnes, exhibited potential as diagnostic markers for BC and may contribute significantly to antitumor activity. Nevertheless, the molecular mechanisms governing their interactions with cancer cells are not yet fully understood, necessitating further research to investigate their viability as targets for tumor prevention.IMPORTANCEAlthough a growing number of studies have highlighted the significant role of microorganisms in BC, there is a lack of consensus regarding the specific microbial genera consistently associated with breast cancer. While some studies have identified certain genera in the breast cancer environment, the results are often inconsistent and influenced by factors such as study design, population, or methodologies used. Through a comprehensive analysis of five publicly available breast cancer studies, along with validation from an in-house cohort, we found a significantly reduced abundance of Cutibacterium and C. acnes in BC tissues. In vivo and in vitro experiments demonstrated the antitumor effects of C. acnes in BC. Understanding the antitumor mechanisms of C. acnes in BC may provide potential avenues for developing novel therapeutic strategies for this disease.},
}
@article {pmid40548706,
year = {2025},
author = {Xie, Y and Cidan, Y and Cisang, Z and Gusang, D and Danzeng, Q and Basang, W and Zhu, Y},
title = {Effects of warm-season feeding on yak growth, antioxidant capacity, immune function, and fecal microbiota.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0100125},
doi = {10.1128/spectrum.01001-25},
pmid = {40548706},
issn = {2165-0497},
abstract = {The yak (Bos grunniens) is of great importance to the local ecosystem and animal husbandry on the Tibetan Plateau. However, the impacts of different feeding practices on yak growth, health, and ecosystem interactions are not fully understood. This study investigates the effects of warm-season grazing and housing-feeding on yak growth performance, antioxidant capacity, immune function, metabolome, and fecal microbiota. The study found that grazing significantly increased the final body weight and average daily gain of yak (P < 0.05), reduced serum globulin and urea nitrogen levels, and elevated aspartate aminotransferase (AST) levels. Grazing enhanced serum total superoxide dismutase (T-SOD) and total antioxidant capacity (T-AOC). It also increased levels of immunoglobulins (IgA, IgM, IgG) and pro-inflammatory cytokines (IL-2, IL-6, TNF-α, IFN-γ). Meanwhile, grazing decreased levels of IL-4 and IL-10. Additionally, grazing significantly altered the plasma metabolite profile, particularly in bile acid metabolism pathways. The relative abundance of beneficial microbial genera (e.g., Christensenellaceae_R-7_group, Monoglobus, Romboutsia) in the feces of grazing yak was significantly higher, while total short-chain fatty acids were lower than in penned yak. Grazing improved growth performance and nutritional metabolism efficiency, enhanced antioxidant and immune functions, and optimized the structure of the gut microbiota in yak. These findings indicate that grazing can better utilize natural forage resources to promote yak health and improve production performance.IMPORTANCEThis study investigates how different feeding patterns-grazing versus housing-feeding-affect the health, growth, and microbiome of yaks in the warm season. Yaks are vital to the Tibetan Plateau's ecosystem and local livelihoods. Understanding how feeding practices impact their health can help optimize yak management, ensuring better welfare and productivity. Grazing yaks showed improved growth, enhanced antioxidant and immune functions, and a healthier gut microbiota compared to penned yaks. These findings highlight the importance of natural forage in promoting yak health and could guide sustainable yak husbandry practices, benefiting both the animals and the communities that rely on them.},
}
@article {pmid40548623,
year = {2025},
author = {Kim, SH and Yoon, MY and Yoon, SS},
title = {TMAO and the gut microbiome: implications for the CVD-CKD-IBD axis.},
journal = {Annals of medicine},
volume = {57},
number = {1},
pages = {2522324},
doi = {10.1080/07853890.2025.2522324},
pmid = {40548623},
issn = {1365-2060},
mesh = {Humans ; *Methylamines/metabolism ; *Gastrointestinal Microbiome/physiology ; *Cardiovascular Diseases/metabolism/microbiology ; *Renal Insufficiency, Chronic/metabolism/microbiology ; *Inflammatory Bowel Diseases/metabolism/microbiology ; Oxidative Stress ; Animals ; },
abstract = {Trimethylamine N-oxide (TMAO) is a metabolite produced by the gut microbiome from dietary nutrients such as choline and carnitine. Recent research has found that TMAO is strongly associated with cardiovascular disease (CVD), chronic kidney disease (CKD) and, more recently, inflammatory bowel disease (IBD). Although TMAO is linked to conditions characterized by inflammation, oxidative stress, fibrosis and gut microbiome imbalances, its exact role in disease development remains unclear. This review examines TMAO's potential role as a key link in the IBD-CKD-CVD disease spectrum. Highlighting the importance of limiting TMAO production, we propose several promising strategies to achieve its reduction. Specifically, we focus on microbiome therapies as innovative methods for managing TMAO levels. This approach offers a hopeful avenue for addressing the complex interplay between gut health and systemic chronic human diseases.},
}
@article {pmid40548295,
year = {2025},
author = {Diwan, A and Harke, S and Panche, AN},
title = {Exploration of novel bioactive compounds from the microbiome of fish and shellfish as an alternative to replace antibiotic drugs in aquaculture farming.},
journal = {Gut microbiome (Cambridge, England)},
volume = {6},
number = {},
pages = {e8},
pmid = {40548295},
issn = {2632-2897},
abstract = {The use of antibiotics in fish and shrimp aquaculture all over the world was found to be only partially successful in preventing infectious diseases. However, their overuse has resulted in the contamination of closed aquatic ecosystems, reduced antibiotic resistance in organisms that fight infectious diseases, and compromised the effectiveness of various antibiotic medications in controlling diseases. Excessive use of antibiotics damages aquaculture species and impacts human health, also rendering the most potent antibiotics increasingly ineffective, with limited alternatives. Therefore, intensive research efforts have been made to replace antibiotics with other protocols and methods like vaccines, phage therapy, quorum quenching technology, probiotics, prebiotics, chicken egg yolk antibody (IgY), and plant therapy," etc. Though all these methods have great potential, many of them are still in the experimental stage, except for fish vaccines. All these alternative technologies need to be carefully standardized and evaluated before implementation. In recent times, after realizing the importance of the gut microbiome community in maintaining the health of animals, efforts have been made to use the microbiome strains for the prevention of pathogenic bacterial and viral infections. Now it has been experimentally proven that animals should possess a healthy microbiome community in their gut tract to strengthen the immune system and prevent the entry of harmful pathogens. Investigations are now being carried out on the derivation of various bioactive compounds from the gut microbiome strains and their structural profile and functionality using the molecular tools of metagenomics and bioinformatics. Such newly discovered compounds from microbiomes can be used as potential alternatives to replace antibiotic drugs in the aquaculture industry. These alternatives are likely to emerge as breakthroughs in animal health management and farming, with effects on cost efficiency, species health, productivity, and yield enhancement. Therefore, introducing new micro-innovative technologies into an overall health management plan will be highly beneficial.},
}
@article {pmid40548227,
year = {2025},
author = {Hetta, HF and Ahmed, R and Ramadan, YN and Fathy, H and Khorshid, M and Mabrouk, MM and Hashem, M},
title = {Gut virome: New key players in the pathogenesis of inflammatory bowel disease.},
journal = {World journal of methodology},
volume = {15},
number = {2},
pages = {92592},
pmid = {40548227},
issn = {2222-0682},
abstract = {Inflammatory bowel disease (IBD) is a chronic inflammatory illness of the intestine. While the mechanism underlying the pathogenesis of IBD is not fully understood, it is believed that a complex combination of host immunological response, environmental exposure, particularly the gut microbiota, and genetic susceptibility represents the major determinants. The gut virome is a group of viruses found in great frequency in the gastrointestinal tract of humans. The gut virome varies greatly among individuals and is influenced by factors including lifestyle, diet, health and disease conditions, geography, and urbanization. The majority of research has focused on the significance of gut bacteria in the progression of IBD, although viral populations represent an important component of the microbiome. We conducted this review to highlight the viral communities in the gut and their expected roles in the etiopathogenesis of IBD regarding published research to date.},
}
@article {pmid40548185,
year = {2025},
author = {Zhu, J and Sun, Y and Dong, Y and Zhao, Y and Gai, Z and Fang, S},
title = {Efficacy and Safety of Lactobacillus acidophilus LA85 in Preventing Antibiotic-Associated Diarrhea: A Randomized, Placebo-Controlled Study.},
journal = {Food science &amp; nutrition},
volume = {13},
number = {6},
pages = {e70490},
pmid = {40548185},
issn = {2048-7177},
abstract = {Antibiotic-associated diarrhea (AAD) is a common clinical complication resulting from antibiotic-induced gut microbiota dysbiosis. Lactobacillus acidophilus LA85, a probiotic strain illustrated with in vitro antimicrobial and immunomodulatory properties, may offer a preventive approach against AAD. However, clinical evidence on its efficacy remains limited. This randomized, double-blind, placebo-controlled trial evaluated the efficacy and safety of L. acidophilus LA85 in preventing amoxicillin-associated diarrhea. A total of 82 adult participants receiving amoxicillin treatment were randomized to receive either LA85 (2 × 10[9] CFU/day) or placebo for 14 days. The primary outcomes included AAD incidence, diarrhea duration, and stool consistency, while secondary outcomes assessed gastrointestinal quality of life and safety. LA85 supplementation was associated with a trend toward a reduction in the incidence of AAD; however, this difference did not reach statistical significance. Nonetheless, LA85 notably shortened the duration of diarrhea episodes compared to placebo (p = 0.072), suggesting a clinically meaningful improvement. Participants receiving LA85 exhibited less variability in stool consistency scores, assessed by the Bristol stool form scale (BSFS), maintaining scores consistently around 3.5. In contrast, placebo recipients had greater fluctuations between 3.5 and 4.0, indicating less stable stool consistency during antibiotic treatment. Importantly, exploratory subgroup analysis revealed that in younger participants (< 53 years age), LA85 supplementation significantly reduced the incidence of AAD (p = 0.008) and effectively eliminated persistent diarrhea episodes. Gastrointestinal quality of life scores improved significantly in the probiotic group (p < 0.05). No serious adverse events were reported, supporting the safety of LA85. While these findings support the clinical application of LA85 for preventing AAD, further large-scale trials incorporating microbiome analysis and longer follow-up periods are necessary to confirm its long-term benefits and generalizability. Trial Registration: This clinical trial (ClinicalTrials.gov Identifier: NCT05974657) was registered on August 3, 2023.},
}
@article {pmid40548146,
year = {2025},
author = {Vermeulen, A and Bootsma, E and Proost, S and Vieira-Silva, S and Kathagen, G and Vázquez-Castellanos, JF and Tito, RY and Sabino, J and Vermeire, S and Matthys, C and Raes, J and Falony, G},
title = {Dietary convergence induces individual responses in faecal microbiome composition.},
journal = {eGastroenterology},
volume = {3},
number = {2},
pages = {e100161},
pmid = {40548146},
issn = {2976-7296},
abstract = {BACKGROUND: Dietary variation has been identified as a key contributor to microbiome diversification. However, assessing its true impact in a cross-sectional setting is complicated by biological confounders and methodological hurdles. We aimed to estimate the impact of a reduction of dietary variation (dietary convergence) on faecal microbiota composition among individuals consuming a Western-type diet.<br><br>METHODS: 18 healthy volunteers recruited in the region of Flanders (Belgium) were followed up for 21 days. Participants were allowed to consume their habitual diet during a baseline and follow-up period (7 and 8&#x2009;days, respectively), intersected by a 6-day intervention during which dietary options were restricted to oat flakes, whole milk and still water. Faecal samples were collected on a daily basis. Quantitative microbiome profiles were constructed, combining 16S rRNA gene amplicon sequencing with flow cytometry cell counting. Blood samples were taken at the beginning and end of each study week.<br><br>RESULTS: While the intervention did not affect transit time (as assessed through the analysis of stool moisture), consumption of the restricted diet resulted in an increased prevalence of the Bacteroides2 microbiome community type. Microbial load and Faecalibacterium abundance decreased markedly. Despite dietary restrictions, no convergence of microbial communities (reduction of interindividual and intraindividual variation) was observed. The effect size (ES) of the intervention on genus-level microbiome community differentiation was estimated as 3.4%, but substantial interindividual variation was observed (1.67%-16.42%).<br><br>CONCLUSION: The impact of dietary variation on microbiome composition in a Western population is significant but limited in ES, with notable individual exceptions. Dietary convergence does not invariably translate into interindividual convergence of faecal microbial communities.},
}
@article {pmid40547801,
year = {2025},
author = {Bian, S and Zhu, S and Zhang, H and Chang, YF and Li, A},
title = {Editorial: Unveiling the potential of microbiome in semi-wild and wildlife animals: exploring opportunities for disease mitigation and animal health across ecological zones.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1623783},
pmid = {40547801},
issn = {1664-302X},
}
@article {pmid40547164,
year = {2025},
author = {Qiao, SB and Niu, ML and Liang, WT and Zhang, LJ and Chen, X and Zhu, YK},
title = {Analysis of serum S100A12, soluble advanced glycation end products receptor, and gut microbiome in elderly patients with colorectal cancer.},
journal = {World journal of gastrointestinal oncology},
volume = {17},
number = {6},
pages = {106393},
pmid = {40547164},
issn = {1948-5204},
abstract = {BACKGROUND: Colorectal cancer (CRC) ranks among the most prevalent malignancies in elderly populations, and chemotherapy resistance remains a critical clinical challenge. Emerging evidence highlights the interplay between chronic inflammation, gut microbiome dysbiosis, and CRC progression. Proinflammatory cytokines [e.g., interleukin (IL)-6, tumor necrosis factor-alpha (TNF-α)] and mediators like S100 calcium-binding protein A12 (S100A12)/soluble receptor for advanced glycation end products (sRAGE) are implicated in tumorigenesis, while gut microbial imbalances may exacerbate inflammatory microenvironments conducive to chemotherapy resistance. However, the triad relationship between S100A12/sRAGE, gut microbiota profiles, and chemotherapy efficacy in elderly patients with CRC remains unexplored, limiting biomarker-driven therapeutic strategies.<br><br>AIM: To analyze the correlation between serum levels of S100A12, sRAGE, gut microbiome dysbiosis, and systemic inflammation in elderly patients with CRC and to assess their predictive value for chemotherapy efficacy.<br><br>METHODS: A retrospective analysis was conducted on the clinical data of 120 elderly patients with advanced-stage CRC who visited our hospital from August 2023 to May 2024. These patients were enrolled in the study group. Additionally, 120 healthy individuals undergoing routine health check-ups during the same period were selected as the control group. Serum S100A12, sRAGE, IL-6, and TNF-&#x3b1; levels were measured by ELISA, and fresh stool samples were collected before chemotherapy to analyze gut microbiome composition in the study group. Follow-up observations were conducted after chemotherapy. Pearson correlation analysis was used to explore the relationship between serum S100A12, sRAGE levels, and gut microbiome dysbiosis in patients with CRC. The predictive diagnostic value of pre-chemotherapy serum S100A12 and sRAGE levels for chemotherapy efficacy was assessed using receiver operating characteristic curves.<br><br>RESULTS: Pre-chemotherapy serum S100A12, sRAGE, IL-6, and TNF-&#x3b1; levels were significantly elevated in patients with CRC vs controls (all P < 0.05). These biomarkers progressively increased with microbiota dysbiosis severity (severe vs mild dysbiosis: S100A12: 340.26 &#xb1; 52.39 &#x3bc;g/L vs 302.53 &#xb1; 56.97 &#x3bc;g/L; sRAGE: 525.64 &#xb1; 37.32 ng/L vs 441.38 &#xb1; 48.73 ng/L, P < 0.05) and correlated strongly with IL-6 (r = 0.712) and TNF-&#x3b1; (r = 0.698). Post-chemotherapy, biomarker levels decreased (P < 0.05), coinciding with beneficial microbiota recovery (Bifidobacterium 176%, Lactobacillus 153%) and pathogenic taxa reduction (Escherichia coli 62%). The combined S100A12/sRAGE model predicted chemotherapy resistance with an area under the curve of 0.914 (sensitivity = 86.07%, specificity = 88.89%), outperforming individual biomarkers.<br><br>CONCLUSION: Elevated serum S100A12 and sRAGE in elderly patients with CRC reflected gut microbiome dysbiosis and systemic inflammation, driven by IL-6/TNF-&#x3b1; signaling. Their post-chemotherapy decline parallels microbiota restoration, supporting a microbiome-inflammation-biomarker axis. The combined biomarker model offers robust clinical utility for chemotherapy efficacy prediction and personalized therapeutic strategies.},
}
@article {pmid40546666,
year = {2025},
author = {Jeyaraman, N and Jeyaraman, M and Dhanpal, P and Ramasubramanian, S and Nallakumarasamy, A and Muthu, S and Santos, GS and da Fonseca, LF and Lana, JF},
title = {Integrative review of the gut microbiome's role in pain management for orthopaedic conditions.},
journal = {World journal of experimental medicine},
volume = {15},
number = {2},
pages = {102969},
pmid = {40546666},
issn = {2220-315X},
abstract = {The gut microbiome, a complex ecosystem of microorganisms, has a significant role in modulating pain, particularly within orthopaedic conditions. Its impact on immune and neurological functions is underscored by the gut-brain axis, which influences inflammation, pain perception, and systemic immune responses. This integrative review examines current research on how gut dysbiosis is associated with various pain pathways, notably nociceptive and neuroinflammatory mechanisms linked to central sensitization. We highlight advancements in meta-omics technologies, such as metagenomics and metaproteomics, which deepen our understanding of microbiome-host interactions and their implications in pain. Recent studies emphasize that gut-derived short-chain fatty acids and microbial metabolites play roles in modulating neuroinflammation and nociception, contributing to pain management. Probiotics, prebiotics, synbiotics, and faecal microbiome transplants are explored as potential therapeutic strategies to alleviate pain through gut microbiome modulation, offering an adjunct or alternative to opioids. However, variability in individual microbiomes poses challenges to standardizing these treatments, necessitating further rigorous clinical trials. A multidisciplinary approach combining microbiology, immunology, neurology, and orthopaedics is essential to develop innovative, personalized pain management strategies rooted in gut health, with potential to transform orthopaedic pain care.},
}
@article {pmid40546415,
year = {2025},
author = {Bulletti, FM and Giacomucci, E and Guido, M and Palagiano, A and Coccia, ME and Bulletti, C},
title = {Revitalizing reproductive health: innovations and future frontiers in restorative medicine.},
journal = {Therapeutic advances in reproductive health},
volume = {19},
number = {},
pages = {26334941251345844},
pmid = {40546415},
issn = {2633-4941},
abstract = {BACKGROUND: Infertility affects around 17.5% of reproductive-aged individuals worldwide, posing significant personal and public health challenges. Although Medically Assisted Reproduction and Assisted Reproductive Technology (ART; e.g., in vitro fertilization) have advanced outcomes, many couples fail to conceive due to unaddressed pelvic, uterine, or systemic factors.<br><br>OBJECTIVES: We aim to (1) define the current usage of Restorative Reproduction Medicine (RRM) in clinical practice, (2) compare RRM outcomes with conventional ART, and (3) propose an integrated model of RRM plus ART for optimal fertility care.<br><br>DESIGN: A systematic review following PRISMA guidelines was conducted (INPLASY registration no. INPLASY2024110069).<br><br>DATA SOURCES AND METHODS: We searched PubMed, Scopus, and Web of Science (January 1995-October 2024), combining terms such as "restorative reproductive medicine," "intrauterine adhesions," "myomas," "polyps," "hydrosalpinx," "endometritis," "BMI," "thyroid dysfunction," "microbiome," and "assisted reproductive technology." Inclusion criteria: studies on uterine/systemic factors affecting infertility, focusing on surgical/pharmacological RRM interventions and ART limitations. Exclusion criteria: male-only infertility, case reports, narrative reviews, non-English publications. Quality assessment employed the Newcastle-Ottawa Scale and the Cochrane Risk of Bias Tool. We also briefly noted potential publication bias due to language and study-type restrictions.<br><br>RESULTS: From >25,000 initial titles, 3 sequential screenings yielded 145 key articles addressing uterine (septum, myomas, polyps, adhesions) and systemic (body mass index (BMI) extremes, thyroid dysfunction, microbiome imbalance) factors. Surgical corrections (e.g., hysteroscopic removal of polyps/myomas, salpingectomy for hydrosalpinx) significantly improved natural conception and ART success (&#x2a7e;20%-40% increase in clinical pregnancy). Chronic endometritis treatment, endometrial microbiome modulation, and BMI/thyroid optimization further improved pregnancy rates by 15%-20%. Comparisons of RRM versus ART alone indicated that RRM often lowers overall cost and may reduce miscarriage, while ART offers immediate embryo transfer. Combining RRM to correct pathologies prior to ART can boost implantation and live birth rates (&#x2a7e;40%-70% improvement in some studies).<br><br>CONCLUSION: Restorative Reproductive Medicine comprehensively addresses pelvic and systemic abnormalities, thereby enhancing fertility outcomes and complementing ART. A proposed integrated model-RRM diagnostics/interventions followed by ART if needed-maximizes success, reduces time/cost, and emphasizes holistic reproductive health. Further multicenter trials are warranted to standardize protocols and fully realize RRM's potential in modern fertility care.},
}
@article {pmid40546285,
year = {2025},
author = {Pei, X and Liu, M and Yu, S},
title = {How is the human microbiome linked to kidney stones?.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1602413},
pmid = {40546285},
issn = {2235-2988},
mesh = {Humans ; *Kidney Calculi/microbiology ; *Microbiota ; Dysbiosis/microbiology ; Gastrointestinal Microbiome ; Bacteria/classification/metabolism/isolation &amp; purification ; },
abstract = {In recent years, the incidence of kidney stones has continued to rise worldwide, and conventional treatments have limited efficacy in treating stones associated with recurrent or metabolic abnormalities. The microbiome, as the 'second genome' of the host, is involved in the development of kidney stones through metabolic regulation, immune homeostasis and inflammatory response. Studies have shown that the urinary microbiome of healthy people is dominated by commensal bacteria such as Lactobacillus and Streptococcus, which maintain microenvironmental homeostasis, whereas patients with renal stones have a significantly reduced diversity of intestinal and urinary microbiomes, with a reduced abundance of oxalic acid-degrading bacteria (e.g., Bifidobacterium oxalicum, Bifidobacterium bifidum), and a possible concentration of pathogenic bacteria (e.g., Proteus mirabilis). The microbiome regulates stone formation through mechanisms such as metabolites (e.g., short-chain fatty acids), changes in urine physicochemical properties (e.g., elevated pH), and imbalances in the inflammatory and immune microenvironments. For example, urease-producing bacteria promote magnesium ammonium phosphate stone formation through the breakdown of urea, whereas dysbiosis of the intestinal flora increases urinary oxalic acid excretion and exacerbates the risk of calcium oxalate stones. Microbiome-based diagnostic markers (e.g., elevated abundance of Aspergillus phylum) and targeted intervention strategies (e.g., probiotic supplementation, faecal bacteria transplantation) show potential for clinical application. However, technical bottlenecks (e.g., sequencing bias in low-biomass samples), mechanistic complexity (e.g., multistrain synergism), and individual heterogeneity remain major challenges for future research. Integration of multi-omics data, development of personalised therapies and interdisciplinary research will be the core directions to decipher the relationship between microbiome and kidney stones.},
}
@article {pmid40546016,
year = {2025},
author = {Xu, W and Shi, H and Li, Y},
title = {Effect of different feeding times on the structure of the intestinal flora of Rana dybowskii tadpole.},
journal = {Chronobiology international},
volume = {},
number = {},
pages = {1-11},
doi = {10.1080/07420528.2025.2519308},
pmid = {40546016},
issn = {1525-6073},
abstract = {Feeding time is a critical factor influencing the growth, feeding efficiency, and health of animals. This study aimed to investigate the impact of different feeding times on the gut microbiome composition in Rana dybowskii tadpoles over a 50-d period. Using 16S rRNA sequencing, we analyzed the gut microbiome at four feeding times: 6:00, 12:00, 18:00, and 24:00. Our results revealed that tadpoles fed at 12:00 and 18:00 grew significantly faster than those fed at 6:00 and 24:00. The highest microbial abundance and diversity were observed in the 12:00 feeding group. Additionally, three probiotic bacteria-Akkermansia muciniphila, Bacteroides ovatus, and Butyricicoccus pullicaecorum-were identified as dominant species in this group. These findings suggest that feeding time not only influences the composition and structure of the intestinal microbiota in R. dybowskii tadpoles but also affects their growth performance. These results highlight the importance of feeding time in improving tadpole health and farming efficiency.},
}
@article {pmid40545911,
year = {2025},
author = {Pizziolo, PG and Silva-Lovato, CH and Clemente, LM and Carandina, A and Salgado, HC and Silva, TMD and Tobaldini, E and Montano, N and Ribeiro, AB},
title = {The role of oral microbiota and tooth loss in cardiovascular disease risk: a systematic review.},
journal = {Biofouling},
volume = {},
number = {},
pages = {1-15},
doi = {10.1080/08927014.2025.2518280},
pmid = {40545911},
issn = {1029-2454},
abstract = {This systematic review explores the relationship between the oral microbiome in edentulous patients and cardiovascular diseases (CVD). A search was conducted across databases PubMed, Scopus, Web of Science, Embase, and gray literature sources. The review followed PRISMA and AMSTAR guidelines. After removing duplicates, the articles were evaluated by titles and abstracts, and 21 were selected for full-text review, with 9 ultimately included in the final analysis. Oral dysbiosis, linked to systemic conditions like obesity, diabetes, and CVD, is common in inflammatory oral diseases such as periodontitis and denture stomatitis, disrupting original oral microbiota. This imbalance may lead to transient bacteremia and systemic inflammation, contributing to CVD development. Tooth loss reduces salivary microbiome diversity, and denture use in CVD patients is linked to decreased life expectancy compared to dentate individuals. The findings suggest tooth loss, denture use, and oral microbiota dysbiosis are unconventional risk factors for CVD progression.},
}
@article {pmid40545707,
year = {2025},
author = {Nevot, G and Pol Cros, M and Toloza, L and Campamà-Sanz, N and Artigues-Lleixà, M and Aguilera, L and Güell, M},
title = {Engineered Marine Biofilms for Ocean Environment Monitoring.},
journal = {ACS synthetic biology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acssynbio.5c00192},
pmid = {40545707},
issn = {2161-5063},
abstract = {Marine bacteria offer a promising alternative for developing Engineered Living Materials (ELMs) tailored to marine applications. We engineered Dinoroseobacter shibae to increase its surface-associated growth and develop biosensors for ocean environment monitoring. By fusing the endogenous extracellular matrix amyloidogenic protein CsgA with mussel foot proteins, we significantly increased D. shibae biofilm formation. Additionally, D. shibae was engineered to express the tyrosinase enzyme to further enhance microbial attachment through post-translational modifications of tyrosine residues. By exploiting D. shibae's natural genetic resources, two environmental biosensors were created to detect temperature and oxygen. These biosensors were coupled with a CRISPR-based recording system to store transient gene expression in stable DNA arrays, enabling long-term environmental monitoring. These engineered strains highlight D. shibae's potential in advancing marine microbiome engineering for innovative biofilm applications, including the development of natural, self-renewing biological adhesives, environmental sensors, and "sentinel" cells equipped with CRISPR-recording technology to capture and store environmental signals.},
}
@article {pmid40545531,
year = {2025},
author = {Sun, Y and Keat, OB and Rajabi, S},
title = {The role of physical activity and epigenetic changes in colorectal cancer prevention.},
journal = {Cancer cell international},
volume = {25},
number = {1},
pages = {227},
pmid = {40545531},
issn = {1475-2867},
abstract = {Regular and consistent physical activity significantly reduces the risk of colorectal cancer (CRC) by approximately 24% in men and 23% in women. There are several mechanisms through which exercise can help protect against CRC. For example, it can reduce chronic inflammation, boost the immune system, and cause positive epigenetic changes like DNA methylation and histone modifications. It increases the activity of immune cells like natural killer cells and cytotoxic T lymphocytes, shifts macrophages to an anti-tumor state, and promotes a tumor-suppressive microenvironment. Exercise also positively affects the gut microbiome, increasing beneficial bacteria that produce anti-inflammatory short-chain fatty acids like butyrate, which strengthen gut health and support epigenetic regulation. Additionally, physical activity lowers oxidative stress, enhances DNA repair, and regulates hormones like insulin and IGF-1, which are associated with cancer progression. Although exercise benefits vary among individuals, especially between genders, it is still a powerful preventive and therapeutic tool for CRC. For patients and survivors, personalized exercise programs improve physical function, decrease fatigue, and improve overall quality of life. Overall, exercise offers a multifaceted approach to CRC prevention and management by targeting inflammation, immunity, epigenetics, and gut health, as this review explores.},
}
@article {pmid40545407,
year = {2025},
author = {Ricigliano, VA and Fine, JD and Nicklisch, SCT},
title = {Harnessing biotechnology for bee pollinator health.},
journal = {Trends in biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tibtech.2025.05.027},
pmid = {40545407},
issn = {1879-3096},
abstract = {Bees are vital to global food security and biodiversity but their populations are threatened by a steady flux of interacting stressors. Current mitigation strategies are failing to address the complexity and scale of these threats. Biotechnology offers innovative solutions to protect essential pollination services and secure the future of beekeeping. Omic tools guided by artificial intelligence can unlock new possibilities for strengthening bee populations and improve their ability to adapt to emerging challenges. Molecular and bio-based treatments offer precise, nonchemical inputs for managed hives. Synthetic biology enables engineered gut microbiomes, pollinator-friendly crops, and artificial diets that are tailored to bee health. We discuss recent progress and future directions of biotechnology to help bees cope with a rapidly changing world.},
}
@article {pmid40545364,
year = {2025},
author = {Nakanishi, E and Cornette, R and Shimura, S and Kikawada, T},
title = {Microbiome Associated with Polypedilum sp. (Diptera; Chironomidae), a Midge Adapted to an Extremely Acidic Environment.},
journal = {Microbes and environments},
volume = {40},
number = {2},
pages = {},
doi = {10.1264/jsme2.ME24090},
pmid = {40545364},
issn = {1347-4405},
mesh = {Animals ; *Chironomidae/microbiology/physiology/growth &amp; development ; Larva/microbiology ; RNA, Ribosomal, 16S/genetics ; Hydrogen-Ion Concentration ; *Microbiota ; Phylogeny ; *Bacteria/classification/genetics/isolation &amp; purification ; Japan ; Symbiosis ; DNA, Bacterial/genetics ; Rivers/chemistry ; Acids ; Sequence Analysis, DNA ; },
abstract = {Chironomids (Diptera; Chironomidae), non-biting midges, are a highly diverse family of holometabolous insects, many of which are known for their tolerance to extreme environmental conditions, such as desiccation, pollution, and high acidity. The contribution of microbial symbionts to these adaptations was recently suggested. Therefore, we herein exami-ned the microbiome associated with the larvae of the undescribed acid-tolerant chironomid species, Polypedilum sp., which inhabits the Yukawa River (Gunma, Japan), an environment that is characterized by an extremely low pH (≤2) and high concentrations of heavy metal ions (including arsenic). Amplicon sequencing of the 16S rRNA gene revealed a distinct larval microbiome with a lower alpha diversity value and more enriched and specific bacterial taxa than the surrounding river water and detritus. Full-length 16S rRNA gene sequencing using nanopore long-read technology identified several previously undescribed operational taxonomic units (OTUs), among which OTU_Bacillaceae_Yukawa was consistently present in larvae reared in the laboratory for more than 4 months, suggesting persistent, possibly vertically transmitted, symbiosis. An inferred pathway ana-lysis suggested the contribution of the larval microbiome to host nutritional physiology. The possibly acid-sensitive OTU_Bacillaceae_Yukawa localized to midgut segments, indicating internal pH-buffered niches for microbial survival. These results provide novel insights into the ecology of acid-tolerant chironomids and lay the groundwork for further examinations of holobiont-based stress tolerance.},
}
@article {pmid40545329,
year = {2025},
author = {Wolk, R and Kerr, AR},
title = {Diagnostic Adjuncts and Biopsy Techniques for Oral Potentially Malignant Disorders and Oral Cavity Squamous Cell Carcinoma.},
journal = {Dental clinics of North America},
volume = {69},
number = {3},
pages = {357-377},
doi = {10.1016/j.cden.2025.03.003},
pmid = {40545329},
issn = {1558-0512},
mesh = {Humans ; *Mouth Neoplasms/pathology/diagnosis ; Biopsy/methods ; *Carcinoma, Squamous Cell/pathology/diagnosis ; *Precancerous Conditions/pathology/diagnosis ; Microscopy, Confocal ; Leukoplakia, Oral/pathology/diagnosis ; Erythroplasia/pathology/diagnosis ; },
abstract = {Diagnostic adjuncts for oral potentially malignant disorders such as leukoplakia or erythroplakia can aid the clinician in triaging abnormal lesions and facilitate both biopsy site selection and surgical management. No adjuncts replace gold standard biopsy and histopathological examination, and their optimal use requires training and experience. This article covers the potential applications, both in primary and expert settings, of adjuncts, such as tissue autofluorescence, toluidine blues staining, and cytopathology. It covers new and emerging adjuncts such as confocal microscopy, liquid biopsy, oral microbiome testing, and the role of artificial intelligence. Incisional biopsy site selection and techniques will also be discussed.},
}
@article {pmid40545328,
year = {2025},
author = {Mehrnia, N and Sonis, S},
title = {Periodontitis and Oral Cancer Risk.},
journal = {Dental clinics of North America},
volume = {69},
number = {3},
pages = {347-355},
doi = {10.1016/j.cden.2025.03.008},
pmid = {40545328},
issn = {1558-0512},
mesh = {Humans ; *Mouth Neoplasms/etiology ; *Periodontitis/complications ; Risk Factors ; Oxidative Stress ; Disease Progression ; Cytokines ; },
abstract = {An association between periodontitis and oral cancer risk and progression has been suggested. It seems most likely that periodontitis plays an indirect role in oral cancer risk and progression in which its contribution to a chronic inflammatory state characterized by the persistent release of pro-inflammatory cytokines contributes to oxidative stress and DNA damage, potentially favoring carcinogenic processes. Periodontal health status of an individual may serve as a surrogate for general health as those factors which contribute to good general health, environment, lifestyle, and access to care are also determinants of oral health and impact cancer risk.},
}
@article {pmid40545143,
year = {2025},
author = {Ou, KJ and Du, J and Liu, G and Chapagain, A and Nuccio, DA and Singh, P and Kim, WK and Kwon, YM and Lei, XG},
title = {Efficacy and Biosafety of 25-Hydroxyvitamin D3 Biofortified in Egg Yolk in Mice Fed Two Levels of Dietary Fat.},
journal = {The Journal of nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tjnut.2025.06.011},
pmid = {40545143},
issn = {1541-6100},
abstract = {BACKGROUND: Vitamin D inadequacy remains a public health concern, particularly in obese individuals. Biofortified eggs with 25-hydroxyvitamin D3 [25(OH)D3] may increase intakes of the active metabolite of this nutrient by the public.<br><br>OBJECTIVE: This study determined efficacy, biosafety, and gut microbiome impact of 25(OH)D3 biofortified in egg yolk compared with a synthetic form in mice fed a control or high-fat diet (HFD).<br><br>METHODS: Reg3b[+/-] mice (n = 4 males + 4 females/group, 3-5 months old) were fed a control (CON) or HFD (12 or 60% kcal from fat) supplemented (per kg of diet) with 200 IU of 25(OH)D3 from the control yolk (BAS), the BAS + 500 IU of 25(OH)D3 from the synthetic form (SUP), or 700 IU of 25(OH)D3 from the biofortified yolk (YOL) for 8 weeks. Body weight, plasma concentrations of 25(OH)D3, osteocalcin, and receptor activator of nuclear factor kappa beta ligand, bone microtomography, bone-related genes and proteins, and colonic and fecal microbiome were examined. Data were analyzed by two-way analysis of variance.<br><br>RESULTS: The HFD-YOL group had 33.4% (P < 0.01) and 39.2% (P < 0.001) higher plasma 25(OH)D3 concentrations at week 8 than the HFD-SUP and CON-YOL groups, respectively. This elevation was associated with upregulated kidney mRNA levels of cytochrome P450 24A1 (Cyp24a1) and vitamin D receptor (Vdr). Both sources of 25(OH)D3 unaltered body weights, blood glucose concentration, plasma alkaline phosphatase activity, plasma osteocalcin concentrations, or bone characteristics but altered (P < 0.05) fecal microbiome compositions.<br><br>CONCLUSIONS: Compared with the synthetic form, 25(OH)D3 in the biofortified yolk led to higher plasma 25(OH)D3 concentrations in mice fed HFD. However, such efficacy in mice fed CON and impacts on fecal microbiome were similar between the two sources of 25(OH)D3. Our finding suggests biosafety and nutritional relevance for future human study of this novel food source of 25(OH)D3.},
}
@article {pmid40545094,
year = {2025},
author = {Wu, Y and Shao, Y and Shao, X and Yu, H and Wang, M and Wang, J and She, Y and Liu, J and Zhang, T and Li, Z and El-Aty, AMA},
title = {Qingke β-glucan and Lactobacillus mitigate neuroinflammation and enhance cognitive function in an Alzheimer's disease mouse model.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {145427},
doi = {10.1016/j.ijbiomac.2025.145427},
pmid = {40545094},
issn = {1879-0003},
abstract = {Alzheimer's disease (AD) is one of the most prevalent neurodegenerative disorders and substantially impacts cognitive health and quality of life. Qingke β-glucan (Q) and its combination with Lactobacillus (Q&amp;P) demonstrated a notable ability to alleviate anxiety behaviors and improve cognitive and learning memory deficits in APP/PS1 mice, a widely used model for AD. Q&amp;P effectively reduced amyloid-β accumulation and Tau phosphorylation, protecting neurons from degeneration. Additionally, it increased the mRNA expression of BDNF and SYP, reduced synaptic damage, and suppressed neuroinflammation by decreasing the mRNA levels of IL-6, IL-17 A, and IL-22. Q&amp;P also activated the Nrf2 signaling pathway, enhanced SOD activity, mitigated oxidative damage, and restored gut microbiota dysbiosis. Metabolomic and 16S rRNA sequencing analyses revealed significant modulation of the intestinal microbiome and metabolic pathways, with key roles identified for Lactobacillus, Muribaculum, Candidatus_Stoquefichus, and Coriobacteriaceae_UCG-002. These microbiota adjustments influence tryptophan and linoleic acid metabolism, contributing to reduced inflammation and oxidative stress and improving neuronal health. By enhancing the intestinal microenvironment and regulating metabolic and microbial profiles, Q&amp;P offers a sustainable and effective approach for preventing cognitive decline and promoting overall brain health in AD patients.},
}
@article {pmid40545077,
year = {2025},
author = {Yu, H and Dong, K and Fu, M and Wang, H and Wang, J and Zhang, Q and Yue, Y and Geng, L and Wu, N},
title = {The anti-hyperuricemia effects of polysaccharide from Saccharina japonica through gut-kidney axis.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {145336},
doi = {10.1016/j.ijbiomac.2025.145336},
pmid = {40545077},
issn = {1879-0003},
abstract = {Hyperuricemia (HUA), a global health burden affecting adults, drives progressive renal dysfunction and chronic inflammation. Current therapies exhibit limited efficacy and renal toxicity, necessitating safer multi-target agents. Here, we characterize a marine-derived heteropolysaccharide (SHP) from Saccharina japonica and demonstrate its pleiotropic anti-hyperuricemia effects. Hyperuricemic mice were established to evaluate anti-hyperuricemic effect of SHP. The correlative general physical parameters, renal histopathology, renal gene expressions, and gut microbiome were investigated in hyperuricemic mice by an enzyme-linked immunosorbent assay (ELISA), western blotting and Immunohistochemistry (IHC). Our results demonstrated that treatment with SHP significantly reduced serum uric acid, serum urea, and creatinine levels compared to the BLK group. Additionally, SHP downregulated inflammatory markers, and alleviated renal injury. Western blotting and IHC analyses revealed that SHP treatment upregulated the expression of key urate transporters, ABCG2 and galectin-9. Furthermore, 16S rRNA gene sequencing indicated that SHP modulated the gut microbiota by increasing the abundance of Lactobacillus. s. Together, this study provides experimental evidence that the potential of SHP as a natural therapeutic agent for hyperuricemia-related disorders. And also, this work providing new insights into multi-target therapeutic strategies and the critical link between natural polysaccharides and metabolic regulation.},
}
@article {pmid40545001,
year = {2025},
author = {Abrieux, A and Barboza, M and Hirahatake, K and Jacobs, H and Schmitz, HH and Adams, SH and Siegel, JB},
title = {A multi-omics framework to unlock the relationships between wine, food, and gut health.},
journal = {Advances in nutrition (Bethesda, Md.)},
volume = {},
number = {},
pages = {100468},
doi = {10.1016/j.advnut.2025.100468},
pmid = {40545001},
issn = {2156-5376},
abstract = {Wine has long been studied for its cardioprotective effects, exemplified by the French Paradox-the observation of relatively lower cardiovascular disease (CVD) rates in the French population despite high dietary cholesterol and saturated fat intake, historically attributed to resveratrol and other bioactive factors from wine consumption. Recent findings suggest that the moderate consumption of wine could impact health well beyond CVD risk, including effects on intestinal physiology and gut microbial diversity and function. For example, wine contains a rich array of polyphenols, organic acids, and oligosaccharides, which may interact with the gut microbiota to alter microbial communities and to promote metabolism of wine-derived compounds into a diverse range of xenometabolites (microbe-produced metabolites) with local and systemic effects on the host. This interplay underscores the potential mechanisms by which moderate wine consumption impacts gut and systemic health. Furthermore, since wine is often consumed with meals, there is a critical need to understand how specific foods intersect with wine's chemical complexity to influence physiology in the gut and body-wide. This review explores how advancements in multi-omics technologies can be leveraged to characterize wine's "dark matter" and to consider interactions of wine components with complex food matrices to influence gut health. This framework holds potential to enhance our understanding of how moderate consumption of wine influences health and to inform the development of functional food innovations derived from wine's molecular components.},
}
@article {pmid40544839,
year = {2025},
author = {Pina-Vaz, T and Costa Silva, A and Costa, G and Gonçalves, M and Fernandes, A and Carmo Reis, F and Nobre, P and Lisboa, C and Rodrigues, A and Alturas-Silva, J and Martins-Silva, C},
title = {Sexually Transmitted Infections in Prostate Cancer: A Prospective Multicenter Analysis.},
journal = {Urologia internationalis},
volume = {},
number = {},
pages = {1-13},
doi = {10.1159/000545208},
pmid = {40544839},
issn = {1423-0399},
abstract = {OBJECTIVE: Chronic inflammation and infections have been implicated in prostate cancer (PCa) pathogenesis. The association between sexually transmitted infections (STIs) and PCa remains inconclusive. The objective was to evaluate the presence of STI-related pathogens in patients with PCa compared to a control group.<br><br>METHODS: A prospective multicenter study involving 239 male patients with a clinical suspicion of PCa was conducted. Among the participants, 176 had histologically confirmed PCa, while 63 served as controls with benign histology. Urine, glans swabs, and prostate biopsy specimens were collected from each participant and analyzed using polymerase chain reaction (PCR) to detect a broad panel of STI-causing pathogens, including Candida spp., Chlamydia trachomatis, Mycoplasma genitalium, Neisseria gonorrhoeae, Trichomonas vaginalis, herpes simplex virus types 1 and 2, and human papillomavirus.<br><br>RESULTS: A total of 717 samples were processed. The detection frequency of STI-related pathogens was relatively low across all sample types. Mycoplasma genitalium was the most frequently detected pathogen, particularly in prostate biopsy samples. No statistically significant association was found between the presence of these pathogens and the incidence of PCa. Neisseria gonorrhoeae and Candida spp. were not detected in any of the samples.<br><br>CONCLUSION: This study did not find a statistically significant association between the presence of STIs and PCa. The low prevalence of STI pathogens despite the use of highly sensitive PCR methods suggests that these infections may play a limited role in prostate carcinogenesis. Future research should consider focusing on the role of the urinary and prostatic microbiome in chronic prostatic inflammation.},
}
@article {pmid40544684,
year = {2025},
author = {Eckermann, C and Klein, CJ and Schäfer, F and Thiel, M and Weiss, AV and Motz, C and Lienkamp, K and Hannig, M and Schneider, M},
title = {Probiotics-embedded polymer films for oral health: Development, characterization, and therapeutic potential.},
journal = {Colloids and surfaces. B, Biointerfaces},
volume = {255},
number = {},
pages = {114886},
doi = {10.1016/j.colsurfb.2025.114886},
pmid = {40544684},
issn = {1873-4367},
abstract = {The oral microbiome plays a crucial role in maintaining homeostasis, and microbial imbalances contribute to diseases such as periodontitis. Probiotic strains such as Lactobacillus rhamnosus and Lactobacillus reuteri have shown potential in restoring microbial balance in the oral cavity. However, their application remains challenging due to limited survival and adherence under intraoral conditions. Thus, we aimed to develop and evaluate mucoadhesive polymer films for local probiotic delivery. L. rhamnosus and L. reuteri were microencapsulated via spray drying and embedded in films composed of hydroxypropyl methylcellulose-polyvinyl alcohol (HPMC-PVA) and foamed polyvinyl alcohol (PVA). The films were characterized in terms of bacterial viability, tensile strength, folding endurance, and mucoadhesive properties. A proof-of-concept in vivo study was conducted by intraorally exposing enamel samples to two volunteers for eight hours, followed by confocal imaging and morphological analysis of adherent bacteria. Microencapsulation preserved high bacterial viability. The resulting films exhibited suitable mechanical properties and strong mucoadhesion. Biological evaluation revealed clear effects: films containing microencapsulated bacteria led to a statistically significant increase in adherent rod-shaped lactobacilli and a consistent reduction in coccoid bacteria associated with dysbiosis. The foamed PVA formulation showed the most pronounced modulation of the enamel-associated microbiota. These findings demonstrate that probiotic films can enable both bacterial stabilization and effective oral delivery. The system enhances colonization by beneficial bacteria while reducing potentially pathogenic cocci. This approach presents a promising strategy for microbiome-based prevention of oral diseases and merits further clinical investigation.},
}
@article {pmid40544677,
year = {2025},
author = {Bortoluzzi, C and Watson, M and Iuspa, MA and Lumpkins, B and Mathis, G and Jones, M and Hofacre, C},
title = {Precision biotics enhance growth performance in broiler chickens by selectively modifying their intestinal microbiome to better respond to enteric challenges.},
journal = {Poultry science},
volume = {104},
number = {9},
pages = {105454},
doi = {10.1016/j.psj.2025.105454},
pmid = {40544677},
issn = {1525-3171},
abstract = {Precision biotics (PB) are innovative feed additives designed to influence key metabolic pathways in the microbiome, particularly those involved in short-chain fatty acid (SCFA) production. These SCFAs are crucial for the healthy development and functionality of the gastrointestinal tract (GIT) in chickens. Our hypothesis was that adding a glycan-based PB to the diet would steer microbial metabolism towards increased SCFA production in the ceca, thereby reducing the adverse effects of necrotic enteritis (NE) in chickens. These studies evaluated the supplementation of PB on the cecal microbiome and growth performance in broiler chickens exposed to a necrotic enteritis (NE) challenge. Experiment 1: Day-old chicks were assigned to three treatment groups: a control, a challenged control, and a challenged group supplemented with PB. The birds were vaccinated for coccidiosis at day 0 and challenged with Clostridium perfringens. Cecal content was collected from one bird per pen on days 22 and 42 for microbiome analysis. Experiment 2: Day-old chicks were again assigned to three treatments: control, challenged control, and challenged with PB. All birds were vaccinated for coccidiosis and challenged with Eimeria maxima on day 14 and later with C. perfringens. On day 21, birds were euthanized for NE lesion scoring. In Exp. 1, the supplementation of PB significantly improved (P < 0.05) the growth performance of the challenged birds. An increased relative abundance of species related to SCFA production was observed on day 42, including several Faecalibacterium species (P < 0.05). This was paired with an increased relative abundance of both propionate (P<0.05) and butyrate pathways in birds with PB supplementation. In Exp. 2, on day 21, the challenge impaired growth performance, but the supplementation of PB counteracted this effect (P < 0.05). On day 42, the supplementation of PB improved BW by 10 % (P < 0.0001), and the FCR by 8.4 % (P < 0.0001) when compared to the challenged group. The supplementation of PB reduced NE associated mortality (5.5 vs 0.5 %; P = 0.002) and reduced the lesions characteristic of NE (P < 0.0001). Taken together, the microbiome metabolic shift observed with the supplementation of PB explains the improvement in growth performance, resilience to enteric stress and faster recovery of the intestine, which consequently improves welfare and the sustainability of poultry production.},
}
@article {pmid40544564,
year = {2025},
author = {Wang, B and Sun, W and Ye, X and Hoskins, TD and Han, Y and Yuan, X and Chen, Q and Liu, Z and Zhang, H},
title = {Sustained exposure to triclocarban and triclosan at environmental relevant concentration disrupts gut-liver axis in the black-spotted frog.},
journal = {Aquatic toxicology (Amsterdam, Netherlands)},
volume = {286},
number = {},
pages = {107463},
doi = {10.1016/j.aquatox.2025.107463},
pmid = {40544564},
issn = {1879-1514},
abstract = {Triclocarban (TCC) and triclosan (TCS) are broad-spectrum biocides that are extensively utilized frequently contaminate water bodies and have high environmental persistence. However, the safety of TCC and TCS for wild organisms remains largely unknown. Here, we evaluated the potential health risks for black-spotted frogs (Pelophylax nigromaculatus) when exposed to TCC and TCS at concentrations of 1, 10, and 100 μg/L for 21 consecutive days. TCC and TCS significantly disrupted the gut microbiome, specifically phylum Proteobacteria, which resulted in elevated serum levels of lipopolysaccharide (LPS), a bacterial endotoxin. After entering the bloodstream, LPS subsequently passes through the liver, where inflammatory cytokines are stimulated, including interleukin-1 β, interleukin-6, and tumor necrosis factor-alpha. Genes related to the inflammatory processes are also activated. This inflammatory response led to an increase in the activity of superoxide anion radicals and oxidative stress markers in the liver, mainly superoxide dismutase, catalase, glutathione peroxidase, and malondialdehyde. In addition to oxidative stress, damage to the liver has also been reported as elevated concentrations of alanine aminotransferase (ALT) and aspartate aminotransferase (AST). Collectively, these findings suggest that TCC and TCS exert hepatotoxic effects on frogs by disrupting the gut-liver axis, thereby inducing hepatic inflammation and oxidative stress. This study highlights the potential health risks posed by TCC and TCS exposure in wild organisms.},
}
@article {pmid40544522,
year = {2025},
author = {Zhong, F and Wei, X and Huang, M and Yan, H and Fu, L and Liu, X and Ru, H and Mo, X and Su, Z and Yan, L},
title = {Significance of Fusobacterium nucleatum Combined with SFRP2 and SDC2 Gene Methylation Detection in Early Screening of Colorectal Cancer.},
journal = {Polish journal of microbiology},
volume = {74},
number = {2},
pages = {218-231},
doi = {10.33073/pjm-2025-018},
pmid = {40544522},
issn = {2544-4646},
mesh = {Humans ; *Colorectal Neoplasms/diagnosis/genetics/microbiology ; *Syndecan-2/genetics/metabolism ; *Fusobacterium nucleatum/genetics/isolation &amp; purification ; *Early Detection of Cancer/methods ; *Membrane Proteins/genetics/metabolism ; *DNA Methylation ; Male ; Female ; Middle Aged ; Biomarkers, Tumor/genetics ; Feces/microbiology ; Aged ; },
abstract = {This study aimed to explore the combined detection of secreted frizzled-related protein-2 (SFRP2), Syndecan-2 (SDC2), and Fusobacterium nucleatum (Fn) in fecal samples for early colorectal cancer (CRC) screening. Public datasets were analyzed to evaluate the expression of SFRP2, SDC2, and Fn. The study included 30 pairs of tissue and 196 fecal samples. Gene expression of SFRP2, SDC2, F. nucleatum antigen adhesinA (fadA), and N-utilization substance G (nusG) was measured by qPCR. Correlations with Ki67, P53 expression, and immune infiltration were examined. The diagnostic performance of the combined markers was assessed using ROC curve analysis. SFRP2 and SDC2 were underexpressed (p < 0.001), while Fn was notably enriched in CRC (p < 0.0001). Expression of SFRP2 and SDC2 correlated with immune cell infiltration, whereas Fn abundance showed a negative correlation with immune infiltration. ROC analysis indicated that the combined detection of these markers outperformed single-gene tests, CEA, and FOBT in early CRC detection. This combined detection approach offers a promising, non-invasive, and cost-effective method for early CRC screening.},
}
@article {pmid40544520,
year = {2025},
author = {Zhang, E and Gong, GA and Huang, S and Bao, Y and Ji, L and Yang, S and Shen, Q and Wang, X and Wu, P and Liu, Y and Zhang, W},
title = {Viral Metagenomics of the Bharal (Pseudois nayaur) within the Qinghai-Tibet Plateau Revealed Diverse Viruses.},
journal = {Polish journal of microbiology},
volume = {74},
number = {2},
pages = {143-152},
doi = {10.33073/pjm-2025-012},
pmid = {40544520},
issn = {2544-4646},
mesh = {Animals ; *Metagenomics ; Phylogeny ; Genome, Viral ; Tibet ; Feces/virology ; *Viruses/genetics/classification/isolation &amp; purification ; Genetic Variation ; },
abstract = {The Qinghai-Tibetan Plateau (QTP) provides a home to diverse flora and fauna, and its ecosystems are unique worldwide. The study focused on the bharal, an endemic species found in the QTP and adjacent regions. We applied viral metagenomics technology to extract samples from the feces of 10 wild bharal. Viral nucleic acids were isolated, enriched, and sequenced from these samples, revealing the presence of a novel strain of Astroviridae virus. Phylogenetic analysis and sequence comparison identified this virus as part of the Mamastro-virus, forming a cluster with other Mamastrovirus species. Recombination analysis confirmed a multiple recombination event, suggesting that the new strain may be a potential recombinant. Additionally, nearly complete genome sequences of viruses belonging to the family Circoviridae were characterized, and a phylogenetic tree was constructed based on genotyping and predicted amino acid sequence analysis of the rep protein. Overall, this study helps us better understand the viral communities in the gut microbiome of the rare bharal. Moreover, the new recombinant discovered in this study will provide insights into the origin, genetic diversity, and evolution of bharal from the QTP and play a crucial role in future research on its presence in the intestinal ecology of sheep.},
}
@article {pmid40544519,
year = {2025},
author = {Yu, X and Liang, J and Yang, R and Gai, W and Zheng, Y},
title = {Clinical Features and Value of Tracheal Aspirate Metagenomic Next-Generation Sequencing for Severe Pneumonia in Children in Pediatric Intensive Care Unit.},
journal = {Polish journal of microbiology},
volume = {74},
number = {2},
pages = {192-205},
doi = {10.33073/pjm-2025-016},
pmid = {40544519},
issn = {2544-4646},
mesh = {Humans ; Infant ; *High-Throughput Nucleotide Sequencing ; Male ; Child, Preschool ; Female ; *Metagenomics/methods ; Child ; Intensive Care Units, Pediatric ; *Trachea/microbiology ; *Pneumonia/microbiology/diagnosis/virology ; Microbiota/genetics ; Bacteria/genetics/classification/isolation &amp; purification ; Coinfection/microbiology ; },
abstract = {Pneumonia is a leading cause of mortality in children. While metagenomic next-generation sequencing (mNGS) has the potential to detect all the microorganisms in pneumonia patients, the relationship between these microorganisms and the patients' clinical characteristics remains to be established. Fifty-five children, diagnosed with severe pneumonia and undergoing tracheal aspirate (TA) mNGS for pathogen detection at The Heilongjiang Hospital of Beijing Children's Hospital between July 2021 and November 2022, were included in this study. The clinical characteristics, pathogen distribution, and microbiome features of these children were analyzed. Results showed that the rate of mixed infections was notably high (80%, 44/55), with bacterial-viral infections being the most common. Streptococcus pneumoniae, Mycoplasma pneumoniae (MP), Candida albicans, and Respiratory syncytial virus (RSV) were the most common pathogens in this cohort. Furthermore, RSV and S. pneumoniae were the most prevalent pathogens in children younger than 12 months (infants), while MP and Haemophilus influenzae were more commonly identified in children between 12 and 144 months. Increased richness and diversity of the microbiota were observed in the TA of the older children. Linear discriminant analysis (LDA) effect size (LEfSe) analysis identified that RSV and Streptococcus mitis were the specific species associated with infants. In contrast, Human bocaparvovirus 1 and Prevotella histicola were significantly enriched in the older children. In addition, the top 20 most abundant species exhibited correlations with neutrophil count and C-reactive protein. This study emphasizes the significance of employing mNGS to understand better the clinical characteristics and microbial diversity in pediatric patients with severe pneumonia.},
}
@article {pmid40544517,
year = {2025},
author = {Cen, L and Qin, L and Chen, W and Wei, L and Tang, C and Teng, X and Tian, Z},
title = {Causal Relationship between Gut Microbiota and Pulmonary Embolism: An Analysis Using Mendelian Randomization.},
journal = {Polish journal of microbiology},
volume = {74},
number = {2},
pages = {153-164},
doi = {10.33073/pjm-2025-013},
pmid = {40544517},
issn = {2544-4646},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Mendelian Randomization Analysis ; *Pulmonary Embolism/microbiology/genetics ; Polymorphism, Single Nucleotide ; Genome-Wide Association Study ; Bacteria/classification/genetics/isolation &amp; purification ; },
abstract = {Previous research has demonstrated a connection between an unbalanced gut microbiome (GM) and lung diseases, suggesting that gut bacteria may affect lung health through the "gut-lung" axis. However, the direct connection between GM and pulmonary embolism (PE) is unclear. Mendelian randomization studies were used to investigate GM's genetic relationship with PE. A total of 18,340 independent genewide association studies (GWAS) yielded single nucleotide polymorphisms (SNPs) linked to the GM, which were then used as instrumental variables in a multiple regression analysis (MR) to examine the effect of GM on the risk of PE within the IEU Open GWAS project, which included 2,118 PE cases and 359,076 controls. The principal analytical methodology utilized in this research was inverse variance weighting (IVW), complemented by assessments for pleiotropy and heterogeneity to confirm the results' resilience. The findings of this study are predominantly derived from the IVW method, providing evidence for causal associations between four distinct genera of GM and the risk of PE. Specifically, our analysis suggests that Slackia (p = 0.031), Oscillospira (p = 0.038), Bacteroides (p = 0.032), and Clostridium sensu stricto 1 (p = 0.049) may be linked to a decreased likelihood of developing PE. Importantly, our analysis yielded no evidence of heterogeneity or pleiotropy. In this MR study, we have established through genetic analysis that specific GM are significantly involved in the development of PE, underscoring the connection between the gut-lung axis and suggesting avenues for future research into the impact of GM on PE.},
}
@article {pmid40544514,
year = {2025},
author = {Gao, Y and Ma, J and Wang, K and Ma, K and Zhao, W and Su, J and Ma, L},
title = {Roles of Gut Microbiota and Associated Metabolites in Clostridioides difficile Infection.},
journal = {Polish journal of microbiology},
volume = {74},
number = {2},
pages = {206-217},
doi = {10.33073/pjm-2025-017},
pmid = {40544514},
issn = {2544-4646},
mesh = {*Gastrointestinal Microbiome ; Humans ; *Clostridium Infections/microbiology/metabolism ; *Clostridioides difficile ; Mendelian Randomization Analysis ; Male ; Female ; Bacteria/classification/metabolism/genetics/isolation &amp; purification ; Netherlands ; Proteobacteria/metabolism/genetics ; },
abstract = {Clostridioides difficile infection (CDI), is the most common healthcare problem primarily involving the colon of individuals who's gut microbiota has been disrupted. Proteobacteria (officially updated and recognized as Pseudomonadota), a minor gut-associated microbial community within a healthy host, could serve as a metric for CDI. However, the alterations of specific members of Proteobacteria in the context of CDI are not thoroughly understood. Based on the summary data of microbiome from 7,738 participants in the Dutch cohort, linkage disequilibrium score regression (LDSC) was used to explore the causal effect of 207 gut microbiome on CDI. Secondly, we performed a Mendelian randomization analysis to investigate the causal relationship between 31 microbiota taxa affiliated with Proteobacteria and CDI. Finally, three significant taxa (p < 0.05, OR > 1) were utilized to conduct the mediation analysis of 1,400 metabolites based on a two-step Mendelian randomization study (two-step MR). The inverse-variance weighted method was conducted as a primary analysis to estimate the causal effect, and the robustness of the results was tested via sensitivity analysis using multiple methods. Bivariate LDSC analysis identified a strong correlation between four populations affiliated with Proteobacteria (Pasteurellaceae, Haemophilus, Pasteurellales and Haemophilus parainfluenzae) and CDI. In two-step MR, Burkholderiales order exerted detrimental effects on CDI by decreasing the levels of 3-hydroxylaurate (OR 0.896; 95%CI, 0.803-0.998; p = 0.047), indicating that metabolite did act as mediator between gut microbiota and CDI. We conducted a study to assess the relations between genetically predicted gut microbiota and metabolite levels with CDI. These results highlight the potential of targeting Burkholderiales and 3-hydroxylaurate as a new antimicrobial strategy against CDI.},
}
@article {pmid40544396,
year = {2025},
author = {Li, P and Sun, Z and Chen, X and Shao, Q and Wu, H},
title = {Mapping current research status and emerging frontiers of lipidomics: a comprehensive data-mining-based study.},
journal = {Metabolomics : Official journal of the Metabolomic Society},
volume = {21},
number = {4},
pages = {85},
pmid = {40544396},
issn = {1573-3890},
support = {LHGJ20240576, LHGJ20190948)//Union Project of Medical and Technology Research Program of Henan Province/ ; },
mesh = {*Lipidomics/methods/trends ; Humans ; *Data Mining/methods ; Bibliometrics ; *Lipid Metabolism ; Lipids ; },
abstract = {BACKGROUND: Lipids are crucial biomolecules involved in various biological processes, with changes in lipid profiles closely linked to the development of multiple disorders. Recent advances in lipidomics have transformed our understanding of lipid metabolism, yet challenges remain, highlighting the need for a comprehensive bibliometric study to identify current research status and emerging frontiers in this rapidly evolving field.<br><br>METHODS: This study collected publications related to lipidomics from the Web of Science Core Collection database. Bibliometric visualization was conducted using VOSviewer, CiteSpace, and an online analytical platform. A variety of bibliometric methods were employed, including co-authorship analysis, co-occurrence analysis, co-citation analysis, cluster analysis, and burst detection.<br><br>RESULTS: A total of 7989 papers including 6961 research articles and 1028 review papers were identified. Over the past two decades, the annual number of publications on lipidomics has shown an overall increasing trend (R[2]&#x2009;=&#x2009;0.933). In terms of contributors, the United States and China have maintained their prominence, with the highest output and the most financial support. At the institutional and individual levels, the University of California System and professor Han Xianlin produced the largest number of papers related to lipidomics. By analyzing the trends in disciplinary flow, this study reveals the increasingly close relationship between fields such as molecular biology, genetics, and clinical medicine, as well as materials science. Obesity was the most studied disease in this domain, followed by Alzheimer's disease, non-alcoholic fatty liver disease, type 2 diabetes, as well as metabolic syndrome. Keywords analysis reveals that the current research focus in the field centered around omics approaches in lipidomics, inflammation and oxidative stress, biomarkers and diagnostic applications, analytical techniques of lipidomics, and lipid metabolism and disease mechanisms. And in the future, the following topics including lipid metabolism and disease pathology, microbiome and lipid interactions, ferroptosis and lipid peroxidation, emerging therapeutic approaches and technologies, as well as technological advancements in lipidomics, are continuing to receive sustained attention.<br><br>CONCLUSIONS: This bibliometric analysis, for the first time, provides a detailed overview of the knowledge structure and highlights the evolving research trends in lipidomics over the past two decades. The systematic summary offers a clear and comprehensive understanding of lipidomics, and also deliver valuable perspectives for future research in this field.},
}
@article {pmid40544319,
year = {2025},
author = {Cao, X and Yuan, Q and Hu, C and Zhang, H and Sun, X and Yan, B and Ma, X and Zhang, L and Huang, L and Li, S and Zhang, Z},
title = {Wild wisdom meets cultivation: comparative rhizomicrobiome analysis unveils the key role of Paraburkholderia in growth promotion and disease suppression in Coptis chinensis.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {150},
pmid = {40544319},
issn = {2049-2618},
support = {2060302-2301-09//Key project at central government level/ ; 2060302-2101-13//Key project at central government level/ ; },
mesh = {Rhizosphere ; Soil Microbiology ; *Coptis/microbiology/growth &amp; development ; *Plant Diseases/microbiology/prevention &amp; control ; *Burkholderiaceae/isolation &amp; purification/genetics/physiology/classification ; Plant Roots/microbiology ; *Microbiota ; Phylogeny ; Fungi/classification/isolation &amp; purification/genetics ; },
abstract = {BACKGROUND: The sustained monoculture and irregular planting practices rendered the cultivated Coptis chinensis more prone to various diseases compared to its wild counterparts. Rewilding the rhizomicrobiome of cultivated plants has emerged as a promising strategy to promote plant growth, but ancestral microbiota suitable for C. chinensis remain largely uncharted.<br><br>RESULTS: The amplicon data analyses revealed that habitat transition strongly influenced the rhizosphere microbial communities. The rhizomicrobiomes of wild C. chinensis encompassed a more diverse array of ecological groups and exhibited a greater functional diversity compared to their cultivated counterparts. A higher proportion of beneficial fungi was observed in the rhizosphere of wild C. chinensis, while the cultivated plants had a higher population of pathogenic fungi. Furthermore, a well-documented plant-growth-promoting rhizobacterium genus, Paraburkholderia, was found to play an essential role in the resistance of the wild C. chinensis to potential disease caused by Ilyonectria. Two strains of Paraburkholderia (Paraburkholderia nemoris and Paraburkholderia phytofirmans) were isolated, and in vitro experiments confirmed that these isolates possess various growth-promoting properties and antagonistic activities against known pathogens for C. chinensis root rot. Both of the Paraburkholderia isolates could markedly promote the plant immune response and enhance the overall health of the cultivated C. chinensis.<br><br>CONCLUSIONS: By a comprehensive comparison of the rhizosphere microbiome between wild and cultivated C. chinensis, the promising bacterial genus Paraburkholderia was identified as a beneficial microbe significantly promoting the growth of C. chinensis, providing pivotal insights for future endeavors aimed at engineering the rhizosphere microbiome of C. chinensis, as well as other medicinal herbs. Video Abstract.},
}
@article {pmid40544290,
year = {2025},
author = {Chege, MN and Ferretti, P and Webb, S and Macharia, RW and Obiero, G and Kamau, J and Alberts, SC and Tung, J and Akinyi, MY and Archie, EA},
title = {Eukaryotic composition across seasons and social groups in the gut microbiota of wild baboons.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {70},
pmid = {40544290},
issn = {2524-4671},
support = {R01 AG071684/NH/NIH HHS/United States ; R01 AG071684/NH/NIH HHS/United States ; DEB 1840223//National Science Foundation/ ; },
abstract = {BACKGROUND: Animals coexist with complex microbiota, including bacteria, viruses, and eukaryotes (e.g., fungi, protists, and helminths). While high-throughput sequencing is commonly used to characterize bacterial communities in animal microbiota, these methods are less often applied to gut eukaryotic composition. Here we used shotgun metagenomic sequencing to characterize eukaryotic diversity in the microbiomes of wild baboons and tested the degree to which eukaryotic community composition was predicted by host social group membership, sex, age, sequencing depth, and season of sample collection.<br><br>RESULTS: We analyzed a total of 75 fecal samples collected in 2012 and 2014 from 73 wild baboons in the Amboseli ecosystem in Kenya. DNA from these samples was subjected to shotgun metagenomic sequencing, revealing members of the kingdoms Protista, Chromista, and Fungi in 90.7%, 46.7%, and 20.3% of all samples, respectively (percentages indicate the percent of samples in which each kingdom was observed). Social group membership explained 11.2% of the global diversity in gut eukaryotic species composition, but we did not detect statistically significant effects of season, host age, or host sex. Across samples, the most prevalent protists were Entamoeba coli (74.66% of samples), Enteromonas hominis (53.33% of samples), and Blastocystis subtype 3 (38.66% of samples), while the most prevalent fungi included Pichia manshurica (14.66% of samples), and Ogataea naganishii (6.66% of samples).<br><br>CONCLUSIONS: Protista, Chromista, and Fungi are common members of the gut microbiome of wild baboons. More work on eukaryotic members of primate gut microbiota is important for primate health monitoring and management strategies.},
}
@article {pmid40544285,
year = {2025},
author = {Kilama, J and Islam, S and Amat, S},
title = {Correction: Bovine ocular microbiome: the next frontier in managing pinkeye in cattle.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {69},
pmid = {40544285},
issn = {2524-4671},
}
@article {pmid40544178,
year = {2025},
author = {Qiu, YS and Ye, C and Li, Q and Jiang, LC and Zhou, CC and Fu, H and Li, DJ and Chen, D and Shen, FM},
title = {Improved gut microbiota by selenium-enriched Bifidobacterium longum DD98 alleviates chemotherapy-induced intestinal mucositis via inhibiting the STING pathway.},
journal = {NPJ science of food},
volume = {9},
number = {1},
pages = {107},
pmid = {40544178},
issn = {2396-8370},
support = {82003638//National Natural Science Foundation of China/ ; 82204537//National Natural Science Foundation of China/ ; 24SF1900902//Shanghai Science and Technology Innovation Action Plan/ ; },
abstract = {Intestinal mucositis, a common chemotherapy side effect, lacks effective treatments. This study evaluated the protective effect of selenium-enriched Bifidobacterium longum DD98 (SeDD98) on irinotecan-induced intestinal mucositis. Irinotecan caused intestinal mucositis, characterized by weight loss, severe diarrhea, damaged intestinal structure, reduced tight junction proteins, and gut dysbiosis. These effects could be inhibited by SeDD98. Additionally, fecal microbiota from SeDD98-treated mice protected against intestinal mucositis. Mechanistically, irinotecan activated the stimulator of interferon genes (STING) / nuclear factor kappa-B (NF-κB) pathway, whereas SeDD98 and fecal microbiota from SeDD98-treated mice suppressed this activation. Furthermore, depletion of gut microbiota by a broad-spectrum antibiotic cocktail (ABX) blunted the protective effect of SeDD98 and its inhibition of the STING/NF-κB pathway. These findings suggest that SeDD98 could protect against intestinal mucositis via inhibiting the STING/NF-κB pathway, likely through improving gut microbiota. Overall, SeDD98 may be a potential therapeutic agent for preventing chemotherapy-induced intestinal mucositis via gut microbiome improvement.},
}
@article {pmid40543864,
year = {2025},
author = {Peng, P and Yan, X and Chen, L and Li, X and Yang, H and Miao, Y and Zhao, F},
title = {Electroactive biofilm enhances synergistic degradation of sulfamethoxazole and roxarsone in actual livestock wastewater: extracellular electron transfer drives metabolic network remodeling.},
journal = {Environmental research},
volume = {},
number = {},
pages = {122173},
doi = {10.1016/j.envres.2025.122173},
pmid = {40543864},
issn = {1096-0953},
abstract = {Livestock wastewater is characterized by high concentrations of organic matter and diverse antibiotics. A major challenge in its anaerobic treatment is the effective degradation and thorough removal of coexisting antibiotic contaminants. In this study, an external voltage was applied to establish an electroactive biofilm, thereby enhancing the co-metabolic degradation of sulfamethoxazole and roxarsone. Application of +0.6 V (Ag/AgCl) increased the 72 h TOC removal efficiency to 52.1%. At the same time, sulfamethoxazole and roxarsone removal efficiencies reached 90.8% and 100%, respectively. The results from liquid chromatography-mass spectrometry (HPLC-MS/MS) and density functional theory (DFT) calculations revealed sulfamethoxazole degradation pathways: N-O bond cleavage and hydroxylation. Roxarsone degradation primarily involved nitro group reduction and C-As bond cleavage. The pharmacophore of sulfamethoxazole was effectively removed, and inorganic arsenic from roxarsone degradation was efficiently immobilized. Toxicity analysis confirmed that the electroactive biofilm notably reduced toxic intermediate accumulation. Elevated concentrations of NADH and ATP in the electroactive biofilm indicated enhanced microbial substrate metabolism and generation of more electron donors. The higher absolute abundance of the sulfamethoxazole degradation gene (SadABC) in the electroactive biofilm indicated that sulfamethoxazole degrading enzyme (sadABC) gained more electrons. Microbiome analysis revealed the upregulation of genes linked to extracellular electron transfer (EET), the tricarboxylic acid (TCA) cycle, nitro-reduction, and sulfate reduction pathway, confirming the electroactive biofilm enhances substrate metabolism and co-metabolic antibiotic degradation. Electroactive biofilm offers a viable strategy for antibiotic removal in livestock wastewater.},
}
@article {pmid40543709,
year = {2025},
author = {Brehm, V and Wang, Z and Rocha, L and Jones, B and Jenq, RR and Chang, CC and Cheng, GS and Hsu, J and Sharifi, H and Yanik, G and Luna, L and Waqar, A and Zaveri, J and Dickey, BF and Bashoura, L and Shpall, EJ and Zinter, M and O'Dwyer, D and Champlin, RE and Chen, G and Alousi, A and Paczesny, S and Peterson, CB and Sheshadri, A},
title = {Inflammatory markers and microbiome dysbiosis in hematopoietic cell transplant recipients with lung graft-versus-host disease.},
journal = {Transplantation and cellular therapy},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jtct.2025.06.020},
pmid = {40543709},
issn = {2666-6367},
abstract = {Bronchiolitis obliterans (BOS) is a manifestation of pulmonary chronic graft versus host disease (cGVHD) and is a devastating complication of allogenic hematopoietic stem cell transplantation (HCT). Early detection and treatment of BOS may improve outcomes, but biomarkers which accurately identify BOS early are lacking. We aimed to determine whether certain validated cGVHD markers could also accurately diagnose BOS as compared to patients without BOS and with or without extrapulmonary cGVHD. In addition, we sought to determine whether dysbiosis of gut or oral microbiomes was associated with BOS or with inflammatory biomarkers. We enrolled 43 allogenic HCT recipients, of whom 16 had BOS. For each patient, we obtained pulmonary function tests, measured the levels of nine serum biomarkers utilizing enzyme linked immunosorbent assays, and analyzed both the oral and gut microbiome using microbial DNA amplification and sequencing. We compared biomarker levels to lung function, both at baseline and over time, as well as to microbiome diversity. Higher IL1RL1 (p = 0.002) and IL-17 (p = 0.041) at enrollment were negatively correlated with FEV1% lung function over time. Increases in IL1RL1 (p = 0.035), IL-17 (p = 0.009), and WFDC2 (p = 0.045) levels over time were associated with worsened lung function/FEV1% over time. There were minimal correlations between gut microbiome diversity and lung function or serum biomarkers. Oral microbiome alpha diversity was lower in subjects with BOS than without (p = 0.00057), and oral beta diversity was associated with FEV1% and with levels of several biomarkers. Our pilot study suggests that certain serum cGVHD markers may identify allogeneic HCT recipients at higher risk for pulmonary impairment over time, and should be followed with robust, controlled studies.},
}
@article {pmid40543454,
year = {2025},
author = {Kang, M and Jo, J and Shin, H and Kang, HW},
title = {Therapeutic potential of wavelength-dependent photobiomodulation on gut inflammation in an in vitro intestinal model.},
journal = {Journal of photochemistry and photobiology. B, Biology},
volume = {269},
number = {},
pages = {113201},
doi = {10.1016/j.jphotobiol.2025.113201},
pmid = {40543454},
issn = {1873-2682},
abstract = {Recently, photobiomodulation (PBM) has emerged as a novel therapeutic approach for modulating the gut microbiome, offering potential for the regulation of intestinal inflammation. Although PBM has been primarily used for various clinical applications, recent studies suggest that its effects may extend to the regulation of microbial imbalances and chronic inflammation. The biological effects of PBM are wavelength-dependent, as the wavelength of light determines tissue penetration depth and cellular response. The current study aimed to compare the inflammation-modulatory effects of PBM at four different wavelengths (405, 532, 635, and 808 nm) and to elucidate the underlying molecular mechanisms of PBM in intestinal inflammation. An in vitro co-culture model consisting of Caco-2 cells and Lactobacillus was established to simulate the intestinal environment. Cellular inflammation was induced by lipopolysaccharide (LPS) stimulation, followed by wavelength-dependent PBM treatment at a dosage of 10 J/cm[2] (100 mW/cm[2] for 100 s, applied as a single irradiation). Among the wavelengths, 635 nm significantly reduced nitric oxide production and suppressed the expression of pro-inflammatory cytokines (TNF-α, IL-6, IL-1β, and iNOS). Furthermore, western blot and qPCR analyses revealed that 635 nm PBM downregulated key signaling factors in the MAPK/NF-kB pathway, indicating a potential molecular mechanism for its anti-inflammatory effect. These findings suggest that PBM, particularly at 635 nm, may serve as an effective strategy for modulating intestinal inflammation. Further studies will investigate the anti-inflammation and microbiome modulation effects of PBM in an in vivo model of inflammatory bowel disease.},
}
@article {pmid40543238,
year = {2025},
author = {Liu, L and Liu, L and Zhuang, H and Li, A and Liu, Z and Jiao, M and Li, J and Xue, S and Li, J and Ren, Y and Mao, Y},
title = {Intestinal microbiota responses to environmental microbiomes and factors across populations of the Manila clam Ruditapes philippinarum.},
journal = {Marine environmental research},
volume = {210},
number = {},
pages = {107296},
doi = {10.1016/j.marenvres.2025.107296},
pmid = {40543238},
issn = {1879-0291},
abstract = {Intestinal microbiota is essential for the health, immune defense, and environmental adaptability of aquatic animals. Still, the interactions involving the intestinal microbiota of the Manila clam Ruditapes philippinarum, the microbiomes of their habitat, and environmental factors remain unclear. This study analyzed the microbial community structure and functional characteristics in clam intestine, water, and sediment across three distribution areas in Laizhou Bay (LZ), Jiaozhou Bay (JZ), and Sanggou Bay (SG) on the Shandong Peninsula, China. Correlations between microbial communities and water parameters were also examined. The results revealed distinct microbial communities in the intestine and habitats across the three areas, with water parameters serving as key drivers of geographic microbial variation. Intestinal selective pressures overwhelmed environmental factors in shaping intestinal microbiota. Intestinal microbiota closely resembled water microbiomes in richness, diversity, and dominant species abundance, indicating that water microbiomes likely served as the primary source of the clam intestinal microbiota. Microbial networks facilitated environmental adaptation by constructing large networks or boosting network density and modularity. Functional differentiation in the intestinal microbiota, driven by environmental influences, facilitated diverse ecological adaptation strategies. Moreover, low salinity, high dissolved oxygen, and high nutrient contents in the water favored specialized intestinal microbiota with narrower niche breadth, while high salinity, low chlorophyll a, and broader nutrient contents promoted stochastic microbiota with broader niche breadth. These findings provide valuable knowledge on the interactions between clam intestinal microbiota and environmental factors, providing a scientific basis for microbiome management strategies in clam seedling production and aquaculture practices.},
}
@article {pmid40542443,
year = {2025},
author = {Kadharusman, MM and Syahputra, RA and Kurniawan, R and Hadinata, E and Tjandrawinata, RR and Taslim, NA and Romano, R and Santini, A and Nurkolis, F},
title = {Seagrass Enhalus acoroides extract mitigates obesity and diabetes via GLP-1, PPARγ, SREBP-1c modulation and gut microbiome restoration in diabetic zebrafish.},
journal = {Diabetology &amp; metabolic syndrome},
volume = {17},
number = {1},
pages = {235},
pmid = {40542443},
issn = {1758-5996},
abstract = {BACKGROUND: The global rise in obesity and type 2 diabetes highlights the need for safe and effective therapeutic interventions. Enhalus acoroides is a tropical seagrass rich in carotenoids and other bioactives. Its potential for metabolic regulation has been suggested in vitro, but in vivo efficacy and molecular mechanisms remain unexplored. This study aimed to evaluate the anti-obesity and anti-diabetic effects of Enhalus acoroides extract (SEAE) in a zebrafish model of diet- and glucose-induced metabolic dysfunction.<br><br>METHODS: Adult zebrafish were subjected to overfeeding and glucose immersion, after overfeeding and 14 days of glucose immersion to induce diabetes, adult zebrafish were randomized into three groups: untreated diabetic, SEAE-treated (5&#xa0;mg/L), and metformin-treated (3.3&#xa0;mg/L) for 20 days. Body weight, fasting blood glucose, lipid profile, gene expression (GLP-1, PPAR&#x3b3;, SREBP-1c), and gut microbiota profiles via 16&#xa0;S rRNA sequencing were assessed.<br><br>RESULTS: SEAE significantly reduced body weight and blood glucose in diabetic zebrafish (p&#x2009;<&#x2009;0.05), with efficacy comparable to or exceeding Metformin. It upregulated GLP-1 and downregulated PPAR&#x3b3; and SREBP-1c. SEAE also reduced total cholesterol, triglycerides, and LDL levels, while increasing HDL levels. Moreover, SEAE restored the Firmicutes/Bacteroidetes ratio, increased alpha diversity, and shifted beta diversity toward healthy controls. SEAE-treated fish showed microbial profiles closer to normal than those treated with Metformin.<br><br>CONCLUSIONS: SEAE exhibits strong anti-obesity and anti-hyperglycemic effects by modulating key metabolic pathways and restoring gut microbial homeostasis. These findings highlight SEAE as a promising marine-derived therapeutic candidate for metabolic syndrome and warrant further investigation as a functional food or nutraceutical.<br><br>CLINICAL TRIAL: Not applicable.},
}
@article {pmid40542437,
year = {2025},
author = {Duran-Pinedo, A and Solbiati, JO and Teles, F and Yanping, Z and Frias-Lopez, J},
title = {Correction: Longitudinal host-microbiome dynamics of metatranscription identify hallmarks of progression in periodontitis.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {147},
pmid = {40542437},
issn = {2049-2618},
}
@article {pmid40542387,
year = {2025},
author = {Wang, H and Sheng, L and Yazdi, Z and Li, X and Liu, Z and Canakapalli, S and Zhou, Y and Liao, C and Emami, S and Kelly, AM and Roy, LA and Soto, E and Wang, L},
title = {The impact of florfenicol treatment on the microbial populations present in the gill, intestine, and skin of channel catfish (Ictalurus punctatus).},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {68},
pmid = {40542387},
issn = {2524-4671},
support = {National Institute of Food and Agriculture under Grant #2019-06093-1022268//U.S. Department of Agriculture/ ; National Institute of Food and Agriculture under Grant #2019-06093-1022268//U.S. Department of Agriculture/ ; National Institute of Food and Agriculture under Grant #2019-06093-1022268//U.S. Department of Agriculture/ ; National Institute of Food and Agriculture under Grant #2019-06093-1022268//U.S. Department of Agriculture/ ; National Institute of Food and Agriculture under Grant #2019-06093-1022268//U.S. Department of Agriculture/ ; National Institute of Food and Agriculture under Grant #2019-06093-1022268//U.S. Department of Agriculture/ ; National Institute of Food and Agriculture under Grant #2019-06093-1022268//U.S. Department of Agriculture/ ; National Institute of Food and Agriculture under Grant #2019-06093-1022268//U.S. Department of Agriculture/ ; National Institute of Food and Agriculture under Grant #2019-06093-1022268//U.S. Department of Agriculture/ ; National Institute of Food and Agriculture under Grant #2019-06093-1022268//U.S. Department of Agriculture/ ; National Institute of Food and Agriculture under Grant #2019-06093-1022268//U.S. Department of Agriculture/ ; National Institute of Food and Agriculture under Grant #2019-06093-1022268//U.S. Department of Agriculture/ ; },
abstract = {BACKGROUND: Florfenicol is a broad-spectrum antimicrobial approved in many countries for treating bacterial infections in production animals. Although florfenicol has been widely used in the US catfish industry, its impact on the native microbiota within catfish tissues remains largely unknown. Florfenicol treatment is followed by a mandatory withdrawal period to ensure drug residues fall below regulatory limits before harvest. This interval also allows for the potential recovery of the native microbiota. In particular, the skin and gill microbiota have often been overlooked in aquaculture microbiome research. Moreover, the dynamics of microbial communities and resistome profiles following drug withdrawal are still poorly understood, despite their ecological significance.<br><br>RESULTS: A significant increase in intestinal microbial diversity was observed at the end of the withdrawal period. The highest alpha diversity (Shannon index) was observed in catfish intestines. This increase indicated the restoration of the normal microbiota in catfish intestine. The predominant bacterial phyla shared among catfish gill, intestine, and skin are Proteobacteria (62%), Bacteroidetes (18%), Actinobacteriota (12%), Firmicutes (3%), Patescibacteria (2%), and Verrucomicrobiota (1%). Florfenicol application can have lasting effects through the withdrawal period, particularly altering the intestinal microbial community.<br><br>CONCLUSION: The result of this study underscores the impact of florfenicol treatment on the bacterial landscape and antibiotic resistance in catfish, highlighting significant changes in microbial composition in the catfish intestine and at the end of the withdrawal period. These findings address the need for monitoring and managing antibiotic resistance in fish farming environments.},
}
@article {pmid40542287,
year = {2025},
author = {Fierer, N and Leung, PM and Lappan, R and Eisenhofer, R and Ricci, F and Holland, SI and Dragone, N and Blackall, LL and Dong, X and Dorador, C and Ferrari, BC and Goordial, J and Holmes, SP and Inagaki, F and Korem, T and Li, SS and Makhalanyane, TP and Metcalf, JL and Nagarajan, N and Orsi, WD and Shanahan, ER and Walker, AW and Weyrich, LS and Gilbert, JA and Willis, AD and Callahan, BJ and Shade, A and Parkhill, J and Banfield, JF and Greening, C},
title = {Guidelines for preventing and reporting contamination in low-biomass microbiome studies.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {40542287},
issn = {2058-5276},
support = {SR200100005//Department of Education and Training | Australian Research Council (ARC)/ ; FT240100502//Department of Education and Training | Australian Research Council (ARC)/ ; DE250101210//Department of Education and Training | Australian Research Council (ARC)/ ; DE230100542//Department of Education and Training | Australian Research Council (ARC)/ ; APP1178715//Department of Health | National Health and Medical Research Council (NHMRC)/ ; RGY0058/2022//Human Frontier Science Program (HFSP)/ ; RGY0058/2022//Human Frontier Science Program (HFSP)/ ; },
abstract = {Numerous important environments harbour low levels of microbial biomass, including certain human tissues, the atmosphere, plant seeds, treated drinking water, hyper-arid soils and the deep subsurface, with some environments lacking resident microbes altogether. These low microbial biomass environments pose unique challenges for standard DNA-based sequencing approaches, as the inevitability of contamination from external sources becomes a critical concern when working near the limits of detection. Likewise, lower-biomass samples can be disproportionately impacted by cross-contamination and practices suitable for handling higher-biomass samples may produce misleading results when applied to lower microbial biomass samples. This Consensus Statement outlines strategies to reduce contamination and cross-contamination, focusing on marker gene and metagenomic analyses. We also provide minimal standards for reporting contamination information and removal workflows. Considerations must be made at every study stage, from sample collection and handling through data analysis and reporting to reduce and identify contaminants. We urge researchers to adopt these recommendations when designing, implementing and reporting microbiome studies, especially those conducted in low-biomass systems.},
}
@article {pmid40541719,
year = {2025},
author = {Theise, ND and Kohnehshahri, MN and Chiriboga, LA and Fyfe, B and Cao, W and Zee, S and Imam, R and Pichler-Sekulic, S and Wells, RG},
title = {EVIDENCE OF INTERSTITIAL CONTINUITY WITHIN AND BEYOND THE HUMAN PANCREAS.},
journal = {Human pathology},
volume = {},
number = {},
pages = {105855},
doi = {10.1016/j.humpath.2025.105855},
pmid = {40541719},
issn = {1532-8392},
abstract = {Bodies have continuous reticular networks, comprising collagens and other extracellular matrix components, through all tissues and organs. We recently validated fluid flow through human interstitium and demonstrated that they are filled with hyaluronic acid by staining with biotinylated hyaluronic acid binding protein. Their continuity across tissue boundaries (skin and subcutis), and between organs (colon and mesentery) and along vessels (within adventitia) and nerves (within perineurium) has been demonstrated in this manner. We aim to evaluate the continuity of interstitium within human pancreas and beyond into adjoining tissues. Tissue blocks of histologically normal pancreas from nine pancreatectomy specimens were sectioned in parallel for staining with hematoxylin and eosin, Picrosirius red, and biotinylated hyaluronic acid binding protein. Also, specimens of invasive pancreatic cancer were assessed for interstitial tumor invasion. Picrosirius red ensheathes all microscopic units of the endocrine and exocrine pancreas, including acini, islets, and ducts, adventitia of blood vessels and perineurium, and into adjacent duodenum. Interstitial spaces within the fibrous tissue are filled with hyaluronic acid by staining and are also continuous through all microscopic structures of the pancreas, into adjoining duodenum and along vessels (within adventitia) and nerves (within perineurium). Invasive carcinoma is seen spreading through pre-existing interstitial spaces. Interstitium of the human pancreas is continuous within and beyond the pancreas. This continuity suggests the capacity to be a route of molecular, microbiome, and cellular trafficking and communication. In particular, it is a route of cancer spread.},
}
@article {pmid40541587,
year = {2025},
author = {Pletsch, EA and Smith, AD and Ragonese, JS and Narrowe, AB and Cheung, L and Chen, CT and Wang, TTY and Dawson, HD},
title = {Broccoli consumption alters microbial diversity, metatranscriptome and host transcriptome in mice fed a Total Western Diet.},
journal = {The Journal of nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tjnut.2025.05.041},
pmid = {40541587},
issn = {1541-6100},
abstract = {BACKGROUND: Cruciferous vegetables (CV) are a source of dietary fiber and phytochemicals that alter the microbiome in animals and humans. Constituent CV compounds, such as glucosinolates, have demonstrated anti-inflammatory properties in animal models, though often using doses and basal diets that are not relevant to humans. The mechanism(s) are unclear, but the gut microbiota may metabolize these compounds into bioactive molecules that influence immune pathways.<br><br>OBJECTIVE: We investigated the effects of a broccoli powder-supplemented Total Western Diet (TWD) on changes in the gut microbiome, the host transcriptome and the metatranscriptome at levels relevant to the human diet to understand how these changes affect metabolic and immune functions.<br><br>METHODS: C57BL/6 male mice (n = 40) were fed a TWD control diet for six weeks followed by supplementation with 0, 0.5, 1 or 2.5% broccoli powder (BP) (reflecting a human intake from &#xbc; -1 cup per day) for three weeks. Microbial communities from cecal contents were taxonomically profiled using 16S rRNA amplicon and shotgun metagenomic sequencing, and metatranscriptomics was used to assess functionality of the microbial communities. The host cecal transcriptome was also assessed.<br><br>RESULTS: Beta diversity was significantly higher (p = 1.20E-03) for mice fed the 2.5% BP diet compared to the control group at the species level. Lachnospiraceae MD335 was significantly more abundant in mice fed higher levels of broccoli, and analysis of bacterial RNA transcripts indicated a dose-dependent increase in transcription of genes associated with butyrate and acetate production, plant cell wall degradation and carbohydrate utilization. Activation of the aryl hydrocarbon receptor pathway in the cecum was evident.<br><br>CONCLUSIONS: Consumption of a broccoli-supplemented TWD induces changes in the gut microbiome, host and microbial gene expression that affect immune health and inflammation in the gut at levels that are achievable in the human diet.},
}
@article {pmid40541131,
year = {2025},
author = {Delcourt, H and Verbrugghe, L and Vandenplas, Y and Huysentruyt, K},
title = {Systematic review and meta-analysis of randomized controlled trials on pre-, pro-, post- and synbiotic supplementation in follow-on formula.},
journal = {Clinical nutrition (Edinburgh, Scotland)},
volume = {51},
number = {},
pages = {101-114},
doi = {10.1016/j.clnu.2025.05.022},
pmid = {40541131},
issn = {1532-1983},
abstract = {BACKGROUND &amp; AIM: The remarkable plasticity of the gut microbiome during the first three years of life offers a critical window of opportunity to influence gut health. The aim of this study is to summarize high quality evidence from randomized controlled trials on the health benefits (respiratory tract infections, diarrheal episodes, febrile days, antibiotic use, microbiome modulation and secretory IgA) of prebiotics, probiotics, synbiotics and postbiotics added to follow-on formula.<br><br>METHODS: A comprehensive literature search for randomized controlled trials (RCTs) using Medline, Embase, Lilacs, and Cochrane was performed up to February 2025 (PROSPERO CRD42024500457). Only RCTs involving healthy children between six months and three years were considered. Quality assessment was done using the ROBINS II tool. Random effects models were used to obtain odd ratio (OR) and number needed to treat (NNT) via meta-analysis.<br><br>RESULTS: Out of 2755 search results, 23 studies were included (n = 6984 children) with an overall low risk of bias (14/23) as assessed by the Robins II tool. The OR for respiratory tract infections in pro-,pre- and synbiotics added to a follow-on formula was 0.22 (95 % CI: 0.05-1.09; NNT = 82; CI 95 %: 67-674), 0.84 (95 % CI: 0.66-1.07; NNT = 28; 95 % CI: 11-75) and 0.75 (95 % CI: 0.54-1.05; NNT = 18; 95 % CI: 9-102), respectively. The OR for diarrheal episodes in pre- and synbiotics added to a follow-on formula 1.40 (95 % CI: 0.71-2.79; NNT = 40, 95 % CI: 10-53) and 1.26 (95 % CI: 0.96-1.66; NNT = 17, 95%CI: 8-94), respectively. For the combination of other interventions with other outcomes insufficient studies were available to perform a meta-analysis.<br><br>CONCLUSION: Pre- and synbiotics may help protect against respiratory tract infection, though they do not appear to offer the same benefit for preventing diarrheal episodes. High quality evidence for the effect of biotics added to follow-on formula on health outcomes is sparse. More research is needed to confirm the observed health effects.},
}
@article {pmid40541100,
year = {2025},
author = {Tang, X and Mao, M and Zhang, X and Gao, H and Wang, Z and Fang, R and Cheng, HW and Jiang, S},
title = {Cecal microbiota transplantation enhances calcium retention through modulation of gut microbiota and intestinal calcium transporter gene expression in chicks.},
journal = {Poultry science},
volume = {104},
number = {9},
pages = {105437},
doi = {10.1016/j.psj.2025.105437},
pmid = {40541100},
issn = {1525-3171},
abstract = {Bone development during early life is crucial for maintaining skeletal health and productivity in laying hens. The aim of this study was to investigate the effects of transferring cecal bacterial material of healthy adult hens on growth performance, gut integrity, microbial development, and bone metabolism of recipient chicks. Cecal contents were collected from 12 healthy Lohmann Pink-shell laying hens aged 47 weeks (donors). A total of 120 1-day-old Lohmann Pink chicks (recipients) were randomly assigned to 2 treatments for a 34-day trial: CONT (0.1 mL saline, Control) and CMT (0.1 mL cecal microbial solution). Each group had 10 replicates and 6 chicks per replicate. The pooled cecal sample as well as saline was administered via oral gavage once daily from day 1 to day 10, and then boosted on days 16, 23, and 30. One bird from each replicate was randomly taken for sample collection at day 34 (n=10). The results showed that CMT chicks had significantly higher Ca and P retention rates than CONT chicks. The mRNA expressions of intestinal Ca transporters, CaBP-D28K and VDR in the ileum and NCX1 in the jejunum, were also upregulated in CMT chicks. Additionally, the mRNA expression of a tight junction protein, ZO-1, was upregulated in the duodenum of CMT chicks. CMT chicks also had higher mRNA expressions of pro-inflammatory cytokines, IL-6, IL-1β, and TNF-α, in the intestinal tract. Furthermore, CMT chicks had a more diverse and mature gut microbial community compared to CONT chicks. The relative abundances of SCFA-produced bacteria (e.g., Bacteroides, Rikenellaceae_RC9_gut_group, and Prevotellaceae_UCG-001) were increased, while the relative abundances of Alistipes, Lactobacillus, and Barnesiella were reduced in CMT chicks. However, there were no CMT effects on body weight, organ indexes, bone morphology, and gene expression-associated with bone metabolism. This study demonstrates that transferring cecal bacteria from adult laying hens enhances calcium absorption and retention in newly hatched chicks by upregulating key calcium transporters and enhancing intestinal barrier integrity via modulating the gut microbiome.},
}
@article {pmid40541049,
year = {2025},
author = {Lazarus, BE and Mueller, RC and Germino, MJ},
title = {Soil-microbial communities respond less than plant communities to synthetic- or bio-herbicides applied to address the exotic grass-fire cycle in rangelands.},
journal = {The Science of the total environment},
volume = {991},
number = {},
pages = {179831},
doi = {10.1016/j.scitotenv.2025.179831},
pmid = {40541049},
issn = {1879-1026},
abstract = {The exotic grass-fire cycle is degrading semiarid rangelands, such as the vast areas of shrub-steppe in North America now invaded by fire-promoting cheatgrass. Chemical- or bio-herbicides are sprayed onto soils to inhibit the invaders, but information on chemical- or bio-herbicide impacts to soil microbial communities is limited. We asked how the soil-microbiome responded to the bioherbicide Pseudomonas fluorescens strain ACK55 in comparison to the separate and combined effects of a conventional pre-emergent chemical herbicide, imazapic, in two cheatgrass-invaded sagebrush-steppe sites. First-year microbial responses were evaluated using targeted sequencing of the 16S and LSU rRNA genes for bacteria+archaea and fungi, respectively, and were related to plant-community responses. A strong cheatgrass reduction with imazapic at one site was accompanied by a small shift in bacteria+archaea (16S) community composition with no effect on microbial alpha diversity, and this shift was small in comparison to natural microbiome variation between sites. ACK55 was not detected in soil a year after application, and it caused only transient and marginally significant reductions in annual grass cover accompanied by small reductions in soil fungi species richness. Full-length sequencing of the ACK55 16S rRNA gene and phylogenetic analyses revealed that ACK55 is more likely P. salmonii than P. fluorescens. Knowledge gaps remain on the duration and consequences of microbial-community shifts with imazapic and why molecular analyses showed ACK55 did not persist in soils. Confusion regarding microbial biopesticides can result where isolation, effectiveness testing, commercial release, and regulation are not guided by molecular taxonomic analyses.},
}
@article {pmid40540864,
year = {2025},
author = {Shi, B and Liu, C and Wang, J and Du, Z and Hou, K and Wang, J and Wang, J and Li, B and Zhu, L},
title = {3,6-dibromocarbazole have a significant effect on diversity, community and function of soil microorganisms.},
journal = {Journal of hazardous materials},
volume = {495},
number = {},
pages = {138962},
doi = {10.1016/j.jhazmat.2025.138962},
pmid = {40540864},
issn = {1873-3336},
abstract = {In recent years, polyhalogenated carbazoles (PHCZs) have been increasingly detected in soil, potentially posing risks to soil health. 3,6-dibromocarbazole (3,6-BCZ), a representative PHCZ, is frequently found in the soil environment. However, the effects of 3,6-BCZ contamination on microbial communities remain largely unexplored. In this study, we investigated the impact of varying concentrations of 3,6-BCZ on the soil microbiome using 16S rDNA gene amplicon sequencing and quantitative PCR techniques at 3, 10, 80 days (pre-, mid-, final-). α-Diversity analysis revealed that bacterial Shannon indices increased with 3,6-BCZ exposure (0.1 mg kg[-1] 1.45 %, 1 mg kg[-1] 4.73 %, 10 mg kg[-1] 4.45 %, 100 mg kg[-1] 5.97 %) at 80 d, compared to solvent soil group (SC). The concentration of 1, 10 and 100 mg kg[-1] 3,6-BCZ significantly increased bacterial diversity and altered community structure, enriching genera such as Bacillus, Adhaeribacter, and Nitrospira genera. Network analysis further demonstrated that bacterial interactions within the soil microbiome became more complex and competitive under 3,6-BCZ exposure. Additionally, functional prediction via FAPROTAX indicated significant alterations in microbial community functional groups, particularly those related to carbon and nitrogen cycling. Specifically, 3,6-BCZ promoted bacterial metabolic functions such as aerobic nitrite oxidation, nitrification, nitrogen fixation, hydrocarbon degradation, and methylotrophy, while inhibiting ureolysis and chitinolysis after 80 days of exposure. Notable changes were also observed in genes associated with nitrogen fixation (nifH), nitrification (AOA-amoA and AOB-amoA), and carbon cycling (cbbLR and cbbLG). Overall, our findings suggest that PHCZs can impact soil health and microbial functionality, highlighting the need for further research to inform risk-based policy development.},
}
@article {pmid40540838,
year = {2025},
author = {Conti Taguali, S and Pöter, R and Aloi, F and Fernández-Trujillo, C and Acedo, A and La Spada, F and Li Destri Nicosia, MG and Pane, A and Schena, L and Cacciola, SO},
title = {Influence of environmental and agronomic variables on soil microbiome in citrus orchards: A comparative analysis of organic and conventional farming system.},
journal = {Microbiological research},
volume = {299},
number = {},
pages = {128260},
doi = {10.1016/j.micres.2025.128260},
pmid = {40540838},
issn = {1618-0623},
abstract = {Crop health and productivity depend on the structure and functionality of soil microbiota associated with the root system of plants. The agricultural policy of the European Union promotes organic farming systems to ensure environmental sustainability and food safety. The objective of this study was to investigate the impact of organic farming on soil microbiome in citrus orchards. The soil microbiota of eight conventionally and seven organically managed commercial citrus orchards across eastern Sicily was characterised using Illumina sequencing and BeCrop® primers for PCR amplification. The structure (diversity and relative abundance) and functionality of soil bacterial and fungal communities depended primarily on the sampling site. Other variables influencing the soil microbiome included soil total carbon content, seasonality, rootstock genotype, soil tillage and irrigation system. The latter three exerted differential effects on either bacterial or fungal communities. Conversely, age and visible health status of the tree had negligible influence on both communities. The differences between organically and conventionally managed citrus orchards accounted for a significant proportion of the variability, indicating a relevant effect of the farming system on soil microbiome. Organically managed orchards compared to those managed conventionally exhibited higher microbial diversity and a unique composition of nutrient-cycling microbes. In particular, organic farming promoted beneficial microbial functions, such as nitrogen fixation and phosphorus solubilization. Findings provide insights into the dynamic and complex interactions between environmental variables and soil microbial communities in citrus orchards, confirming the potential of microbial diversity as an indicator of sustainability in agricultural systems.},
}
@article {pmid40540603,
year = {2025},
author = {Chen, HY and Wu, PS and Li, ZY and Liu, YC and Yeh, SR and Duan, BC and Cheng, KW and Hsu, CC and Chiu, YL and Lee, WT and Fan, SZ and Wang, PY},
title = {Gut microbiome and host TOR pathway interact to regulate predator-induced aversive memory in Drosophila melanogaster.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {25},
pages = {e2422928122},
doi = {10.1073/pnas.2422928122},
pmid = {40540603},
issn = {1091-6490},
support = {111-2320-B-002-018 112-2320-B-002-026 113-2321-B-418-005 113-2320-B-002-021-MY3//National Science and Technology Council (NSTC)/ ; 113-2321-B-418-005//National Science and Technology Council (NSTC)/ ; NHRI-12A1-CG-CO-08-2325-2//National Health Research Institutes (NHRI)/ ; 112L895401//National Taiwan University ()/ ; 113-UN0065//National Taiwan University Hospital (NTUH)/ ; },
abstract = {The gut microbiome has emerged as a key factor influencing a wide range of host physiological processes and behaviors, though the mechanisms behind these effects remain only partially understood. In this study, we explored the role of the gut microbiome in memory regulation using a parasitoid wasp-induced oviposition depression paradigm in Drosophila melanogaster. Our findings show that flies with depleted gut microbiota, either through axenic culture or antibiotic treatment, exhibited significant memory impairments. However, reintroducing the commensal bacterium Lactobacillus plantarum alone was sufficient to restore memory, while coinoculation with Acetobacter pomorum further enhanced memory performance. Hemolymph metabolomic analyses revealed reduced amino acid levels in antibiotic-treated flies, which were linked to impaired Drosophila target of rapamycin (dTOR) signaling. Additionally, genetic manipulation of dTOR or dietary supplementation with branched-chain amino acids either mimicked or rescued the memory deficits caused by antibiotic treatments. These results suggest that the gut microbiome is essential for regulating memory function by maintaining amino acid homeostasis and proper dTOR signaling, with profound implications for advancing knowledge of cognitive regulation.},
}
@article {pmid40540565,
year = {2025},
author = {Chen, N and Cai, P and Lin, X and Song, ZM and He, J and Li, Z and Li, Z and Zhang, D and Song, Y and Li, YX},
title = {Autoinducing peptides regulate antibiotic production to potentially shape root microbiome.},
journal = {Science advances},
volume = {11},
number = {25},
pages = {eadw5076},
pmid = {40540565},
issn = {2375-2548},
abstract = {Microbes use signaling molecules to regulate multiple physiological processes and mediate chemical interactions. Decoding these chemical languages is instrumental in comprehending microbial regulatory mechanisms within complex microbiota. Here, we discover previously unidentified autoinducing peptides (AIPs) derived from the plant probiotic bacterium Paenibacillus polymyxa, identified as Pp-AIPs. Omics analyses coupled with genetic manipulations revealed that Pp-AIP1 could effectively modulate the production of multiple antimicrobial secondary metabolites at nanomolar concentration, expanding known AIP functions. Furthermore, through inoculating P. polymyxa in the natural rhizosphere microbiome and analyzing its antagonistic interactions against root microbes, we suggest that Pp-AIPs may influence the microbial community composition through modulating the antimicrobial spectrum. Global analysis of biosynthetic gene clusters (BGCs) reveal widespread co-occurrence of uncharacterized AIPs with secondary metabolite BGCs. This study underscores the unreported roles of AIPs in antibiotic regulation and the microbiome interactions, advancing knowledge of quorum-sensing mechanisms in microbial ecosystems.},
}
@article {pmid40540444,
year = {2025},
author = {Shi, Y and Yan, F and Wang, W and Li, X},
title = {Letter to the editor - intratumoral fusobacterium nucleatum associates with advanced-stage colorectal cancer and poor prognosis in a Chinese cohor.},
journal = {International journal of surgery (London, England)},
volume = {},
number = {},
pages = {},
doi = {10.1097/JS9.0000000000002655},
pmid = {40540444},
issn = {1743-9159},
}
@article {pmid40540409,
year = {2025},
author = {Wang, HB and Liu, XP and Shu, YC and Li, G and Sun, CL and Jones, DL and Zhu, YG and Lin, XY},
title = {Molecular Composition of Exogenous Dissolved Organic Matter Regulates Dissimilatory Iron Reduction and Carbon Emissions in Paddy Soil.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c03323},
pmid = {40540409},
issn = {1520-5851},
abstract = {Soil carbon (C) cycling under anoxic conditions is mechanistically linked to dissimilatory iron (Fe) reduction, potentially influenced by exogenous dissolved organic matter (DOM). However, the impact of complex exogenous DOM on soil microbial activity and C-Fe coupling in paddy soils remains underexplored. With a 100-day microcosm experiment, we found that biochar-DOM significantly promoted Fe reduction and accelerated CH4 and CO2 emissions, and manure-DOM increased soil CO2 emissions. These effects may be caused by the following mechanisms: DOM molecules with high aromaticity and high double bond equivalence (DBE), including lignins-polyphenols, lignins-polycyclic aromatics, and condensed aromatics-polycyclic aromatics, promoted soil Fe reduction and CH4 emissions with enrichment of soil Fe-reducing bacteria, r-strategists, and reduction of methanotrophs at the early stage of incubation. Conversely, DOM with low aromaticity, low DBE, and high H/C enhanced CO2 emissions with the enhancement of recalcitrant C degradation and CH4 oxidation at the late stage of incubation. In conclusion, our study highlights the importance of the molecular composition of organic amendment-derived DOM in regulating soil Fe reduction and greenhouse gas emissions. The findings offer novel insights into the effective utilization of agricultural resources and the potential mitigation of greenhouse gas production and emissions.},
}
@article {pmid40540354,
year = {2025},
author = {Roichman, A and Reyes-Castellanos, G and Chen, Z and Chen, Z and Mitchell, SJ and MacArthur, MR and Sawant, A and Levett, L and Powers, JR and Burgo, V and Gomez-Jenkins, M and Ibrahim, M and Xu, X and Tomlinson, B and Hang, X and Pamer, EG and Wei, Y and Kang, Y and White, EP and Rabinowitz, JD},
title = {Dietary Fiber Lacks a Consistent Effect on Immune Checkpoint Blockade Efficacy Across Diverse Murine Tumor Models.},
journal = {Cancer research},
volume = {},
number = {},
pages = {},
doi = {10.1158/0008-5472.CAN-24-4378},
pmid = {40540354},
issn = {1538-7445},
abstract = {Immune checkpoint blockade (ICB) has transformed cancer treatment, but success rates remain limited. Recent research suggests that dietary fiber enhances ICB efficacy through microbiome-dependent mechanisms. However, prior studies in mice compared grain-based chow (high-fiber) to low-fiber purified diet, but these diets also differed in other dimensions, including phytochemicals. Therefore, further work is needed to establish the robustness of the effect of fiber on ICB across cancer types and dietary contexts. Here, we investigated gut microbiome composition, metabolite levels, and ICB activity in mice fed grain-based chow or purified diets with differing quantities of isolated fibers (cellulose and inulin). Compared to dietary fiber content, consumption of chow versus purified diet had a greater effect on the gut microbiome and a much stronger impact on the metabolome. Studies in multiple tumor models revealed that fiber has a weaker impact on ICB (anti-PD-1) efficacy than previously reported. While diet impacted ICB in some models, the effect was not directionally consistent. None of the models tested displayed the pattern expected if fiber controlled ICB efficacy: strong efficacy in both chow and high-fiber purified diet but low efficacy in low-fiber purified diet. Thus, dietary fiber appears to have limited or inconsistent effects on ICB efficacy in mouse models, and other dietary factors that correlate with fiber intake may underlie clinical correlations between fiber consumption and immunotherapy efficacy.},
}
@article {pmid40540179,
year = {2025},
author = {Agrawal, A and Acharya, AB and Sahu, B and Barik, TK and Patel, AK},
title = {Bacterial community composition and diversity associated with developmental stages of Anopheles subpictus.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {},
number = {},
pages = {},
pmid = {40540179},
issn = {1618-1905},
support = {DST/INSPIRE FELLOWSHIP/2020/IF200208//Department of Science and Technology, Ministry of Science and Technology, India/ ; },
abstract = {Malaria remains the deadliest vector-borne disease globally. Among different malaria vectors, Anopheles subpictus has been regarded as the potent vector across many Indian states. Microbiota in mosquitoes are critical determinants for their development, physiology, and vector competence, which differ significantly among mosquito species, life stages, and environmental parameters. Microbial profiles linked with various life stages of the emerging malaria vector, An. subpictus remain unexplored. In this study, 16S rRNA amplicon sequencing (V1-V9 regions) was used to explore and analyze the microbial community dynamics within and between life stages. A total of 287,077 bacterial reads were generated and distributed into 40 phyla, 75 classes, 160 orders, 334 families, 961 genera, and 2398 species. Diversity analyses revealed that bacterial community structure varied significantly across the three life phases (larvae, pupae, adult) of An. subpictus. The larval stage has higher species richness compared to subsequent developmental stages. The sequence-based taxonomic profiling revealed that Methylobacterium, Clostridium, Bradyrhizobium, Cytophaga, Roseateles, Mitsuaria, Sphingomonas and Wolbachia were the dominant bacterial genera across the different life stages. Moreover, Methylobacterium sp. (51.6%) was the most abundant taxa in the adult female stage, whereas the larval stage was mainly dominated by Cytophaga (15.2%). This research advances our understanding of bacterial community composition and dynamics across the developmental succession of An. subpictus. The finding pinpoints dominant bacterial candidates that could be harnessed to develop microbial-based control strategies aimed at limiting mosquito-borne diseases.},
}
@article {pmid40540085,
year = {2025},
author = {Aminurrasyid, AHB and Mohd Ikmal, A and Nadarajah, KK},
title = {The Rice-Microbe Nexus: Unlocking Productivity Through Soil Science.},
journal = {Rice (New York, N.Y.)},
volume = {18},
number = {1},
pages = {56},
pmid = {40540085},
issn = {1939-8425},
support = {Fundamental Research Grant FRGS/1/2023/STG01/UKM/01/1//Ministry of Higher Education, Malaysia/ ; Fundamental Research Grant FRGS/1/2023/STG01/UKM/01/1//Ministry of Higher Education, Malaysia/ ; Fundamental Research Grant FRGS/1/2023/STG01/UKM/01/1//Ministry of Higher Education, Malaysia/ ; },
abstract = {Rice is a staple crop and a primary food source for nearly half of the global population. Its cultivation is heavily dependent on irrigation systems, which is crucial in determining productivity. Beyond irrigation, the genetic characteristic of rice significantly influences its growth, resilience, and yield. These factors are closely connected to the soil microbiome within the rhizosphere, where interactions between plants, soil, and microbes occur, ultimately affecting agricultural outcomes. Different rice genotypes and agricultural practices shape soil microbiomes uniquely, impacting crop resilience and yield. Additionally, the growth stage of rice influences root exudation patterns, which in turn affects the composition and functionality of the rhizospheric microbiome. As the plant matures, the quantity and quality of root exudates evolve alongside its physiological changes, further modifying microbial communities in the surrounding soil. This review explores the complex interplay among irrigation strategies, rice genotypes, and growth phases, examining their collective impact on soil microbial diversity, offering insights into leveraging soil microbiomes for sustainable crop management and enhanced production. In addition it also highlights biotechnological tools and approaches that may be utilized in sustainable rice farming.},
}
@article {pmid40539946,
year = {2025},
author = {Theirlynck, T and Staat, L and Servania, D and Engelen, AH and van Tussenbroek, BI and Muyzer, G and Visser, PM and Amaral-Zettler, L},
title = {Nutrient-driven growth and microbiome shifts in the brown alga Sargassum fluitans III.},
journal = {Journal of phycology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jpy.70045},
pmid = {40539946},
issn = {1529-8817},
support = {CEECINST/00114/2018//Portuguese national fund, Foundation for Science and Technology/ ; LA/P/0101/2020 (DOI:10.54499/LA/P/0101/2020)//Portuguese national fund, Foundation for Science and Technology/ ; UIDB/04326/2020 (DOI:10.54499/UIDB/04326/2020)//Portuguese national fund, Foundation for Science and Technology/ ; NWOCA.1 of the Sargassum Call2 research program//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; },
abstract = {Since 2011, holopelagic Sargassum has been accumulating in a region of the tropical Atlantic now referred to as the Great Atlantic Sargassum Belt (GASB). Among the hypothesized contributors to these accumulations are the increased inputs of nitrogen (N) and phosphorus (P) in the tropical Atlantic Ocean. Little is known about the effects of N and P additions on Sargassum physiology and its microbiome. We studied the effects of N, P, and NP additions on the growth, photosynthetic efficiency, and microbiome composition of Sargassum fluitans III in a six-day experiment on the Caribbean Island of Curaçao. Sargassum fluitans III took up most nitrate and phosphate within 3 days with respective uptake rates of 0.343 and 0.0399 μmol · g[-1] DW · h[-1]. Fv/Fm decreased in the control after 6 days but remained constant in nutrient treatments. Growth rates did not differ significantly among treatments, but a trend in higher growth rates in the NP treatment was discerned, suggesting a possible NP co-limitation. The relative abundance of epiphytic Cyanobacteria such as Schizothrix and bacteria such as Lentilitoribacter increased under N and P addition, while heterotrophic Rhodobacteraceae decreased in abundance. Microeukaryotic communities responded with varying changes in alpha diversity, possibly steered by increased photosynthesis and growth of S. fluitans III or bacterial interactions. The physiological response to N and P and rapid change of the microbiome demonstrates that the studied S. fluitans III can quickly benefit from increased nutrient concentrations, which might contribute to its growth success in the GASB.},
}
@article {pmid40539808,
year = {2025},
author = {Sun, H and Chen, Q and Zhang, D and Hu, L and Li, S and Lu, M and Wang, Y and Su, H and Gao, Y and Guo, J and Zhao, Y and Du, J and Liu, C and Xia, H and Xu, Y and Ge, X and Yang, Q},
title = {Integrative study of pulmonary microbiome and clinical diagnosis in pulmonary tuberculosis patients.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0156324},
doi = {10.1128/spectrum.01563-24},
pmid = {40539808},
issn = {2165-0497},
abstract = {UNLABELLED: This study investigated the diagnostic potential of mNGS for detecting MTB in pulmonary tuberculosis patients. We analyzed pulmonary microbiome data to assess its impact on mNGS diagnostic accuracy and explored the association between microbiome profiles and clinical diagnosis. Bronchoalveolar lavage fluid samples were collected from 236 patients with pulmonary infections, and the diagnostic performance of mNGS was compared with traditional methods in detecting MTB. Furthermore, the incidence of false negatives and false positives, as well as the characteristics of the lung microbiota in TB patients, was analyzed to improve the diagnostic precision of mNGS. We observed that among all detection methods, mNGS showed the highest sensitivity (73.33%), followed by X-pert (60.00%), culture (53.33%), RT-PCR (53.33%), and sputum smear (23.33%). Notably, mNGS produced 3 false positive results in 236 samples, yielding a specificity of 98.54%. Analysis of the pulmonary microbiome revealed significant differences in both α-diversity and β-diversity between patients with TB and uninfected controls (P<0.05). Shannon index and Chao1 index were identified as significant predictors associated with MTB infection. ROC curve analysis demonstrated an AUC of 0.765, indicating good discriminatory performance. This study suggested that integrating wet-laboratory techniques with bioinformatics analysis can further enhance the diagnostic accuracy of mNGS for TB. Furthermore, microbiome analysis holds significant potential for the diagnosis of MTB infection.<br><br>IMPORTANCE: This study focuses on the application of next-generation sequencing (NGS) technology in detecting Mycobacterium tuberculosis in bronchoalveolar lavage fluid and explores the impact of M. tuberculosis infection on the pulmonary microbiome. By optimizing the methods and conducting microbial analyses, the accuracy of metagenomic NGS for detecting M. tuberculosis has been improved.},
}
@article {pmid40539779,
year = {2025},
author = {Monod, V and Hofstetter, V and Viret, O and Zufferey, V and Gindro, K and Croll, D},
title = {Landscape-scale endophytic community analyses in replicated grapevine stands reveal that dieback disease is unlikely to be caused by specific fungal communities.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0078225},
doi = {10.1128/aem.00782-25},
pmid = {40539779},
issn = {1098-5336},
abstract = {Tree diebacks are complex and multifactorial diseases with suspected biotic and abiotic components. Microbiome effects on plant health are challenging to assess due to the complexity of fungal and bacterial communities. Grapevine wood dieback is the main threat to sustainable production worldwide, and no causality with microbial species has been established despite long-standing claims of fungal drivers. Here, we aimed to test the hypothesis that grapevine esca disease progression has reproducible drivers in the fungal species community. For this, we analyzed a set of 21 vineyards planted simultaneously with a single susceptible cultivar to provide unprecedented replication at the landscape scale. We sampled a total of 496 plants at the graft union across vineyards in 2 different years to perform deep amplicon sequencing analyses of the fungal communities inhabiting grapevine trunks. The communities were highly diverse with a total of 4,129 amplified sequence variants assigned to 697 distinct species. We detected trunk fungal community shifts over years of sampling, vineyards and climatic conditions, as well as disease status. However, we detect no specific fungal species driving symptom development across vineyards, contrary to long-standing expectations. The high degree of environmental standardization in the decade-long experimental plots and the well-powered replication provide the clearest evidence yet that grapevine wood dieback is most likely caused by environmental factors rather than specific pathogens. Furthermore, our study shows how landscape-scale replicated field surveys allow for powerful hypothesis testing for complex dieback disease drivers and prioritize future research directions.IMPORTANCETree diebacks are complex diseases suspected to be caused by both biological and environmental drivers. Grapevine wood dieback is a major threat to vineyards worldwide, but no specific microbial species have been experimentally implicated, despite claims that fungi are causing the symptoms. Here, we tested whether the progression of grapevine esca disease is driven by specific fungal species. We analyzed 21 long-established vineyards planted at the same time with the same susceptible grape variety to ensure consistent conditions. Over the years, we observed changes in the fungal communities inhabiting the trunk depending on the vineyard, climate, and disease status. However, contrary to expectations, we did not detect any specific fungal species that consistently could cause symptoms across the vineyards. The high level of environmental control and replication in our study provides strong evidence that grapevine wood dieback is more likely caused by environmental factors rather than specific pathogens.},
}
@article {pmid40539731,
year = {2025},
author = {Lee, S and Kim, G and Seong, SM and Cho, CG and Park, SW and Shin, H and Kim, S and Kim, JY},
title = {Nasal Microbial Community Shifts Following Treatment in Chronic Rhinitis: An Observational Study.},
journal = {The Laryngoscope},
volume = {},
number = {},
pages = {},
doi = {10.1002/lary.32295},
pmid = {40539731},
issn = {1531-4995},
support = {NRF-2021R1I1A1A01056576//National Research Foundation of Korea/ ; RS-2024-00358007//Ministry of Science and ICT, South Korea/ ; //Dongguk University, College of Medicine Research Fund/ ; },
abstract = {OBJECTIVES: Nasal microbiome helps maintain mucosal homeostasis and immune function. Previous studies suggested the pathogenesis of chronic rhinitis and the nasal microbiome were related. This study aimed to evaluate the treatment effect on the nasal microbiome in chronic rhinitis through analyzing microbial diversity and composition in pre- and post-treatment status.<br><br>METHODS: In participants diagnosed with chronic rhinitis, nasal microbiome samples were collected before and after treatment. Treatment regimens included intranasal corticosteroid spray, oral antihistamines, and/or oral leukotriene receptor antagonists. The degree of symptom improvement was measured by rhinitis symptom questionnaires assessing four nasal symptoms, two ocular symptoms, and quality of life (QOL). Laboratory tests were performed at baseline, including serum total immunoglobulin E, blood eosinophil percentage, and skin prick test.<br><br>RESULTS: A total of 22 patients were enrolled. Total nasal symptom score (TNSS), TNSS eye (TNSS with two ocular symptoms), and QOL questionnaire scores all significantly decreased after treatment (p&#x2009;<&#x2009;0.001). Alpha diversity showed no significant changes, while intra-group distances were significantly decreased for both unweighted and weighted distances after treatment (p&#x2009;<&#x2009;0.05). The relative abundance of Staphylococcus increased, while that of Alloprevotella decreased after treatment (p&#x2009;<&#x2009;0.05). Predominant genera in most subjects were Staphylococcus, Acinetobacter, and Burkholderiaceae, and all significantly correlated to QOL improvement after treatment (p&#x2009;<&#x2009;0.05).<br><br>CONCLUSIONS: This study investigated the impact of chronic rhinitis treatment on the nasal microbiome and its association with symptom improvement. The changes in the nasal microbiome following treatment may enhance our understanding of its role in chronic rhinitis pathophysiology and therapeutic response.},
}
@article {pmid40539526,
year = {2025},
author = {Mu, M and Xu, Q and Hao, Q and Li, X and Wu, Z and Zhang, Q and Liu, S and Man, X and Xiao, L and Zou, Y and Li, S and He, N},
title = {Multiomics Analysis of Bacteroides cellulosilyticus Anticolitis via Gut Microbiota Metabolite-Mediated PI3K-Akt Signaling Pathway.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c00637},
pmid = {40539526},
issn = {1520-5118},
abstract = {Ulcerative colitis (UC) is a chronic inflammatory bowel disease characterized by mucosal inflammation and dysbiosis of the gut microbiota. Bacteroides cellulosilyticus (B. cellulosilyticus) is a multifunctional carbohydrate-degrading bacterium that may serve as a probiotic to enhance gut health by regulating gut microbiota. However, its specific role and mechanisms in UC remain unclear. This study utilized a population cohort and combined microbiome, metabolome, and transcriptome analyses to explore the therapeutic effects and potential mechanisms of B. cellulosilyticus on dextran sulfate sodium (DSS)-induced colitis in mice. After B. cellulosilyticus treatment, mice exhibited a 10.3% increase in body weight recovery (p < 0.01), a 12.9% reduction in disease activity index (DAI) scores (p < 0.05), and significant decreases in pro-inflammatory cytokine levels, including a 21.9% drop in IL-6 and a 24.6% reduction in TNF-α (p < 0.05; p < 0.0001). Notably, B. cellulosilyticus significantly inhibited the PI3K/Akt signaling pathway by effectively reducing the phosphorylation levels of both PI3K and Akt proteins. Additionally, metabolomic analysis revealed that B. cellulosilyticus significantly affected the gut metabolic profile. It led to increased levels of metabolites related to gut health, such as hypoxanthine. These metabolic changes were closely associated with the improvement of the microbial community composition. B. cellulosilyticus effectively restored microbial diversity and abundance in DSS-induced colitis. The integrated analysis of multiple omics approaches indicates that B. cellulosilyticus has the potential to serve as a probiotic therapeutic agent for UC. It offers new dietary and therapeutic strategies for managing UC by regulating the gut microbiota, altering metabolic profiles, and downregulating the PI3K-Akt signaling pathway.},
}
@article {pmid40539103,
year = {2025},
author = {Lin, ZY and He, SS and Mo, ZT and Liao, XT and Feng, ZS and Kong, J and Zhu, L and Li, Y and Tan, HY and Su, ZW and Jia, CH and Wu, F},
title = {Integrated analysis of serum metabolomics and fecal microbiome in infants with necrotizing enterocolitis.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1584041},
pmid = {40539103},
issn = {1664-302X},
abstract = {BACKGROUND: Necrotizing enterocolitis (NEC), a lethal gastrointestinal disorder in preterm infants, remains poorly understood in its pathology, and early diagnosis are critically limited. Multi-omics approaches present unprecedented opportunities to elucidate NEC pathogenesis and identify clinically translatable biomarkers.<br><br>METHODS: Infants with Bell stage II-III NEC and gestational age-matched controls were enrolled. Serum/stool samples from NEC patients at acute (NEC-D) and recovery (NEC-R) phases, and controls (non-NEC) were collected. Fecal metagenomic sequencing and serum untargeted metabolomic profiling were performed. Clinical parameters were compared.<br><br>RESULTS: The study comprised seven NEC and seven non-NEC infants. Baseline neonatal characteristics and maternal perinatal parameters showed no significant differences between NEC-D and non-NEC except for markedly lower leukocyte counts in NEC infants. Fecal metagenomics revealed severely diminished alpha diversity in NEC-D versus both non-NEC controls and NEC-R, characterized with lower Chao1 index. NEC-D exhibited elevated Escherichia coli relative abundance alongside reduced Staphylococcus haemolyticus, Staphylococcus aureus, Staphylococcus epidermidis, and Lactobacillus paracasei. Correspondingly, KEGG functional gene analysis demonstrated impaired metabolism in NEC-D. Serum metabolomics identified significantly decreased ornithine, DL-arginine, L-threonine, leucine, and D-proline in NEC-D versus non-NEC. NEC-D also showed lower taurodeoxycholic acid, glycocholic acid, and chenodeoxycholic acid compared to NEC-R. Integrative analysis revealed a positive correlation between the metabolites D-proline and ornithine and the Lactobacillus paracasei, Staphylococcus epidermidis, and Staphylococcus aureus abundance.<br><br>CONCLUSION: NEC is characterized by gut microbiota dysbiosis with reduced diversity, altered functional gene expression, and disrupted host-microbiota metabolic crosstalk. The identified serum metabolite-microbiome correlations provide mechanistic insights into NEC pathogenesis and potential diagnostic biomarkers.},
}
@article {pmid40539101,
year = {2025},
author = {Cui, X and Ding, Z and Ji, Y and Liu, J and Chang, Z and Zhang, J and Wang, X and Liu, K and Liu, Y},
title = {Stir-baked Xanthii fructus ameliorates adjuvant arthritis by regulating gut microbiota, short-chain fatty acids and metabolites.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1599529},
pmid = {40539101},
issn = {1664-302X},
abstract = {INTRODUCTION: Rheumatoid arthritis (RA) is a common and widespread autoimmune disease whose incidence is increasing. Stir-baked Xanthii fructus (XF) is used to treat RA in clinic. However, it's in vivo efficacy and mechanistic pathways remain unclear. This study aimed to explored XF's therapeutic effects and its mechanisms by comprehensive serum metabolomics and gut microbiota analysis.<br><br>METHODS: The components in XF were identified using the UPLC-MS technique. A rat model of adjuvant arthritis was established using complete Freund's adjuvant to evaluate the efficacy of XF. The in vivo mechanisms were explored through microbiome, short-chain fatty acid (SCFAs), and metabolomics analysis.<br><br>RESULTS: In total, 27 components were identified in XF. The treatment effectively suppressed inflammatory factors and alleviated pannus and cartilage damage. In addition, this article revealed a substantial remodeling of the gut microbiota composition, characterized by a reduced abundance of pro-inflammatory bacteria, increased populations of immunomodulatory bacteria and restored levels of SCFAs. Serum metabolomic profiling identified 17 arthritis-associated metabolites, primarily involved in glycerophospholipid metabolism and bile acid biosynthesis. Then, a strong correlation was found between gut microbiota and serum metabolites, indicating that XF exerts its therapeutic effects through immunomodulation, energy homeostasis regulation, and redox balance maintenance via the gut-joint axis.<br><br>DISCUSSION: This study provides new insights for further research into the targeted therapy of XF to ameliorate adjuvant arthritis.},
}
@article {pmid40538825,
year = {2025},
author = {Hofman, J and Brenerova, P and Borilova Linhartova, P},
title = {State-of-the-art approaches in the investigation of human seminal bacteriome using metagenomic methods.},
journal = {Frontiers in reproductive health},
volume = {7},
number = {},
pages = {1557912},
pmid = {40538825},
issn = {2673-3153},
abstract = {Although the understanding of the causes of infertility is the key to its successful treatment, recent studies have shown that as many as 50% of male-caused infertility cases are considered idiopathic. The microbial colonization of the male reproductive system was shown to be associated with reduced male reproductive fitness. Investigation of the seminal microbiome, however, remains challenging. This article aimed to improve this situation by creating the first comprehensive review of literature on the metagenomic methods (including the pre-analytical and analytical approaches) used in the research on human seminal bacteriome (total bacterial DNA in the matrix), published in 2018-2024. A total of 29 studies addressing the analysis of the human seminal bacteriome were identified. The analysis typically involved DNA extraction from the supernatant using commercial kits, amplification of the gene for 16S rRNA, and sequencing of amplicons. Where the separation of seminal plasma was performed, centrifugation was the dominant method used for this purpose. The significant heterogeneity in individual steps of methodological approaches in the analysis of the human seminal bacteriome complicates the comparison of results among studies and the establishment of standard procedures, hindering clinical advancements. For this reason, a protocol for the analysis of the human seminal plasma bacteriome is proposed here, which could lead to improved comparability of results among studies and make future research more efficient. This protocol is founded on rigorous quality control measures, compliance with the WHO laboratory manual for sample collection, extensive pretreatment involving mechanical and enzymatic lysis, DNA extraction using the QIAamp DNA Mini Kit (Qiagen), and short-read sequencing conducted on the MiSeq platform (Illumina).},
}
@article {pmid40538755,
year = {2025},
author = {Krama, T and Krams, R and Popovs, S and Gudrā, D and Ustinova, M and Fridmanis, D and Trakimas, G and Contreras-Garduño, J and Cīrule, D and Rantala, MJ and Adams, CB and Jõers, P and Krams, IA},
title = {Effects of Trichomonas gallinae infection and diet on blood microbiome composition in european greenfinches (Chloris chloris).},
journal = {Frontiers in physiology},
volume = {16},
number = {},
pages = {1576833},
pmid = {40538755},
issn = {1664-042X},
abstract = {Recent research has reported microbial invasion of the bloodstream in various disease-associated conditions. In this study, we investigated the role of trichomonosis outbreak (caused by the Trichomonas gallinae parasite) and food availability in shaping the blood microbiome composition of wintering greenfinches (Chloris chloris). Data were collected during two periods: before the outbreak (December) and during the outbreak (February). No bacterial contamination was observed in pre-epidemic blood samples. All individuals were infected during the outbreak, but greenfinches with irregular food access exhibited lower bacterial contamination in their blood. Individuals with permanent food access had a greater proportional representation of specific microbial taxa and higher alpha diversity in their blood microbiomes. However, beta diversity did not differ between the two groups. We demonstrated that trichomonosis infection and feeding regime play critical roles in mediating septic conditions of peripheral circulation during an outbreak, with food accessibility influencing blood microbial contamination. These findings integrate the impacts of feeding regimes and hematological responses to improve our understanding of the complex interactions between diet, disease, and physiological resilience in wild birds.},
}
@article {pmid40538713,
year = {2025},
author = {Kuang, X and Shen, J and Zheng, L and Duan, Y and Ma, Y and Leung, EL and Dai, L},
title = {Applications of bacteriophages in precision engineering of the human gut microbiome.},
journal = {Engineering microbiology},
volume = {5},
number = {1},
pages = {100189},
pmid = {40538713},
issn = {2667-3703},
abstract = {As our understanding of the role of the gut microbiome in human diseases deepens, precision engineering of the gut microbiome using bacteriophages has gained significant attention. Herein, we review the recent advances in bacteriophage-mediated modulation of the gut microbiome, discuss approaches at the ecological and genetic levels, and summarize the challenges and strategies pertinent to each level of intervention. Drawing on the structural attributes of bacteriophages in the context of precision engineering, we examined the latest developments in the field of phage administration. Gaining a nuanced understanding of microbiome manipulation will yield tailored strategies and technologies. This could revolutionize the prevention and treatment of diseases linked to gut pathogens and offer new avenues for the therapeutic use of bacteriophages.},
}
@article {pmid40538711,
year = {2025},
author = {Lathakumari, RH and Vajravelu, LK and Gopinathan, A and Vimala, PB and Panneerselvam, V and Ravi, SSS and Thulukanam, J},
title = {The gut virome and human health: From diversity to personalized medicine.},
journal = {Engineering microbiology},
volume = {5},
number = {1},
pages = {100191},
pmid = {40538711},
issn = {2667-3703},
abstract = {The human gut virome plays a crucial role in the gut and overall health; its diversity and regulatory functions influence bacterial populations, metabolism, and immune responses. Bacteriophages (phages) and eukaryotic viruses within the gut microbiome contribute to these processes, and recent advancements in sequencing technologies and bioinformatics have greatly expanded our understanding of the gut virome. These advances have led to the development of phage-based therapeutics, diagnostics, and artificial intelligence-driven precision medicine. The emerging field of phageomics shows promise for delivering personalized phage therapies that combat antimicrobial resistance by specifically targeting pathogenic bacteria while preserving beneficial microbes. Moreover, CRISPR-Cas systems delivered via phages have shown success in selectively targeting antibiotic resistance genes and enhancing treatment effectiveness. Phage-based diagnostics are highly sensitive in detecting bacterial pathogens, offering significant benefits for human health and zoonotic disease surveillance. This synthesis of the current knowledge highlights the pivotal role of the gut virome in regulating microbial communities and its transformative potential in personalized medicine, emphasizing its importance in advancing therapeutic and diagnostic strategies for improving health outcomes.},
}
@article {pmid40538528,
year = {2025},
author = {Alqam, ML and Jones, BC and Hitchcock, TM},
title = {Safety Evaluation of Topical Products Containing Live Cultures and Ferment of Cutibacterium Acnes Subspecies Defendens Strain XYCM42 in Individuals Predisposed to Acne Vulgaris.},
journal = {The Journal of clinical and aesthetic dermatology},
volume = {18},
number = {5},
pages = {44-53},
pmid = {40538528},
issn = {1941-2789},
abstract = {BACKGROUND: For individuals with acne-prone skin, identifying a topical regimen that does not lead to progression of their inflammatory issues often poses a challenge. A topical skin probiotic regimen containing a specific strain of Cutibacterium acnes (C. acnes) subspecies defendens, XYCM42, has been shown to be beneficial in improving skin health and appearance in individuals with generally healthy skin, but the use of the skin probiotic has not been sufficiently assessed in individuals with acne-prone skin.<br><br>OBJECTIVE: The purpose of this study was to evaluate the safety and efficacy of daily application of a topical skin biome care regimen containing a living C. acnes subsp. defendens derivative strain, XYCM42, its ferment, and adjunct topicals in individuals with acne-prone skin.<br><br>METHODS: This eight-week study was conducted at five locations and included 136 total participants. At baseline, Week 1, Week 4, and Week 8, subjects completed product questionnaires and symptom severity surveys. Of the study subjects, 20 were enrolled for clinical efficacy evaluation at all timepoints. Clinical assessments included blemish lesion counts, Investigator's Global Assessment (IGA) of acne lesion severity, and clinical grading of skin cosmetic and safety parameters.<br><br>RESULTS: As early as Week 1 of regimen application, clinical observations demonstrated statistically significant improvements in acne severity scores, with no subjects reporting increased or worsened acne during the study. By Week 4, subjects showed significant changes in nearly all skin cosmetic parameters assessed, including skin texture, clarity, tone, fine wrinkling, undereye dark circles, dryness, and erythema. Lesion counts were significantly reduced from baseline at all timepoints, with 100 percent of subjects experiencing fewer non-inflammatory lesions and 70 percent and 30 percent with fewer papule and pustule inflammatory lesions, respectively, by the end of the study. No adverse events were reported.<br><br>CONCLUSION: This at-home use study demonstrates that use of the XYCM42-based topical skin biome care regimen is both safe and appropriate for individuals with acne-prone skin. More broadly, the outcomes of this study provide further support toward the beneficial and commensal nature of C. acnes subsp. defendens in promoting skin health.},
}
@article {pmid40538297,
year = {2025},
author = {van Hees, K and van Velzen, R and Thijssen, J and Hofmans, L and Dijkman, R and Ducatelle, R and Molenaar, RJ},
title = {New Method for Early Detection of Gut Health Issues in Broilers.},
journal = {Avian pathology : journal of the W.V.P.A},
volume = {},
number = {},
pages = {1-21},
doi = {10.1080/03079457.2025.2521354},
pmid = {40538297},
issn = {1465-3338},
abstract = {Flocks differ in levels for Lactobacillales, Lachnospiraceae and Ruminococcaceae.Gut Damage Ratio between broilers with or without gut health problems differ.Results of both assays in broilers of 21 days of age relate significantly to SW.},
}
@article {pmid40538224,
year = {2025},
author = {Sun, S and Xin, Q and Ma, Z and Gao, W and Cheng, J and Liu, Y and Huang, Y and Zhang, H and Yang, Y and Lin, X and Zheng, L and Xu, X and Ding, C and Li, J},
title = {Self-Assembled Photothermal Particles Boost Synergistic Biofilm Eradication and Remineralization in Early Dental Caries Treatment.},
journal = {Small (Weinheim an der Bergstrasse, Germany)},
volume = {},
number = {},
pages = {e2503224},
doi = {10.1002/smll.202503224},
pmid = {40538224},
issn = {1613-6829},
support = {2022YFC2405905//National Key Research and Development Program of China/ ; 52373295//National Natural Science Foundation of China/ ; U22A20158//National Natural Science Foundation of China/ ; 52473311//National Natural Science Foundation of China/ ; RD-03-202409//Interdisciplinary Innovation Project of West China Hospital of Stomatology/ ; sklpme 2023-2-02//State Key Laboratory of Polymer Materials Engineering/ ; 2024NSFSC0241//Sichuan Science and Technology Program/ ; },
abstract = {Dental caries, driven by dietary habits and microbial biofilms, remains a significant global health issue. In situ biomimetic remineralization is considered a promising method, but its low efficiency is a key challenge. Additionally, the interference of cariogenic bacteria further exacerbates the problem. In this study, self-assembled photothermal particles (PAEB) with light-boosted synergistic biofilm eradication and remineralization properties for caries treatment are reported. Composed by polyaspartic acid-stabilized amorphous calcium phosphate (Pasp-ACP) and ε-poly-L-lysine/baicalein (EPL-BC), PAEB enable efficient light-to-heat conversion under near-infrared light exposure due to polymerization and stacking of baicalein. The localized hyperthermia, accompanied with EPL-BC disrupts bacterial membranes and eradicates biofilm by more than 99%, which is seven times higher than the non-radiation group (12.86%) and ≈21 times higher than the fluoride group (4.35%). Meanwhile, the releasing of calcium and phosphate ions is accelerated for rapid remineralization, with highest hardness recovery (1.96 GPa) of all groups, comparable to untreated healthy enamel. Moreover, in vivo microbiome analysis confirms that PAEB selectively reduces the abundance of cariogenic Streptococcus spp. while maintaining overall microbial diversity and oral ecological balance, presenting a promising solution for non-invasive dental caries treatment. This photothermal-enhanced strategy gives a reference for the design of bioactive therapeutic dental materials.},
}
@article {pmid40538021,
year = {2025},
author = {Abs, E and Saleska, SR and Allison, SD and Ciais, P and Song, Y and Weintraub, MN and Ferriere, R},
title = {Microbiome Adaptation Could Amplify Modeled Projections of Global Soil Carbon Loss With Climate Warming.},
journal = {Global change biology},
volume = {31},
number = {6},
pages = {e70301},
doi = {10.1111/gcb.70301},
pmid = {40538021},
issn = {1365-2486},
support = {891576//H2020 Marie Sk&#x142;odowska-Curie Actions/ ; PIA-10-LBX-54//MemoLife Laboratory of Excellence/ ; //FACE Partner University Fund, CNRS Mission pour l'Interdisciplinarit&#xe9;, PSL University/ ; //Ecole Doctorale 474 - Fronti&#xe8;res de l'Innovation en Recherche et &#xc9;ducation/ ; DE-SC0016440//Basic Energy Sciences/ ; DE-SC0025551//Basic Energy Sciences/ ; //Schmidt Sciences/ ; 2022070//Division of Environmental Biology/ ; DEB-1831493//Division of Environmental Biology/ ; },
abstract = {Warming alters soil microbial traits through ecological and evolutionary processes, directly influencing the decomposition of organic matter, which significantly affects global soil carbon emissions. Yet, soil carbon models largely ignore these processes and their implications for global responses to warming. Here, we incorporate eco-evolutionary theory into a mechanistic model describing microbial soil carbon decomposition to address the question of whether such processes could have consequential effects on climate carbon feedbacks globally. We assume that a key trait of microbes, their resource allocation to production of exoenzymes (which facilitate decomposition of organic matter)-is optimized to environmental temperatures by natural selection. We find that eco-evolutionary optimization results in microbes allocating more resources to enzyme production under warming. When applied at the global scale, eco-evolutionary optimization enhances the biological realism of soil carbon models and significantly amplifies global soil carbon loss by 2100. Our results highlight the significant potential of microbial eco-evolutionary responses to influence carbon cycle feedbacks to climate change, and motivate an urgent need for more comprehensive data to accurately quantify the adaptive potential of microbiomes in response to climate change.},
}
@article {pmid40537904,
year = {2025},
author = {Khongkool, K and Taweechotipatr, M and Payungporn, S and Sawaswong, V and Lertworapreecha, M},
title = {Characterization and Evaluation of Lactobacillus plantarum LC5.2 Isolated from Thai Native Pigs for its Probiotic Potential in Gut Microbiota Modulation and Immune Enhancement.},
journal = {Journal of microbiology and biotechnology},
volume = {35},
number = {},
pages = {e2503028},
doi = {10.4014/jmb.2503.03028},
pmid = {40537904},
issn = {1738-8872},
abstract = {Probiotic supplementation, particularly with Lactobacillus species, enhances growth performance, maintains gastrointestinal microbial balance, and prevents infections in livestock. This study isolated Lactobacillus strains from the feces of healthy native pigs in southern Thailand and assessed their probiotic properties and safety through both in vitro and in vivo evaluations. Nine Lactobacillus strains showed probiotic potential, with Lactobacillus plantarum LC5.2 demonstrating the best characteristics. This strain tolerated both acid and bile (100% tolerance) and exhibited strong adhesion properties, including high auto-aggregation (69.74%), cell surface hydrophobicity (77.14%), adhesion to Caco-2 cells (9.31%), and biofilm formation. It also exhibited antibacterial activity, inhibiting EHEC, EPEC, and Salmonella Typhimurium through organic acid production. Co-aggregation with these pathogens ranged from 60.83% to 74.09%. Safety evaluations showed no hemolytic activity, susceptibility to antibiotics, and co-existence with other probiotics. In mice, L. plantarum LC5.2 showed no toxicity, with normal food intake, behavior, and weight gain. No abnormalities were found in the small intestine, colon, liver, or spleen. Mice administered the probiotic had significantly higher intestinal IgA levels. Gut microbiome analysis revealed no notable structural alterations but indicated an increase in beneficial bacteria, including Lactobacillus. These results suggest that L. plantarum LC5.2 demonstrates strong probiotic potential, safety, and benefits for gut health, making it a promising candidate for livestock applications.},
}
@article {pmid40537897,
year = {2025},
author = {Jung, W and Son, YM},
title = {Nanoparticle-Driven Modulation of Mucosal Immunity and Interplay with the Microbiome.},
journal = {Journal of microbiology and biotechnology},
volume = {35},
number = {},
pages = {e2404033},
doi = {10.4014/jmb.2504.04033},
pmid = {40537897},
issn = {1738-8872},
abstract = {Mucosal surfaces are dynamic immunological interfaces that play a critical role in maintaining host defense and microbial homeostasis. Disruptions in the interaction between the mucosal immune system and its commensal microbiota have been associated with the onset of several diseases, including inflammatory bowel disease, asthma, and bacterial vaginosis. This review examines recent advances in nanoparticle (NP)-based strategies aimed at modulating mucosal immunity and restructuring microbial communities. It highlights how organic and inorganic NPs such as polysaccharide-based carriers, lipid NPs, and metallic nanomaterials enhance the delivery and stability of probiotics, prebiotics, and synbiotics, and facilitate targeted immunomodulation across gastrointestinal, respiratory, and female reproductive mucosal tissues. NP-based strategies are particularly emphasized for their ability to penetrate mucus barriers, facilitate microbial colonization, modulate cytokine activity, and enhance the restoration of epithelial barrier function. Disease-specific applications, including NP-based therapies for colitis, respiratory inflammation, and vaginal dysbiosis, are also discussed. In addition, this review outlines current challenges related to biosafety, targeting specificity, and clinical translation, and suggests future directions for research. Altogether, NP platforms offer a promising avenue for the precise modulation of mucosal immunity and microbiota, with significant potential in the prevention and treatment of mucosal-associated diseases.},
}
@article {pmid40537892,
year = {2025},
author = {Kang, J and Choi, Y and Keum, GB and Doo, H and Kwak, J and Kim, H and Chae, Y and Lee, S and Yang, H and Kim, S and Sun, X and Kim, HB and Yoo, SJ},
title = {Effect of Diet and Lifestyle Changes on Gut Microbial Diversity in Healthy Adolescents.},
journal = {Journal of microbiology and biotechnology},
volume = {35},
number = {},
pages = {e2503018},
doi = {10.4014/jmb.2503.03018},
pmid = {40537892},
issn = {1738-8872},
abstract = {The human gut microbiome is a complex ecosystem shaped by both intrinsic and extrinsic factors, with external elements such as diet and exercise significantly influencing its diversity and composition. In this study, we evaluated gut microbiome shifts in adolescents participating in a four-week camp with controlled diets, lifestyle, and a healthy living environment. Stool samples were collected before and after the camp period and analyzed through 16S rRNA gene sequencing to assess changes in microbial composition and diversity. Post-intervention, gut microbiome diversity increased significantly, with notable changes in the relative abundance of taxa such as Lachnospira, Alistipes, and Barnesiella, which are associated with enhanced immune function and gut health. Additionally, functional prediction using PICRUSt indicated an increase in genes associated with energy production and metabolism, suggesting a broader functional impact of lifestyle modifications on gut microbial functionalities. These findings revealed the potential causal relationships between lifestyle modifications and gut microbiome shifts, providing valuable insights into the interactions between environment, diet, and the gut microbiota.},
}
@article {pmid40537703,
year = {2025},
author = {Tronel, A and Roger-Margueritat, M and Plazy, C and Cunin, V and Mohanty, I and Dorrestein, PC and Soranzo, T and Le Gouellec, A},
title = {Untargeted and semi-targeted metabolomics approach for profiling small intestinal and fecal metabolome using high-resolution mass spectrometry.},
journal = {Metabolomics : Official journal of the Metabolomic Society},
volume = {21},
number = {4},
pages = {84},
pmid = {40537703},
issn = {1573-3890},
support = {2021/0931//Association Nationale de la Recherche et de la Technologie/ ; 2021/0931//Association Nationale de la Recherche et de la Technologie/ ; RF20230503289//Association Vaincre la Mucoviscidose/ ; ANR-15-IDEX-02//ANR/ ; },
abstract = {INTRODUCTION: The gut microbiome is a complex ecosystem stratified that varies along different sections of the gut. It comprises a wide array of metabolites originating from both food, host, and microbes. Microbially-derived metabolites, such as bile acids, short-chain fatty acids, and indole derivatives, are of significant interest due to their direct interactions with host physiology and regulating function. Most current studies on the gut microbiome focus on fecal samples, which do not fully represent the upper parts of the gut due to its stratification. To collect microbiome samples from the proximal gut microbiome, endoscopic methods or new non-invasive medical devices can be used.<br><br>OBJECTIVES: To enable comprehensive profiling of the gut metabolome and analyze key metabolites, we developed a combined approach combining untargeted and semi-targeted metabolomics using a Q-Exactive Plus Orbitrap mass spectrometer.<br><br>METHODS: Initially, we selected 49 metabolites of interest for the gut metabolome based on four distinct criteria. We validated these metabolites through repeatability and linearity tests and created a compound database using the software TraceFinder (ThermoFisher Scientific). For untargeted metabolomics, we established a workflow for the annotation and discovery of molecules.<br><br>RESULTS: Finally, 37 metabolites were validated for semi-targeted metabolomics, and we conducted a proof of concept on small intestinal and fecal samples form a clinical trial (NCT05477069).<br><br>CONCLUSION: Our combined approach, facilitated by molecular networking, demonstrated the potential to discover new metabolites.},
}
@article {pmid40537586,
year = {2025},
author = {King, A},
title = {Single-celled organisms set for greater role in gut health.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {40537586},
issn = {1476-4687},
}
@article {pmid40537478,
year = {2025},
author = {Sommer, AJ and Skarlupka, JH and Teseo, S and Otani, S and Suen, G and Coon, KL and Sapountzis, P},
title = {Genomic evidence for flies as carriers of zoonotic pathogens on dairy farms.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {111},
pmid = {40537478},
issn = {2055-5008},
support = {WIS04039//United States Department of Agriculture | National Institute of Food and Agriculture (NIFA)/ ; },
abstract = {Dairy farms are major reservoirs of zoonotic bacterial pathogens, which harbor antimicrobial resistance genes (ARGs), and raise critical questions about their dissemination on and off the farm environment. Here, we investigated the role of coprophagous muscid flies (Diptera: Muscidae) as carriers of zoonotic pathogens and antimicrobial resistance. We collected cow manure and flies on a dairy farm and used shotgun metagenomics to identify the presence of clinically relevant bacteria, virulence factors, and ARGs in both environments. Our results reveal that, although the fly microbiome is largely composed of manure-associated taxa, they also harbor specific insect-associated bacteria, which may be involved in nutrient provisioning to the host. Furthermore, we identifed shared ARGs, virulence factors, and zoonotic pathogens enriched within the fly gastrointestinal tract (GIT). Our study illustrates the potential flow of pathogenic microorganisms from manure to coprophagous flies, suggesting that flies may pose an important zoonotic threat on dairy farms.},
}
@article {pmid40537474,
year = {2025},
author = {Bradshaw, CS and Plummer, EL and Muzny, CA and Mitchell, CM and Fredricks, DN and Herbst-Kralovetz, MM and Vodstrcil, LA},
title = {Bacterial vaginosis.},
journal = {Nature reviews. Disease primers},
volume = {11},
number = {1},
pages = {43},
pmid = {40537474},
issn = {2056-676X},
abstract = {Bacterial vaginosis (BV) is a vaginal microbiome disorder that is associated with preterm birth and spontaneous abortion, increased risk of HIV infection and sexually transmitted infections, and has negative effects on quality of life. BV affects one in four women globally, with the highest burden in resource-limited settings. Marked alterations in vaginal microbiome composition, in pro-inflammatory cytokines and chemokines, and in the proteome and metabolome characterize BV and contribute to adverse sequelae. Despite its prevalence, the exact aetiologic agent of BV is unknown and its pathophysiology is poorly understood. These knowledge gaps impede diagnostic and management approaches, with recommended treatment strategies resulting in recurrence that exceeds 50% over 3-6 months. New data on the sexual transmission of BV, including evidence that male-partner treatment improves cure, have improved our understanding of its aetiology and pathogenesis, and provide opportunities for developing optimal diagnostic, treatment and prevention strategies. Other factors probably also contribute to the low efficacy of current treatments, including biofilm and/or antimicrobial resistance, and failure to recolonize a favourable vaginal microbiome after treatment. The complex pathophysiology of BV highlights that individualized and multifaceted management approaches will be required to manage the refractory and adverse sequelae of BV.},
}
@article {pmid40537372,
year = {2025},
author = {Kolodkin-Gal, I and Frenkel-Morgenstern, M},
title = {Liquid biopsy for microbiome profiling through nucleotide analysis.},
journal = {Trends in biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tibtech.2025.05.021},
pmid = {40537372},
issn = {1879-3096},
abstract = {Liquid biopsy for microbiome analysis is an emerging field that aims to study the composition and dynamics of microbial communities by analyzing biological fluids such as blood, urine, or saliva. This noninvasive method offers a useful approach to understanding microbiome dynamics. It provides insights into different pathologies, enables unbiased pathogen detection through noninvasive sampling, and offers rapid turnaround times. Clinical applications of liquid biopsy are emerging for microbiome exploration, particularly in areas such as infectious disease management, cancer diagnostics, and personalized medicine for chronic bowel diseases. This review highlights the role of liquid biopsy in infection and microbiome exploration, potentially revolutionizing diagnostics and tailored medicine by enabling the real-time monitoring of microbial shifts.},
}
@article {pmid40537345,
year = {2025},
author = {Zhang, C and Turnbaugh, PJ},
title = {Mining microbial metabolites of GPCR-targeted drugs.},
journal = {Trends in pharmacological sciences},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tips.2025.05.014},
pmid = {40537345},
issn = {1873-3735},
abstract = {G protein-coupled receptors (GPCRs) are a large superfamily of receptors critical for mammalian cell-cell communication and a common drug target. A new study has revealed that the human gut microbiome can metabolize GPCR-targeted drugs into both expected and surprising metabolites, with potentially broad implications for the treatment of disease.},
}
@article {pmid40537117,
year = {2025},
author = {Khouri Chalouhi, D and Bertani, I and Esposito, A and Piazza, S and Bez, C and Venturi, V},
title = {An in Planta Enrichment Route to Identify Bacterial Root Endophytes.},
journal = {Environmental microbiology reports},
volume = {17},
number = {3},
pages = {e70136},
doi = {10.1111/1758-2229.70136},
pmid = {40537117},
issn = {1758-2229},
support = {//Arturo falaschi PhD scholarship/ ; PGR10061//MAE-CI/ ; },
abstract = {Microorganisms live in close association with plants, forming ecological interaction webs and providing beneficial traits such as nutrition, growth, and tolerance to biotic and abiotic stresses. Via the rhizosphere, plants recruit bacteria which colonise internal plant tissues, creating a spatial gradient between the rhizosphere and the endosphere. This study presents a high throughput in planta endophyte enrichment scheme designed for the identification of 'super'-endophytic bacteria which can serially colonise the rice root endosphere. Oryza sativa (rice) plants were grown in bulk soil, and endophytes were then recovered from roots. The recovered endophyte mixture was used as inoculum for the first generation of rice plantlets, which were then grown under no stress or nitrogen (N) depletion. The total endophytic community was then purified and used as a second inoculum for a new set of plants; this procedure was repeated for four generations. Enrichment patterns of root bacterial endophytes were observed, such as Kosakonia in the non-stressed plants and Ferrovibrio in plants grown under nitrogen starvation. This enrichment method proved to be suitable for the identification of endophytes which can efficiently colonise the root endosphere.},
}
@article {pmid40536601,
year = {2025},
author = {Gan, B and Zhang, X and Xin, J and Duan, L and Sun, N and Chen, Y and Zeng, J and Lian, Y and Li, H and Wang, H and Ni, X and Ma, H},
title = {Lactobacillus johnsonii HL79 mitigate plateau environment-induced hippocampal dysfunction in mice.},
journal = {AMB Express},
volume = {15},
number = {1},
pages = {96},
pmid = {40536601},
issn = {2191-0855},
support = {U23A20476//Joint Funds of the National Natural Science Foundation of China/ ; U23A20476//Joint Funds of the National Natural Science Foundation of China/ ; U23A20476//Joint Funds of the National Natural Science Foundation of China/ ; U23A20476//Joint Funds of the National Natural Science Foundation of China/ ; U23A20476//Joint Funds of the National Natural Science Foundation of China/ ; U23A20476//Joint Funds of the National Natural Science Foundation of China/ ; U23A20476//Joint Funds of the National Natural Science Foundation of China/ ; U23A20476//Joint Funds of the National Natural Science Foundation of China/ ; U23A20476//Joint Funds of the National Natural Science Foundation of China/ ; U23A20476//Joint Funds of the National Natural Science Foundation of China/ ; U23A20476//Joint Funds of the National Natural Science Foundation of China/ ; U23A20476//Joint Funds of the National Natural Science Foundation of China/ ; LSKJ202309//Key Science and Technology Project of Lhasa, Tibet/ ; LSKJ202309//Key Science and Technology Project of Lhasa, Tibet/ ; LSKJ202309//Key Science and Technology Project of Lhasa, Tibet/ ; LSKJ202309//Key Science and Technology Project of Lhasa, Tibet/ ; LSKJ202309//Key Science and Technology Project of Lhasa, Tibet/ ; LSKJ202309//Key Science and Technology Project of Lhasa, Tibet/ ; LSKJ202309//Key Science and Technology Project of Lhasa, Tibet/ ; LSKJ202309//Key Science and Technology Project of Lhasa, Tibet/ ; LSKJ202309//Key Science and Technology Project of Lhasa, Tibet/ ; LSKJ202309//Key Science and Technology Project of Lhasa, Tibet/ ; LSKJ202309//Key Science and Technology Project of Lhasa, Tibet/ ; LSKJ202309//Key Science and Technology Project of Lhasa, Tibet/ ; 2023ZYJM001//Key Research and Development Project of the Tibet Autonomous Region/ ; 2023ZYJM001//Key Research and Development Project of the Tibet Autonomous Region/ ; 2023ZYJM001//Key Research and Development Project of the Tibet Autonomous Region/ ; 2023ZYJM001//Key Research and Development Project of the Tibet Autonomous Region/ ; 2023ZYJM001//Key Research and Development Project of the Tibet Autonomous Region/ ; 2023ZYJM001//Key Research and Development Project of the Tibet Autonomous Region/ ; 2023ZYJM001//Key Research and Development Project of the Tibet Autonomous Region/ ; 2023ZYJM001//Key Research and Development Project of the Tibet Autonomous Region/ ; 2023ZYJM001//Key Research and Development Project of the Tibet Autonomous Region/ ; 2023ZYJM001//Key Research and Development Project of the Tibet Autonomous Region/ ; 2023ZYJM001//Key Research and Development Project of the Tibet Autonomous Region/ ; 2023ZYJM001//Key Research and Development Project of the Tibet Autonomous Region/ ; },
abstract = {Plateau environment represents a common terrestrial characterized by multistress conditions including hypobaric hypoxia, low temperature, and intense radiation, yet sustain over 100 million permanent or transient inhabitants. While this extreme environment exerts profound impacts on cerebral architecture and gut microbiota homeostasis, precipitating cognitive deficits and microbiome-derived intestinal pathologies, the mechanistic interplay between plateau environment adaptation and microbial dynamics remains contentious. Here, we employ a microbiota-gut-brain axis framework to investigate whether probiotic intervention can ameliorate hippocampal impairments induced by simulated plateau environment exposure (3500-4000 m) in mice. Through simulated plateau environment exposure experiments, we revealed that extreme high-altitude conditions induced hippocampal memory dysfunction in mice, exacerbated oxidative stress damage in hippocampal tissues, and altered synaptic plasticity-related biomarkers including CREB transcription factor, BDNF protein levels, and electrophysiological power spectra. Administration of HL79 alleviated these burdens, including memory dysfunction and tissue damage, though complete reversal was not achieved. Combined hippocampal transcriptomic analyses suggested that HL79's beneficial effects primarily involved modulation of lipid-related gene expression in the hippocampus, consistent with prior reports of plateau environmental impacts on gene expression. Serum metabolomic results further reinforced this inference that differential metabolites regulated by HL79 are mainly enriched in bile secretion, taurine and hypotaurine metabolism, linoleic acid metabolism, and PPAR signaling pathways, though the precise regulatory mechanisms require further elucidation. This research provides a novel microbiota-gut-brain axis-based regulatory strategy for adaptation to extreme plateau environments and offers new evidence for understanding the relationship between gut microbiota and plateau environment adaptation at high elevations.},
}
@article {pmid40536441,
year = {2025},
author = {Xia, K and Jiao, Y and Zhang, L and Gao, R and Wang, F and Pan, Y and Cui, S and Lin, Y and Wu, T and Li, L and Wu, X and Ruan, Y and Sun, J and Yin, L and Chen, C and Lin, M},
title = {Multi-Omics Analysis of Ileal Mucosa and Mesentery Before and After Ileocecal Resection in Crohn's Disease.},
journal = {United European gastroenterology journal},
volume = {},
number = {},
pages = {},
doi = {10.1002/ueg2.70069},
pmid = {40536441},
issn = {2050-6414},
abstract = {Crohn's disease (CD), a type of inflammatory bowel disease (IBD), is a chronic disorder involving any part of the gastrointestinal tract. Ileocecal resection may serve as a more effective treatment option for early CD. However, the potential relationship and mechanisms between the ileocecum and remission induction of CD are still elusive. In this study, we conducted 16S rRNA sequencing and liquid chromatography-tandem mass spectrometry (LC-MS/MS) on 68 terminal ileal mucosa and mesentery samples from 34 patients with CD. The results showed an improvement in the microbial health of the ileal mucosa and mesentery in patients with CD after ileocecal resection. In addition, specific spatial alterations in microbiota and metabolites were observed before and after surgery. Furthermore, differentially expressed metabolites in the ileal mucosa and mesentery were subjected to Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. The findings of this study support the therapeutic value of ileocecal resection in CD from a multi-omics perspective and may guide the clinical translation of microbiome-based strategies for precise treatment of CD.},
}
@article {pmid40536191,
year = {2025},
author = {Dietz, M and Gates, TJ and Sikdar, R and Subramanian, S and Elias, MH and Staley, C},
title = {Impeding Quorum Sensing Among the Intestinal Microbiota Impacts the Metastatic Rate of Colorectal Cancer.},
journal = {Cancer medicine},
volume = {14},
number = {12},
pages = {e71009},
pmid = {40536191},
issn = {2045-7634},
support = {//Norm and Pat Wells Grant/ ; //Minnesota Colorectal Cancer Research Foundation/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Colorectal Neoplasms/pathology/microbiology/drug therapy/genetics ; Female ; Male ; Mice ; *Quorum Sensing/drug effects ; Mice, Inbred C57BL ; Neoplasm Metastasis ; Disease Models, Animal ; Feces/microbiology ; Humans ; },
abstract = {BACKGROUND: The gut microbiota is associated with colorectal cancer (CRC) risk and CRC metastatic potential. However, the role of bacteria in CRC progression and metastasis remains unclear.<br><br>AIMS: Here, we hypothesized that microbial communication, mediated through quorum sensing (QS), was a critical component regulating microbial functions related to cancer progression and metastasis.<br><br>MATERIALS &amp; METHODS: To test this, male and female C57BL/6 mice were injected with organoids modeling aggressive colon cancer (CRC), carrying mutations in Apc, Kras, p53, and Smad4. Two groups of mice were treated with two different quorum quenching (QQ) lactonases (GcL or SsoPox) for 8&#x2009;weeks (n&#x2009;=&#x2009;10/group/sex). Fecal samples were collected weekly and characterized by Illumina next-generation sequencing, with tissues collected during necropsy.<br><br>RESULTS: Male mice treated with SsoPox had fewer metastases than control mice (&#x3c7;[2]&#x2009;=&#x2009;3.206, p&#x2009;=&#x2009;0.073), with no SsoPox-treated male developing a metastasis. In contrast, female mice treated with SsoPox had more metastases than control mice (&#x3c7;[2]&#x2009;=&#x2009;2.554, p&#x2009;=&#x2009;0.110), and every female, SsoPox-treated mouse that developed a primary tumor also developed metastasis by the experimental endpoint. However, QQ treatment was shown to minimally affect the gut microbiome composition. Similarly, no significant differences were observed in inflammatory response as assessed by immunofluorescent staining or fecal concentrations of immunoglobulin A, calprotectin, or lipocalin-2. Differences in fecal short-chain fatty acid concentrations also did not differ significantly.<br><br>DISCUSSION: These results suggest that QQ treatment has a sex-based effect on CRC metastatic rate.<br><br>CONCLUSION: Targeting communication among the gut microbiome may be a promising avenue for the development of CRC therapies that minimally impact microbial community composition and host immune response.},
}
@article {pmid40535760,
year = {2025},
author = {Yoo, JY and Dutta, M},
title = {Editorial: Microbiome: the modulator of human health.},
journal = {Frontiers in pharmacology},
volume = {16},
number = {},
pages = {1625412},
pmid = {40535760},
issn = {1663-9812},
}
@article {pmid40535543,
year = {2025},
author = {Meyers, M and Stoffels, CBA and Frache, G and Letellier, E and Feucherolles, M},
title = {Microbiome in cancer metastasis: biological insights and emerging spatial omics methods.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1559870},
pmid = {40535543},
issn = {2235-2988},
mesh = {Humans ; *Microbiota ; *Neoplasm Metastasis/pathology ; Tumor Microenvironment ; *Neoplasms/microbiology/pathology ; Metabolomics/methods ; Genomics/methods ; Proteomics/methods ; Animals ; },
abstract = {The role of the microbiome in cancer metastasis has emerged as a critical area of research, with growing evidence suggesting that microbial composition and interactions within the tumour microenvironment may significantly influence metastatic progression. This review explores the role of the microbiome in cancer metastasis, as well as potential key bacteria and their mechanisms through which they could impact tumour dissemination, seeding and growth. Biological models used to study metastasis are discussed to provide context for the further investigation of these interactions. In order to answer unresolved questions regarding the microbiome's involvement in metastatic dissemination, recent advancements in spatial biology techniques are examined, including spatial genomics, transcriptomics, proteomics and metabolomics, which enable the spatial mapping of microbial interactions within the tumour microenvironment. Additionally, multimodal-omics imaging approaches are highlighted for their potential to integrate multiple molecular layers, offering comprehensive insights into the microbiome's role in cancer metastasis. The review also addresses the challenges and limitations of these techniques, underscoring the complexity of studying microbiome-tumour interactions and offering directions for future research to better explore and target the microbiological landscape in metastatic cancer.},
}
@article {pmid40535353,
year = {2025},
author = {Huang, L and Meng, J and Lin, S and Peng, Z and Zhang, R and Shen, X and Zheng, W and Zheng, Q and Wu, L and Wang, X and Wang, Y and Mao, R and Sun, C and Li, X and Feng, ST},
title = {Integrating Gut Microbiome and Metabolomics with Magnetic Resonance Enterography to Advance Bowel Damage Prediction in Crohn's Disease.},
journal = {Journal of inflammation research},
volume = {18},
number = {},
pages = {7631-7649},
pmid = {40535353},
issn = {1178-7031},
abstract = {PURPOSE: Cumulative bowel damage (BD) critically influences the progression and prognosis of Crohn's disease (CD). Although the Lémann Index (LI) remains the standard for BD assessment, its clinical utility is limited by heavy reliance on extensive clinical data. Multiparametric magnetic resonance enterography (MRE) provides noninvasive macroscopic evaluation of BD severity, however, it fails to characterize microscopic alterations. We therefore integrated MRE with gut microbiome and metabolomic data to uncover mechanistic insights and develop a comprehensive model for better prediction of BD.<br><br>METHODS AND RESULTS: In this prospective two-center study, 309 CD patients were stratified into BD and non-BD groups using LI. Patients underwent MRE, fecal 16S rRNA gene sequencing, and fecal/serum metabolomic analysis. Thirty healthy controls were included for comparison. The relationships between microbial/metabolic factors and MRE features were explored using correlation and mediation analyses. Seven machine learning algorithms, each paired with seven distinct combinations of multi-omics features, were evaluated using nested 5-fold cross-validation to construct an optimal prediction model. BD patients exhibited reduced gut microbial diversity (P<0.05), with Erysipelatoclostridium and [Ruminococcus]_gnavus_group as key discriminators. Metabolomics revealed elevated fecal aromatic amino acids and depleted serum glycerophospholipids/sphingolipids (P<0.05) linked to MRE-quantified features through mediation by microbial pathways (eg, 22.8% mediation effect of Prevotella_9 on penetration, P ACME=0.022). The optimal Xtreme Gradient Boosting Classifier (XGBC) model integrating three microbial genera, six fecal metabolites, three serum metabolites, and three MRE features achieved superior performance (AUC 0.857 and 0.829 in the derivation and external validation cohorts, respectively). SHapley Additive exPlanations (SHAP) analysis prioritized perianal diseases, Erysipelatoclostridium, and fecal alanine as key contributors.<br><br>CONCLUSION: Our study underscores the interplay between gut microbial dysbiosis, metabolic alterations, and MRE-quantified structural changes in BD patients. The integrated multi-omics model provides a promising tool for BD prediction, enabling precise CD severity stratification and personalized clinical decision-making.},
}
@article {pmid40535324,
year = {2025},
author = {Liu, S and Lin, Z and Zhou, J and Yang, X and You, L and Yang, Q and Li, T and Hu, Z and Zhan, X and Jiang, Y and Sun, B},
title = {Distinct Airway Microbiome and Metabolite Profiles in Eosinophilic and Neutrophilic Asthma.},
journal = {Journal of asthma and allergy},
volume = {18},
number = {},
pages = {1003-1022},
pmid = {40535324},
issn = {1178-6965},
abstract = {BACKGROUND: Asthma is a chronic, heterogeneous disease driven by inflammatory phenotypes, primarily eosinophilic asthma (EA) and neutrophilic asthma (NEA). While allergen triggers are well-known, the role of the airway microbiome and metabolites in asthma exacerbations remains poorly understood.<br><br>METHODS: We recruited 64 participants (24 EA, 20 NEA, 20&#xa0;healthy controls [HC]) for the discovery cohort, with validation in an external cohort (10 EA, 8 NEA, 8&#xa0;HC). Induced sputum samples were analyzed using 16S rRNA sequencing to profile bacterial composition and non-targeted metabolomics to assess airway metabolites. Random forest models identified diagnostic markers, validated in the external cohort.<br><br>RESULTS: Significant shifts in airway microbiota were observed, particularly between NEA and HC, and between EA and NEA. Four bacterial general-Stenotrophomonas, Streptococcus, Achromobacter, and Neisseria-were consistently identified across groups. Veillonella was more abundant in NEA vs HC, while Achromobacter was enriched in NEA vs EA, indicating distinct microbial signatures. Metabolomic profiling revealed distinct pathways: pyrimidine metabolism (EA vs HC), tryptophan metabolism (NEA vs HC), and arachidonic acid metabolism (EA vs NEA). Microbial-metabolite correlations indicated microbiota-driven metabolic activity. Biomarker candidates were validated in the external cohort.<br><br>CONCLUSION: The airway microbiota and metabolites are intricately linked to asthma exacerbations, with distinct patterns between EA and NEA. These findings highlight their potential as diagnostic biomarkers and therapeutic targets for personalized asthma management.},
}
@article {pmid40535110,
year = {2025},
author = {Raimi, A and Adeleke, R},
title = {High-throughput sequencing analysis of community diversity and functional structure of endophytic bacteria in edible vegetable crops: potential implication on plant microbiological quality.},
journal = {3 Biotech},
volume = {15},
number = {7},
pages = {216},
pmid = {40535110},
issn = {2190-572X},
abstract = {UNLABELLED: This study evaluated the diversity and functional structure of endophytic bacterial communities residing within four common leafy vegetables: Brassica oleracea, Lactuca sativa, Allium cepa, and Spinacia oleracea, cultivated under organic (OF) and conventional (CF) farming systems. Utilizing high-throughput 16S rRNA gene sequencing and the PICRUSt2 pipeline, the research assessed the influence of plant species, organ (leaf/root), and fertilizer type on these microbial communities. Findings revealed that plant species and organ type significantly shaped endophytic bacterial community composition and diversity. Onion communities were distinct, and roots exhibited higher diversity and richness compared to leaves. Fertilizer type significantly impacted overall bacterial diversity, with CF farms showing higher diversity than OF. Microbial network analysis identified keystone taxa, including network hubs like Serratia and Streptomyces, and module hubs like Solirubrobacter, Corynebacterium, and Mycobacterium. Functional predictions indicated diverse metabolic capabilities, with organ type significantly affecting pathway abundance (leaves enriched in carbohydrate degradation, roots in nutrient metabolism/degradation). OF farms showed higher predicted abundance of some potential virulence pathways, while CF farms had higher abundance of certain biotechnological pathways. Vegetable nutrient content significantly correlated with both bacterial community composition and predicted metabolic pathways. This study highlights the complex interplay between farming practices, plant factors, endophytic microbiomes, and their functional potential, underscoring implications for vegetable microbiological quality and potential human health.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-025-04380-9.},
}
@article {pmid40535082,
year = {2025},
author = {Wang, C and Hu, B and Liang, Q and Jiang, H and Yuan, L and Li, S},
title = {Oral microbiome and risk of lung cancer: results from a two-sample mendelian randomization analysis.},
journal = {Translational lung cancer research},
volume = {14},
number = {5},
pages = {1715-1723},
pmid = {40535082},
issn = {2218-6751},
abstract = {BACKGROUND: Numerous studies have suggested that the oral microbiome may function as a biomarker for lung cancer screening. However, the relationship between oral microbiome and lung cancer has not been thoroughly investigated. Consequently, investigating the causal relationship between oral microbiome and lung cancer was the primary goal of this study.<br><br>METHODS: We conducted a two-sample Mendelian randomization (MR) analysis to investigate the causal relationship between the oral microbiome and lung cancer. Summary statistics for the oral microbiomes were obtained from large-scale metagenome-genome-wide association studies (mgGWAS), while genome-wide association study (GWAS) summary statistics for lung cancer were sourced from the IEU-OpenGWAS online platform. We employed inverse variance weighted (IVW) analysis and Wald ratio methods to evaluate the causal associations between the oral microbiome and lung cancer. Finally, we performed MR Steiger's test to strengthen the validity of the causal associations.<br><br>RESULTS: Three oral microbiomes were causally associated with lung cancer. Gemella haemolysans (pheno.388) from saliva and an unclassified species (pheno.844) of Clostridia from saliva were protective factors for lung cancer, and an unclassified species (pheno.1354) of Prevotella from tongue was a risk factor for lung cancer. And there is no bidirectional association of causality between oral microbiomes and lung cancer.<br><br>CONCLUSIONS: The oral microbiomes, Gemella haemolysans (pheno.388) from saliva, an unclassified species (pheno.844) of Clostridia from saliva and an unclassified species (pheno.1354) of Prevotella from tongue, were causally associated with lung cancer. Oral microbiology holds significant potential for clinical applications in etiologic exploration, early screening, prevention, and enhancing survival in lung cancer. Regarding treatment, personalized therapy based on oral flora may provide novel therapeutic strategies for lung cancer.},
}
@article {pmid40535022,
year = {2025},
author = {Blaustein, RA and Smith, JE and Toro, M and Pachepsky, Y and Stocker, MD},
title = {Water metagenomes reflect physicochemical water quality throughout a model agricultural pond.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1535096},
pmid = {40535022},
issn = {1664-302X},
abstract = {Agricultural ponds are essential irrigation resources, though may also serve as reservoirs for pathogens and antimicrobial resistance (AMR) genes. While monitoring microbiological water quality is critical for food safety, the influence of sampling factors (e.g., when and where to collect samples) in making risk assessments and potential applications for using environmental covariates as indicators remain unclear. Here, we explored the hypothesis that metagenomes of agricultural waters change with spatiotemporal shifts in physicochemical water quality, i.e., across water depths over time. Water samples and underlying sediments were collected at a model pond at the surface and within the water column (0, 1, 2 m depths) throughout one day (i.e., 9:00, 12:00, 15:00). All samples were processed for shotgun metagenomic sequencing analysis and enumeration of various water quality parameters (e.g., temperature, nutrient concentrations, turbidity, pH, culturable Escherichia coli). At the pond surface, Microcystis aeruginosa and members of Cyanobacteria, along with genes encoding pathways related to photosynthesis and nucleotide biosynthesis, were enriched throughout the day. In contrast, within the water column (1-2 m depths) and sediments, diverse members of Proteobacteria and Actinobacteria were more dominant, along with encoded pathways related to respiration and amino acid biosynthesis. Various aspects of water quality (i.e., chlorophyll dissolved organic matter, ammonia, E. coli concentrations) correlated with water metagenome diversity, albeit not with any specific AMR genes or virulence factors. Nevertheless, de novo assembly of sequenced reads uncovered 22 unique strains encoding several AMR, virulence, or stress response genetic elements, thus linking metagenome functional potential to key taxa. Overall, our findings highlight distinctions in agricultural pond water metagenomes at the surface and in the water column and demonstrate the potential for metagenomic surveillance in water quality monitoring to support food safety.},
}
@article {pmid40535009,
year = {2025},
author = {He, S and Qi, Y},
title = {The microbiota, the malarial parasite, and the mice-a three-sided relationship.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1615846},
pmid = {40535009},
issn = {1664-302X},
abstract = {In recent years, the role of gut microbiota in modulating malaria susceptibility and infection progression has emerged as a pivotal focus in interdisciplinary research. While existing reviews have delineated mechanisms by which mosquito-associated gut microbiota regulate Plasmodium development, a systematic synthesis of the tripartite interplay among host gut microbiota, Plasmodium and host immunometabolic networks remains absent. Compared with previous studies predominantly focusing on single species or unitary mechanisms, this review fills the gap in cross-species integrated analysis of host-microbiota-pathogen interactions. By consolidating metagenomic, metabolomic, and immunological data, this review transitions from unitary mechanistic explanations to multi-omics-driven systematic analyses, demonstrating that murine microbiota suppresses Plasmodium proliferation through adaptive immune activation and metabolic product regulation. Meanwhile, Plasmodium infection induces decreased microbial diversity and functional pathway deviation in murine microbiota, exacerbating host immunometabolic imbalance. These advancements not only elucidate core biological principles governing "microbiota-host-pathogen" interactions but also transcend traditional pathogen-centric perspectives by pioneering precise intervention strategies based on microbiota homeostasis restoration. This provides theoretical foundation for developing microbiome-targeted precision prevention approaches, which will continue to make substantial contributions to malaria research.},
}
@article {pmid40534981,
year = {2025},
author = {Hodgson, RJ and Cando-Dumancela, C and Liddicoat, C and Ramesh, SA and Edwards, RA and Breed, MF},
title = {Strong Host Modulation of Rhizosphere-to-Endosphere Microbial Colonisation in Natural Populations of the Pan-Palaeotropical Keystone Grass Species, Themeda triandra.},
journal = {Ecology and evolution},
volume = {15},
number = {6},
pages = {e71595},
pmid = {40534981},
issn = {2045-7758},
abstract = {Soil microbiota can colonise plant roots through a two-step selection process, involving recruitment of microbiota first from bulk soil into plant rhizospheres, then into root endospheres. This process is poorly understood in all but a few model species (e.g., Arabidopsis), which is surprising given its fundamental role in plant and soil ecology. Here, we examined the microbial community assembly processes across the rhizospheres and root endospheres in eight natural populations of the pan-palaeotropical C4 grass, Themeda triandra, in southern Australia. Using a space-for-time substitution approach, we assessed whether bacterial root colonisation patterns conformed to the two-step model and tested whether community assembly was driven more by deterministic or stochastic processes. Our results show that the two-step selection process shaped bacterial recruitment dynamics across these natural T. triandra populations, and we provide clear evidence that host plants influence microbial assembly via deterministic pressures that produce strong community convergence within endospheres. These findings highlight the central role of host filtering in shaping a conserved 'core' endosphere microbiome. However, limited understanding of these endosphere communities constrains efforts to harness these important relationships to, for example, improve plant propagation and revegetation practices.},
}
@article {pmid40534416,
year = {2025},
author = {Wang, Z and Wei, M and Wan, J and He, W and Zhou, J and Zhang, Y and Liu, Y and Liu, Y and Liu, D and Zhu, Q and Wang, X and Wu, K},
title = {Oral Microbiota Dysbiosis Initiated by Chronic Colitis and the Possible Role in Oral Mucosa Changes.},
journal = {Oral diseases},
volume = {},
number = {},
pages = {},
doi = {10.1111/odi.15344},
pmid = {40534416},
issn = {1601-0825},
support = {LCA202206//National Clinical Research Center for Oral Diseases of China/ ; LX2023408//New Technologies of School of Stomatology, Air Force Medical University Fund/ ; 82341223//National Natural Science Foundation of China/ ; 2023-YBSF-171//Key Program of Science Technology in Shaanxi Province/ ; 22JK0547//Special Scientific Research Project of Shaanxi Provincial Education Department/ ; 2019JZ33//Key Program of Natural Science Basic Research Plan in Shaanxi Province/ ; },
abstract = {OBJECTIVE: To investigate oral microbiota dysbiosis and cytopathological changes in oral mucosa of murine chronic colitis model and the correlation between them.<br><br>METHODS: Dextran sodium sulfate (DSS) induced chronic colitis was established in SPF C57BL/6 male mice, oral microbiome characterization was performed using 16S rRNA gene sequencing, and cytopathological and immunohistochemistry assessment was performed in oral mucosa.<br><br>RESULTS: When chronic colitis was induced, the overall microbial composition of the oral microbiome was altered with increased abundance in phylum Proteobacteria (82.2%), Actinobacteria (2.6%) and decreased abundance in Firmicutes (12.7%), Bacteroidetes&#xa0;(1.1%). Among the top 10 most abundance genera, Streptococcus was the only genera significantly decreased in colitis mice oral cavity. Meanwhile, oral epithelial hyperplasia was identified in the murine chronic colitis model, and the ki67 expression was significantly upregulated in oral epithelium (p&#x2009;<&#x2009;0.05). The chronic course of colitis did not lead to obvious inflammatory infiltration in the oral mucosa. Spearman analysis indicated a strong inverse correlation (r&#x2009;=&#x2009;-0.52, p&#x2009;=&#x2009;0.03) between oral Streptococcus and epithelium thickness.<br><br>CONCLUSIONS: The chronic colitis mice displayed epithelial hyperplasia in the oral mucosa without obvious inflammatory infiltration, which might be associated with oral dysbiosis, especially a decreased abundance of Streptococcus.},
}
@article {pmid40534245,
year = {2025},
author = {Sierra-Cruz, M and Vilalta, A and Miguéns-Gómez, A and Park, H and Rodríguez-Gallego, E and Blay, MT and Ardévol, A and Pinent, M and Behmoaras, J and Beltrán-Debón, R and Terra, X},
title = {Grape Seed Proanthocyanidins: A Potential Microbiome-Targeted Intervention for Healthy Aging in Rats.},
journal = {Molecular nutrition &amp; food research},
volume = {},
number = {},
pages = {e70150},
doi = {10.1002/mnfr.70150},
pmid = {40534245},
issn = {1613-4133},
support = {945413//H2020 Marie Sk&#x142;odowska-Curie Actions/ ; PID2021-122636OB-I00//Agencia Estatal de Investigaci&#xf3;n/ ; 2021SGR00201//Ag&#xe8;ncia de Gesti&#xf3; d'Ajuts Universitaris i de Recerca (AGAUR) del Departament de Recerca i Universitats de la Generalitat de Catalunya/ ; },
abstract = {Aging and age-related metabolic complications are global health issues that pose a serious threat to public health. Gut dysfunction and dysbiosis contribute to age-related health decline. Grape seed-derived procyanidins (GSPE) have shown efficacy in mitigating adaptive homeostasis decline in young animal models, but their impact on intestinal health and the gut microbiome in aged animals remains unexplored. Twenty-one-month-old female rats were treated with 500 mg GSPE/kg of body weight for 10 days. After 11 weeks, GSPE anti-aging potential was evaluated by measuring plasma lipopolysaccharide, gut integrity gene expression, ex vivo gut barrier function, myeloperoxidase activity, and fecal microbiome composition. GSPE shifted the microbiota toward a younger profile, even restoring lost strains in aged rats. Despite the presence of metabolic aging markers, there was minimal deterioration in gut barrier function. Neither ex vivo permeability tests, transcriptional analysis of barrier function, nor gut histology showed significant impairment in gut. Only jejunal myeloperoxidase activity was increased in aged rats and reduced by GSPE. Intestinal barrier function showed mild deterioration in this model of aged rats. GSPE improved the aging process by modulating the gut microbiome, suggesting its potential as a microbiome-targeted intervention for promoting healthy aging.},
}
@article {pmid40534235,
year = {2025},
author = {Renaldi, R and Wiguna, T and Persico, AM and Tanra, AJ},
title = {p-Cresol and p-Cresyl Sulphate Boost Oxidative Stress: A Systematic Review of Recent Evidence.},
journal = {Basic &amp; clinical pharmacology &amp; toxicology},
volume = {137},
number = {1},
pages = {e70065},
pmid = {40534235},
issn = {1742-7843},
support = {//Center for Higher Education Funding and Assessment/ ; //Ministry of Higher Education/ ; //Science, and Technology of the Republic of Indonesia/ ; },
mesh = {*Cresols/toxicity/metabolism ; Humans ; *Oxidative Stress/drug effects ; *Sulfuric Acid Esters/toxicity/metabolism ; Animals ; Reactive Oxygen Species/metabolism ; Renal Insufficiency, Chronic/metabolism ; Biomarkers/metabolism ; Uremic Toxins/metabolism/toxicity ; Neurodegenerative Diseases/metabolism ; },
abstract = {Recent studies have emphasized the significant role of p-cresol and its conjugated form, p-cresyl sulphate (PCS), in enhancing oxidative stress, leading to potential detrimental effects on various biological systems. Both p-cresol and PCS contribute to increased production of reactive oxygen species (ROS), which can result in tissue damage, inflammation and a cascade of physiological abnormalities. Elevated p-cresol levels have been associated with greater clinical severity in autism spectrum disorder, correlating with more severe behavioural manifestations and a history of regression. This systematic review explores the recent evidence on how these compounds promote oxidative stress and their impact on different health conditions. This review also addresses the involvement of p-cresol and PCS in conditions such as chronic kidney disease, Parkinson's disease and other neurodegenerative disorders, where oxidative damage contributes to disease progression. Furthermore, this review highlights the need for further research to understand the precise mechanisms by which p-cresol and PCS modulate oxidative stress and their potential as biomarkers for clinical diagnosis and disease management. SUMMARY: This focused review systematically summarizes recent evidence that oxidative stress plays an important role in the damage of biological systems produced by two uremic toxins, p-cresol and its conjugated form, p-cresyl sulphate (PCS). p-cresol coming from environmental sources or produced by some gut bacterial strains, modulates various conditions, like chronic kidney disease, Parkinson's disease and autism spectrum disorder, among others. Oxidative damage and inflammation seemingly contribute to disease onset, progression and/or severity. The exact mechanism by which p-cresol and PCS promote oxidative stress, their influence on disease trajectory and their potential role as biomarkers merit further investigation.},
}
@article {pmid40533873,
year = {2025},
author = {Härer, A and Kurstjens, E and Rennison, DJ},
title = {Host traits and environmental variation shape gut microbiota diversity in wild threespine stickleback.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {67},
pmid = {40533873},
issn = {2524-4671},
support = {458274593//Deutsche Forschungsgemeinschaft/ ; },
abstract = {BACKGROUND: Despite the growing recognition of the importance of gut microbiota in host ecology and evolution, our understanding of the relative contributions of host-associated and environmental factors shaping gut microbiota composition within and across wild populations remains limited. Here, we investigate how host morphology, sex, genetic divergence, and environmental characteristics influence the gut microbiota of threespine stickleback fish populations from 20 lakes on Vancouver Island, Canada.<br><br>RESULTS: Our findings reveal substantial variation in gut microbiota composition and diversity among populations, with host traits exerting a relatively stronger influence on bacterial alpha diversity than environmental characteristics. Previous studies have suggested a link between stickleback body shape and niche specialization, and our results indicate that aspects of host morphology may be associated with gut microbiota divergence among populations, though whether this is related to trophic ecology remains to be explored. Within and across populations, we only observed a weakly defined core microbiota and limited sharing of amplicon sequence variants (ASVs) among hosts, indicating that gut microbiota composition is individualized. Additionally, we detected sex-dependent differences in microbial diversity, opening avenues for future research into the mechanisms driving this variation.<br><br>CONCLUSIONS: In sum, our study emphasizes the need to consider both host-associated and environmental factors in shaping gut microbiota dynamics and highlights the complex interplay between host organisms, their associated microbial communities, and the environment in natural settings. Ultimately, these insights add to our understanding of the eco-evolutionary implications of host-microbiota interactions while underscoring the need for further investigation into the underlying mechanisms.},
}
@article {pmid40533851,
year = {2025},
author = {Rahman, N and McCullough, T and Orozco, DF and Walkowiak, S and Farzan, A and Shekarriz, S and Surette, MG and Cicek, N and Derakhshani, H},
title = {Genomic characterization of antimicrobial resistance and mobile genetic elements in swine gut bacteria isolated from a Canadian research farm.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {66},
pmid = {40533851},
issn = {2524-4671},
support = {(RGPIN-2023-04359)//NSERC Discovery Grant/ ; },
abstract = {INTRODUCTION: The widespread use of antimicrobials in the livestock industry has raised global concerns regarding the emergence and spread of antimicrobial resistance genes (ARGs). Comprehensive databases of ARGs specific to different farm animal species can greatly improve the surveillance of ARGs within the agri-food sector and beyond. In particular, defining the association of ARGs with mobile genetic elements (MGEs)-the primary agents responsible for the spread and acquisition of resistant phenotypes among bacterial populations-could help assess the transmissibility potential of clinically relevant ARGs. Recognizing the gut microbiota as a vast reservoir of ARGs, we aimed to generate a representative isolate collection and genome database of the swine gut microbiome, enabling high-resolution characterization of ARGs in relation to bacterial host range and their association with MGEs.<br><br>RESULTS: We generated a biobank of bacteria from different sections of the gastrointestinal tracts of four clinically healthy pigs housed at a research farm in Ontario, Canada. The culturing was performed under anaerobic conditions using both selective and general enrichment media to ensure the capture of a diverse range of bacterial families within the swine gut microbiota. We sequenced the genomes of 129 unique isolates encompassing 44 genera and 25 distinct families of the swine gut microbiome. Approximately 85.3% (110 isolates) contained one or more ARGs, with a total of 246 ARGs identified across 38 resistance gene families. Tetracycline and macrolide resistance genes were the most prevalent across different lineages of the swine gut microbiota. Additionally, we observed a wide range of MGEs, including integrative conjugative elements, plasmids, and phages, frequently associated with ARGs, indicating that the swine gut ecosystem is conducive to the horizontal transfer of ARGs. High-throughput alignment of the identified ARG-MGE complexes to large-scale metagenomics datasets of the swine gut microbiome suggests the presence of highly prevalent and conserved resistome sequences across diverse pig populations.<br><br>CONCLUSION: Our findings reveal a highly diverse and relatively conserved reservoir of ARGs and MGEs within the gut microbiome of pigs. A deeper understanding of the microbial host range and potential transmissibility of prevalent ARGs in the swine microbiome can inform development of targeted antimicrobial resistance surveillance and disease control programs.},
}
@article {pmid40533779,
year = {2025},
author = {Liu, YC and Tang, XY and Lang, JX and Qiu, Y and Chen, Y and Li, XY and Cao, Y and Zhang, CD},
title = {Effects of antibiotic exposure on risks of colorectal tumors: a systematic review and meta-analysis.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {682},
pmid = {40533779},
issn = {1479-5876},
support = {JYTMS20230108//the Scientific Study Project for Institutes of Higher Learning, Ministry of Education, Liaoning Province/ ; RXXM202302//the Young Backbone Talents of China Medical University/ ; LTKMZ20221139//the Scientific Study Project for Institutes of Higher Learning, Ministry of Education, Liaoning Province/ ; },
mesh = {Humans ; *Colorectal Neoplasms/chemically induced/epidemiology/microbiology ; *Anti-Bacterial Agents/adverse effects/therapeutic use ; Risk Factors ; Publication Bias ; Odds Ratio ; Gastrointestinal Microbiome/drug effects ; },
abstract = {BACKGROUND: Increasing evidence suggests that the gut microbiome may play an important role in the development of colorectal tumors. Antibiotic use can affect the gut microbiome and may increase the risks of benign and malignant colorectal tumors.<br><br>METHODS: Eligible studies assessing the relationship between antibiotic exposure and the risk of developing benign or malignant colorectal tumors were identified. Odds ratios (ORs) were pooled for antibiotic use versus no use using a random-effects model. Further subgroup and sensitivity analyses were conducted to confirm the consistence and robustness of the main findings. The study protocol was registered with PROSPERO.<br><br>RESULTS: Twenty-three studies including 1,145,853 participants were finally included in the analysis. People who had used antibiotics had a 13% increased risk of colorectal tumors compared with those who had never used antibiotics [OR: 1.13; 95% confidence interval (CI) 1.04-1.22; P&#x2009;<&#x2009;0.01]. Subgroup analysis showed that antibiotic exposure was associated with increased risks of both benign (OR: 1.13; 95% CI 1.00-1.27; P&#x2009;<&#x2009;0.01) and malignant colorectal tumors (OR: 1.13; 95% CI 1.03-1.23; P&#x2009;<&#x2009;0.01). In addition, colorectal tumor risk was significantly increased by antibiotic exposure, especially the use of combined antibiotics and a longer period after antibiotic exposure. The main findings were consistent and robust across most subgroups and sensitivity analyses.<br><br>CONCLUSIONS: The current findings suggested that antibiotic use increased the risk of developing benign or malignant colorectal tumors. These results highlighted the need for clinicians to prescribe antibiotics cautiously, to reduce colorectal cancer risk.},
}
@article {pmid40533562,
year = {2025},
author = {White, Z and Cabrera, I and Mei, L and Clevenger, M and Ochoa-Raya, A and Kapustka, I and Dominguez, JR and Zhou, J and Koster, KP and Anwar, S and Wang, Q and Ng, C and Sagoshi, S and Matsuo, T and Jayawardena, D and Kim, SH and Kageyama, T and Mitchell, BJ and Rivera, D and Dudeja, PK and Lutz, SE and Kim, KW and Yoshii, A and Chevrier, N and Inoue, M and Sano, T},
title = {Gut inflammation promotes microbiota-specific CD4 T cell-mediated neuroinflammation.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {40533562},
issn = {1476-4687},
abstract = {The microbiota has been recognized as a critical contributor to various diseases[1], with multiple reports of changes in the composition of the gut microbiome in contexts such as inflammatory bowel disease[2,3] and neurodegenerative diseases[4]. These microbial shifts can exert systemic effects by altering the release of specific metabolites into the bloodstream[5,6], and the gastrointestinal microbiota has also been reported to exhibit immunomodulatory activity through the activation of innate and adaptive immunity[7,8]. However, it remains unclear how the microbiota contributes to inflammation in the central nervous system (CNS), where these microorganisms are typically absent. Here we report that T cells that recognize gut-colonizing segmented filamentous bacteria can induce inflammation in the mouse intestine and CNS in the absence of functional regulatory T cells. Gut commensal-specific CD4 T cells (Tcomm cells) that are dysregulated in the inflamed gut can become licensed to infiltrate into the CNS regardless of their antigen specificity and have the potential to be re-stimulated by host protein-derived antigens in the CNS via molecular mimicry, whereupon they produce high levels of GM-CSF, IFNγ and IL-17A, triggering neurological damage. These infiltrated Tcomm cells initiate CNS inflammation by activating microglia through their IL-23R-dependent encephalitogenic programme and their IL-23R-independent GM-CSF production. Together, our findings reveal potential mechanisms whereby perturbation of Tcomm cells can contribute to extraintestinal inflammation.},
}
@article {pmid39710259,
year = {2025},
author = {Callaway, T and Perez, HG and Corcionivoschi, N and Bu, D and Fluharty, FL},
title = {International Symposium on Ruminant Physiology: The holobiont concept in ruminant physiology-More of the same, or something new and meaningful to food quality, food security, and animal health?.},
journal = {Journal of dairy science},
volume = {108},
number = {7},
pages = {7567-7575},
doi = {10.3168/jds.2024-25847},
pmid = {39710259},
issn = {1525-3198},
abstract = {The holobiont concept has emerged as an attempt to recognize and describe the myriad interactions and physiological signatures inherent to a host organism, as affected by the microbial communities that colonize and co-inhabit the environment within which the host resides. The field acknowledges and draws upon principles from evolution, ecology, genetics, and biology, and in many respects has been pushed by the advent of high throughput DNA sequencing and, to a lesser extent, other omics-based technologies. Despite the explosion in data generation and analyses, much of our current understanding of the human and ruminant holobiont is based on compositional forms of data and thereby, restricted to describing host phenotypes via associative or correlative studies. So, where to from here? We will discuss some past findings arising from ruminant and human gut microbiota research and seek to evaluate the rationale, progress, and opportunities that might arise from the holobiont approach to the ruminant and human host. In particular, we will consider what is a "good" or "bad" host gastrointestinal microbiome in different scenarios, as well as potential avenues to sustain or alter the holobiont. Although the holobiont approach might improve food quality, food security, and animal health, these benefits will most likely be achieved via a judicious and pragmatic compromise in data generation, both in terms of its scale as well as its generation, in context with the forgotten knowledge of ruminant and human physiology.},
}
@article {pmid40533471,
year = {2025},
author = {Eggers, S and Hoggarth, ZE and Nagdeo, K and Banas, MJ and Lane, JM and Rechtman, E and Gennings, C and O'Neal, E and Peppard, PE and Sethi, AK and Safdar, N and Malecki, KM and Schultz, AA and Midya, V},
title = {Food insecurity modifies the association between the gut microbiome and the risk of cognitive impairment in adults.},
journal = {npj aging},
volume = {11},
number = {1},
pages = {47},
pmid = {40533471},
issn = {2731-6068},
support = {R00ES032884/ES/NIEHS NIH HHS/United States ; P30ES005605/ES/NIEHS NIH HHS/United States ; P30ES023515/ES/NIEHS NIH HHS/United States ; P30ES023515/ES/NIEHS NIH HHS/United States ; },
abstract = {This study investigated the role of food insecurity as an effect modifier between the gut microbiome, including groups of microbes (cliques), and risk of cognitive impairment (RCI). The analytical sample (n = 360) included adult participants of the Survey of the Health of Wisconsin with complete data on food insecurity, RCI, and 16S rRNA sequencing from stool samples. Microbial cliques associated with RCI were identified using an interpretable machine-learning-based algorithm. All analyses were stratified by food insecurity level, and adjusted for relevant confounders. We identified two cliques whose associations with RCI were modified by food insecurity status. The presence of the clique with either Eisenbergiella or Eubacterium was more strongly associated with RCI for the food-insecure group (β = 0.29, p < 0.0001). A clique representing the presence of Ruminococcus torques, Bacteroides, CAG-352F, and/or Eubacterium had a stronger association with RCI for the food-secure group (β = 0.1, p < 0.0001). Findings suggest food security be considered in RCI etiology.},
}
@article {pmid40533417,
year = {2025},
author = {Li, Z and He, Q and He, X and Xing, X and Fu, S and Sun, X and Ma, M and Wang, D and Mi, N and Zhao, J and Yuan, J and Yang, K},
title = {Long-Term or Recurrent Antibiotic Use in Early Life and the Risk of Type 2 Diabetes: A Population-Based Prospective Cohort and a Case-Control Study.},
journal = {Journal of diabetes},
volume = {17},
number = {6},
pages = {e70113},
doi = {10.1111/1753-0407.70113},
pmid = {40533417},
issn = {1753-0407},
support = {20JR10FA667//Gansu Province Endocrine Disease Clinical Medical Research Center/ ; 19ZDA142//the Major Project of the National Social Science Fund of China: Research on the Theoretical System, International Experience and Chinese Path of Evidence-based Social Science/ ; },
mesh = {Humans ; Case-Control Studies ; *Diabetes Mellitus, Type 2/epidemiology/chemically induced ; Male ; Female ; *Anti-Bacterial Agents/adverse effects ; Prospective Studies ; Risk Factors ; Middle Aged ; Adult ; United Kingdom/epidemiology ; Child ; Gastrointestinal Microbiome/drug effects ; Follow-Up Studies ; Adolescent ; },
abstract = {BACKGROUND: Antibiotics in childhood are commonly used and have been linked to gut microbiome dysbiosis and metabolic disorders. However, direct evidence regarding the association between long-term or recurrent antibiotic use (LRAU) during early life and diabetes was scarce. We performed this study to investigate this association in two population-based studies.<br><br>METHODS: We undertook a prospective analysis encompassing 147&#x2009;010 participants from the UK Biobank. Cox proportional hazard regression was used to calculate hazard ratios (HRs) and 95% confidence intervals (CIs) of self-reported LRAU during early life on diabetes risk. We also conducted a case-control study within the Chinese population, in which 263 diabetes cases and 526 controls were matched for age and living location. Odds ratios (ORs) and 95% CI were was calculated using logistic regression models.<br><br>RESULTS: We identified 4314 incident cases of type 2 diabetes over 1&#x2009;840&#x2009;944 person-years of follow-up in the UK Biobank. LRAU during early life was associated with a 26% higher risk of diabetes after accounting for putative risk factors (HR, 1.26; 95% CI, 1.16-1.37) in the UK biobank. We observed a more evident association between LRAU and an elevated risk of diabetes in the case-control study (OR, 3.32; 95% CI, 2.06-5.38). The primary finding was robust to several subgroup analyses and sensitivity analyses.<br><br>CONCLUSIONS: LRAU during early life may increase the risk of type 2 diabetes. Caution should be exercised when prescribing long-term or recurrent antibiotics to children and adolescents.},
}
@article {pmid40533342,
year = {2025},
author = {Pedroso, I and Kumbhare, SV and Johnson, S and Muthukumar, KM and Saravanan, SK and Irudayanathan, C and Sharma, G and Tabone, L and Sinha, R and Almonacid, DE and Szoka, N},
title = {Microbiome and genetic predictors of weight loss 12 months postsleeve gastrectomy: insights from a pilot retrospective cohort study.},
journal = {Surgery for obesity and related diseases : official journal of the American Society for Bariatric Surgery},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.soard.2025.05.008},
pmid = {40533342},
issn = {1878-7533},
abstract = {BACKGROUND: Gut microbiome and genetic biomarkers are increasingly guiding obesity treatment. Bariatric surgery leads to shifts in gut microbial composition and function, while genome-wide association studies reveal genetic underpinnings of polygenic obesity, informing risk, therapeutic outcomes, and nutrigenomics-based interventions.<br><br>OBJECTIVES: This pilot study aimed to identify gut microbiome and genetic biomarkers associated with weight loss 12 months after sleeve gastrectomy (SG).<br><br>SETTING: Single academic institution university clinic.<br><br>METHODS: Sixty-seven patients 12 months post-SG were enrolled: 34 had successful excess weight loss (EWL &#x2265;50%), while 33 had unsuccessful EWL (EWL <50%). Microbiome and genetic profiles were collected and analyzed using ANOVA and regression methods.<br><br>RESULTS: The genus Akkermansia was significantly associated with EWL (P = 9.9 &#xd7; 10[-6]). Several microbial pathways, including propionate synthesis and menaquinone (vitamin K2) production, showed nominally significant (P < .05) associations with greater weight loss. No differences emerged in the Firmicutes/Bacteroidetes ratio. Genetic analyses revealed significant correlations between EWL and polygenic scores for dietary needs and metabolic responses, including distinct vitamin D and K requirements, as well as higher LDL cholesterol levels and predisposition for major depression.<br><br>CONCLUSIONS: These findings suggest that both the gut microbiome and genetics may modulate weight loss following bariatric surgery. Integrating microbiome and genetic profiling into bariatric care pathways could enhance personalized obesity treatment. While this pilot, exploratory, and proof-of-concept study has limitations, it supports prior work linking gut microbial pathways to weight loss and suggests new associations. Follow-up studies are warranted to validate these results and further inform precision obesity interventions.},
}
@article {pmid40533327,
year = {2025},
author = {Sullivan, O and Sie, C and Ng, KM and Cotton, S and Rosete, C and Hamden, JE and Singh, AP and Lee, K and Choudhary, J and Kim, J and Yu, H and Clayton, CA and Carranza Garcia, NA and Voznyuk, K and Deng, BD and Plett, N and Arora, S and Ghezzi, H and Huan, T and Soma, KK and Yu, JJ and Tropini, C and Ciernia, AV},
title = {Corrigendum to "Early-life gut inflammation drives sex-dependent shifts in the microbiome-endocrine-brain axis" [Brain Behav. Immun. 125 (2025) 117-139].},
journal = {Brain, behavior, and immunity},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.bbi.2025.06.007},
pmid = {40533327},
issn = {1090-2139},
}
@article {pmid40533309,
year = {2025},
author = {Xie, QY and Danska, JS},
title = {Large-scale microbiome data initiatives call for diversity.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2025.06.001},
pmid = {40533309},
issn = {1878-4380},
abstract = {High variability in human gut microbiota is a challenge in the identification of consistent microbe-disease associations. Two Cell papers by Nishijima et al. and Abdill, Graham, et al. addressed this by curating large public microbiome datasets. They highlight long overlooked drivers of gut microbiome variance, such as fecal microbial biomass and geographical locations of study participants, necessitating diverse population representation in microbiome research.},
}
@article {pmid40533209,
year = {2025},
author = {Stolberg-Mathieu, G and Mikkelsen, LS and Gottlieb, AD and Mølgaard, C and Roager, HM},
title = {The MOTILITY Mother-Child Cohort: a Danish prospective longitudinal cohort study of the infant gut microbiome, nutrition and bowel habits - a study protocol.},
journal = {BMJ open},
volume = {15},
number = {6},
pages = {e094965},
doi = {10.1136/bmjopen-2024-094965},
pmid = {40533209},
issn = {2044-6055},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Infant ; Denmark ; Longitudinal Studies ; Prospective Studies ; Female ; Infant, Newborn ; *Defecation/physiology ; Milk, Human ; *Nutritional Status ; Male ; Child Development ; Mothers ; Feces/microbiology ; },
abstract = {INTRODUCTION: Concurrent with infants' progression in dietary complexity and gut microbiome diversity, infants gradually change their defecation patterns during the first year of life. However, the links between bowel habits, the gut microbiota and early life nutrition remain unclear. The primary outcome is to characterise the gut microbiome development from birth to 1 year of age. Second, to investigate how bowel habits and nutrition in early life relate to the gut microbiome and metabolome during this period of life, and to explore how the development of the gut microbiome associates with host development.<br><br>METHODS AND ANALYSIS: The MOTILITY Mother-Child Cohort (MOTILITY) is a Danish prospective longitudinal cohort study enrolling up to 125 mother-infant dyads. Assessments occur at 36 weeks gestation (visit 1), birth (screening of infant) and 3, 6, 9 and 12 months (&#xb1;2 weeks) post partum (visits 2-5). At visit 1, maternal anthropometrics, self-collected faecal and urine samples, and questionnaires on bowel habits and lifestyle are obtained. Between visits, infant faecal (biweekly), urine (monthly) and maternal breast milk (monthly until 6 months of age) samples are collected at home, and bowel habits and dietary intake are assessed biweekly by self-reported questionnaires. At visits 2-5, infant blood and saliva samples are collected, and anthropometric measurements are obtained. In addition, dietary intake is recorded thrice throughout the study period for mother and infant, respectively, and infant whole-gut transit time is estimated by sweet corn tests at 9 and 12 months of age. Birth, growth, motor development, sleep patterns, tooth development, overall health and well-being are assessed using questionnaires. Univariate and multivariate statistics will be applied to identify associations between the gut microbiome, early life nutrition and host physiology including bowel habits during the first year of life.<br><br>ETHICS AND DISSEMINATION: The MOTILITY study has been approved by the Research Ethics Committee for the Capital Region of Denmark (reference number: H-21063016). Selected results will be made available to the participants in the form of a summary document. Results will be published in peer-review journals and by means of national and international conferences.<br><br>TRIAL REGISTRATION NUMBER: NCT05491161.},
}
@article {pmid40533202,
year = {2025},
author = {Andrews, C and Vodapally, S and Foster, LP and Lawandy, I and Murphy, M and Castellanos, M and Moncada, D and Mourao, ML and Bhushan, B and Berger, PK and Fichorova, R and Monthé-Drèze, C and Freedman, SD and Angelidou, A and Martin, CR and Sen, S},
title = {Cohort profile: Mother and Infant Metabolome and Microbiome (MIMM) study, a prospective cohort study of mothers and infants in Boston, Massachusetts.},
journal = {BMJ open},
volume = {15},
number = {6},
pages = {e096957},
doi = {10.1136/bmjopen-2024-096957},
pmid = {40533202},
issn = {2044-6055},
mesh = {Humans ; Female ; Prospective Studies ; *Breast Feeding/statistics &amp; numerical data ; Infant ; *Milk, Human/chemistry/microbiology/metabolism ; Adult ; Infant, Newborn ; Boston ; *Metabolome ; *Microbiota ; Male ; Mothers ; Pregnancy ; },
abstract = {PURPOSE: Breastfeeding is beneficial to the health of both the mother and infant. Despite recommendations to breastfeed by organisations including the WHO and the American Academy of Pediatrics, rates of breastfeeding remain below public health goals. The Mother and Infant Metabolome and Microbiome (MIMM) study is a prospective cohort study of healthy mother-term infant dyads designed to comprehensively assess the perinatal, maternal, neonatal and infant factors that are associated with breastfeeding outcomes and human milk composition.<br><br>PARTICIPANTS: MIMM participants were recruited from two medical centres in Boston, Massachusetts, from 2019 to 2023 and are followed for 2 years. Dyads were included if the mother delivered a singleton infant at &#x2265;37 weeks' gestation, was discharged home <72&#x2009;hours after vaginal delivery or <6&#x2009;days after caesarean delivery, spoke English, planned to breastfeed (either exclusively or with formula supplementation) and was willing and able to conduct follow-up through 2 years. Dyads were excluded from the study if the infant was admitted to the neonatal intensive care unit for longer than 72 hours. A total of 156 dyads were enroled in the study; however, eight participants dropped out prior to hospital discharge and will be excluded from all analyses (ie, no data was collected), resulting in a final cohort sample size of 148 mother-infant dyads. Approximately 62% of participants were White, 20% were Black or African American, 11% were Asian and 7% were more than one or unknown race. The cohort was highly educated, with 87% of participants having at least a college degree. Median maternal pre-pregnancy body mass index was 24.8 kg/m[2] and infant gestational age was 39.3 weeks. Approximately 43% of infants were born via caesarean delivery, and 45.5% were female.<br><br>FINDINGS TO DATE: MIMM study procedures include longitudinal (1) collections of maternal blood, vaginal swab, stool and milk and infant blood and stool samples and (2) assessments of breastfeeding status, child neurodevelopment and growth and maternal health at birth, 6 weeks and 6, 12, 18 and 24 months. Data collection through 18 months is complete. The overall objective of the MIMM study is to identify potential targets to improve breastfeeding outcomes, human milk composition and ultimately, maternal and child health. Preliminary analyses, reported in conference presentations (with ongoing analyses and results manuscripts pending), have found that (1) mothers with higher levels of stress were less likely to be exclusively breastfeeding their infants at 6 weeks; (2) higher breastfeeding intensity was associated with greater postpartum weight loss at 6 weeks; (3) feeding type was a more relevant predictor of feeding frequency and volume compared with feeding mode; (4) infants who received exclusive human milk had higher food enjoyment compared with those who received any formula; and (5) infants of mothers with obesity had higher average feeding volume per feed.<br><br>FUTURE PLANS: Data collection for the final 24-month visit is expected to be completed by August 2025. We expect that all sample assays will be completed by December 2025. Findings will continue to be submitted for presentation at scientific conferences, and we expect to publish the first findings from this cohort in manuscript format in 2025.},
}
@article {pmid40533070,
year = {2025},
author = {Russell, M and Cain, E and Bazzano, L and De Anda, I and Woo, JG and Urbina, EM},
title = {Collecting at-Home Biometric Measures for Longitudinal Research From the i3C: Feasibility and Acceptability Study.},
journal = {JMIR human factors},
volume = {12},
number = {},
pages = {e71103},
doi = {10.2196/71103},
pmid = {40533070},
issn = {2292-9495},
mesh = {Humans ; Female ; Male ; Middle Aged ; Feasibility Studies ; Longitudinal Studies ; Adult ; Aged ; Wearable Electronic Devices ; },
abstract = {BACKGROUND: The use of individual wearable devices or internet-based applications to collect biometric data from research participants is popular, but several devices may be needed to replace a full set of research measurements.<br><br>OBJECTIVE: In this study, we assessed the feasibility of a "Virtual Home Clinic" within the context of long-term epidemiologic studies.<br><br>METHODS: Participants from 3 study cohorts were recruited. Devices were sent to the home to measure anthropometrics, resting metabolic rate, blood pressure (BP), heart rate (HR), heart rhythm, oxygen saturation, glucose, total cholesterol, physical activity, diet, sleep duration or quality, and arterial stiffness over the course of 1 week. Stool and saliva were also self-collected for microbiome, DNA, and cotinine. Feasibility and acceptability of collecting measurements using home devices were assessed.<br><br>RESULTS: A total of 134 participants were enrolled (87% female, 31% Black; mean age 54.2, SD 8.4 years). Furthermore, 91% (N=122) performed at least one of the home tests. At least two-thirds of participants were able to complete all of the requested readings for glucose, electrocardiogram, BP, diet record, and resting metabolic rate. The scale that measured weight, body composition, and pulse wave velocity (PWV) was more difficult to use (113/134, 84% participants recorded at least one weight and 84/134, 63% recorded a PWV). The device to measure total cholesterol was least successful (32/134, 24% participants completed all readings, 72/134, 54% provided at least one result). Return of biospecimens was highly successful (115/134, 86% returned saliva and 113/134, 84% returned stool). Of 95 who responded to the user acceptability survey, 38 (40%) participants preferred home assessment, 36 (38%) preferred clinic, and 21 (22%) did not have a preference. The mean user acceptability score across devices for ease of use was 4.3 (SD 1.0), for instructions was 4.5 (SD 0.7), and for time to use was 3.9 (SD 1.1; scale of 1-5, with higher scores indicating greater acceptability). The study team documented several regulatory or IT, connectivity or account, data retrieval, and logistical issues encountered during the study.<br><br>CONCLUSIONS: Despite several complications involved with managing multiple devices and applications, most of the components of the virtual home clinic were reasonably feasible and acceptable to participants.},
}
@article {pmid40532960,
year = {2025},
author = {Johnstone, N and Kadosh, KC},
title = {A randomised controlled trial of the effects of Galacto-Oligosaccharides on the gut brain-axis of young females.},
journal = {Brain, behavior, and immunity},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.bbi.2025.06.020},
pmid = {40532960},
issn = {1090-2139},
abstract = {Galacto-oligosaccharides (GOS) are prebiotics that modulate gut microbiota and are implicated in the gut-brain axis (GBA), with preclinical models reporting effects on neurochemistry, brain function, and cognition. Here we report the results of a randomised, double-blind, placebo-controlled trial in 83 healthy females (17-25 years), who received GOS or placebo for 28 days. Assessments occurred at baseline, endline, and 28 days post-supplementation. The primary outcome was trait anxiety, secondary outcomes were brain-based levels of GABA and glutamate in the dorsolateral prefrontal cortex (dlPFC), anterior cingulate cortex, and inferior occipital gyrus (IOG) (measured with [1]H-MRS), and gut microbiome composition. Tertiary outcomes included social anxiety, depression, emotion behaviour, reaction times, and nutritional intake. Analyses included intention-to-treat, per-protocol, and sensitivity approaches. Trait anxiety did not differ between groups at endline (p = 0.443), though trends favoured lower anxiety in the GOS group at follow-up (p = 0.069). GOS reduced GABA at trend significance in the IOG (p = 0.053) in the Intention to Treat (ITT) population and dlPFC (p = 0.088) in high-anxious participants, with effects persisting at follow-up. GOS transiently increased Bifidobacterium abundance (p = 0.001) but did not affect microbiome diversity. Tertiary outcomes showed no significant changes in social anxiety or depression but faster reaction rates in high-anxious participants for simple (p = 0.036) and choice tasks (p < 0.001). Nutritional intake was unaffected. While GOS supplementation did not significantly reduce trait anxiety, it produced neurochemical changes and transient modulations of the gut microbiome in Bifidobacterium abundance, indicating GOS-induced changes can be traced along the GBA.},
}
@article {pmid40532868,
year = {2025},
author = {Krishnapriya, and Kishanchand, DK and Rishikesh, and Venkatachalam, S and Alikunju, AP and Deepti, A and Sivan, U and Sasidharan, BCP},
title = {Remodelling the Gut Ecosystem: A Dysbiosis Model to Elucidate Gut-Organ Axis Dynamics in Mice.},
journal = {Physiology &amp; behavior},
volume = {},
number = {},
pages = {115000},
doi = {10.1016/j.physbeh.2025.115000},
pmid = {40532868},
issn = {1873-507X},
abstract = {Gut dysbiosis, an imbalance in intestinal microbiota composition, influences various physiological and pathological processes. We present a refined method to induce gut dysbiosis in mice, offering a valuable tool for investigating the gut-organ axis. Using an antibiotic cocktail, we induced dysbiosis and characterised its effects on host physiology and gut microbiota. Our analysis revealed significant alterations in bacterial diversity and composition, with the test group showing an increased abundance of potentially pathogenic genera like Clostridia_vadinBB60_group_ge and Escherichia-Shigella and decreased presence of beneficial microbes such as Prevotellaceae_UCG-001 and Muribaculaceae_ge. These changes were accompanied by shifts in predicted metabolic pathways, suggesting widespread functional alterations in the gut ecosystem. Notably, our dysbiosis model exhibited a 'subclinical' state, meaning that despite significant microbial shifts and physiological changes - including increased faecal water content, prolonged gastrointestinal transit time, elevated ileal acetylcholinesterase activity, and enlarged cecum - it was characterized by the absence of overt inflammation, alongside increased glutathione levels in the colon and an intact gut barrier. This unique model allows for exploring subtle, long-term effects of microbiome disruption on distant organ systems, providing a valuable platform for investigating the gut-organ axis in various diseases. Our findings offer promising avenues for research into therapeutic interventions targeting the gut microbiome and its extensive physiological impacts.},
}
@article {pmid40532867,
year = {2025},
author = {Graf, M and Murgueitio, N and Sheridan, MA and Quinn, RA and Carlson, AL and Vogel, SC and Styner, MA and Alex, AM and Stephens, RL and Roach, J and Sagarnaga, N and Mills-Koonce, WR and Azcarate-Peril, MA and Short, SJ and Knickmeyer, RC and Propper, CB},
title = {Gut microbiome is associated with insula structure in neonates.},
journal = {Physiology &amp; behavior},
volume = {},
number = {},
pages = {115001},
doi = {10.1016/j.physbeh.2025.115001},
pmid = {40532867},
issn = {1873-507X},
abstract = {The infant brain and gut microbiome both develop rapidly in early infancy. Growing evidence indicates that the gut microbiome plays a critical role in shaping neurodevelopment early in life, possibly through effects on brain regions involved in affective, interoceptive, and sensory processes. This study used brain magnetic resonance imaging (MRI) and whole genome sequencing of fecal samples to examine associations between the gut microbiome and brain structures in infants at 2 weeks of age. We identified significant relationships between specific gut microbiome characteristics and brain volumes in key regions involved in affective, sensory, and interoceptive processing. Our most consistent findings were associations between gut microbiome composition and insula volume, suggesting that the insula may be particularly sensitive to gut microbiome influences during the neonatal period. Specifically, a significant negative association between insula volume and the abundance of Veillonella was observed. Alpha diversity (Shannon) and functional pathways were also related to insula structure. Enterobacter was negatively associated with thalamus volume. These findings contribute to the growing evidence of a developing gut-brain axis, highlighting links between the gut and brain as early as 2 weeks of age. Future research should investigate the mechanisms by which specific microbial taxa and diversity patterns impact neurodevelopment by way of the insula, as well as explore the potential long-term implications of these early relationships on sensory, interoceptive, and affective processing, and behavioral outcomes.},
}
@article {pmid40532861,
year = {2025},
author = {Biswas, I and Mitra, D and Mallik, C and Das Mohapatra, PK},
title = {Characterization and toxicity assessment of metabiotic produced through natural tannin fermentation by newly isolated probiotic Lactiplantibacillus plantarum PKI15 and study of its effect on gut microbiome through metagenomics approach.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {107815},
doi = {10.1016/j.micpath.2025.107815},
pmid = {40532861},
issn = {1096-1208},
abstract = {Metabiotic fabrication has been done by mixed plant fermentation of Terminalia bellirica and Phyllanthus emblica fruit extract with probiotic bacteria Lactiplantibacillus plantarum PKI15 and showed considerable tannase (0.36 U/ml), gallic caid and pyrogallol production. Fermentative end-product analysis through FTIR, LC-MS and GC-MS analysis result indicates the presence of several bioactive compounds confirming the presence of gallic acid and pyrogallol respectively. Molecular docking analysis of the identified bioactive compounds with the protein myeloperoxidase denotes quercetin-3β-D-glucoside as the best ligand showing a binding score of -9.5 Kcal/mol. The formulated metabiotic revealed potential antibacterial and antioxidant properties activities. In-vivo toxicity assessment was done on the laboratory rats. Results revealed reduced body weight, urea content and creatinine level. Increase in superoxide dismutase, catalase activity and reduced content of conjugated diene, glutamate pyruvate transaminase and glutamic-oxaloacetic transaminase further supports the antioxidative potential of the metabiotic. Further study through histological sectioning of liver, kidney and spleen showed no structural abnormalities. Finally, metagenomics analysis of the gut microbiome of the experimental rats was done to check the influence of the formulated metabiotic on the gut commensals and it was found that species of Bifidobacterium and Pseudomonas are the most prevalent members of the examined groups, while, the relative proportion of other bacterial genera, such as Lactobacillus, Lactococcus, and Bacillus, were found to vary among the groups. Thus, both the in vivo and in silico studies proved that the formulated metabiotic is non-toxic and safe in use.},
}
@article {pmid40532696,
year = {2025},
author = {Er, YX and Lee, SC and Aneke, C and Conlan, S and Muslim, A and Deming, C and Che, Y and Yap, NJ and Tee, MZ and Abdull-Majid, N and Shahrizal, S and Leong, KF and Han, J and Shen, Z and Than, LTL and Park, M and Mohd Sayed, I and , and Seyedmousavi, A and Kong, HH and Loke, P and Segre, JA and Lim, YAL},
title = {Trichophyton concentricum fungal infections and skin microbiomes of Indigenous Peninsular Malaysians.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2025.05.034},
pmid = {40532696},
issn = {1097-4172},
abstract = {Recent outbreaks of multidrug-resistant fungi infecting human skin emphasize the importance of understanding fungal pathophysiology and spread. In efforts to address health concerns with various Indigenous Peninsular Malaysians (Orang Asli [OA]), tinea imbricata-a Trichophyton concentricum fungal skin infection-emerged as a particular concern. We investigated the etiology and transmission of tinea imbricata by culturing, testing antifungal sensitivities, and sequencing T. concentricum isolates in remote OA villages. Among regionally conserved isolates, we identified the emergence of terbinafine-resistant T. concentricum microbiologically and genomically. Investigating the skin microbiomes of 82 Indigenous OA, we found unique microbiota and lower relative abundances of bacterial commensals (Cutibacterium acnes, Staphylococcus epidermidis) among OA versus Malaysian and US urban populations, emphasizing how understudied populations provide unprecedented knowledge on host-microbiome co-evolution. These findings provide valuable insights into clinical, microbiological, and genomic features of chronic fungal skin infections, offering the potential to inform strategies to address drug resistance and effective therapy.},
}
@article {pmid40532695,
year = {2025},
author = {Sepela, RJ and Jiang, H and Shin, YH and Hautala, TL and Clardy, J and Hibbs, RE and Bellono, NW},
title = {Environmental microbiomes drive chemotactile sensation in octopus.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2025.05.033},
pmid = {40532695},
issn = {1097-4172},
abstract = {Microbial communities coat nearly every surface in the environment and have co-existed with animals throughout evolution. Whether animals exploit omnipresent microbial cues to navigate their surroundings is not well understood. Octopuses use "taste-by-touch" chemotactile receptors (CRs) to explore the seafloor, but how they distinguish meaningful surfaces from the rocks and crevices they encounter is unknown. Here, we report that secreted signals from microbiomes of ecologically relevant surfaces activate CRs to guide octopus behavior. Distinct molecules isolated from individual bacterial strains located on prey or eggs bind single CRs in subtly different structural conformations to elicit specific mechanisms of receptor activation, ion permeation and signal transduction, and maternal care and predation behavior. Thus, microbiomes on ecological surfaces act at the level of primary sensory receptors to inform behavior. Our study demonstrates that uncovering interkingdom interactions is essential to understanding how animal sensory systems evolved in a microbe-rich world.},
}
@article {pmid40532682,
year = {2025},
author = {Lu, N and Yao, Y and Gao, M and Liu, Z and Xie, H and Liu, J and Jiao, Q},
title = {Investigating the Impact of the Gut Microbiota on Nasal Polyp Development: Insights from Mendelian Randomization.},
journal = {International archives of allergy and immunology},
volume = {},
number = {},
pages = {1-24},
doi = {10.1159/000546793},
pmid = {40532682},
issn = {1423-0097},
abstract = {BACKGROUND: Chronic rhinosinusitis with nasal polyps has a high post-surgery recurrence, suggesting complex pathology. However, research into underlying mechanisms and contributing factors, such as gut microbiota, is lacking.<br><br>OBJECTIVE: We investigated the cause-and-effect relationship between nasal polyps and the gut microbiota and determined the influence of metabolic pathways&#xa0;as possible mediators. &#xa0; Methods: This study utilized genetic data from genome-wide association studies. The datasets included nasal polyp data from FinnGen (6,841 cases and 308,457 control samples), microbial metabolic pathway data from the Dutch Microbiome Project (7,738 samples), and single nucleotide polymorphisms of the gut microbiota from MiBioGen (18,340 samples). First, two-sample Mendelian randomization (MR) analyses were conducted on the gut microbiota, nasal polyps, and metabolic pathways. Next, a two-step MR was employed for mediation analysis to investigate whether metabolic pathways serve as mediators between the gut microbiota and nasal polyps and to estimate the proportion of the effect of metabolism-mediated gut microbiota on nasal polyps.<br><br>RESULTS: MR analysis revealed that Alcaligenaceae was associated with a higher risk of nasal polyps by inhibiting enopyranuronate degradation, whereas Desulfovibrionales had the opposite effect by promoting l-isoleucine biosynthesis. In addition, Actinomyces reduced the risk of nasal polyps by inhibiting L-glutamate degradation but also increased the risk by inhibiting sulfate reduction.<br><br>CONCLUSION: This study identified a causal relationship between the gut microbiota and nasal polyps, with metabolic pathways as mediators. Our study provides new perspectives and possibilities for the study and treatment of chronic rhinosinusitis with nasal polyps.},
}
@article {pmid40532622,
year = {2025},
author = {Rio-Aige, K and Selma-Royo, M and Massot-Cladera, M and Everard, A and Castell, M and Rodríguez-Lagunas, MJ and Collado, MC and Pérez-Cano, FJ},
title = {A diet rich in fibre and vegetable protein during gestation and lactation shapes maternal immunity, intestinal microbiota and lipid metabolism.},
journal = {EBioMedicine},
volume = {117},
number = {},
pages = {105784},
doi = {10.1016/j.ebiom.2025.105784},
pmid = {40532622},
issn = {2352-3964},
abstract = {BACKGROUND: Establishing optimal maternal nutritional habits during pregnancy, breastfeeding, and early life is crucial for the health and welfare of both the mother and the child. However, research is lacking to understand the associated mechanisms linking maternal diet to health outcomes. The objective of this study was to assess the potential influence of two distinct diets, consumed during gestation and lactation, on the microbiota composition, immunity and lipid metabolism of Lewis dams.<br><br>METHODS: Diet 1 (D1, Mediterranean diet-like) was characterized by a high fibre content, vegetable protein, and fish oil; whereas Diet 2 (D2, slightly Western diet-like) was enriched with animal protein and lard. Fecal samples were collected weekly throughout the nutritional intervention. Blood, tissue samples (adipose tissue, intestine, mammary gland, spleen and liver) and cecal content were collected from the mother at the end of lactation (day 21) to examine the effects on the epithelial barrier, lipid metabolism, microbiota composition and metabolites, as well as the mucosal immunity.<br><br>FINDINGS: According to our findings, consumption of the D1 diet had a beneficial impact on the mothers compared to the D2 diet. D1 increased the intestinal surface area and enhanced the mucosal immunity, as evidenced by a rise in fecal immunoglobulin (Ig) A and Ig-coated bacteria levels, along with an increase in total IgG in the mesenteric lymph nodes, as well as elevated levels of T helper (Th)1-associated IgG2c isotype. Furthermore, D1 influenced the adiposity and exerted an anti-obesogenic effect on brown adipose tissue by up-regulating the expression of the genes Ucp-1, Cidea, Prdm16 and Gpr43. D1 also influenced the cecal microbiota composition, impacting its functions such as the production of short-chain fatty acids in the caecum. D1 reduced microbiota diversity by increasing beneficial taxa, such as Ruminococcaceae family and Turicibacter genus, among others. These genera showed correlations with the analysed immune and lipid metabolism parameters suggesting that microbiome modulation serves as a link between the observed systemic effects and the dietary intervention.<br><br>INTERPRETATION: The study highlights that a diet rich in fibre, vegetable protein, and fish oil, consumed during gestation and lactation, enhances maternal health by improving intestinal function, mucosal immunity, and exerting anti-obesogenic effects on lipid metabolism, likely mediated by modifications in the cecal microbiota composition and function.<br><br>FUNDING: The study was supported by LaMarat&#xf3;-TV3 (DIM-2-ELI, ref. 2018-27/30-31).},
}
@article {pmid40532561,
year = {2025},
author = {Oh, S and Byeon, H and Wijaya, J},
title = {Digital health framework for the predictive surveillance and diagnosis of atopic dermatitis.},
journal = {Water research},
volume = {284},
number = {},
pages = {124012},
doi = {10.1016/j.watres.2025.124012},
pmid = {40532561},
issn = {1879-2448},
abstract = {Atopic dermatitis (AD) is an inflammatory skin disease with immunological and environmental triggers that reduces the quality of life and increases the burden on health services. It is thus important to establish effective surveillance and diagnosis methods for the development of preventive and therapeutic interventions. In line with this, the present study established a digital health framework combining urban big data analytics, machine learning modeling, and environmental bioinformatics for the predictive surveillance and diagnosis of the nationwide AD prevalence in Korea. In this process, urban big data from environmental (e.g., immune response inducers), crowdsourced (web search keywords related to AD symptoms), and municipal microbiome sources (AD-associated bacteria detectable in wastewater) were combined and employed as input variables. Data preprocessing (i.e., feature selection, scaling, and normalization), model testing and selection, and hyperparameter tuning were then used to improve the prediction accuracy for AD prevalence. By applying explainable artificial intelligence methods, highly explanatory predictors, such as specific skin disease keywords associated with AD patients and environmental and inflammatory factors, were identified. Environmental genomics revealed that Streptococcus strains were dominant in human-derived wastewater, with operational taxonomic units that were strongly associated with inflammation-inducing bacteria originating from AD patients. Bioinformatic analysis subsequently revealed the pathogenotype and resistotype of these inflammation-related bacteria. Overall, our digital health framework holds great promise as an alternative to conventional complex and costly surveillance systems for the proactive guidance of the decision-making of health professionals regarding the surveillance, diagnosis, and therapeutic treatment of environmental diseases.},
}
@article {pmid40532026,
year = {2025},
author = {Matsumoto, Y and Hitaka, Y and Hirata, H and Yamamoto, Y and Kobayashi, K and Isoyama, N and Matsubara, T and Watanabe, K and Mizukami, Y and Nakagawa, S and Mishima, K and Harada, K and Shiraishi, K},
title = {Exploration of predictive factors based on oral and intestinal bacterial flora for treating patients with urothelial carcinoma.},
journal = {PloS one},
volume = {20},
number = {6},
pages = {e0324814},
doi = {10.1371/journal.pone.0324814},
pmid = {40532026},
issn = {1932-6203},
mesh = {Humans ; Male ; Female ; *Gastrointestinal Microbiome ; Saliva/microbiology ; Middle Aged ; Aged ; Feces/microbiology ; RNA, Ribosomal, 16S/genetics ; Immune Checkpoint Inhibitors/therapeutic use ; *Mouth/microbiology ; Phylogeny ; Case-Control Studies ; Adult ; *Urologic Neoplasms/microbiology/drug therapy ; },
abstract = {PURPOSE: The role of intestinal flora in carcinogenesis and chemotherapy efficacy has been increasingly studied; however, comparisons between oral and intestinal flora remain limited. Given the oral microbiome's role in systemic inflammation and immune modulation, it may significantly influence cancer progression and response to immunotherapy. This study aimed to identify the microbial changes in urothelial carcinoma (UC) by analyzing oral saliva and stool samples from healthy individuals and UC patients. We also examined the association between microbial composition and immune checkpoint inhibitor (ICI) response.<br><br>METHODS: A total of 20 healthy individuals and 38 patients with UC were analyzed. Among them, 27 patients with UC underwent ICI treatment. Oral saliva and stool samples were analyzed for 16S rRNA sequences to assess bacterial composition. Operational taxonomic units were generated, and phylogenetic analysis was performed using the Illumina BaseSpace.<br><br>RESULTS: Patients with UC showed higher Veillonellaceae and Prevotellaceae levels in saliva and stool, with lower levels of these bacteria associated with more prolonged overall survival and progression-free survival, particularly Veillonellaceae in stool. A higher neutrophil-to-lymphocyte ratio correlated with increased levels of these bacteria.<br><br>CONCLUSION: Veillonellaceae and Prevotellaceae are potential microbial biomarkers of survival outcomes and ICI efficacy in patients with UC. Non-invasive oral microbial sampling may facilitate personalized cancer treatment strategies.},
}
@article {pmid40531585,
year = {2025},
author = {Gevelinger, MM and Khemmani, M and Joyce, C and John, J and Sohail, S and Nasse, A and Fontes Noronha, M and Acevedo-Alvarez, M and Pham, T and Wolfe, AJ and Mueller, ER},
title = {Resilience of the Urogenital Microbiota Following Urogynecologic Surgery.},
journal = {Urogynecology (Philadelphia, Pa.)},
volume = {31},
number = {7},
pages = {650-659},
pmid = {40531585},
issn = {2771-1897},
mesh = {Humans ; Female ; *Microbiota ; Longitudinal Studies ; Middle Aged ; Adult ; Postmenopause ; *Vagina/microbiology ; Premenopause ; Aged ; RNA, Ribosomal, 16S ; *Urogenital System/microbiology ; *Pelvic Floor Disorders/surgery ; Postoperative Period ; Urinary Bladder/microbiology ; *Gynecologic Surgical Procedures ; },
abstract = {IMPORTANCE: Little is known about the resilience of the urogenital microbiota in response to urogynecologic surgery.<br><br>OBJECTIVES: The aim of this study was to determine if the urogenital microbiota are disrupted after surgery and if the postoperative composition returns to a preoperative baseline. We also sought to determine if the process of recovery differs in premenopausal women versus postmenopausal women.<br><br>STUDY DESIGN: Women undergoing surgery for pelvic floor disorders were invited to participate in this longitudinal descriptive study. Catheterized urine specimens and vaginal swabs were obtained at 4 timepoints: (1) day of surgery prior to antibiotic administration and surgical preparation; (2) immediately postoperatively; (3) 3-week postoperative visit; and (4) 12-week postoperative visit. Bacterial DNA was extracted, sequenced by 16S rRNA gene sequencing and classified taxonomically. Longitudinal data analyses were performed using linear mixed-effects models evaluating Jensen-Shannon divergence and &#x3b1; diversity measures.<br><br>RESULTS: Forty women, 50% of whom were postmenopausal, were included. There were significant alterations in &#x3b1; diversity over time (P time &#x2264;0.05 for all comparisons), except richness in the bladder. There was perturbation immediately postoperatively, with a return to preoperative baseline at 3 and 12 weeks postoperatively. At each timepoint, premenopausal participant microbiota were not diverse, whereas postmenopausal women had diverse compositions. Jensen-Shannon divergence indices were stable in both the bladder (P = 0.95) and vagina (P = 0.88) over time in premenopausal women but showed divergence from the preoperative vagina for postmenopausal women (P = 0.004).<br><br>CONCLUSIONS: The urogenital microbiome is altered after urogynecologic surgery. In premenopausal versus postmenopausal women, the composition, stability, and process of recovery differ.},
}
@article {pmid40531331,
year = {2025},
author = {Yu, Y and Park, S and Jeon, J and Lee, SH and Kim, H and Seo, D and Park, M and Park, E and Kim, JY and Cho, SJ and Jo, S and Park, G and Yang, JY},
title = {The radioprotective role of human Alistipes onderdonkii identified by multi-omic analysis in patients with prostate cancer.},
journal = {Discover oncology},
volume = {16},
number = {1},
pages = {1142},
pmid = {40531331},
issn = {2730-6011},
support = {2018R1A5A2023879//National Research Foundation of Korea (NRF) grant funded by the Korea government (MSIT)/ ; 2018R1A5A2023879//National Research Foundation of Korea (NRF) grant funded by the Korea government (MSIT)/ ; 2018R1A5A2023879//National Research Foundation of Korea (NRF) grant funded by the Korea government (MSIT)/ ; 2018R1A5A2023879//National Research Foundation of Korea (NRF) grant funded by the Korea government (MSIT)/ ; 2018R1A5A2023879//National Research Foundation of Korea (NRF) grant funded by the Korea government (MSIT)/ ; 2018R1A5A2023879//National Research Foundation of Korea (NRF) grant funded by the Korea government (MSIT)/ ; RS-2024-00460591//Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education/ ; A21IP13//Korea Hydro &amp; Nuclear Power CO., LTD/ ; A21IP13//Korea Hydro &amp; Nuclear Power CO., LTD/ ; A21IP13//Korea Hydro &amp; Nuclear Power CO., LTD/ ; A21IP13//Korea Hydro &amp; Nuclear Power CO., LTD/ ; A21IP13//Korea Hydro &amp; Nuclear Power CO., LTD/ ; A21IP13//Korea Hydro &amp; Nuclear Power CO., LTD/ ; A21IP13//Korea Hydro &amp; Nuclear Power CO., LTD/ ; A21IP13//Korea Hydro &amp; Nuclear Power CO., LTD/ ; A21IP13//Korea Hydro &amp; Nuclear Power CO., LTD/ ; A21IP13//Korea Hydro &amp; Nuclear Power CO., LTD/ ; A21IP13//Korea Hydro &amp; Nuclear Power CO., LTD/ ; A21IP13//Korea Hydro &amp; Nuclear Power CO., LTD/ ; RS-2023-00301938//Learning &amp; Academic research institution for Master's&#xb7;PhD students, and Postdocs (LAMP) Program of the National Research Foundation of Korea (NRF) grant funded by the Ministry of Education/ ; RS-2023-00301938//Learning &amp; Academic research institution for Master's&#xb7;PhD students, and Postdocs (LAMP) Program of the National Research Foundation of Korea (NRF) grant funded by the Ministry of Education/ ; RS-2023-00301938//Learning &amp; Academic research institution for Master's&#xb7;PhD students, and Postdocs (LAMP) Program of the National Research Foundation of Korea (NRF) grant funded by the Ministry of Education/ ; RS-2023-00301938//Learning &amp; Academic research institution for Master's&#xb7;PhD students, and Postdocs (LAMP) Program of the National Research Foundation of Korea (NRF) grant funded by the Ministry of Education/ ; RS-2023-00301938//Learning &amp; Academic research institution for Master's&#xb7;PhD students, and Postdocs (LAMP) Program of the National Research Foundation of Korea (NRF) grant funded by the Ministry of Education/ ; },
abstract = {BACKGROUND: Advances in medical science improved cancer treatment outcomes, and radiotherapy became a common modality used by 50% of cancer patients. However, radiotherapy induces gastrointestinal distress, and it can severely impair patients' quality of life. During irradiation, the gut microbiome is critical in maintaining intestinal health and influences the body's response. This study examines the alterations in the gut microbiome and serum metabolites of prostate cancer patients undergoing radiotherapy. We investigate the potential radioprotective effects of Alistipes (A.) onderdonkii.<br><br>METHODS: Ten patients with prostate cancer receiving radiotherapy were included in this study. Fecal and serum samples were collected, and diarrhea symptoms were monitored along with each radiotherapy section.<br><br>RESULTS: After radiotherapy, nine microbiomes and 129 serum metabolites displayed significant changes associated with irradiation-induced gastrointestinal toxicity. Dehydroascorbic acid and A. onderdonkii found a correlation in the analysis between metabolites and the microbiome. Administration of A. onderdonkii significantly improved survival and reduced intestinal damage in mice after radiation exposure, suggesting A. onderdonkii as a protective agent in radiotherapy.<br><br>CONCLUSIONS: This result highlights A. onderdonkii as a potential microbial candidate for mitigating irradiation-induced damage in the gastrointestinal tract. It appears to alleviate oxidative stress and support mucosal integrity, thereby promoting resistance to radiation-induced injury.<br><br>IMPACT: This finding establishes the foundation for developing microbiome-based therapeutics for the gut health of cancer patients undergoing radiotherapy.},
}
@article {pmid40530883,
year = {2025},
author = {Ganote, CL and Caesar, L and Rice, DW and Whitaker, RJ and Newton, ILG},
title = {Evolutionary trends in Bombella apis CRISPR-Cas systems.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0016625},
doi = {10.1128/msystems.00166-25},
pmid = {40530883},
issn = {2379-5077},
abstract = {UNLABELLED: Bacteria and archaea employ a rudimentary immune system, CRISPR-Cas, to protect against foreign genetic elements such as bacteriophage. CRISPR-Cas systems are found in Bombella apis. B. apis is an important honey bee symbiont, found primarily in larvae, queens, and hive compartments. B. apis is found in the worker bee gut but is not considered a core member of the bee microbiome and has therefore been understudied with regard to its importance in the honey bee colony. However, B. apis appears to play beneficial roles in the colony, by protecting developing brood from fungal pathogens and by bolstering their development under nutritional stress. Previously, we identified CRISPR-Cas systems as being acquired by B. apis in its transition to bee association, as they are absent in a sister clade. Here, we assess the variation and distribution of CRISPR-Cas types across B. apis strains. We found multiple CRISPR-Cas types, some of which have multiple arrays, within the same B. apis genomes and also in the honey bee queen gut metagenomes. We analyzed the spacers between strains to identify the history of mobile element interaction for each B. apis strain. Finally, we predict interactions between viral sequences and CRISPR systems from different honey bee microbiome members. Our analyses show that the B. apis CRISPR-Cas systems are dynamic; that microbes in the same niche have unique spacers, which supports the functionality of these CRISPR-Cas systems; and that acquisition of new spacers may be occurring in multiple locations in the genome, allowing for a flexible antiviral arsenal for the microbe.<br><br>IMPORTANCE: Honey bee worker gut microbes have been implicated in everything from protection from pathogens to breakdown of complex polysaccharides in the diet. However, there are multiple niches within a honey bee colony that host different groups of microbes, including the acetic acid bacterium Bombella apis. B. apis is found in the colony food stores, in association with brood, in worker hypopharyngeal glands, and in the queen's digestive tract. The roles that B. apis may serve in these environments are just beginning to be discovered and include the production of a potent antifungal that protects developing bees and supplementation of dietary lysine to young larvae, bolstering their nutrition. Niche specificity in B. apis may be affected by the pressures of bacteriophage and other mobile elements, which may target different strains in each specific bee environment. Studying the interplay between B. apis and its mobile genetic elements (MGEs) may help us better understand microbial community dynamics within the colony and the potential ramifications for the honey bee host.},
}
@article {pmid40530879,
year = {2025},
author = {Ke, Z and Ma, Q and Ye, X and Jin, Y and Wang, Y and Zhao, X and Su, Z},
title = {Oral delivery of GLP-1 peptide using recombinant Lactobacillus gasseri for the treatment of type 2 diabetes mellitus.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0282824},
doi = {10.1128/spectrum.02828-24},
pmid = {40530879},
issn = {2165-0497},
abstract = {Glucagon-like peptide-1 (GLP-1) is an effective therapeutic peptide for the treatment of type 2 diabetes mellitus (T2DM). Here, we constructed an effective probiotic-based oral GLP-1 delivery system by engineering the probiotic strain of Lactobacillus gasseri (Lgs[GPA]) to secrete GLP-1 fusion peptide, which combines GLP-1 with protein transduction domain (PTD) and a serum albumin binding peptide (ABP), GLP-1-PTD-ABP (GPA). The supernatants of Lgs[GPA] cultures significantly upregulated the expression of PDX-1 and stimulated insulin release in Min6 cells. Daily oral administration of Lgs[GPA] in db/db mice significantly alleviated insulin resistance, hyperglycemia, and dyslipidemia. Simultaneously, the abundance of unclassified_f_Erysipelotrichaceae and Intestinimonas was significantly reduced in db/db mice, while the average abundance of Akkermansia increased in the SD rats. These findings demonstrate that the probiotic-based delivery system represents a versatile and effective strategy for the oral administration of therapeutic peptides. Collectively, our results highlight the potential of this probiotic-based approach as a promising therapeutic and preventive intervention for T2DM.IMPORTANCEIt is important to develop the oral delivery strategy for therapeutic peptides. Due to issues with patient adherence and the low oral bioavailability of current administration methods, researchers have been exploring oral delivery strategies for GLP-1 analogs for many years, including the use of advanced microbiome therapeutics (AMTs). AMTs offer the potential to use engineered microbes for innovative therapeutic applications, such as the oral delivery of GLP-1 analogs. Our approaches offer a general oral delivery strategy for therapeutic peptides. The probiotic-based approach represents a promising method for treating and preventing T2DM.},
}
@article {pmid40530826,
year = {2025},
author = {Carolak, E and Czajkowska, J and Stypułkowska, A and Waszczuk, W and Dutkiewicz, A and Grzymajlo, K},
title = {Being a better version of yourself: genetically engineered probiotic bacteria as host defense enhancers in the control of intestinal pathogens.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2519696},
doi = {10.1080/19490976.2025.2519696},
pmid = {40530826},
issn = {1949-0984},
mesh = {*Probiotics ; Humans ; *Gastrointestinal Microbiome ; Genetic Engineering ; Animals ; *Microorganisms, Genetically-Modified/genetics ; *Bacteria/genetics ; },
abstract = {Intestinal pathogens pose a significant global health burden, and traditional antibiotic treatments often disrupt the beneficial gut microbiota that plays a crucial role in maintaining host health through pathogen prevention and immune regulation. Although probiotics have emerged as promising therapeutic agents, their efficacy is limited by strain-dependent variations, survival challenges in the gastrointestinal tract, and inconsistent immune responses. Recent advances in genetic engineering, particularly CRISPR-Cas systems and their combinations with complementary technologies, such as Cre-lox and RecE/T, have enabled the precise modification of probiotic strains to enhance their therapeutic potential. These enhanced probiotics demonstrate improved functionality through multiple mechanisms, including increased adhesion via the expression of specific proteins (InlA, FnBPA, and LAP), targeted antimicrobial activity through engineered sensing systems (Lactococcus lactis detecting Vibrio cholerae CAI-1), and enhanced immunomodulation through cytokine production. Results have demonstrated the potential of genetically modified probiotics in preventing and treating gastrointestinal infections through mechanisms that include competitive exclusion, bacteriocin production, intestinal barrier reinforcement, and immune modulation. However, challenges remain in ensuring genetic stability and preventing horizontal gene transfer. Future research should focus on optimizing probiotic strains for targeted applications while addressing biosafety concerns. By understanding the complex interplay between probiotics, pathogens, and host immunity, innovative strategies can be developed to harness the full therapeutic potential of probiotic interventions in maintaining gut health.},
}
@article {pmid40530746,
year = {2025},
author = {Lee, E and Yang, SI and Suh, DI and Kim, HB and Lee, SY and Kwon, SO and Hong, SJ},
title = {Environmental factors shaping atopic dermatitis: Lessons from longitudinal cohort studies.},
journal = {Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology},
volume = {36},
number = {6},
pages = {e70130},
doi = {10.1111/pai.70130},
pmid = {40530746},
issn = {1399-3038},
support = {//Korea Environment Industry &amp; Technology Institute (KEITI)/ ; RS-2022-KE002048//Ministry of Environment (Republic of Korea)/ ; 2008-E33030-00//Korea National Institute of Health/ ; 2009-E33033-00//Korea National Institute of Health/ ; 2011-E33021-00//Korea National Institute of Health/ ; 2012-E33012-00//Korea National Institute of Health/ ; 2013-E51003-00//Korea National Institute of Health/ ; 2014-E51004-00//Korea National Institute of Health/ ; 2014-E51004-01//Korea National Institute of Health/ ; 2014-E51004-02//Korea National Institute of Health/ ; 2017-E67002-00//Korea National Institute of Health/ ; 2017-E67002-01//Korea National Institute of Health/ ; 2017-E67002-02//Korea National Institute of Health/ ; 2020E670200//Korea National Institute of Health/ ; 2020E670201//Korea National Institute of Health/ ; 2020E670202//Korea National Institute of Health/ ; 2023E120300//Korea National Institute of Health/ ; 2023E120301//Korea National Institute of Health/ ; 2023E120302//Korea National Institute of Health/ ; BCRI-25076//Chonnam National University Hospital Biomedical Research Institute/ ; },
mesh = {Humans ; *Dermatitis, Atopic/etiology/epidemiology/immunology ; *Environmental Exposure/adverse effects ; Longitudinal Studies ; Female ; Pregnancy ; Infant ; Exposome ; Gastrointestinal Microbiome ; },
abstract = {Atopic dermatitis (AD) is a prevalent chronic inflammatory skin disease arising from a multifaceted interplay between genetic susceptibility and environmental exposures. Longitudinal cohort studies have been instrumental in elucidating the contribution of environmental factors to both the onset and persistence of AD. This review synthesizes evidence from such studies to delineate key environmental determinants across various domains. Early-life exposures, including delivery mode and antibiotic exposure, modulate microbial composition and function, thereby influencing immune development and predisposing individuals to AD. Both outdoor and indoor air pollutants, such as particulate matter and volatile organic compounds, have been shown to impair skin barrier integrity and dysregulate immune responses, facilitating the initiation and progression of AD. Nutritional factors, encompassing maternal and infant dietary patterns, shape gut microbiota and metabolite profiles and systemic immune activity, further modulating AD risk. Moreover, psychological stress during the prenatal and postnatal periods has been associated with alterations in immune function and epigenetic programming, which may heighten susceptibility to AD. Environmental influences also appear to vary by AD phenotype and trajectory, underscoring the need for individualized prevention strategies. Advances in exposome research, encompassing both external and internal environmental components, have enhanced mechanistic understanding and facilitated the identification of candidate biomarkers. Collectively, current evidence supports the notion that early-life environmental exposures act not as isolated determinants but in concert with genetic, microbial, and immunologic factors to shape AD pathogenesis. A comprehensive framework integrating exposomics and multiomics may ultimately inform the development of targeted preventive and therapeutic strategies for children with AD.},
}
@article {pmid40530272,
year = {2025},
author = {Jia, Y and Wang, J and Lin, X and Liang, T and Dai, H and Wu, B and Yang, M and Zhang, Y and Li, R},
title = {Integrated metabolomics and metagenomics reveal plant-microbe interactions driving aroma differentiation in flue-cured tobacco leaves.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1588888},
pmid = {40530272},
issn = {1664-462X},
abstract = {Current research on tobacco aroma predominantly focuses on single-omics approaches. In this study, we conducted a comprehensive investigation of the relationships between tobacco metabolite profiles, microbial communities, and aroma characteristics. Untargeted metabolomics and metagenomic analyses were performed on flue-cured upper tobacco leaves to compare light aromatic tobacco (LAT) and strong aromatic tobacco (SAT). The results showed that sugar metabolite levels in LAT were significantly higher than those in SAT, whereas levels of specific acids and amino acid metabolites in SAT exceeded those in LAT. Redundancy analysis (RDA) and metabolomic correlation analyses indicated that the genera Methylorubrum and Pseudomonas may promote sugar metabolite accumulation, while Pseudokineococcus potentially regulates both sugar and acid metabolites. In contrast, Methylobacterium and Sphingomonas were associated with acid and amino acid metabolism, with Methylobacterium additionally exhibiting inhibitory effects on sugar metabolism. Metagenomic analysis revealed that Methylorubrum, Pseudomonas, and Pseudokineococcus were abundant in LAT, whereas Methylobacterium and Sphingomonas dominated in SAT. Notably, the bidirectional regulation of aromatic metabolites by microbial genera such as Pseudokineococcus highlights the universality of plant-microbe interactions in shaping metabolic networks-a mechanism potentially applicable to other crop systems. These findings reveal conserved microbial functional traits (e.g., metabolic pathway modulation) that may drive plant phenotypic differentiation beyond tobacco, offering insights into microbiome-mediated crop quality improvement. The results provide theoretical guidance for tobacco aging and aroma regulation and underscore the broader significance of microbial community engineering in agriculture for manipulating plant metabolic outputs.},
}
@article {pmid40530238,
year = {2025},
author = {Welham, Z and Li, J and Tse, B and Engel, A and Molloy, MP},
title = {Gut Mucosal Microbiome of Patients With Low-Grade Adenomatous Bowel Polyps.},
journal = {Gastro hep advances},
volume = {4},
number = {8},
pages = {100687},
pmid = {40530238},
issn = {2772-5723},
abstract = {BACKGROUND AND AIMS: Colorectal cancer etiology is multifactorial and influenced by colonic environmental exposures leading to the accumulation of genetic lesions in precancerous polyps. There is growing recognition for a role of the gut microbiome in colorectal cancer progression, but the structure of the gut mucosal microbiome in the early stages of polyp growth is limited. The aim of this study was to characterize the gut mucosal microbiome from patients with low-grade conventional bowel neoplasia compared to symptomatic but polyp-free patients.<br><br>METHODS: In this case-control study conducted at a tertiary referral hospital, 148 symptomatic patients undergoing colonoscopy were prospectively recruited. Mucosal biopsies adjacent to low-grade dysplasia (LGD) adenomatous polyps were used for 16S rRNA gene amplicon sequencing to define bacterial taxonomies relative to polyp-free controls.<br><br>RESULTS: Minimal differences in gut mucosa community diversity measures were observed between participants with or without LGD adenomas. After correcting for clinical covariates, patients with adenomas in the proximal colon revealed elevated amplicons from Parabacteroides distasonis, Bacteroides uniformis, and unassigned Lachnospiraceae spp. Bacteroides/Phocaeicola massiliensis was the only microbe consistently found to be decreased in the gut mucosa of LGD adenoma patients compared with controls. Participants with LGD polyps in the distal colon showed more amplicons from Howardella sp. and Blautia faecicola.<br><br>CONCLUSION: This study identified microbial candidates in the colonic mucosa that are associated with adenomatous LGD bowel neoplasia as an early step in the colorectal carcinogenesis pathway.},
}
@article {pmid40530108,
year = {2025},
author = {Frias, J and Martins, M and Peixoto, A and Macedo, G},
title = {Rifaximin as a Therapeutic Ally in the Modulation of Dysbiosis: A Narrative Review of Its Applicability in Gastrointestinal Disorders.},
journal = {GE Portuguese journal of gastroenterology},
volume = {},
number = {},
pages = {1-15},
pmid = {40530108},
issn = {2341-4545},
abstract = {BACKGROUND: The gastrointestinal microbiota is vital for a well-functioning digestive tract, nutrient metabolism, immune support, and protection against pathogenic microorganisms. Disruption of this balance is known as dysbiosis. Rifaximin, an oral antibiotic with selective action, reduces harmful gut bacteria while preserving beneficial species, aiding in microbiota restoration.<br><br>SUMMARY: Alterations in the intestinal microbiota are implicated in many gastrointestinal disorders. Rifaximin, by targeting and modulating the microbiota, may serve as a powerful tool in the approach of these conditions.<br><br>KEY MESSAGES: This narrative review summarizes the main uses of rifaximin in gastrointestinal disorders like irritable bowel syndrome, diverticular disease, small intestinal bacterial overgrowth, traveler's diarrhea, hepatic encephalopathy, Clostridioides difficile infection, and inflammatory bowel disease.},
}
@article {pmid40529595,
year = {2025},
author = {Li, Y and Ash, KT and Joyner, D and Williams, DE and Hazen, TC},
title = {SARS-CoV-2 virus in raw wastewater from student residence halls with concomitant 16S rRNA bacterial community structure changes.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1589029},
pmid = {40529595},
issn = {1664-302X},
abstract = {The detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in sewage is well-established, but the concomitant changes in microbial compositions during the pandemic remain insufficiently explored. This study investigates the impact of the SARS-CoV-2 virus on microbial compositions in raw sewage, utilizing high-throughput 16S rRNA amplicon sequencing to analyze wastewater samples collected from six dormitories over a one-year field trial at the University of Tennessee, Knoxville. The concentration of SARS-CoV-2 RNA was assessed using a reverse transcription-quantitative polymerase chain reaction. Significant variations in bacterial composition were evident across the six dormitories, highlighting the importance of independently considering spatial differences when evaluating the raw wastewater microbiome. Positive samples for SARS-CoV-2 exhibited a prominent representation of exclusive species across all dormitories, coupled with significantly reduced bacterial diversity compared to negative samples. The correlation observed between the relative abundance of enteric pathogens and potential pathogens at sampling sites introduces a significant dimension to our understanding of COVID-19, especially the notable correlation observed in positive SARS-CoV-2 samples. Furthermore, the significant correlation in the relative abundance of potential pathogens between positive and negative SARS-CoV-2 raw sewage samples may be linked to the enduring effects of microbial dysbiosis observed during COVID-19 recovery. These findings provide valuable insights into the microbial dynamics in raw sewage during the COVID-19 pandemic.},
}
@article {pmid40529587,
year = {2025},
author = {Lee, CK and Lee, HJ and Jeong, SH and Lee, SJ},
title = {Precision targeting of genetic variations in mixed bacterial cultures using CRISPR-Cas12a-programmed λ phages.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1575339},
pmid = {40529587},
issn = {1664-302X},
abstract = {The CRISPR-Cas system, an adaptive immune mechanism in prokaryotes against bacteriophages, has been developed into a versatile tool for recognizing and cleaving target nucleic acid sequences. In this study, we developed a model system by integrating CRISPR-Cas12a into the genome of temperate bacteriophage λ, enabling precise regulation of lysogeny and lysis in Escherichia coli. We confirmed that λ phage, armed with Cas12a nuclease and CRISPR RNA (crRNA) targeting specific sequences, could inhibit the lysogenic cycle of E. coli cells. We demonstrated that the CRISPR-Cas12a-loaded temperate λ phage mimicked a lytic phage by selectively killing cells carrying the target genomic sequence. Furthermore, by employing truncated crRNA to enhance target recognition specificity, we found that the synthetic phage could distinguish single nucleotide variations in the genomic target DNA, enabling precise targeting and selective elimination of target cells in homogeneous bacterial cultures. To further validate its specificity, we tested this system in mixed bacterial cultures, wherein Cas12a nuclease and truncated crRNA-loaded bacteriophages selectively eliminated only those cells carrying the target sequences perfectly matching the crRNA. These results highlight the potential of this approach for advancing precision microbiome modulation.},
}
@article {pmid40529581,
year = {2025},
author = {Xu, D and Lu, Z and Li, Q and Cheng, Y and Yang, Z},
title = {Decoding the gut-sleep Nexus: a bibliometric mapping of gut microbiota and sleep disorders.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1598173},
pmid = {40529581},
issn = {1664-302X},
abstract = {BACKGROUND: An increasing number of studies have focused on the interaction between gut microbiota and sleep disorders. However, there is currently no bibliometric analysis of the literature on gut microbiota and sleep disorders. This study employs bibliometric methods to analyze the current research status and hotspots in the field of gut microbiota and sleep disorders, providing a reference for future research in this area.<br><br>METHODS: Articles related to gut microbiota and sleep disorders were retrieved from the WOS core database, covering the period from the database's inception to December 31, 2024. After rigorous screening, VOSviewer and CiteSpace were used to conduct analyses on quantity, collaboration networks, clustering, and citation bursts.<br><br>RESULTS: The number of articles on gut microbiota and sleep disorders has increased annually, with a significant surge after 2022. China has the highest number of publications, while the United States has the highest citation count. The institution with the most publications is Shanghai Jiao Tong University, and the institution with the most citations is Deakin University. The top 10 journals by publication volume are all ranked above Q2 in the JCR. The most cited article is "Gut microbiome diversity is associated with sleep physiology in humans" by Smith et al., published in PLOS ONE in 2019. The top 10 most frequent keywords are gut microbiota, sleep, depression, inflammation, chain fatty acids, anxiety, brain, oxidative stress, obesity, and health. The keyword cluster "obstructive sleep apnea" is a focal research direction, while fecal microbiota transplantation is a current research hotspot.<br><br>CONCLUSION: This study reveals the publication trends, collaboration relationships among countries, regions, and authors, and recent research hotspots in the field of gut microbiota and sleep disorders through bibliometric methods, providing an objective data reference for scientific research in this domain.},
}
@article {pmid40529484,
year = {2025},
author = {Lee, B and Ko, MM and Ahn, YM and Park, HJ and Jung, SY and Jung, HA and Lee, H and Kim, PW and Choi, Y and Han, K and Shin, S and Jung, J},
title = {Effect of herbal medicine Bojungikgi-tang on gut microbiome and symptoms in anorexic patients with atopic dermatitis: a randomized controlled trial.},
journal = {Frontiers in pharmacology},
volume = {16},
number = {},
pages = {1593477},
pmid = {40529484},
issn = {1663-9812},
abstract = {INTRODUCTION: Atopic dermatitis (AD) is often associated with gastrointestinal symptoms, including anorexia and alterations in the gut microbiome. A traditional East Asian herbal medicine Bojungikgi-tang (BJT; Buzhongyiqi-tang in Chinese, Hochuekki-To in Japanese) has been commonly used to manage AD and anorexia. This study aimed to evaluate the effects and safety of BJT in anorexic patients with AD and to investigate its therapeutic mechanism through gut microbiome analysis.<br><br>METHODS: The trial included 26 adults with AD and anorexia, randomized (1:1) into BJT or waiting list groups for 12&#xa0;weeks, including 8&#xa0;weeks of treatment and 4&#xa0;weeks of follow-up. The severity of anorexia and AD was assessed using the Visual Analog Scale (VAS), SCORing of Atopic Dermatitis (SCORAD), and Dermatology Life Quality Index (DLQI). Serum cytokine concentrations were measured before and after treatment using a multiplex immunoassay. Fecal samples were collected before and after treatment, and 16S rRNA sequencing was performed to analyze the gut microbiota.<br><br>RESULTS: The BJT group showed a significant decrease in anorexia VAS scores compared to the waiting list group at 8&#xa0;weeks. Only the BJT group showed significant improvements in SCORAD and DLQI scores compared to baseline, with effects maintained through follow-up. No serious adverse events related to BJT were reported. Among the serum cytokines, IL-1&#x3b2; significantly decreased only in the BJT group, while IL-4 and IL-17 significantly decreased in both groups, with a more pronounced reduction observed in the BJT group. After 8&#xa0;weeks of BJT treatment, significant changes were observed in the gut microbiome, including alterations in the Gemella genus, Gemmiger formicilis, and Blautia_uc species.<br><br>CONCLUSION: BJT may improve symptoms of anorexia and AD without serious adverse events, potentially through modifications in the gut microbiota.<br><br>CLINICAL TRIAL REGISTRATION: The study protocol was registered at the Clinical Research Information Service (KCT0006784, https://cris.nih.go.kr/cris/search/detailSearch.do?seq=21298&amp;search_page=L).},
}
@article {pmid40529475,
year = {2025},
author = {Burma, NE and Ramien, ML},
title = {Cutaneous and Gut Dysbiosis in Alopecia Areata: A Review.},
journal = {JID innovations : skin science from molecules to population health},
volume = {5},
number = {4},
pages = {100363},
pmid = {40529475},
issn = {2667-0267},
abstract = {Alopecia areata (AA) is a common, immune-mediated nonscarring alopecia. Breakdown of immune privilege combined with local immune cell infiltration is central to the development of AA; yet, the instigating factors causing immune dysregulation remain elusive. Recent attention has focused on the microbiome in AA, where alterations to the usual composition of healthy microorganisms is observed. This review examines the current evidence for bacterial dysbiosis affecting the scalp and gut of patients with AA and summarizes the potential influence of altered microbial composition on immune dysregulation in AA. Although the literature supports changes to the bacterial composition of patients with AA, a causal link between microbial dysbiosis and AA pathogenesis remains to be established.},
}
@article {pmid40529471,
year = {2025},
author = {Grashoff, P and Mutters, NT and Kramer, A and Ilschner, C and Rausch, M and Gebel, J},
title = {Development of the active ingredient composition of hand antiseptics in Germany from 2004 to 2022 with special consideration of ethanol as active agent.},
journal = {GMS hygiene and infection control},
volume = {20},
number = {},
pages = {Doc17},
pmid = {40529471},
issn = {2196-5226},
abstract = {AIM: The number of active agents used in hand antiseptics (HA) in Germany was analyzed using the disinfectant lists of the Association for Applied Hygiene (VAH) for the years 2004, 2012 and 2022 to evaluate the development regarding the use of unnecessary or critical active agents in alcohol-based hand rubs (ABHR).<br><br>RESULTS: While 20 different active agents were used in the HAs (97 listed HAs) in 2004, only 14 were used in 2012 (201 listed HAs) and 15 in 2022 (332 listed HAs). Benzoic acid, clorocesol, chlorophene, octenidine dihydrochloride, peracetic acid, polihexanide and triclosan are no longer used as additives to ABHR. At the same time, the number of active ingredients per product fell.In the period from 2002 to 2022, there was an increase in ABHR, so that in 2022, only four HAs did not contain alcohol: three were based on PVP iodine and one was based on quaternary ammonium compounds.While 2-propanol still dominated as the first-named active ingredient in 2004 and 2022, in 2022 mainly ABHR with ethanol as the first-named active ingredient were certified. The percentage share of ethanol in ABHR, measured against all VAH-listed HA and as the main active ingredient, increased by 43.4% between 2004 and 2022. At the same time, there has been a 33.2% decrease in ABHR of 2-propanol as active ingredient.<br><br>DISCUSSION: There are probably two reasons for the decrease in the total number of active ingredients used. The addition of antiseptic agents to ABHR does not increase their residual effectiveness. In addition, the antimicrobial antiseptics added to ABHR are less well tolerated than alcohols. Consequently, for ethical reasons it makes sense not to add these antimicrobials to the formulas. The increase of ethanol-based hand rubs (EBHR) suggests that these are preferred by users. One explanation may be that, unlike ethanol, 1-propanol can have an irritating effect on both healthy and atopic skin.<br><br>CONCLUSION: Ethanol must be retained as an active ingredient for ABHR for the following reasons: ethanol is the only active ingredient that can be used for HA with comprehensive efficacy against non-enveloped viruses; both propanols are less physiological for the human organism than ethanol; ethanol is better tolerated by the skin than 1-propanol; and an adverse effect on the skin microbiome has been ruled out for ethanol. This must be considered when discussing the possible biocide classification of ethanol as CMR, especially because such a classification has absolutely no scientific basis.},
}
@article {pmid40529420,
year = {2025},
author = {Starck, C and Blumfield, M and Petocz, P and Duve, E and Downey, L and Abbott, K and Fayet-Moore, F},
title = {A1 protein free milk benefits mood and subjective cognition in free-living Australian adults: a pragmatic, exploratory, open label randomised controlled trial.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1579986},
pmid = {40529420},
issn = {2296-861X},
abstract = {BACKGROUND: Adverse effects of milk containing A1-type β-casein on digestion, immune response, and cognition have been identified in milk-intolerant individuals, but health effects in healthy individuals without symptoms of milk intolerance are yet to be examined.<br><br>OBJECTIVE: The objective was to explore the impact of reducing A1 type &#x3b2;-casein intake via switching milk type from conventional A1/A2-type &#x3b2;-casein milk (A1/A2 milk) to A1-type &#x3b2;-casein protein free milk (A1PF) on brain, immune response, gastrointestinal, and skin (BIGS) outcomes in a real-world setting.<br><br>METHODS: An open-label, pragmatic, exploratory randomised controlled trial was conducted in 997 healthy, free-living Australian older adolescents and adults (16-65&#x202f;years) who regularly consume A1/A2 protein-containing milk and milk products. Participants were randomised into two groups, to consume &#x2265;250&#x202f;mL/day of A1/A2 milk (control) or to switch to &#x2265;250&#x202f;mL/day of A1PF milk (intervention) for 28&#x202f;days, while continuing to follow their usual diet (including up to 1 serve a day of A1/A2 dairy products). A sub-group of 265 participants conducted stool, saliva and cognitive testing on days 0 and 28. All participants completed subjective questionnaires on days 0, 14, and 28.<br><br>RESULTS: No differences in gut microbiome composition, alpha-diversity, or function were found by switching milk type. After switching to A1PF milk, a small increase in stool consistency was reported (-0.16, p&#x202f;=&#x202f;0.007), and females experienced a marginal reduction in gastrointestinal symptoms (p&#x202f;=&#x202f;0.015) and improved subjective cognition (p&#x202f;=&#x202f;0.03). Switching to A1PF milk reduced anxiety (-0.61; p&#x202f;=&#x202f;0.002), depression (-0.56; p&#x202f;=&#x202f;0.023), stress (-0.70, p&#x202f;=&#x202f;0.012) and fatigue (p&#x202f;=&#x202f;0.001; females only), compared to drinking A1/A2 milk, with stronger effects in females. No consistent effects on markers of immune response or skin health were identified.<br><br>CONCLUSION: Switching from conventional A1/A2 milk to A1PF milk may benefit mood and subjective cognition, particularly in females, without the need for complete elimination of A1 &#x3b2;-casein from the diet. Further investigations are warranted.<br><br>CLINICAL TRIAL REGISTRATION: https://www.anzctr.org.au/Trial/Registration/TrialReview.aspx?id=385966, identifier ACTRN12623000628640.},
}
@article {pmid40529306,
year = {2025},
author = {Xu, J and Zhang, M and Yan, Y and Li, Z and Lu, X},
title = {Intestinal flora metabolites indole-3-butyric acid and disodium succinate promote IncI2 mcr-1-carrying plasmid transfer.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1564810},
pmid = {40529306},
issn = {2235-2988},
mesh = {*Plasmids/genetics ; Reactive Oxygen Species/metabolism ; *Indoles/metabolism/pharmacology ; *Gastrointestinal Microbiome/drug effects ; Escherichia coli/genetics/drug effects ; *Gene Transfer, Horizontal/drug effects ; Conjugation, Genetic/drug effects ; *Succinic Acid/metabolism ; Cell Membrane Permeability/drug effects ; Drug Resistance, Bacterial/genetics ; },
abstract = {INTRODUCTION: Plasmid-driven horizontal transfer of resistance genes in bacterial communities is a major factor in the spread of resistance worldwide. The gut microbiome, teeming with billions of microorganisms, serves as a reservoir for resistance genes. The metabolites of gut microorganisms strongly influence the physiology of their microbial community, but the role of the metabolites in the transfer of resistance genes remains unclear.<br><br>METHODS: A dual-fluorescence conjugation model was established. We assessed the effects of different concentrations of indole-3-butyric acid (IBA) and disodium succinate (DS) on plasmid transfer using conjugation assays. The growth of bacteria (donors, recipients, and transconjugants), the reactive oxygen species (ROS) levels and membrane permeability were measured under IBA and DS exposure. The plasmid copy number, and transcriptional levels of conjugation-related genes (including the related genes of the regulation of ROS production, the SOS response, cell membrane permeability, pilus generation, ATP synthesis, and the type IV secretion system (T4SS)) were evaluated by qPCR.<br><br>RESULTS: In this study, we demonstrated that IBA and DS at low concentrations, which can also be ingested through diet, enhance the interspecies transfer ratio of IncI2 mcr-1-carrying plasmid in Escherichia coli. At 20 mg/L, the transfer ratios in the presence of IBA or DS increased by 2.5- and 2.7-fold compared to that of the control, respectively. Exposure to this concentration of IBA or DS increased the production of reactive oxygen species (ROS), the SOS response, cell membrane permeability, and plasmid copy number. The transcription of genes of the related pathways and of pilus, ATP, and the T4SS was upregulated.<br><br>DISCUSSION: Our findings revealed that low-dose gut microbiota metabolites-particularly those with dietary origins-promote plasmid-mediated resistance gene dissemination through multifaceted mechanisms involving oxidative stress, SOS activation, and conjugation machinery enhancement. This highlights potential public health risks associated with microbiota metabolites, especially those utilized in food production.},
}
@article {pmid40529304,
year = {2025},
author = {Chen, Z and Jin, D and Hu, J and Guan, D and Bai, Q and Gou, Y},
title = {Microbiota and gastric cancer: from molecular mechanisms to therapeutic strategies.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1563061},
pmid = {40529304},
issn = {2235-2988},
mesh = {*Stomach Neoplasms/therapy/microbiology/pathology ; Humans ; *Gastrointestinal Microbiome ; Dysbiosis/complications/microbiology ; Tumor Microenvironment ; Probiotics/therapeutic use ; Fecal Microbiota Transplantation ; },
abstract = {Gastric cancer, a prevalent malignancy globally, is influenced by various factors. The imbalance in the gut microbiome and the existence of particular intratumoural microbiota could have a strong connection with the onset and progression of gastric cancer. High-throughput sequencing technology and bioinformatics analysis have revealed a close correlation between abnormal abundance of specific microbial communities and the risk of gastric cancer. These microbial communities contribute to gastric cancer progression through mechanisms including increasing cellular genomic damage, inhibiting DNA repair, activating abnormal signaling pathways, exacerbating tumor hypoxia, and shaping a tumor immune-suppressive microenvironment. This significantly impacts the efficacy of gastric cancer treatments, including chemotherapy and immunotherapy. Probiotic, prebiotic, antibiotic, carrier-based, dietary interventions, fecal microbiota transplantation, and traditional Chinese medicine show potential applications in gastric cancer treatment. However, the molecular mechanisms regarding dysbiosis of microbiota, including gut microbiota, and intra-tumoral microbiota during the progression of gastric cancer, as well as the therapeutic efficacy of microbiota-related applications, still require extensive exploration through experiments.},
}
@article {pmid40529156,
year = {2025},
author = {Fotouh, B and Kyser, AJ and Mahmoud, MY and Frieboes, HB},
title = {Dual probiotic and antibiotic therapy targeting bacterial vaginosis: an integrated experimental/computational modeling perspective.},
journal = {Biomedical engineering advances},
volume = {9},
number = {},
pages = {},
pmid = {40529156},
issn = {2667-0992},
abstract = {A novel strategy delivering both metronidazole and L. crispatus via 3D-printed scaffolds was recently shown to target pathogens in bacterial vaginosis (BV) while promoting beneficial microflora with sustained probiotic release, with the objective to facilitate user treatment adherence. This study developed an integrated experimental/computational platform to evaluate dual therapeutic strategy efficacy over a wide range of system dynamics, towards the goal of personalized therapy design. Experiments evaluated Gardnerella and L. crispatus interactions under controlled glucose concentrations in vitro, including bacterial growth, glucose consumption, lactic acid production, and pH. These data informed parameters of a novel computational model simulating the vagina, incorporating nutrient dynamics, bacterial interactions, and dual release of antibiotics and probiotics from 3D-printed scaffolds. Efficacy of varying concentrations of antibiotics and probiotics was assessed via sensitivity analyses. Experimental results demonstrate that L. crispatus outcompetes Gardnerella at lower glucose concentrations, while Gardnerella dominates at higher glucose levels. The computational model replicated these dynamics and projected that dual therapy could significantly suppress Gardnerella while promoting L. crispatus, even at lower drug dosages and probiotic CFU counts. Results were validated against data from 3D-printed dual release scaffolds. Simulated dual treatment enhanced lactic acid production and decreased vaginal pH, creating an unfavorable environment for pathogenic bacteria and shifting the microbiome composition towards the beneficial microflora. We conclude that an integrated experimental/computational modeling approach enables detailed evaluation of pathogenic and host bacteria interactions in the vaginal microbiome. This approach could advance personalized treatment for BV that eradicates pathogens while simultaneously restoring beneficial microflora.},
}
@article {pmid40528895,
year = {2025},
author = {Liu, J and Huang, S},
title = {Association between dietary index for gut microbiota and sleep duration in US adults: a cross-sectional study.},
journal = {Current research in microbial sciences},
volume = {9},
number = {},
pages = {100412},
pmid = {40528895},
issn = {2666-5174},
abstract = {BACKGROUND: The microbiota-gut-brain axis underlies the pathogenesis of sleep disorders. The dietary index for gut microbiota (DI-GM) is an innovative diet quality metric related to gut microbiota diversity, with higher scores indicating a healthier gut microbiome. This study aimed to investigate its association with sleep duration.<br><br>METHODS: This cross-sectional study analyzed the National Health and Nutrition Examination Survey (NHANES) data from 2005 to 2018, involving 25,439 participants aged &#x2265;20 years. The DI-GM score was calculated utilizing dietary recall data, encompassing both beneficial (BGMS) and unfavorable (UGMS) to gut microbiota score. Sleep duration was assessed via the question: "How much sleep do you usually get at night on weekdays or workdays?" and categorized as short (<7 h per night), optimal (7-8 h per night), and long (>8 h per night). Multivariable weighted linear and logistic regression models were performed to determine the association between DI-GM and sleep duration. Secondary analyses included restricted cubic splines (RCS) and subgroup analyses.<br><br>RESULTS: In the fully adjusted model, a higher DI-GM score was associated with longer sleep duration (&#x3b2; =0.03, 95 % confidence interval [CI]: 0.01-0.04, P < 0.001), as was a higher BGMS (&#x3b2; =0.04, 95 % CI: 0.02-0.06, P < 0.001). Using optimal sleep as the reference category, both higher DI-GM score and BGMS were significantly associated with lower odds of short sleep (DI-GM: odds ratio [OR] =0.96, 95 % CI: 0.93-0.99, P = 0.010; BGMS: OR =0.93, 95 % CI: 0.89-0.96, P < 0.001). RCS revealed nonlinear associations between DI-GM and both outcomes, while BGMS exhibited linear patterns. Subgroup analyses confirmed consistent associations across demographic, lifestyle, and health strata, with significant effect modification by race/ethnicity (P = 0.015 for sleep duration; 0.016 for short sleep) and physical activity (P = 0.033 and 0.007, respectively).<br><br>CONCLUSIONS: Higher DI-GM scores were associated with longer sleep duration, underscoring the potential of gut microbiota-targeted diets for sleep health.},
}
@article {pmid40528728,
year = {2025},
author = {Bui, TA and O'Croinin, BR and Dennett, L and Winship, IR and Greenshaw, AJ},
title = {Pharmaco-psychiatry and gut microbiome: a systematic review of effects of psychotropic drugs for bipolar disorder.},
journal = {Microbiology (Reading, England)},
volume = {171},
number = {6},
pages = {},
doi = {10.1099/mic.0.001568},
pmid = {40528728},
issn = {1465-2080},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Bipolar Disorder/drug therapy/microbiology ; *Psychotropic Drugs/therapeutic use/pharmacology ; Bacteria/classification/drug effects/genetics ; Adult ; },
abstract = {Despite being one of the most common and debilitating mood disorders, bipolar disorder is often misdiagnosed and undertreated. Its pathogenesis is complex, with significant patient variability and inconsistent treatment effectiveness. The brain-gut-microbiota axis plays a critical role in bipolar disorder by modulating neurotransmitter secretion, gut peptides and systemic inflammation. However, the mechanisms by which psychotropic treatments influence gut microbiota composition and their implications for clinical outcomes remain poorly understood. This systematic review evaluated the impact of psychotropic drugs on gut microbiota and their potential role in bipolar disorder treatment outcomes. A comprehensive search across Ovid MEDLINE, Embase, APA PsycINFO, Scopus and PubMed yielded 314 articles, of which 12 met the inclusion criteria (last search: 13 August 2024). The studies included were those on adults with bipolar disorder type I or II receiving psychopharmacological treatments; those with group comparisons (e.g. healthy controls vs. medicated vs. non-medicated) investigating gut microbiome changes; and no restrictions applied to psychotic features, comorbid anxiety or prior treatment responses. Exclusions involved individual case reports, incomplete conference submissions or early terminated studies lacking efficacy analysis. Cochrane ROBINS-I V2 tool was used to measure the risk of bias, and the GRADE approach was utilized to rate the certainty of evidence in included studies. Two authors independently extracted data into Excel spreadsheets, categorizing demographic and clinical characteristics, describing microbiome analytic methods and summarizing findings on gut microbiome changes post-treatment. Given the high variability in methods and outcome measures across studies, all details were reported without data conversion. Data synthesis reveals that psychotropic treatments, including quetiapine and lithium, influence gut microbiota by increasing the abundance of beneficial bacteria supporting gut health and pathogenic bacteria linked to metabolic dysfunction. Notably, female patients exhibited more significant changes in microbial diversity following psychotropic treatment. Additionally, patients treated with psychotropics showed an increased prevalence of gut bacteria associated with multidrug antibiotic resistance. In bipolar patients treated with quetiapine, responders - those experiencing improved depressive symptom scores - displayed distinct gut microbiome profiles more closely resembling those of healthy individuals compared with non-responders. Responders also exhibited neural connectivity patterns similar to healthy subjects. These findings underscore the complex dual impact of psychotropic medications on gut microbiota, with potential consequences for both gut and mental health. While the enrichment of beneficial bacteria may support gut health, the rise in antibiotic-resistant and metabolically disruptive bacteria is concerning. Study limitations include methodological heterogeneity, inclusions of other psychiatric disorders, a high risk of bias in some studies due to incomplete statistical analyses or insufficient control for confounding factors and potential duplication of study populations arising from overlapping authorship. Further research is essential to elucidate the functional consequences of these microbial shifts and their influence on treatment efficacy. Nevertheless, this review highlights the potential of utilizing gut microbiota profiles to inform personalized treatment strategies, optimize therapeutic outcomes and minimize side effects in bipolar disorder. This study was registered with Open Science Framework (https://doi.org/10.17605/OSF.IO/3GUZR).},
}
@article {pmid40528662,
year = {2025},
author = {Soto-Moreno, A and Haselgruber-de Francisco, S and León-Pérez, J and García-Moronta, C and Cuenca Barrales, C and Arias-Santiago, S and Molina Leyva, A},
title = {The Microbiome in Hidradenitis Suppurativa Tunnels: A Systematic Review.},
journal = {International journal of dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1111/ijd.17892},
pmid = {40528662},
issn = {1365-4632},
abstract = {Hidradenitis suppurativa (HS) is a chronic inflammatory disease that affects the pilosebaceous units, particularly in large skin folds. The pathophysiology of HS is multifactorial, with evidence suggesting that the microbiome plays a crucial role in perpetuating inflammation. The persistent nature of HS tunnels, coupled with potential dysbiosis in these lesions, may help explain the recurrent episodes of HS, even with systemic treatment. To explore this further, a literature search was conducted on June 20, 2024. A total of eight studies, involving 418 patients, 632 HS lesions, 360 HS tunnels, and 300 controls, were included. The findings from these studies suggested that HS tunnels are characterized by a polymicrobial microbiome, predominantly dominated by anaerobic bacteria such as Porphyromonas, Parvimonas, Fusobacterium, and Prevotella. In contrast, HS tunnels exhibit a notable reduction in saprophytic species like Cutibacterium acnes and Staphylococcus epidermidis, which are commonly found in healthy skin. Disease stage, as classified by the Hurley system, is the most significant factor influencing the microbiome composition of HS tunnels, with advanced lesions showing a greater presence of dysbiotic and pathogenic flora. Interestingly, no significant differences in bacterial colonization were observed based on variables such as sex, age, smoking status, body mass index (BMI), or anatomical location. Larger biofilms with active bacteria were found in tunnels and anaerobic regions of hair follicles. Overall, these results highlight the distinct polymicrobial, predominantly anaerobic bacterial flora of HS tunnels and the significant reduction in commensal bacteria typically found in healthy skin. This specific microbiome may help explain both the pathogenic characteristics and therapeutic challenges associated with HS tunnels.},
}
@article {pmid40528272,
year = {2025},
author = {Guitart-Matas, J and Vera-Ponce de León, A and Pope, PB and Hvidsten, TR and Fraile, L and Ballester, M and Ramayo-Caldas, Y and Migura-Garcia, L},
title = {Multi-omics surveillance of antimicrobial resistance in the pig gut microbiome.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {65},
pmid = {40528272},
issn = {2524-4671},
support = {10385//European Molecular Biology Organization/ ; RYC2019-027244-I//Ministerio de Ciencia e Innovaci&#xf3;n/ ; RTI2018-095586-B-C22//Ministerio de Econom&#xed;a y Competitividad/ ; },
abstract = {BACKGROUND: High-throughput sequencing technologies play an increasingly active role in the surveillance of major global health challenges, such as the emergence of antimicrobial resistance. The post-weaning period is of critical importance for the swine industry and antimicrobials are still required when infection occurs during this period. Here, two sequencing approaches, shotgun metagenomics and metatranscriptomics, have been applied to decipher the effect of different treatments used in post-weaning diarrhea on the transcriptome and resistome of pig gut microbiome. With this objective, a metagenome-assembled genome (MAG) catalogue was generated to use as a reference database for transcript mapping obtained from a total of 140 pig fecal samples in a cross-sectional and longitudinal design to study differential gene expression. The different treatments included antimicrobials trimethoprim/sulfamethoxazole, colistin, gentamicin, and amoxicillin, and an oral commercial vaccine, a control with water acidification, and an untreated control. For metatranscriptomics, fecal samples from pigs were selected before weaning, three days and four weeks post-treatment.<br><br>RESULTS: The final non-redundant MAGs collection comprised a total of 1396 genomes obtained from single assemblies and co-assemblies per treatment group and sampling time from the metagenomics data. Analysis of antimicrobial resistance genes (ARGs) at this assembly level considerably reduced the total number of ARGs identified in comparison to those found at the reads level. Besides, from the metatranscriptomics data, half of those ARGs were detected transcriptionally active in all treatment groups. Differential gene expression between sampling times after treatment found major number of differential expressed genes (DEGs) against the group treated continuously with amoxicillin, with DEGs being correlated with antimicrobial resistance. Moreover, at three days post-treatment, a high number of significantly downregulated genes was detected in the group treated with gentamicin. At this sampling time, this group showed an altered expression of ribosomal-related genes, demonstrating the rapid effect of gentamicin to inhibit bacterial protein synthesis.<br><br>CONCLUSIONS: Different antimicrobial treatments can impact differently the transcriptome and resistome of microbial communities, highlighting the relevance of novel sequencing approaches to monitor the resistome and contribute to a more efficient antimicrobial stewardship.},
}
@article {pmid40528248,
year = {2025},
author = {Mohamed, AH and Shafie, A and Al-Samawi, RI and Jamali, MC and Ashour, AA and Felemban, MF and Alqarni, A and Ahmad, I and Mansuri, N and Ahmad, F and Yousif, AAM},
title = {The role of probiotics in promoting systemic immune tolerance in systemic lupus erythematosus.},
journal = {Gut pathogens},
volume = {17},
number = {1},
pages = {45},
pmid = {40528248},
issn = {1757-4749},
support = {RGP-2/202/45//Deanship of Research and Graduate Studies at King Khalid University/ ; },
abstract = {Systemic lupus erythematosus (SLE) is an autoimmune disorder branded via over-activation of the immune system, resulting in atypical roles of natural and adaptive immune cells and the making of numerous autoantibodies against nuclear components. The causes and pathogenesis of this disease are not completely realized. The gut microbiota plays a significant character in human health and disorder, particularly in autoimmune diseases.Gut microbiome dysbiosis can affect the host immune system as suggested by several recent studies, balance and activity of the gut microbiome, which are influenced by daily diet, might be associated with disease activity in SLE. There are rising signs to support the immunomodulatory abilities of certain probiotics. Numerous investigational and clinical surveys have demonstrated the useful effects of certain probiotic bacteria, mainly strains of Lactobacillus and Bifidobacterium, in patients with SLE. Various species of bacteria were found to be positively or negatively associated with SLE gut microbiomes. A better comprehension of the Studying the gut microbiota will provide a good opportunity to identify microbes involved in tolerance in systemic lupus patients. The purpose of this study is to review the existing literature on probiotics that have the ability to restore tolerance and modulate the levels of inflammatory or anti-inflammatory cytokines that play a role in SLE.},
}
@article {pmid40528245,
year = {2025},
author = {Yang, Q and Zhang, H and Qiu, JW and Huang, D and Zhou, X and Zheng, X},
title = {Symbiotic Symbiodiniaceae mediate coral-associated bacterial communities along a natural thermal gradient.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {72},
pmid = {40528245},
issn = {2524-6372},
support = {2022YFC3102003//National Key Research and Development Program of China/ ; 2020017//he Scientific Research Foundation of the Third Institute of Oceanography, Ministry of Natural Resources of China/ ; 2019017//the Scientific Research Foundation of the Third Institute of Oceanography, Ministry of Natural Resources of China/ ; 42376110//the National Natural Science Foundation of China/ ; 2023J06043//the Fujian Provincial Natural Science Funds for Distinguished Young Scholar/ ; },
abstract = {The coral-associated microbiome plays a vital role in the holobiont, enabling coral adaptation to diverse environments by modulating its composition and mediating interactions among its constituents. However, the responses of coral microbiomes, particularly the interactions between Symbiodiniaceae and bacteria, to environmental changes remain unclear. To fill this knowledge gap, we examined Pocillopora acuta, an environmentally sensitive coral species, collected from three sites along the southeastern coast of Hainan which exhibit moderate environmental differences. We measured the physiological characteristics of Symbiodiniaceae and conducted amplicon sequencing to analyze the structure of Symbiodiniaceae and bacterial communities. Our results revealed that P. acuta in southeastern Hainan maintains stable symbiosis with Symbiodiniaceae sub-clades such as C1, C42.1, C3, D1, D4, and D6, as evidenced by ΔF/Fm' values ranging from 0.45 for P. acuta dominated by Durusdinium (PaD) to 0.6 for counterparts dominated by Cladocopium (PaC). However, the composition of Symbiodiniaceae varied among the three sites, primarily due to differences in the abundance of dominant sub-clades. These variations may reflect adaptations to distinct environmental conditions, which in turn significantly influence the associated bacterial communities. Notably, our results suggest that Symbiodiniaceae may exert a greater regulatory role on the coral-associated bacterial community than environmental differences. Specific bacteria, such as Endozoicomonas and Synechococcus_CC9902, exhibit strong correlations with particular Symbiodiniaceae genera or sub-clades, indicating that the dominant Symbiodiniaceae shape bacterial community dynamics. Despite the observed variations, we identified modular co-occurrence patterns in bacterial networks, with PaC exhibiting a more complex and stable structure. Overall, these results highlight the critical role of various Symbiodiniaceae genera in influencing bacterial community dynamics, emphasizing their importance in maintaining coral health and resilience in the face of changing environmental conditions.},
}
@article {pmid40528214,
year = {2025},
author = {Zhang, Y and Luo, J and Chen, K and Li, N and Luo, C and Di, S and Qin, J and Zhang, F and Chen, H and Dai, M},
title = {Cross-cohort analysis identifies shared gut microbial signatures and validates microbial risk scores for colorectal cancer.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {676},
pmid = {40528214},
issn = {1479-5876},
support = {2022-I2M-1-0031//Institute of Chinese Materia Medica, China Academy of Chinese Medical Science/ ; 82173606//National Natural Science Foundation of China/ ; 82273726//National Natural Science Foundation of China/ ; 20230484397//Beijing Nova Program of Science and Technology/ ; },
mesh = {Humans ; *Colorectal Neoplasms/microbiology ; *Gastrointestinal Microbiome/genetics ; Cohort Studies ; Risk Factors ; Risk Assessment ; Reproducibility of Results ; Male ; Female ; Middle Aged ; Metagenomics ; Case-Control Studies ; },
abstract = {BACKGROUND: Microbiome-wide association studies showed links between colorectal cancer (CRC) and gut microbiota. However, the clinical application of gut microbiota in CRC prevention has been hindered by the diversity of study populations and technical variations. We aimed to determine CRC-related gut microbial signatures based on cross-regional, cross-population, and cross-cohort metagenomic datasets, and elucidate its application value in CRC risk assessment.<br><br>METHODS: We used the MMUPHin tool to perform a meta-analysis of our own cohort and seven publicly available metagenomics datasets to identify gut microbial species associated with CRC across different cohorts, comprising of 570 CRC cases and 557 controls. Based on differential species sets, we constructed the microbial risk score (MRS) using &#x3b1;-diversity of the sub-community (MRS&#x3b1;), weighted/unweighted summation methods and machine learning algorithms. Cohort-to-cohort training and validation were performed to demonstrate the transferability.<br><br>RESULTS: We found that MRS&#x3b1; of core species was better validated and more interpretable than those constructed with summation methods or machine learning algorithms. Six species, including Parvimonas micra, Clostridium symbiosum, Peptostreptococcus stomatis, Bacteroides fragilis, Gemella morbillorum, and Fusobacterium nucleatum, were included in MRS&#x3b1; constructed by half or more of the cohorts. The AUC of MRS&#x3b1;, calculated based on the sub-community of six species, varied between 0.619 and 0.824 across the eight cohorts.<br><br>CONCLUSION: We identified six CRC-related species across regions, populations, and cohorts. The constructed MRS&#x3b1; could contribute to the risk prediction of CRC in different populations.},
}
@article {pmid40528206,
year = {2025},
author = {Luo, M and Xin, K and Luo, T},
title = {A comment on "Association between oral microbiome diversity and chronic obstructive pulmonary disease in the US population".},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {667},
pmid = {40528206},
issn = {1479-5876},
}
@article {pmid40528192,
year = {2025},
author = {Li, Y and Yang, D and Zhao, H and Dou, L and Chen, Q and Cheng, Y and Hu, B and Tang, Y and Duan, Y and Guo, C and Sakandar, A and Li, D},
title = {The pasteurized Weissella cibaria alleviates sepsis-induced acute lung injury by modulation of intestinal mucus barrier and gut microbiota.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {661},
pmid = {40528192},
issn = {1479-5876},
support = {82302431//National Natural Science Foundation of China/ ; 242102311155//Henan Provincial Science and Technology Research Project/ ; },
mesh = {Animals ; *Sepsis/complications/microbiology ; *Gastrointestinal Microbiome ; *Weissella/physiology ; *Intestinal Mucosa/microbiology/pathology ; *Acute Lung Injury/microbiology/etiology/pathology/therapy ; Cytokines/metabolism/blood ; Mice ; Male ; Lung/pathology ; Dysbiosis/complications ; Mice, Inbred C57BL ; Inflammation/pathology ; Lipopolysaccharides ; },
abstract = {BACKGROUND: Dysbiosis of intestinal microecology caused by sepsis plays a crucial role in the onset and progression of sepsis-induced acute lung injury (SALI). As a postbiotic type, inactivated probiotic bacteria can regulate the gut microbiome. Pasteurized bacteria are considered safer than live bacteria in immune dysregulation disorders. Weissella cibaria (W. cibaria) is considered a candidate probiotic with certain beneficial functions. However, whether inactivated W. cibaria can alleviate SALI and the underlying mechanisms remain unclear. This study aimed to investigate whether inactivated W. cibaria can regulate intestinal mucosal barrier function and gut microbiota, thereby improving SALI.<br><br>METHODS: Following gavage of pasteurized W. cibaria in septic mice, lung tissue damage and inflammation levels were assessed. Circulating LPS levels and inflammatory cytokine concentrations in the blood were measured. Additionally, colonic tissue inflammation, intestinal mucosal barrier integrity, and alterations in the gut microbiota were evaluated.<br><br>RESULT: Pasteurized W. cibaria increases survival rates in SALI mice and improves pathological damage and cell apoptosis in lung tissue. Pasteurized W. cibaria also reduces the lung inflammatory response in septic mice by lowering pro-inflammatory cytokine levels and increasing anti-inflammatory cytokine levels. Pasteurized W. cibaria appears to exert its effects by improving the intestinal mucosal barrier and reversing gut microbiota dysbiosis caused by sepsis. Specifically, pasteurized W. cibaria alleviates intestinal barrier damage and inflammation in SALI mice, enhancing the integrity of the intestinal mucosal barrier. Additionally, pasteurized W. cibaria increases the abundance of anti-inflammatory bacteria such as Muribaculaceae. Pasteurized W. cibaria also decreases the levels of LPS-producing bacteria, including Escherichia-Shigella and Helicobacter, leading to significant attenuation in metabolic endotoxemia, which in turn alleviates excessive lung inflammation in septic mice.<br><br>CONCLUSIONS: Pasteurized W. cibaria has the potential to act as a postbiotic agent, improving sepsis-induced gut microbiota dysbiosis and acute lung injury, and providing a novel strategy for treating SALI.},
}
@article {pmid40527992,
year = {2025},
author = {Kozycki, CT and Sharma, R and Bharti, K and Lee, RWJ},
title = {Is there a link between gut microbes and ageing?.},
journal = {Nature},
volume = {642},
number = {8068},
pages = {572},
doi = {10.1038/d41586-025-01905-3},
pmid = {40527992},
issn = {1476-4687},
}
@article {pmid40527932,
year = {2025},
author = {Liu, YR and Wen, S and Singh, BK and Zhang, W and Liu, Z and Hao, X and Hao, YY and Delgado-Baquerizo, M and Tan, W and Huang, Q and Rillig, MC and Zhu, YG},
title = {Vulnerability of soil food webs to chemical pollution and climate change.},
journal = {Nature ecology &amp; evolution},
volume = {},
number = {},
pages = {},
pmid = {40527932},
issn = {2397-334X},
support = {42425701//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Soil food webs are critical for maintaining ecosystem functions but are challenged by various stressors including climate change, habitat destruction and pollution. Although complex multitrophic networks can, in theory, buffer environmental stress, the effects of anthropogenic chemicals on soil food webs under climate change remain poorly understood. Here we propose that the effects of chemical pollution on soil communities have been largely underestimated, particularly for climate change-affected ecosystems. We explore the interactive effects of environmental stressors on soil food webs and the importance of integrating chemical pollution impacts into assessing soil food web stability. We also discuss a conceptual framework involving microbiome manipulation, community compensatory dynamics and interaction modulation to mitigate the combined effects of chemical pollution and climate change on soil food webs.},
}
@article {pmid40527658,
year = {2025},
author = {Li Lin, CY and Huang, YJ and Lin, HC and Tsai, ML and Ku, JT and Lee, FC and Chang, H},
title = {Increased incidence of attention-deficit/hyperactivity disorder is associated with early and prolonged exposure to antibiotics: A population-based retrospective cohort study.},
journal = {Pediatrics and neonatology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.pedneo.2025.03.008},
pmid = {40527658},
issn = {2212-1692},
abstract = {BACKGROUND: Medication exposure has been shown to alter the composition of healthy gut microbiome, thereby disrupting the microbiota-gut-brain axis. Gut dysbiosis has been linked to increasing cases of neurodevelopmental disorders. To identify any correlation between antibiotics use and one of the most prevalent childhood disorders - ADHD - we conducted a nationwide study spanning over a decade in Taiwan.<br><br>METHODS: Two million individuals were randomly sampled between the years 2005 and 2018 ranging from the time of birth to the age of 8. They were categorized into three groups based on age of initial exposure to antibiotics and further stratified by exposure duration. The hazard ratios and 95 % confidence interval for ADHD were compared using a Cox proportional hazard model. Cumulative incidence curves were generated using the Kaplan-Meier method and analyzed using a log-rank test.<br><br>RESULTS: ADHD risk was highest in individuals exposed to antibiotics before the age of 2 years, regardless of the duration of exposure. In children aged >2 years, increased ADHD risk was observed alongside prolonged antibiotic exposure.<br><br>CONCLUSIONS: In clinical practice, we may consider the potential adverse impact of prescribing antibiotics in young children, particularly in children aged <2 years. If antibiotic use is necessary, duration of administration should be shortened whenever practicable.},
}
@article {pmid40527519,
year = {2025},
author = {Lajoie, G and Dariel, L},
title = {How Useful Are Plant Traits in Explaining Variation in Phyllosphere Microbial Abundance and Composition Across Hosts?.},
journal = {Environmental microbiology},
volume = {27},
number = {6},
pages = {e70123},
doi = {10.1111/1462-2920.70123},
pmid = {40527519},
issn = {1462-2920},
mesh = {*Plant Leaves/microbiology ; *Microbiota ; *Plants/microbiology ; *Bacteria/classification/isolation &amp; purification/genetics ; *Fungi/classification/isolation &amp; purification/genetics ; },
abstract = {Plant taxonomy has emerged as a key driver of plant-microbe associations, but the mechanisms underlying these associations remain poorly understood. By defining selective environmental gradients for microbial taxa, plant traits can provide more proximate explanations of microbial taxonomic turnover across plants than plant taxonomy alone. Whether key plant traits may generally predict plant-microbe associations, however, remains unknown. Here, we conducted a systematic review of the phyllosphere literature to evaluate whether specific plant traits consistently explained variation in the abundance and composition of leaf microbes within and among plant species. Drawing on results from over 100 studies, we showed that plant traits linked to development, primary metabolism and defence consistently shaped the composition of leaf bacterial and fungal communities, highlighting the relevance of these traits in predicting plant-microbe associations in the phyllosphere. Since most plant traits tested did not influence leaf microbial composition more frequently than expected by chance, our study underscores the importance of: (1) rethinking the scale and selection of plant traits used to investigate microbiome assembly; (2) refining the taxonomic resolution at which microbial communities are analysed and (3) considering alternative explanations such as stochastic processes or historical factors for improving our understanding of plant-microbe associations.},
}
@article {pmid40527467,
year = {2025},
author = {Gonzalez Moreno, C and Funiciello-Mendez, S and Torres Luque, A and Fayek, P and Chapwanya, A and Otero, MC},
title = {Progesterone-controlled internal drug release-based estrous synchronization induces vaginal dysbiosis and enrichment of potential pathogens in Braford heifers.},
journal = {American journal of veterinary research},
volume = {},
number = {},
pages = {1-10},
doi = {10.2460/ajvr.25.03.0093},
pmid = {40527467},
issn = {1943-5681},
abstract = {OBJECTIVE: To evaluate the effects of an estrus synchronization program on the resident microbial population of the vagina in Braford heifers.<br><br>METHODS: Nulliparous Braford heifers were enrolled in a 9-day progesterone-controlled internal drug release-based estrous synchronization protocol. Vaginal swabs were collected on day (D) 0 and D11 of the synchronization protocol and again on D60 to profile changes in vaginal bacterial communities though 16S ribosomal DNA gene sequencing.<br><br>RESULTS: Analysis of samples from 10 heifers revealed that the most abundant phyla were the Proteobacteria, Firmicutes, Bacteroidetes, Tenericutes, Fusobacteria, and Actinobacteria. Principal coordinate analysis showed significant differentiation among the vaginal profiles of the microbial communities at D11 compared to D0 and D60. The bacterial clustering may be due to estrous synchronization. Significant differences were observed at the genus level. The relative abundances of known endometrial pathogens Fusobacterium, Helcococcus, Ureaplasma, and Leptotrichiaceae significantly increased from D0 to D11.<br><br>CONCLUSIONS: This study describes, for the first time, transient changes in the diversity of the vaginal microbiota of Braford heifers in response to estrus manipulations. The presence (or absence) of certain recognized pathogens, such as Fusobacterium, Helcococcus, and Ureaplasma, may negatively affect reproductive health, justifying further investigation.<br><br>CLINICAL RELEVANCE: These results may help in advances of the diagnosis and treatment of infertility.},
}
@article {pmid40527462,
year = {2025},
author = {Jones, KR and Becker, MH and Walke, JB and Belden, LK},
title = {Natural recolonization of the amphibian skin bacterial community following disruption by antibiotics.},
journal = {Proceedings. Biological sciences},
volume = {292},
number = {2049},
pages = {20250855},
doi = {10.1098/rspb.2025.0855},
pmid = {40527462},
issn = {1471-2954},
support = {//Virginia Tech Department of Biological Sciences/ ; //Fralin Life Sciences Institute/ ; //NSF/ ; },
mesh = {Animals ; *Skin/microbiology ; *Anti-Bacterial Agents/pharmacology/adverse effects ; RNA, Ribosomal, 16S/genetics/analysis ; *Microbiota/drug effects ; *Bacteria/drug effects/genetics/classification ; },
abstract = {Despite the ubiquity of microbial communities, we lack a thorough understanding of how host-associated communities respond to disturbances. We explored the response of the skin bacterial communities of Notophthalmus viridescens (eastern, red-spotted newts) to disturbance by exposing newts to antibiotics, returning them to pond enclosures and assessing bacterial community composition through periodic skin swabs over 28 days. Through 16S rRNA gene amplicon sequencing and qPCR, we observed immediate shifts in bacterial abundance and community composition following antibiotic exposure. Bacterial communities recovered compositionally by the experiment's conclusion; however, bacterial abundance did not recover to pre-exposure levels. Additionally, community composition on all newts shifted over the course of the experiment. Our results provide evidence for lasting consequences of disturbance on bacterial communities, highlight the potential disconnect between recovery in terms of community structure and bacterial abundance and emphasize the importance of incorporating natural community shifts into evaluations of community recovery.},
}
@article {pmid40527418,
year = {2025},
author = {Celorrio, M and Shumilov, K and Ni, A and Ayerra, L and Self, WK and de Francisca, NLV and Rodgers, R and Schriefer, LA and Garcia, B and Aymerich, MS and Layden, BT and Egervari, G and Baldridge, MT and Friess, SH},
title = {Short-chain fatty acids are a key mediator of gut microbial regulation of T cell trafficking and differentiation after traumatic brain injury.},
journal = {Experimental neurology},
volume = {},
number = {},
pages = {115349},
doi = {10.1016/j.expneurol.2025.115349},
pmid = {40527418},
issn = {1090-2430},
abstract = {The gut microbiota has emerged as a pivotal regulator of host inflammatory processes after traumatic brain injury (TBI). However, the mechanisms by which the gut microbiota communicates to the brain in TBI are still under investigation. We previously reported that gut microbiota depletion (GMD) using antibiotics after TBI resulted in increased microglial activation, reduced neurogenesis, and reduced T cell infiltration. In the present study, we have demonstrated that intestinal T cells contribute to the pool of cells infiltrating the brain after TBI. Depletion or genetic deletion of T cells before injury reversed GMD induced reductions in post-TBI neurogenesis. Short-chain fatty acid supplementation increased T regulatory and T helper1 cell infiltration to the brain along with restoring neurogenesis and microglia activation after TBI with GMD. These data suggest that T cell subsets are essential cellular mediators by which the gut microbiota modulates TBI pathogenesis, a finding with important therapeutic implications.},
}
@article {pmid40527395,
year = {2025},
author = {Su, J and Hansen, BE and Ma, Z and Peppelenbosch, MP},
title = {Effects of one month of intermittent fasting on the blood microbiome in healthy volunteers (OMIF): A randomized controlled crossover study protocol.},
journal = {Contemporary clinical trials},
volume = {},
number = {},
pages = {107986},
doi = {10.1016/j.cct.2025.107986},
pmid = {40527395},
issn = {1559-2030},
abstract = {BACKGROUND: It is hypothesized that the presence of microorganisms in the gut is reflected in circulating blood through small DNA fragments resulting from the degradation of these organisms. Cross-sectional studies have not yet provided a definitive answer regarding the validity of this hypothesis, and the potential presence of a so-called common blood-microbiome remains highly controversial. Both bioinformatical pipelines (which may produce false-positive results) and environmental contamination may obscure the less than 5 % microbial DNA that is postulated to be present within the total blood DNA.<br><br>METHOD/DESIGN: This study aims to validate the existence of the blood microbiome using one month of intermittent fasting (OMIF). Through a prospective, randomized, controlled cross-over trial, we will evaluate the effect of OMIF on the composition and function of the blood microbiome in healthy volunteers, with secondary outcomes on clarifying the relationship between the gut and blood microbiome. Healthy volunteers aged 18-65 will be enrolled. All volunteers will undergo OMIF, a washout period and an ad libitum diet for another month, with the order of the interventions assigned randomly. We will assess the dynamics in blood microbiome in response to OMIF versus those seen during an ad libitum diet, using shotgun sequencing. Physiological changes will be monitored A dietary recall interview will be conducted during the trial to evaluate energy intake, and movement data collected from Health App will be used to assess changes in physical activity.<br><br>CONCLUSION: If successful, this trial provides a proof-of-concept study documenting the existence of a bona fide blood microbiome.<br><br>CLINICAL TRIAL REGISTRATION: NCT06678516.},
}
@article {pmid40527211,
year = {2025},
author = {Ghosh, S and Nath, S and Chakraborty, A and Bhowmick, S and Majumdar, KK and Mukherjee, S and Pramanik, S},
title = {Long-term arsenic exposure perturbs gut microbial diversity, composition and predicts metabolic dysregulation.},
journal = {Journal of hazardous materials},
volume = {495},
number = {},
pages = {138836},
doi = {10.1016/j.jhazmat.2025.138836},
pmid = {40527211},
issn = {1873-3336},
abstract = {The present study documents significant alterations in human gut microbial composition in arsenic exposed populations of West Bengal, India through amplicon sequencing of human stool metagenomic DNA. A notable reduction in α-diversity underscored a reduced species richness and an altered predominance. β- diversity analysis revealed prominent inter-individual differences. Among the 26 phyla detected, significant perturbation was noted in Bacteroidetes, Actinobacteria, Proteobacteria, and Firmicutes. Species analysis identified significant increase in Bifidobacterium adolescentis, B.longum, Blautia luti, B.wexlerae, Clostridium saudiense, Romboutsia timonensis and Streptococcus salivarius whereas members of Faecalibacterium prausnitzii, Megasphaera elsdenii, Prevotella copri and P. stercorea were found to be highly diminished due to As stress. PICRUSt analysis predicted significant upregulation (pT-test< 0.05) in gene families associated with carbohydrate, amino acid, nucleotide and lipid metabolism along with fermentation and secondary metabolite/ vitamin synthesis pathways in exposed group confirmed through Linear Discriminant Analysis. B.longum, B.luti and S.salivarius were found to be associated with obesity and ulcerative colitis. Network interactions were also characterized with major disruptions in keystone species interaction. The major findings of this study shall drive future studies like community-based metagenomics, metabolomics and in-vitro microbial verifications for designing of microbial therapeutics targeting gut health to combat the harmful impact of As exposure.},
}
@article {pmid40527040,
year = {2025},
author = {Azizsoltani, A and Niknam, B and Taghizadeh-Teymorloei, M and Ghoodjani, E and Dianat-Moghadam, H and Alizadeh, E},
title = {Therapeutic implications of obeticholic acid, a farnesoid X receptor agonist, in the treatment of liver fibrosis.},
journal = {Biomedicine &amp; pharmacotherapy = Biomedecine &amp; pharmacotherapie},
volume = {189},
number = {},
pages = {118249},
doi = {10.1016/j.biopha.2025.118249},
pmid = {40527040},
issn = {1950-6007},
abstract = {Liver fibrosis, a serious consequence of chronic liver disease, is characterized by excessive extracellular matrix (ECM) accumulation and impaired liver function. Obeticholic acid (OCA) is an agonist of the farnesoid X receptors (FXRs) that modulates multiple pathways, including bile acid and lipid metabolism, intestinal microbiome balance, and inflammatory responses. Recently, OCA has been investigated as a treatment for liver fibrosis. This review emphasizes the therapeutic potential of OCA and explores the complex cellular and molecular mechanisms underlying liver fibrosis. Furthermore, the review summarizes preclinical and clinical data on OCA, highlighting significant milestones in its development for primary biliary cholangitis and metabolic dysfunction-associated steatohepatitis. While OCA shows promise in improving liver fibrosis, its clinical use is limited by safety concerns, regulatory challenges, and adverse events, including dose-dependent pruritus, elevated LDL cholesterol, gallstones, and potential hepatotoxicity. Consequently, combination therapy strategies are being evaluated to increase therapeutic outcomes and minimize side effects. This reflects the ongoing need for safer and more effective FXR-targeted treatments for liver fibrosis. Additionally, this review discusses the prospects of using OCA clinically for various liver diseases. The findings underscore the need for further research to optimize OCA therapy and address the complexities of managing liver fibrosis.},
}
@article {pmid40526755,
year = {2025},
author = {Zheng, Q and Zhong, Y and Lian, H and Zhuang, J and Wang, L and Chen, J and Wang, H and Wang, H and Ye, X and Huang, Z and Yang, K},
title = {Gut Microbial Signatures Associated With Clinical Remission in Inflammatory Bowel Disease Treated With Biologics: A Comprehensive Multi-Cohort Analysis.},
journal = {United European gastroenterology journal},
volume = {},
number = {},
pages = {},
doi = {10.1002/ueg2.70064},
pmid = {40526755},
issn = {2050-6414},
support = {No. 82300619//National Natural Science Foundation of China/ ; 2023A04J2245//Science and Technology Project in Guangzhou/ ; No. 20231800936102//Dongguan Science and Technology of Social Development Program/ ; No. 2022E02125//Science and Technology Aid Project of Xinjiang Uygur Autonomous Region/ ; },
abstract = {BACKGROUND AND AIMS: The relationship between gut microbiota and biological treatment response in inflammatory bowel disease (IBD) remains incompletely understood. We sought to characterize microbial signatures associated with clinical remission and develop a prediction model for clinical remission.<br><br>METHODS: We analyzed 16&#xa0;S rRNA gene sequencing data from two independent public cohorts (n&#xa0;=&#xa0;231) treated with biologics (infliximab: n&#xa0;=&#xa0;23; adalimumab: n&#xa0;=&#xa0;22; ustekinumab: n&#xa0;=&#xa0;186). Microbial diversity and taxonomic compositions were compared between the remission and non-remission groups. Random Forest algorithm was employed to construct a prediction model using differential genera and clinical features, with performance evaluated through cross-validation. The model was further validated in a local cohort (n&#xa0;=&#xa0;29).<br><br>RESULTS: Significant differences in alpha and beta diversity were observed between the remission and non-remission groups (p&#xa0;<&#xa0;0.05). MaAsLin2 analysis identified 25 differentially abundant genera (p&#xa0;<&#xa0;0.05). Among these, we selected the top 10 genera with highest importance scores (Parabacteroides_B_862066, Agathobaculum, Ruminococcus_E, Sutterella, Clostridium_R_135822, Hominilimicola, Onthenecus, Butyricimonas, Bariatricus, Hominenteromicrobium) to build the Random Forest model, notably all enriched in remission patients. The model demonstrated robust predictive performance for clinical remission (AUC: 0.895), which was further validated in the local cohort (AUC: 0.750).<br><br>CONCLUSION: There is a relationship between gut microbial signatures and biological treatment outcomes in IBD patients. A predictive model based on gut microbiota composition may help stratify patients for treatment response. Further investigation of microbiome modulation strategies may enhance therapeutic efficacy.},
}
@article {pmid40526720,
year = {2025},
author = {Burtnyak, L and Yuan, Y and Stojek, E and Pan, X and Gunaratne, L and Silveira d'Almeida, G and Fergus, C and Martinelli, M and J Reed, C and Fernandez, J and Patel, BI and Marquez, I and Ehrenhofer-Murray, AE and Swairjo, MA and Alfonzo, JD and Green, BD and Kelly, VP and de Crécy-Lagard, V},
title = {The oncogene SLC35F2 is a high-specificity transporter for the micronutrients queuine and queuosine.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {25},
pages = {e2425364122},
doi = {10.1073/pnas.2425364122},
pmid = {40526720},
issn = {1091-6490},
support = {GM132254//HHS | NIH (NIH)/ ; GM146075//HHS | NIH (NIH)/ ; HRB-USIRL-2019-2//Science Foundation Ireland (SFI)/ ; MC PC 18038//UKRI | Medical Research Council (MRC)/ ; STL/5460/18//Health and Social Care in Northern Ireland (HSCNI)/ ; EH237/ 19-1//Deutsche Forschungsgemeinschaft (DFG)/ ; EPSPG/2022/390//Irish Research Council (IrishResearch)/ ; },
mesh = {Humans ; *Nucleoside Q/metabolism ; HeLa Cells ; Schizosaccharomyces/metabolism/genetics ; Trypanosoma brucei brucei/metabolism/genetics ; Biological Transport ; *Membrane Transport Proteins/metabolism/genetics ; *Schizosaccharomyces pombe Proteins/metabolism/genetics ; Guanine/analogs &amp; derivatives ; },
abstract = {The nucleobase queuine (q) and its nucleoside queuosine (Q) are micronutrients derived from bacteria that are acquired from the gut microbiome and/or diet in humans. Following cellular uptake, Q is incorporated at the wobble base (position 34) of tRNAs that decode histidine, tyrosine, aspartate, and asparagine codons, which is important for efficient translation. Early studies suggested that cytosolic uptake of queuine is mediated by a selective transporter that is regulated by mitogenic signals, but the identity of this transporter has remained elusive. Here, through a cross-species bioinformatic search and genetic validation, we have identified the solute carrier family member SLC35F2 as a unique transporter for both queuine and queuosine in Schizosaccharomyces pombe and Trypanosoma brucei. Furthermore, gene disruption in human HeLa cells revealed that SLC35F2 is the sole transporter for queuosine (Km 174 nM) and a high-affinity transporter for the queuine nucleobase (Km 67 nM), with the additional presence of second low-affinity queuine transporter (Km 259 nM). Ectopic expression of labeled SLC35F2 reveals localization to the cell membrane and Golgi apparatus via immunofluorescence. Competition uptake studies show that SLC35F2 is not a general transporter for other canonical ribonucleobases or ribonucleosides but selectively imports q and Q. The identification of SLC35F2, an oncogene, as the transporter of both q and Q advances our understanding of how intracellular levels of queuine and queuosine are regulated and how their deficiency contributes to a variety of pathophysiological conditions, including neurological disorders and cancer.},
}
@article {pmid40526718,
year = {2025},
author = {Kumar, R and Sykes, DJ and Band, VI and Schaller, ML and Patel, R and Vitvitsky, V and Sajjakulnukit, P and Singhal, R and Wong, HKA and Hourigan, SK and Ichinose, F and Lyssiotis, CA and Shah, YM and Banerjee, R},
title = {Gut sulfide metabolism modulates behavior and brain bioenergetics.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {25},
pages = {e2503677122},
doi = {10.1073/pnas.2503677122},
pmid = {40526718},
issn = {1091-6490},
support = {R35GM130183//HHS | NIH (NIH)/ ; R01CA248160/GF/NIH HHS/United States ; R01CA148828 R01CA245546//HHS | NIH (NIH)/ ; },
mesh = {Animals ; *Energy Metabolism ; Mice ; *Brain/metabolism ; *Hydrogen Sulfide/metabolism ; *Quinone Reductases/metabolism/genetics/deficiency ; Colon/metabolism ; Gastrointestinal Microbiome/physiology ; Methionine/metabolism ; *Sulfides/metabolism ; Male ; Mice, Inbred C57BL ; *Behavior, Animal ; Mitochondria/metabolism ; },
abstract = {The host-microbiome interface is rich in metabolite exchanges and exquisitely sensitive to diet. Hydrogen sulfide (H2S) is present at high concentrations at this interface and is a product of both microbial and host metabolism. The mitochondrial enzyme, sulfide quinone oxidoreductase (SQOR), couples H2S detoxification to oxidative phosphorylation; its inherited deficiency presents as Leigh disease. Since an estimated two-thirds of systemic H2S metabolism originates in the gut, it raises questions as to whether impaired sulfide clearance in this compartment contributes to disease and whether it can be modulated by dietary sulfur content. In this study, we report that SQOR deficiency confined to murine intestinal epithelial cells perturbs colon bioenergetics that is reversed by antibiotics, revealing a significant local contribution of microbial H2S to host physiology. We also find that a 2.5-fold higher methionine intake, mimicking the difference between animal and plant proteins, synergizes with intestinal SQOR deficiency to adversely impact colon architecture and alter microbiome composition. In serum, increased thiosulfate, a biomarker of H2S oxidation, reveals that intestinal SQOR deficiency combined with higher dietary methionine affects sulfide metabolism globally and perturbs energy metabolism as indicated by higher ketone bodies. The mice exhibit lower exploratory locomotor activity while brain MRI reveals an atypical reduction in ventricular volume, which is associated with lower aquaporin 1 that is important for cerebrospinal fluid secretion. Our study reveals the dynamic interaction between dietary sulfur intake and sulfide metabolism at the host-microbe interface, impacting gut health, and the potential for lower dietary methionine intake to modulate pathology.},
}
@article {pmid40526476,
year = {2025},
author = {Tignat-Perrier, R and Bramanti, L and Giordano, B and van de Water, JAJM and Manea, E and Allemand, D and Ferrier-Pagès, C},
title = {Microbiome Dynamics in Early Life Stages of the Precious Mediterranean Red Coral Corallium rubrum.},
journal = {Environmental microbiology reports},
volume = {17},
number = {3},
pages = {e70127},
doi = {10.1111/1758-2229.70127},
pmid = {40526476},
issn = {1758-2229},
support = {//Fondation CHANEL/ ; //Government of the Principality of Monaco/ ; //Prince Albert II of Monaco Foundation/ ; //COST Action CA20102 Marine Animal Forests of the World/ ; 101062275//Marie Curie Actions, the project RESTORE/ ; },
mesh = {Animals ; *Anthozoa/microbiology/growth &amp; development ; *Microbiota ; *Bacteria/classification/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Symbiosis ; Larva/microbiology ; Phylogeny ; Mediterranean Sea ; Coral Reefs ; DNA, Bacterial/genetics ; Sequence Analysis, DNA ; },
abstract = {Microbial colonisation in the early life stages of corals plays a critical role in their fitness, but the mechanisms by which microbial symbionts are acquired-whether from parental colonies, the environment, or both-remain poorly understood, particularly in octocorals. Although they are the second most abundant coral group on tropical reefs and contribute significantly to the structural complexity of Mediterranean coral reefs, their microbial dynamics are largely unexplored. In this study, we investigated the acquisition of the bacterial microbiota in the red coral Corallium rubrum, a precious coral. By analysing the composition of the bacterial community at different early life stages, including newly released larvae, 5- and 10-day-old larvae, 3-month-old settlers, 1-year-old recruits and 3-year-old juveniles, we are gaining new insights into the development of its microbiome. Using a direct PCR-based 16S rRNA metabarcoding approach, we performed high-resolution microbiome analyses at the level of individual larvae and settlers. Our results show that the bacterial microbiota of C. rubrum matures after the first year of life. Notably, dominant symbionts, such as Spirochaetaceae and BD72BR169 Gammaproteobacteria, were absent in larvae, settlers and recruits, suggesting that they were likely acquired horizontally from the environment. These findings improve our understanding of the microbial colonisation and development of C. rubrum and shed light on the potential role of its bacterial community in holobiont function.},
}
@article {pmid40525968,
year = {2025},
author = {Lopez-Echartea, E and Dusek, N and Misialek, M and Mahmud-Un-Nabi, MA and Williamson, R and Marathe, K and Geddes, BA},
title = {Culturomics from field-grown crop plants using dilution to extinction, two-step library preparation and amplicon sequencing.},
journal = {Microbiology (Reading, England)},
volume = {171},
number = {6},
pages = {},
doi = {10.1099/mic.0.001571},
pmid = {40525968},
issn = {1465-2080},
mesh = {RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/isolation &amp; purification/growth &amp; development ; *Zea mays/microbiology ; *Microbiota/genetics ; Phylogeny ; DNA, Bacterial/genetics ; Plant Roots/microbiology ; *Pisum sativum/microbiology ; *Crops, Agricultural/microbiology ; High-Throughput Nucleotide Sequencing ; Sequence Analysis, DNA ; Gene Library ; Soil Microbiology ; },
abstract = {Culturomics approaches have advanced microbial research by enabling the high-throughput isolation and characterization of a broader range of bacterial taxa, including some previously considered unculturable. Here, we present the testing and optimization of a protocol for isolating and identifying hundreds of cultivable microbes from field-grown plants. This protocol was tested and optimized using the root microbiomes of field-grown corn and pea plants under varying environmental conditions in ND, USA. By employing dilution-to-extinction culturing and a two-step barcoding PCR strategy targeting the V4 region of the 16S rRNA gene, we identified over 200 unique bacterial isolates. The optimized bioinformatic pipeline, built around the DADA2 package, ensured accurate amplicon sequence variant detection and taxonomy assignment. The resulting bacterial isolates span diverse phylogenetic groups, including plant-associated taxa known for promoting plant growth and mitigating stress. Our findings highlight the value of culturomics in generating microbial collections for synthetic community design and advancing plant-microbe interaction research. The protocol's scalability, cost-effectiveness and robust performance demonstrate its potential for widespread application in agricultural microbiome studies.},
}
@article {pmid40525868,
year = {2025},
author = {Wang, H and Xue, W and Cheng, J and He, Y and Song, Y and Hu, D and Peng, A and Li, C and Bao, H},
title = {Altered fecal microbial and metabolic profiles reveal potential mechanisms underlying anemia in patients with chronic renal failure.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0316624},
doi = {10.1128/spectrum.03166-24},
pmid = {40525868},
issn = {2165-0497},
abstract = {The gut microbiomes communicate with the kidney and may play a crucial role in the development of anemia in patients with chronic renal failure (CRF). However, the alterations in microbiota and their association with functional metabolites remain unclear. We performed metagenomics and untargeted metabolomics in a cohort of 30 patients with anemia of CRF and 20 healthy controls (HCs) to identify the characteristics of the gut microbiome and explore its potential interactions with the host. Decreased microbiota diversity and significant compositional differences were observed in the patients with anemia of CRF. We identified six gut microbiotas significantly changed in the patients with anemia of CRF, particularly Faecalibacterium prausnitzii, Prevotella copri, and Escherichia coli, which were closely correlated with hemoglobin (Hb) levels and estimated glomerular filtration rate (eGFR). These changes were accompanied by functional alterations in distinctive microbial pathways. Further fecal and serum metabolomics revealed fecal 12-KETE-LTB4 in arachidonic acid metabolism, uracil and L-aspartic acid in beta-alanine metabolism, gulonic acid in ascorbate and aldarate metabolism, accompanied by the top 15 differential serum metabolites that were closely correlated with Hb levels. Furthermore, we observed a complex co-occurrence between anemia of CRF-related gut microbiota species and the characterized metabolites. Moreover, a non-invasive model incorporating Faecalibacterium prausnitzii and Prevotella copri, combined with fecal 12-KETE-LTB4, uracil, L-aspartic acid, and gulonic acid, distinguished the patients with anemia of CRF from HCs (area under the curve: 0.879). Collectively, our results suggest that a disordered gut microbiome associated with functional metabolites may be a non-invasive diagnostic and therapeutic target for anemia of CRF.IMPORTANCEAnemia is a prevalent complication in patients with chronic renal failure (CRF), which is associated with a high burden of morbidity and adverse clinical outcomes. Various evidence suggests that gut microbiota dysbiosis may contribute to the pathogenesis of anemia in CRF, although the mechanism is still obscure. This work provides substantial evidence identifying the specific characteristics of the gut microbiomes accompanied by functional alterations in anemia of CRF. We highlight the intricate interactions among the anemia of CRF-related gut microbiome and the functional metabolites, which may regulate toxic accumulation, oxidative stress, and immune-inflammatory responses to induce and exacerbate anemia in patients with CRF. Furthermore, we found that evaluating the gut microbiota and fecal metabolites in combination might be a non-invasive prognostic indicator of CRF-induced anemia. These findings provide important insights into the role of gut microbiota in the mechanism of anemia in CRF.CLINICAL TRIALSThis study is registered with ClinicalTrials.gov as NCT05543291.},
}
@article {pmid40525799,
year = {2025},
author = {Šarac, J and Havaš Auguštin, D and Šunić, I and Michl, K and Berg, G and Cernava, T and Marjanović, D and Jakobsen, RR and Lovrić, M},
title = {Linking the bed dust microbiome with environmental factors and child respiratory health.},
journal = {Annals of human biology},
volume = {52},
number = {1},
pages = {2509606},
doi = {10.1080/03014460.2025.2509606},
pmid = {40525799},
issn = {1464-5033},
mesh = {Humans ; *Dust/analysis ; *Microbiota ; Child ; *Asthma/microbiology/epidemiology ; Adolescent ; Child, Preschool ; Male ; Female ; RNA, Ribosomal, 16S/analysis/genetics ; Bacteria/classification/genetics/isolation &amp; purification ; Housing ; Air Pollution, Indoor ; },
abstract = {BACKGROUND: Humans spend up to 90% of their time indoors and are exposed to a significant number of microbes in their homes, which can have important implications for their health.<br><br>AIM: This study focused on analysing the influence of environmental factors on microbiome diversity and abundance in bed dust and linking the exposure to dust bacteria with asthma.<br><br>SUBJECTS AND METHODS: A total of 90 dust samples were collected from homes of asthmatic patients (n&#x2009;=&#x2009;59) and controls (n&#x2009;=&#x2009;31) aged 5-18&#x2009;years. The bacterial fraction of the microbiome was analysed using 16S rRNA gene high-throughput sequencing on the Illumina MiSeq platform and downstream analyses in QIIME2 and R. Microbiome profiles were associated with asthma and relevant environmental and household data.<br><br>RESULTS: Higher bacterial &#x3b2;-diversity in the environment was shown to be inversely associated with asthma (p&#x2009;=&#x2009;0.009). Also, living environment (p&#x2009;=&#x2009;0.002), housing type (p&#x2009;=&#x2009;0.004), presence of pets in the household (p&#x2009;=&#x2009;0.001), and cleaning practices (p&#x2009;=&#x2009;0.006 for dusting and p&#x2009;=&#x2009;0.011 for vacuuming) were prominent environmental factors affecting the bed dust microbiome.<br><br>CONCLUSION: Our results suggest significant differences in bacterial community composition between individuals with and without asthma and the interaction between indoor microbiome and asthma is mediated by environmental factors in the household.},
}
@article {pmid40525692,
year = {2025},
author = {Jarrett, ZS and Xia, H and O'Neil, ER and Lonergan, TP and Gonzales, M and Sobieszczyk, M and Gibbons, TF and Marcus, JE},
title = {Characterizing Microbiome Changes in Veno-Venous Extracorporeal Membrane Oxygenation: A Case Report of Multidrug-Resistant Bacteremia.},
journal = {ASAIO journal (American Society for Artificial Internal Organs : 1992)},
volume = {},
number = {},
pages = {},
doi = {10.1097/MAT.0000000000002479},
pmid = {40525692},
issn = {1538-943X},
support = {//Clinical Investigations &amp; Research Support (CIRS)/ ; },
abstract = {Microbiome analysis using metagenomics next-generation sequencing (mNGS) is rarely performed in patients receiving extracorporeal membrane oxygenation (ECMO). Patient body sites were swabbed within 72 hours of ECMO cannulation and weekly during ECMO course. Specimens underwent 16S sequencing to identify the microbiome along with mNGS to determine antimicrobial resistance genes. Fifty-two year old male who suffered polytraumatic injuries and developed acute respiratory syndrome was placed on veno-venous (VV) ECMO to treat severe respiratory failure. On ECMO day 1, the patient was undergoing treatment for urinary tract infection due to susceptible Pseudomonas aeruginosa (PsA). On ECMO day 22, the patient developed fulminant septic shock and tracheal aspirate and blood cultures both grew MDR PsA and Enterobacter cloacae complex (ECC) and ultimately died on day 23. There were significant microbiome and antimicrobial resistance changes that preceded sepsis on day 22, as evidenced by the increase in oral PsA colonization and expansion of resistance genes, such as KPC and OXA-50, which suggest several possible reservoirs for infection outside of the circuit. Further application of these methods is needed to understand microbiome changes in ECMO and ultimately guide infection prevention efforts.},
}
@article {pmid40525652,
year = {2025},
author = {Yarmohammadi, H and Soltanipur, M and Rezaei, M and Ejtahed, HS and Raei, M and Razavi, A and Mirhosseini, SM and Zangeneh, M and Doroud, D and Fateh, A and Seyed Siamdoust, S and Siadat, SD},
title = {The Comparison of the Gut Microbiome Composition, Serum Inflammatory Markers and Faecal Short-Chain Fatty Acids Among Individuals With Type 1 and 2 Diabetes Mellitus With Healthy Controls: A Case-Control Study.},
journal = {Endocrinology, diabetes &amp; metabolism},
volume = {8},
number = {4},
pages = {e70071},
doi = {10.1002/edm2.70071},
pmid = {40525652},
issn = {2398-9238},
support = {940604//National Institute for Medical Research Development of Iran/ ; },
mesh = {Humans ; *Diabetes Mellitus, Type 2/microbiology/metabolism/blood ; Male ; Female ; *Gastrointestinal Microbiome/physiology ; *Feces/chemistry/microbiology ; Case-Control Studies ; *Fatty Acids, Volatile/analysis/metabolism ; *Diabetes Mellitus, Type 1/microbiology/metabolism/blood ; Adult ; Middle Aged ; Biomarkers/blood ; Inflammation/blood ; },
abstract = {BACKGROUND: This study aimed to compare the gut microbiome (GM) composition, serum inflammatory markers and faecal short-chain fatty acids among individuals with type 1 and type 2 diabetes mellitus (DM) and healthy controls.<br><br>METHODS: This case-control study examined 49 subjects with type 2 DM, 21 with type 1 DM and 40 healthy controls. Blood and faecal samples were collected. Serum inflammatory markers, including CRP, IL-1&#x3b2;, IL-6, TNF-&#x3b1; and IFN-&#x3b3;, were measured using enzyme-linked immunosorbent assays (ELISA). Bacterial populations were quantified using RT-qPCR and NGS. Faecal metabolites were analysed using gas chromatography.<br><br>RESULTS: Simpson's alpha diversity was higher among types 1 and 2 DM than in the control. The frequency of the bacterial genera Gemmiger, Dorea, Collinsella, Escherichia/Shigella, Dialister, Coprococcus, Achromobacter, Intestinimonas and Allisonella in type 2 DM was higher than in the control, and the frequency of the genera Romboutsia and Clostridium was decreased in type 2 DM. The frequency of the Prevotella, Bacteroides and Faecalibacterium genera in type 1 DM was lower than in the other groups. Acetate, propionate and butyrate levels were significantly higher in type 2 DM patients compared to the other groups. Participants with diabetes had significantly higher hs-CRP, IL1-&#x3b2;, TNF, IL-6 and IFG levels compared to the controls. Compared to healthy controls, both T1DM and T2DM patients showed a significant increase in the abundance of the Lactobacillus genus (p&#x2009;=&#x2009;0.01) and a decrease in Faecalibacterium (p&#x2009;=&#x2009;0.02). Additionally, serum levels of IL-6 and TNF-&#x3b1; were significantly elevated in T2DM patients (p&#x2009;=&#x2009;0.003 and p&#x2009;=&#x2009;0.005, respectively). Faecal levels of butyrate were significantly reduced in both diabetic groups compared to the controls (p&#x2009;=&#x2009;0.004).<br><br>CONCLUSION: By determining the GM alterations in patients with diabetes, interventional strategies could be designed to modulate the GM composition as an adjunctive therapy in diabetes.},
}
@article {pmid40525494,
year = {2025},
author = {Kumagai, A and Mayanagi, K and Hayashi, S and Nakano, S and Ito, S and Fujinami, D},
title = {In Vitro Amyloid Formation by a Bacteriocin From Bifidobacterium longum subsp. infantis.},
journal = {Proteins},
volume = {},
number = {},
pages = {},
doi = {10.1002/prot.70002},
pmid = {40525494},
issn = {1097-0134},
support = {//Japan Society for the Promotion of Science/ ; //Mishima Kaiun Memorial Foundation/ ; //Yakult Bio-Science Foundation/ ; },
abstract = {Bifidobacterium longum subsp. infantis is a probiotic bacterium isolated from human milk-fed infants. This species secretes various metabolites that contribute to gut microbiome development and immune system maturation. In this study, we investigated bacteriocins, ribosomally synthesized peptides that typically exhibit antimicrobial activity. We produced Blon_0434, a B. infantis-derived bacteriocin belonging to the Lactococcin 972 family, by expressing it heterologously in Escherichia coli. Our results demonstrate that recombinant Blon_0434 is secreted via the Sec-dependent pathway but exhibited no detectable antimicrobial activity under the tested conditions. NMR structural analysis suggests that Blon_0434 is thermodynamically unstable, which may account for its inactivity. Unexpectedly, Blon_0434 formed amyloid-like fibrils in vitro, as demonstrated by thioflavin T fluorescence and transmission electron microscopy. The biological implications of Blon_0434 amyloid formation warrant further investigation, particularly regarding microbial interactions and host immune responses.},
}
@article {pmid40525381,
year = {2025},
author = {Karjoo, S and Braglia-Tarpey, A and Chan, AP and Ayala Germán, AG and Herdes, RE and Pai, N and Sierra-Velez, D and Whitehead, B and Quiros-Tejeira, RE and Duro, D},
title = {Evidence-based review of the nutritional treatment of obesity and metabolic dysfunction-associated steatotic liver disease in children and adolescents.},
journal = {Journal of pediatric gastroenterology and nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1002/jpn3.70099},
pmid = {40525381},
issn = {1536-4801},
abstract = {The growing pediatric obesity epidemic has paralleled the surge in metabolic dysfunction-associated steatotic liver disease (MASLD) and metabolic dysfunction-associated steatohepatitis. It develops due to nutritional imbalances, microbiome dysbiosis, gene regulation, hormonal changes, and environmental factors like food deserts, low activity level, and an unhealthy lifestyle. The prevalence of MASLD and obesity is rising every year. Lifestyle changes remain the mainstay treatment for obesity and MASLD. Per the 2023 American Association for the Study of Liver Diseases Practice Guidance on MASLD, achieving ≥5% weight loss can reduce hepatic steatosis, ≥7% weight loss can reduce hepatic inflammation, and ≥10% weight loss can reduce liver fibrosis. Therefore, nutritional interventions can be a powerful tool to help correct metabolic dysfunction and promote healthy weight loss. Current endorsed nutritional interventions for weight loss or MASLD include the Mediterranean diet, low glycemic/low carbohydrate diet, plant-based diet/anti-inflammatory diet, ketogenic diet, and intermittent fasting. This review provides evidence-based insights into current nutritional interventions for children and adolescents with obesity and MASLD to help guide pediatric gastroenterologists in making the best dietary-based recommendations in clinical practice.},
}
@article {pmid40525291,
year = {2025},
author = {Rischard, FP and Hemnes, AR},
title = {Right Ventricular Function, Inflammation, and the Gut Microbiome in Pulmonary Hypertension: A Translational Frontier.},
journal = {Circulation. Heart failure},
volume = {},
number = {},
pages = {e013198},
doi = {10.1161/CIRCHEARTFAILURE.125.013198},
pmid = {40525291},
issn = {1941-3297},
}
@article {pmid40525141,
year = {2025},
author = {de Oliveira, MJK and Yang, Q and Brandão Melo, AD and Marçal, DA and Korth, N and Pavlovikj, N and Benson, AK and Htoo, JKK and Brand, HG and Hauschild, L and Gomes-Neto, JC},
title = {Fecal microbiome of pigs fed diets differing in protein and amino acid content raised in thermoneutral or cyclical heat stress conditions.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1585374},
pmid = {40525141},
issn = {1664-302X},
abstract = {The pig microbiome composition is affected by factors such as dietary changes, genetics, and diseases. Recent evidence suggests that housing temperature may also contribute to the variability in community structure and composition. Therefore, we investigated the interactive effects of different nutritional strategies and heat stress (HS) on the fecal microbiota composition, community structure, taxon distribution, and taxa correlation structure of pigs. Forty-eight (Landrace × Large White) finishing gilts with an average of 67.7 ± 6.2 kg of body weight (BW) were distributed in a 2 × 3 factorial arrangement: two temperatures [thermoneutral (TN, 22°C for 24 h) and cyclic heat stress (CHS, 12 h to 35°C and 12 h to 22°C)] and three diets varying in the dietary crude protein (CP) contents and amino acid (AA) levels [high CP (HP); low CP-free AA-supplemented diet (LPAA); low CP-free AA-supplemented diet and digestible Lys level (+20%), and Lys:AA ratios above recommendations (LPAA+)] originating six treatments (eight replicates of one pig). Pigs were fed ad libitum throughout the study. The 16S ribosomal RNA (rRNA)-based microbiome analysis was conducted in fecal samples collected on days 0 and 27 (endpoint). Overall, microbiome analysis suggested an increased richness in the fecal microbiome of pigs raised in TN conditions fed a diet supplemented with higher levels of AA (LPAA+). In addition, changes in the fecal microbiome composition indicated that Mogibacterium was significantly diminished in the feces of pigs fed the LPAA diet when compared to pigs fed the LPAA+, both in CHS conditions. Oscillospira was reduced in the feces of pigs fed a diet containing exclusively protein-bound as the source of AA, while the more the feed-grade AA was included in the remaining diets, the more the abundance of this taxon in fecal samples. Despite dietary alterations, Corynebacterium was enriched under CHS compared to TN, whereas the enrichment of Prevotella and Eubacterium hallii group was higher in the TN group. Outcomes of this study suggest that changes in fecal microbiota composition were mainly associated with temperature, pointing toward potential taxa that may contribute to physiological adaptation to heat stress.},
}
@article {pmid40372016,
year = {2025},
author = {Cappellozza, BI and Cooke, RF and Amaral, RC and Bach, A and Engle, TE and Ferraretto, LF and Marques, RS and Miller, AC and Moriel, P and Vendramini, JMB},
title = {Ruminant nutrition symposium: novel microbial solutions to optimize production efficiency in beef and dairy systems.},
journal = {Journal of animal science},
volume = {103},
number = {},
pages = {},
doi = {10.1093/jas/skaf165},
pmid = {40372016},
issn = {1525-3163},
mesh = {Animals ; Cattle/physiology ; Animal Feed/analysis ; Animal Nutritional Physiological Phenomena ; *Dairying/methods ; Silage/analysis ; Diet/veterinary ; *Animal Husbandry/methods ; Bacteria ; },
abstract = {The livestock industry is in search of sustainable technologies that enhance the profitability and sustainability of food animal production. Among these technologies, microbial solutions include living bacteria that may support soil, plant, and animal health. Bacterial inoculants have been the most used additives to modulate whole-plant corn silage fermentation, including homo- and heterofermentative bacteria. Bacterial inoculants can improve fermentation characteristics of grass silage, whereas the wide variation in chemical composition and management practices across cool- and warm-season grasses makes the outcome of inoculation less predictable. Tailored recommendations for bacterial inoculant species and strains, based on species and management practices, are necessary to increase the predictability of silage inoculation, including whole-plant corn and grass silage. Microbial solutions are also used as feed additives for beef and dairy cattle, including Bacillus-based direct-fed microbials (DFM). Recent advancements in Bacillus-based DFM supplementation have shown promise for enhancing cow-calf productivity through improved gut health, immune function, and nutrient metabolism. Incorporating Bacillus-based DFM into stocker and feedlot receiving programs can improve feed intake and digestibility, health, and productivity of high-risk cattle. Bacillus-based DFM have also been used in feedlot diets to address public concerns with antimicrobial resistance but also to improve cattle performance and reduce the incidence of diseases. Multispecies bacterial-based DFM are promising alternatives to counteract the potentially adverse effects of Salmonella, as these DFM supported the integrity of the intestinal epithelial cells under in vitro settings. In dairy cattle, most DFM-related research in mature cows has targeted improvements in rumen fermentation and enterocyte health. In general, improvements in milk production due to supplementation of bacteria-based DFM seem to be more consistent than those obtained with yeast-based DFM. Collectively, microbial solutions have the potential to optimize silage quality, enhance feed intake and digestibility by ruminants, and support cattle health and performance while fostering sustainable practices in beef and dairy production systems.},
}
@article {pmid40524921,
year = {2025},
author = {Richardson, H and Keir, HR and Nitza, S and Fong, CJ and Crichton, ML and Dicker, AJ and Chalmers, JD},
title = {Short-term stability of the sputum microbiota in bronchiectasis and cystic fibrosis.},
journal = {ERJ open research},
volume = {11},
number = {3},
pages = {},
pmid = {40524921},
issn = {2312-0541},
abstract = {The microbiome in bronchiectasis shows day to day variability in sputum samples from people with bronchiectasis and cystic fibrosis. This should be taken into account in studies of the airway microbiome in chronic airway disease. https://bit.ly/3URkv42.},
}
@article {pmid40524870,
year = {2025},
author = {Αikepa, D and He, Y and Chen, W and Liang, M and Du, Y and Chen, X and Du, M and Zhu, Y and Wang, J and Sun, Y},
title = {The Effects of Specific Gut Microbiota on Hyperuricemia - A Mendelian Randomization Analysis and Clinical Validation.},
journal = {Diabetes, metabolic syndrome and obesity : targets and therapy},
volume = {18},
number = {},
pages = {1891-1902},
pmid = {40524870},
issn = {1178-7007},
abstract = {BACKGROUND: Hyperuricemia (HUA) is a metabolic disorder caused by an imbalance between uric acid (UA) production and excretion. It is closely associated with various diseases, including gout and kidney disease. The intestines play a significant role in UA excretion, and emerging evidence suggests that gut microbiota modulate UA excretion and degradation. However, the specific functional microbial biomarkers and their roles in HUA remain underexplored.<br><br>METHODS: Based on this, we hypothesize that the Mendelian randomization (MR) analysis method can be used to identify and define microbial biomarkers associated with HUA. Accordingly, we conducted an MR study using gut microbiota data from 18,340 participants across 24 distinct cohorts, including 129&#xa0;HUA patients and 352,232 controls, to investigate the causal relationship.<br><br>RESULTS: We found that the genus Ruminococcus was linked to a lower risk of HUA, while the family Clostridiaceae was associated with a higher risk of HUA. Clinical validation showed that high Clostridiaceae and low Ruminococcus abundance could distinguish HUA patients from healthy individuals, and the predictive diagnostic efficacy of Clostridiaceae was better. The combined model further enhanced diagnostic accuracy.<br><br>CONCLUSION: Our findings provide important information on the micro-biome features of HUA and novel insights into the further determination of the roles of the involved microorganisms, providing a reference for disease diagnosis and the development of microbial therapies.},
}
@article {pmid40524571,
year = {2025},
author = {Mohr, AE and Jasbi, P and van Woerden, I and Bowes, DA and Chi, J and Gu, H and Bruening, M and Whisner, CM},
title = {Longitudinal assessment of food insecurity status on the gut microbiome and metabolome of first year college students.},
journal = {The British journal of nutrition},
volume = {},
number = {},
pages = {1-42},
doi = {10.1017/S0007114525103668},
pmid = {40524571},
issn = {1475-2662},
abstract = {Food insecurity affects the health of college-aged individuals, but its impact on the gut microbiome (GM) over time is poorly understood. This study explored the association between food insecurity and the GM in 85 college students, identifying microbial taxa, metabolites, and pathways linked to food security status and examining GM stability and microbe-metabolite interactions. Longitudinal GM and metabolomic data were collected from first-year students over an academic year, encompassing periods of variable food security status. Participants were categorized into three groups: food insecure (FI, n=13), food secure (FS, n=44), and variable (VAR, n=28) status. GM composition varied significantly between FS classifications (Bray-Curtis dissimilarity, P ≤ 0.005). Stability analysis revealed correlations between stability scores and microbial features, pathways, and metabolites. Specific microbes (e.g., Bifidobacterium species, Faecalibacterium prausnitizii D, and Lachnospiraceae), pathways (energy and microbial turnover), and metabolites (cadaverine, N-acetylcadaverine, putrescine, testosterone sulfate, and creatine) associated with FI status were identified. Multi-omic integration revealed metabolic pathways influenced by differentially abundant microbial species and co-occurring fecal metabolites in food-insecure participants related to the microbial production of polyamines, detoxification, and energy metabolism. The transition from FS to FI showed no significant differences at specific taxonomic, functional, or metabolite levels. This study uncovers complex interactions between food security, GM composition, and metabolism. Significant differences were found in microbial community variability and metabolic pathways associated with food security status, but the transition from food security to insecurity disrupted the GM without clear taxonomic or functional distinctions, emphasizing the need for further research into these mechanisms.},
}
@article {pmid40524502,
year = {2025},
author = {Shen, T and Wu, Q and Tan, Y and Ju, X and Han, G},
title = {Diet-induced gut microbiota shifts in grasshoppers: ecological implications for management and adaptation under varying grazing intensities.},
journal = {Pest management science},
volume = {},
number = {},
pages = {},
doi = {10.1002/ps.8953},
pmid = {40524502},
issn = {1526-4998},
support = {32192463//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: Grasshoppers play a keystone role in health and stability in grassland ecosystems, which are critical for biodiversity and ecological services. Despite this, in the context of the desert steppe, there remains a paucity of knowledge regarding the response of Calliptamus abbreviatus to variations in grazing intensity and the subsequent impact on its gut microbiome and dietary diversity. The present study evaluated the impact of variations in sheep grazing intensity on the composition of plant species, which in turn influences the diet and intestinal microbiota of the grasshopper C. abbreviatus, an abundant species in these ecosystems.<br><br>RESULTS: We found that increased grazing intensity has significant impacts on plant species composition and diversity, reduces grasshopper dietary diversity, increases reliance on Allium tenuissimum, and alters gut microbial community structure. Notably, plant species composition changes associated with high grazing intensity decrease Actinobacteria and Frankia but increase Proteobacteria, potentially affecting grasshopper adaptability and nutrient absorption. Procrustes analysis revealed a significant congruence between diet and gut microbiota, and the plant species changes associated with grazing serve as a pivotal point in the enterotype differentiation of grasshoppers, with enterotype 2 potentially endowing grasshoppers with enhanced nutrient absorption and transport capabilities under grazing, helping them adapt to environmental changes.<br><br>CONCLUSION: Our findings emphasize that the diet and structure and function of grasshopper gut microbial communities are altered by the quality and quantity of food resources. This study provides insights into the long-term interactions between insects and their environment, and these insights are crucial for sustainable grassland management and pest control strategies. &#xa9; 2025 Society of Chemical Industry.},
}
@article {pmid40524314,
year = {2025},
author = {Schumacher, J and Müller, P and Sulzer, J and Faber, F and Molitor, B and Maier, L},
title = {Proton-pump inhibitors increase C. difficile infection risk by altering pH rather than by affecting the gut microbiome based on a bioreactor model.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2519697},
doi = {10.1080/19490976.2025.2519697},
pmid = {40524314},
issn = {1949-0984},
mesh = {*Proton Pump Inhibitors/adverse effects/pharmacology ; *Gastrointestinal Microbiome/drug effects ; Humans ; Hydrogen-Ion Concentration ; *Clostridioides difficile/drug effects/growth &amp; development ; Omeprazole/pharmacology/adverse effects ; *Clostridium Infections/microbiology ; Bioreactors/microbiology ; Bacteria/drug effects/classification/genetics/growth &amp; development/isolation &amp; purification ; Feces/microbiology ; },
abstract = {Clostridioides difficile infections often occur after antibiotic use, but they have also been linked to proton-pump inhibitor (PPI) therapy. The underlying mechanism - whether infection risk is due to a direct effect of PPIs on the gut microbiome or changes in gastrointestinal pH - has remained unclear. To disentangle both possibilities, we studied the impact of the proton-pump inhibitor omeprazole and pH changes on key members of the human gut microbiome and stool-derived microbial communities from different donors in vitro. We then developed a custom multiple-bioreactor system to grow a model human microbiome community and a stool-derived community in chemostat mode and tested the effects of omeprazole exposure, pH changes, and their combination on C. difficile growth within these communities. Our findings show that changes in pH significantly affect the gut microbial community's biomass and the abundances of different bacterial taxa, leading to increased C. difficile growth within the community. However, omeprazole treatment alone did not result in such effects. These findings imply that the higher risk of C. difficile infection following proton-pump inhibitor therapy is probably because of alterations in gastrointestinal pH rather than a direct interaction between the drug and the microbiome. This understanding offers a new perspective on infection risks in proton-pump inhibitor therapy.},
}
@article {pmid40524290,
year = {2025},
author = {Qian, L and Liuchen, X and Yue, Y and Xiaopeng, D and Jie, W and Moye, T and Yuxin, L and Hongfeng, GU and Xuejiao, X},
title = {Xiong's Shiwei Wendan decoction attenuates plaque lesions and balances gut microbiota dysbiosis in ApoE-/- mice with high-fat diet.},
journal = {Journal of traditional Chinese medicine = Chung i tsa chih ying wen pan},
volume = {45},
number = {3},
pages = {508-517},
pmid = {40524290},
issn = {2589-451X},
support = {81603600//National Natural Science Foundation of China: the Anti-Atherosclerotic Mechanism of Xiong's Shiwei Wendan decoction based on the Regulation of Reverse Cholesterol Transport via the MicroRNA-33A Adenosine Triphosphate-binding Cassette Subfamily A Member 1/ Adenosine Triphosphate-binding Cassette Subfamily A Member 1 Pathway/ ; 2021JJ30510//Natural Science Foundation of Hunan Province of China: the Anti-Atherosclerotic Mechanism of Xiong's Shiwei Wendan Decoction based on the Activation of Lipophagy Mediated by the AMP-activated Protein Kinase/Mechanistic Target of Rapamycin Pathway/ ; D202303018265//Health Research Project of Hunan Provincial Health Commission: the An-ti-Atherosclerotic Mechanism of Xiong's Shiwei Wendan Decoction based on Lipophagy Mediated by the MicroRNA-499a-3p/ Autophagy-related 5 Pathway/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Drugs, Chinese Herbal/administration &amp; dosage ; Male ; Mice ; Humans ; Diet, High-Fat/adverse effects ; *Apolipoproteins E/genetics/deficiency/metabolism ; *Atherosclerosis/drug therapy/microbiology/metabolism/genetics ; *Plaque, Atherosclerotic/drug therapy/metabolism/microbiology/genetics ; *Dysbiosis/drug therapy/microbiology/metabolism/genetics ; Mice, Inbred C57BL ; Mice, Knockout ; },
abstract = {OBJECTIVE: To evaluate the anti-atherosclerotic potential and gut microbiota (GM) modulation effects of Xiong's Shiwei Wendan decoction (, XSWD).<br><br>METHODS: For in vitro study, Tsuchiya human peripheral blood mononuclear cell-1 (THP-1) derived foam cells were used to examine the possible anti-atherosclerotic effect of XSWD and XSWD-medicated serum. Atherosclerosis-prone apolipoprotein E-deficient (ApoE-/-) mice were utilized for in vivo analysis. After an 8-week high-fat diet (HFD) adminstration, 25 male ApoE-/- mice were randomly divided into the model group, different doses of XSWD groups (1.25, 2.5, 5 mg/mL), and atorvastatin group (2.6 mg/kg). Following a continuous 8-week intervention, all mice underwent examination for AS lesion formation and assessment of its serum lipid profile. To investigate the effect on the gut microbiome, 16S rRNA gene sequencing targeting the V3-V4 hypervariable region was performed on the colonic content of mice.<br><br>RESULTS: XSWD administration attenuated lipid deposition in THP-1 cells, significantly reduced aortic plaque lesions, improved the lipid profile, and normalized GM composition in HFD-fed ApoE-/- mice.<br><br>CONCLUSION: This study investigated the potential anti-atherosclerotic and gut microbio-ta-restoring effects of XSWD in ApoE-/- mice, with findings suggesting that XSWD may be a promising preventive measure against atherosclerosis through its ability to reduce lipid accumula-tion in foam cells, improve lipid profile, and restore gut microbiota composition.},
}
@article {pmid40524271,
year = {2025},
author = {Serrano-Gómez, G and Yañez, F and Soler, Z and Pons-Tarin, M and Mayorga, L and Herrera-deGuise, C and Borruel, N and Rodriguez-Sinovas, A and Consegal, M and Manjón, I and Vega-Abellaneda, S and Manichanh, C},
title = {Microbiome multi-omics analysis reveals novel biomarkers and mechanisms linked with CD etiopathology.},
journal = {Biomarker research},
volume = {13},
number = {1},
pages = {85},
doi = {10.1186/s40364-025-00802-1},
pmid = {40524271},
issn = {2050-7771},
support = {72190278//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; FI21/00262//Instituto de Salud Carlos III/ ; PI20/00130//Instituto de Salud Carlos III/ ; 2021 SGR 00459//Ag&#xe8;ncia de Gesti&#xf3; d'Ajuts Universitaris i de Recerca/ ; 2021 SGR 00459//Ag&#xe8;ncia de Gesti&#xf3; d'Ajuts Universitaris i de Recerca/ ; 2021 SGR 00459//Ag&#xe8;ncia de Gesti&#xf3; d'Ajuts Universitaris i de Recerca/ ; },
abstract = {BACKGROUND: The gut microbiome plays a key role in the development of inflammatory bowel disease (IBD), as imbalances in microbial composition are associated with immune dysfunction. However, the specific mechanisms by which certain microorganisms contribute to this process remain unclear.<br><br>METHODS: Here, we employed a multi-omics approach on fecal samples to identify novel microbiome markers and elucidate mechanisms underlying IBD. Shotgun metagenomics was applied to 212 samples (850 in total with validation cohort), shotgun metatranscriptomics to 103 samples and metabolomics to 105 samples. Machine learning techniques were used to predict disease and the three omics data were integrated to propose a mechanistic role of the microbiota.<br><br>RESULTS: Metagenomic analysis identified Crohn's disease (CD)-specific microbiome signatures, including a panel of 20 species that achieved a high diagnostic performance, with an area under the ROC curve (AUC) of 0.94 in an external validation set. Metatranscriptomic analysis revealed significant alterations in microbial fermentation pathways in CD, but not in ulcerative colitis (UC), highlighting disruptions that explain the depletion of butyrate-a key anti-inflammatory metabolite-observed in metabolomics analysis. Integrative multi-omics analyses further identified active virulence factor genes in CD, predominantly originating from the adherent-invasive Escherichia coli (AIEC). Notably, these findings unveiled novel mechanisms, including E. coli-mediated aspartate depletion and the utilization of propionate, which drives the expression of the ompA virulence gene, critical for bacterial adherence and invasion of the host's macrophages. Interestingly, these microbiome alterations were absent in UC, underscoring distinct mechanisms of disease development between the two IBD subtypes.<br><br>CONCLUSIONS: In conclusion, our study not only identifies promising novel biomarkers with strong diagnostic potential, which could be valuable in challenging clinical scenarios, but also offers an integrated multi-omics perspective on the microbial mechanisms underlying inflammation and virulence in Crohn's disease.},
}
@article {pmid40524270,
year = {2025},
author = {Mann, AE and Aumend, C and Crull, S and O'Connell, LM and Osagie, E and Akhigbe, P and Obuekwe, O and Omoigberale, A and Rowe, M and Blouin, T and Soule, A and Kelly, C and , and Burne, RA and Coker, MO and Richards, VP},
title = {HIV infection and exposure is associated with increased cariogenic taxa, reduced taxonomic turnover, and homogenized spatial differentiation for the supragingival microbiome.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {144},
pmid = {40524270},
issn = {2049-2618},
support = {R01DE028154/DE/NIDCR NIH HHS/United States ; R01DE028154/DE/NIDCR NIH HHS/United States ; R01DE028154/DE/NIDCR NIH HHS/United States ; R01DE028154/DE/NIDCR NIH HHS/United States ; R01DE028154/DE/NIDCR NIH HHS/United States ; R01DE028154/DE/NIDCR NIH HHS/United States ; R01DE028154/DE/NIDCR NIH HHS/United States ; R01DE028154/DE/NIDCR NIH HHS/United States ; },
mesh = {Humans ; *HIV Infections/microbiology/complications ; *Dental Caries/microbiology ; Child ; *Microbiota ; Female ; Male ; Cross-Sectional Studies ; *Mouth/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Child, Preschool ; Nigeria ; *Gingiva/microbiology ; },
abstract = {BACKGROUND: The oral microbiome consists of distinct microbial communities that colonize various ecological niches within the oral cavity, the composition of which are influenced by nutrient and substrate availability, host genetics, diet, behavior, age, and other diverse host and environmental factors. Unlike other densely populated human-associated microbial ecosystems (e.g., gut, urogenital), the oral microbiome is directly and frequently exposed to external influences, contributing to its relatively lower stability over time. In individuals with compromised immunity, such as those living with HIV, the composition and stability of the oral microbiome may be especially vulnerable to disruption. Cross-sectional studies of the oral microbiome in children living with HIV capture a glimpse of this temporal dynamism, yet a full appreciation of the relative stability, robusticity, and spatial structure of the oral environment is necessary to understand the role of microbial communities in promoting health or disease in the context of HIV. Here, we investigate the spatial and temporal stability of the oral microbiome over three sampling time points in the context of HIV infection and exposure. Individual teeth were sampled from a cohort of 565 Nigerian children with varying levels of tooth decay severity (i.e., caries disease). We collected 1960 supragingival plaque samples and characterized the oral microbiome using a metataxonomic approach targeting an approximately 478 bp region of the bacterial rpoC gene.<br><br>RESULTS: Both HIV infection and exposure have significant, if subtle, effects on the stability of the supragingival plaque microbiome. Specifically, we observed (1) a slight but significant reduction in taxonomic turnover among HIV-exposed and infected children; (2) an association between HIV infection and a more homogenized oral community across the anterior and posterior dentition in children living with HIV; and (3) a relationship between impaired immunity, lower taxonomic turnover over time, and an elevated frequency of cariogenic taxa, including Streptococcus mutans, in children living with HIV.<br><br>CONCLUSIONS: Despite the influence of various contributing factors, we observe an effect of HIV status on both the temporal and spatial stability of the oral microbiome. Specifically, the results presented here indicate that the oral microbiome shows less community change over time in children living with or exposed to HIV, which we hypothesize may be linked to a reduced capacity to adapt to environmental changes. The observed taxonomic rigidity among children living with HIV may signal community dysfunction, potentially leading to a higher incidence of oral diseases, including caries, in this cohort. Video Abstract.},
}
@article {pmid40524217,
year = {2025},
author = {Ncho, CM},
title = {Heat stress and the chicken gastrointestinal microbiota: a systematic review.},
journal = {Journal of animal science and biotechnology},
volume = {16},
number = {1},
pages = {85},
pmid = {40524217},
issn = {1674-9782},
abstract = {Heat stress (HS) has become a significant challenge for poultry farming due to an increase in global temperatures. Existing literature suggests that the health effects of HS in chickens are related to its impact on the gastrointestinal tract. While there is evidence of the detrimental consequences of HS on the gut structure, little is known about the effects of HS on the microbial population inhabiting this organ. Fortunately, recent advancements in "omics" technologies have made investigating the interaction between HS and the gut microbiota possible. Therefore, a systematic review was conducted to assess the effects of HS on chicken gut microbiota. In July 2024, a comprehensive literature search was performed across scientific repositories, including Scopus, PubMed, Science Direct, and Google Scholar. Eighteen studies met the eligibility criteria for inclusion and a qualitative synthesis of their results was conducted according to the PRISMA guidelines. Current evidence indicates that HS poses a significant challenge to the gastrointestinal system of chickens, resulting in a range of physiological reactions. These changes trigger fierce competition among beneficial microbial species for limited nutrients, promote microbial shifts from obligate to facultative anaerobes, and increase the abundance of microbial species with high resistance to elevated environmental temperatures. Furthermore, the proliferation of pathogens is exacerbated. Ultimately, gut microbiota profiling highlights changes in microbial diversity, alterations in the composition of microbial populations, disruptions in specific microbial functional pathways (tricarboxylic acid cycle, amino acid metabolism, antioxidant biosynthesis, and fatty acid degradation), and the breakdown of complex networks that govern microbial interactions. Understanding the complex relationship between HS and microbial shifts within the chicken gut can provide valuable insights for the development of sustainable mitigation strategies. Further research is needed to expand the current knowledge and employ more advanced literature synthesis techniques such as meta-analyses.},
}
@article {pmid40524215,
year = {2025},
author = {Hao, Y and Wang, W and Li, M and Choi, Y and Zhou, M and Wang, Y and Cao, Z and Wang, YJ and Yang, H and Jiang, L and Guan, LL and Li, S},
title = {Microbial diurnal rhythmicity in the rumen fluid impacted by feeding regimes and exogenous microbiome providing novel mechanisms regulating dynamics of the rumen microbiome.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {142},
pmid = {40524215},
issn = {2049-2618},
support = {32130100//National Natural Science Foundation of China/ ; 32130100//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Rumen/microbiology/parasitology ; Cattle ; *Circadian Rhythm ; *Archaea/classification/isolation &amp; purification/genetics ; *Bacteria/classification/genetics/isolation &amp; purification ; *Gastrointestinal Microbiome/physiology ; Female ; Animal Feed ; },
abstract = {BACKGROUND: Diurnal oscillations have been reported on ruminal prokaryotes, but the daily rhythmicity of eukaryotes remains unknown. This study investigated diurnal oscillations of ruminal prokaryotes and eukaryotes under three different feeding managements and rumen fluid transplantation conditions, aiming to elucidate the regulatory mechanisms influencing the dynamic shifts of rumen microbiome through the daily feeding cycle.<br><br>RESULTS: Quantification and profiling of the microbiota of 288 rumen samples collected from lactating dairy cows (n&#x2009;=&#x2009;12) every 6-h over 48-h feeding cycles under ad libitum, restricted feeding at daytime and nighttime, respectively, revealed the rhythmicity in the population and abundance of ruminal bacteria, archaea, and protozoa. Under restricted-feeding regimes, 61.99% bacterial genera including Prevotella and Ruminococcus, and 7.19% archaeal species including Methanosphaera sp. ISO3-F5, and 66.93% protozoa genera including Entodinium and Isotricha showed feeding-time-influenced changes in circadian rhythms. However, 4.76% bacterial genera such as Prevotellaceae_UCG-001, and 0.29% archaeal species such as group 12 sp. ISO4-H5 exhibited non-feeding-time affected circadian rhythm pattern shifts. Further analysis of 176 rumen fluid samples collected after rumen fluid transplantation showed the proportion of bacterial, archaeal, and protozoal taxa displayed consistent (including Anaeroplasma and Fibrobacter), inconsistent (including Bacteroidales_UCG-001 and NK4A214_group), gain (including Prevotella and Succinivibrio), and loss (including Butyrivibrio and Mycoplasma) of circadian rhythms over the 48-h to 7-day period after transplantation. Similar circadian patterns were found among feed intake, ruminal volatile fatty acid concentrations, bacterial functions such as glycolysis/gluconeogenesis, and deterministic assembly processes of bacterial communities. However, different circadian patterns (12-h shifts) were observed for rumination time, ruminal pH, ammonia nitrogen concentration, and bacterial functions such as chemotaxis, nitrogen metabolism, and deterministic assembly processes of archaeal communities. Additionally, cross-lagged effects were observed between the relative abundance of microbial taxa and rumen fermentation parameters, which could affect feed intake, rumination time, microbial population/diversity, and microbial interactions. Video Abstract CONCLUSIONS: The classified feeding-time responsive, multi-factor responsive, consistent, and inconsistent circadian rhythm of microbial taxa underscore the driven factors behind the daily dynamics of rumen microbes, which also filled the gaps for targeting specific microbial taxa for better animal production.},
}
@article {pmid40524209,
year = {2025},
author = {Huda, MN and Kelly, E and Barron, K and Xue, J and Valdar, W and Tarantino, LM and Schoenrock, S and Ideraabdullah, FY and Bennett, BJ},
title = {The impact of early-life exposures on growth and adult gut microbiome composition is dependent on genetic strain and parent- of- origin.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {143},
pmid = {40524209},
issn = {2049-2618},
support = {KES023849A/ES/NIEHS NIH HHS/United States ; R21DK122242/DK/NIDDK NIH HHS/United States ; 2032-51530-025-00D (//Agricultural Research Service/ ; 2019-07731//National Institute of Food and Agriculture/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/genetics/drug effects ; Mice ; Female ; Pregnancy ; Anti-Bacterial Agents/adverse effects/pharmacology ; Male ; Vitamin D Deficiency/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; Protein Deficiency/microbiology ; *Prenatal Exposure Delayed Effects/microbiology ; Dysbiosis/microbiology ; RNA, Ribosomal, 16S/genetics ; *Maternal Exposure/adverse effects ; Feces/microbiology ; Diet ; Mice, Inbred C57BL ; },
abstract = {BACKGROUND: Early-life exposure to environmental factors can have long-lasting impacts on offspring health into adulthood and therefore is an emerging public health concern. In particular, the impact of maternal environmental exposures such as diet and antibiotic use on the establishment of the offspring gut microbiome has been recently highlighted as a potential link to disease risk. However, the long-term effects are poorly understood. Moreover, interindividual host genetic differences have also been implicated in modulating the gut microbiome, suggesting that these differences may modulate susceptibility to environmentally induced dysbiosis and exacerbate related health outcomes. Our understanding of how the developmental environment and genetics interact to modulate offspring long-term gut microbiota and health is still limited.<br><br>METHODS: In this study, we investigated the effects of early exposure to known or putative dietary insults on the microbiome (antibiotic exposure, protein deficiency, and vitamin D deficiency) in a novel population of mice. Dams were maintained on purified AIN93G antibiotic-containing (AC), low-protein (LP), low-vitamin D (LVD), or mouse control (CON) diets from 5&#xa0;weeks prior to pregnancy until the end of lactation. After weaning, mice were transferred to new cages and fed a standardized chow diet. The parent-of-origin&#xa0;(PO) effect was determined via F1 offspring from reciprocal crosses of recombinant inbred intercross (RIX) of Collaborative Cross (CC) mice, where all F1 offspring within a reciprocal pair were genetically identical except for the X- and Y-chromosomes and mitochondrial genomes. We assayed offspring bodyweight and the gut bacterial microbiota via 16S rRNA gene sequencing at 8&#xa0;weeks of age.<br><br>RESULTS: Our study revealed that early developmental exposure to antibiotics, protein deficiency, and vitamin D deficiency had long-lasting effects on offspring bodyweight and gut microbial diversity and composition, depending on the genetic background. Several bacterial genera and ASVs, including Bacteroides, Muribaculaceae, Akkermansia, and Bifidobacterium, are influenced by developmental insults. We also observed a significant effect of PO on offspring gut microbiota and growth. For example, the offspring of CC011xCC001 mice had increased bodyweight, microbial diversity indices, and several differential bacterial abundances, including those of Faecalibaculum, compared with those of the corresponding reciprocal cross CC001xCC011.<br><br>CONCLUSION: Our results show that maternal exposure to nutritional deficiencies and antibiotics during gestation and lactation has a lasting impact on offspring gut microbiota composition. The specific responses to a diet or antibiotic can vary among F1 strains and may be driven by maternal genetics. Video Abstract.},
}
@article {pmid40524025,
year = {2025},
author = {Mallari, P and Rostami, LD and Alanko, I and Howaili, F and Ran, M and Bansal, KK and Rosenholm, JM and Salo-Ahen, OMH},
title = {The Next Frontier: Unveiling Novel Approaches for Combating Multidrug-Resistant Bacteria.},
journal = {Pharmaceutical research},
volume = {},
number = {},
pages = {},
pmid = {40524025},
issn = {1573-904X},
support = {190913//Svenska Kulturfonden/ ; 188147//Svenska Kulturfonden/ ; },
abstract = {BACKGROUND: The rapid occurrence of bacterial antibiotic resistance poses a significant threat to public health worldwide. Since particularly multidrug-resistant (MDR) pathogens are becoming untreatable with currently available antibiotics, new treatment modalities must be deployed.<br><br>OBJECTIVES: This review explores the recent advancements and the enduring challenges in new antibacterial&#xa0;development for drug-resistant organisms.<br><br>RESULTS: We describe how bacterial resistance to antibiotics arises and discuss why the traditional drug discovery&#xa0;routes are inefficient. The best alternative strategies to overcome these challenges might include exploring new&#xa0;bacterial pathways, utilizing compounds with antibacterial activities from the human microbiome, and repurposing&#xa0;existing drugs. Moreover, novel drug delivery mechanisms that leverage, for example, nanotechnology-based&#xa0;carriers may be breakthrough ideas that can increase antibiotic efficacy and, at the same time, reduce toxicity.&#xa0;Current clinical trials of next-generation drugs indicate that some treatments possess excellent potential to&#xa0;overcome the MDR issue.<br><br>CONCLUSION: Despite the substantial obstacles to getting bench findings to the patient, numerous scientists are still&#xa0;working towards this goal. Both the application of antibiotic stewardship principles and timely considerations through&#xa0;the regulatory pathways are needed to release the next generation of antibiotics that are suitable for the fight&#xa0;against superbugs.},
}
@article {pmid40523948,
year = {2025},
author = {Jenkinson, A and Harris, C and Bafadhel, M and Razavi, R and Dassios, T and Greenough, A},
title = {Longitudinal changes in cardiopulmonary outcomes of adults born extremely prematurely: United Kingdom Oscillation Study.},
journal = {Pediatric research},
volume = {},
number = {},
pages = {},
pmid = {40523948},
issn = {1530-0447},
abstract = {BACKGROUND: During puberty, lung function of individuals born extremely prematurely can deteriorate putting them at risk of early chronic obstructive pulmonary disease (COPD). We hypothesise that young adults exposed to postnatal corticosteroids will have poorer lung and cardiac function, higher pulmonary artery pressures and poorer exercise tolerance compared to preterm born adults not exposed to postnatal steroids and term born adults. We further hypothesise lung function differences may be demonstrated depending on mode of ventilation at birth (high frequency oscillatory or conventional ventilation) in preterm born adults.<br><br>METHODS: A prospective study of participants (aged 24-28) from the United Kingdom Oscillation Study (UKOS) and term born controls. Assessments will involve comprehensive lung function, cardiac ultrasound, exercise assessments, inflammatory cell and biomarker profiling and airway microbiome assessment. The primary outcome is the ratio of forced expiratory volume in 1&#x2009;s/forced vital capacity (FEV1/FVC); to detect a significant difference we will recruit 150 individuals. Statistical analysis will involve mixed effect models with adjustment for imbalances and sensitivity analysis.<br><br>DISCUSSION: The results may identify adults born extremely preterm at increased risk of COPD and pulmonary hypertension (PH) who might benefit from interventions to delay the onset of COPD and cardiovascular complications such as PH.<br><br>IMPACT: Adults born extremely prematurely in the modern era of neonatal care are an emerging population whose long-term outcomes have infrequently been reported. This study will describe their cardiac and lung function, pulmonary artery pressures, exercise capacity and immunobiological profile. We aim to identify risk factors for worse outcomes such as early chronic obstructive pulmonary disease onset and pulmonary hypertension. The results will identify those who might benefit from multi-disciplinary follow-up to ensure interventions are employed to delay the onset of COPD and manage longer term cardiovascular problems.},
}
@article {pmid40523927,
year = {2025},
author = {Beckers, KF and Flanagan, JP and Sones, JL},
title = {Correction: Microbiome and pregnancy: focus on microbial dysbiosis coupled with maternal obesity.},
journal = {International journal of obesity (2005)},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41366-025-01817-2},
pmid = {40523927},
issn = {1476-5497},
}
@article {pmid40523923,
year = {2025},
author = {Zhang, M and Liang, C and Li, B and Jiang, F and Song, P and Gu, H and Gao, H and Cai, Z and Zhang, T},
title = {Gut microbiome and diet contribute to ecological niche differentiation between argali (Ovis ammon hodgsoni) and blue sheep (Pseudois nayaur) on the Qinghai-Tibet Plateau.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {930},
pmid = {40523923},
issn = {2399-3642},
mesh = {Animals ; *Gastrointestinal Microbiome ; Tibet ; *Diet/veterinary ; Sheep/microbiology ; Ecosystem ; Herbivory ; },
abstract = {The gut microbiota plays a critical role in plant digestion, nutrient absorption, and ecological adaptation in herbivores. However, how gut microbiota and diet jointly influence ecological niche differentiation in sympatric species remains unclear. Here, we use metagenomic sequencing and plant trnL (UAA) fragment sequencing to examine the gut microbiota and dietary composition of sympatric Tibetan argali (Ovis ammon hodgsoni) and blue sheep (Pseudois nayaur) in the Kunlun Mountains of the Qinghai-Tibet Plateau. Despite inhabiting similar environments, the two species harbor distinct microbial compositions and functional profiles. Interestingly, higher dietary diversity does not correspond to higher microbial diversity. Tibetan argali, despite having a simpler diet, possesses a more diverse and flexible gut microbiome. In contrast, blue sheep show broader dietary preferences and stronger microbial metabolic adaptation to glycan biosynthesis and metabolism. These findings reveal significant associations between gut microbiota composition, function, and diet, supporting a microbial contribution to trophic niche differentiation. Our results highlight distinct microbial-dietary strategies in sympatric herbivores and underscore the role of the gut microbiome in ecological adaptation and species coexistence.},
}
@article {pmid40523636,
year = {2025},
author = {Melotto, KSK and Souza, RBMS and Fernandes, EL and Santos, LNA and Lima, LS and Silva, HL and Oliveira, SG and Félix, AP},
title = {Metronidazole-sulfadimethoxine combination affects diet digestibility, immunity indicators, fermentation metabolites, and intestinal microbiome of puppies.},
journal = {Journal of the American Veterinary Medical Association},
volume = {},
number = {},
pages = {1-9},
doi = {10.2460/javma.25.02.0109},
pmid = {40523636},
issn = {1943-569X},
abstract = {OBJECTIVE: This study aimed to evaluate the effects of a commercial metronidazole-sulfadimethoxine formulation on the apparent digestibility coefficients and metabolizable energy of the diet and immunity, gut permeability, fermentation metabolites, and intestinal microbiome of puppies.<br><br>METHODS: 12 growing Beagles (65 &#xb1; 14 days old) were divided into a control group (n = 6), without administration of antimicrobials, and an antimicrobials group (6), with oral administration (q 24 h) of 15 mg of metronidazole and 15 mg of sulfadimethoxine/kg of body weight for 5 days. Both groups were fed the same dry extruded diet for growing dogs for 80 days. Diet digestibility and fecal characteristic analyses were performed between days 20 and 25. Feces were collected for ammonia, pH, short-chain fatty acids, branched-chain fatty acids, phenols, indoles, biogenic amines, immunoglobulin A, and fecal microbiome analysis. In addition, blood samples were collected to analyze intestinal permeability and inflammatory and oxidative indicators.<br><br>RESULTS: The use of antimicrobials reduced the diet apparent digestibility coefficients of dry matter, organic matter, and crude protein and resulted in lower butyrate and higher branched-chain fatty acid concentrations in feces. The antimicrobials group had higher serum concentrations of nuclear factor &#x3ba;B and higher intestinal permeability. The use of antimicrobials reduced fecal immunoglobulin A (days 50 and 80), bacterial diversity, and genera such as Blautia and Turicibacter.<br><br>CONCLUSIONS: Metronidazole combined with sulfadimethoxine may negatively affect markers of intestinal functionality, increasing inflammation, and compromising the intestinal barrier function in puppies.<br><br>CLINICAL RELEVANCE: Antimicrobials may negatively affect intestinal health indicators in puppies, and veterinarians should consider their use carefully.},
}
@article {pmid40523420,
year = {2025},
author = {Bai, W and Jiang, T and Tang, L and Shao, C and Wei, M and Wang, Z and Zhao, M},
title = {A new anchor point for gut microbiome to regulate complications of allogeneic hematopoietic stem cell transplantation: oxidative stress.},
journal = {Experimental hematology},
volume = {},
number = {},
pages = {104833},
doi = {10.1016/j.exphem.2025.104833},
pmid = {40523420},
issn = {1873-2399},
abstract = {Teaser Abstract: Although there has been a large amount of reviews focusing on the relation between gut microbiome and the major complications after allogeneic hematopoietic stem-cell transplantation (allo-HSCT), few review have referred the role of oxidative stress in this process. The manuscript elucidates the mechanism of oxidative stress on allo-HSCT complications, summarize the interaction between GM and oxidative stress in the body, and highlight the role of GM regulation of oxidative stress in allo-HSCT complications. We hope to offer ideas to clinicians formulating new prophylaxis and treatment strategies of allo-HSCT complications. Finally, we would like to make the following declarations: The work described has not been submitted elsewhere for publication, in whole or in part, and all the authors listed have approved the manuscript that is enclosed. Allogeneic hematopoietic stem cell transplantation (allo-HSCT) is a cure for many malignant hematologic and metabolic diseases, whose complications are an unignorable cause of long-term prognosis. Pre-treatment chemoradiotherapy administered before and after transplantation alters the state of the bone marrow hematopoietic microenvironment. Under the stress of hematopoietic injury, a large number of hematopoietic stem cells (HSC) proliferate and differentiate, that produce large amounts of reactive oxygen species (ROS).And the chemotherapeutic pre-treatment drugs themselves also cause oxidative stress(OS),which can indirectly exacerbated OS of the bone marrow microenvironment. The bone marrow hematopoietic microenvironment and local oxidative stress affects the development of infections, relapse, graft-versus-host disease (GVHD), poor graft function (PGF), persistent thrombocytopenia (PT), chronic fatigue syndrome (CFS), bronchiolitis obliterans (BOS), transplant-associated thrombotic microangiopathy (TA-TMA), etc. Recent studies have demonstrated that the gut microbiome (GM) and its metabolites such as short chain fatty acids (SCFAs), secondary bile acids (SBAs), trimethylamine (TMA) and signaling molecules such as H2S and NO can enter the bloodstream through the intestinal epithelium and reach all parts of the body. This review describes the impact of oxidative stress on the development of allo-HSCT complications. In this paper, we will elucidate the mechanism of oxidative stress on allo-HSCT complications, summarize the interaction between GM and oxidative stress in the body, and highlight the role of GM regulation of oxidative stress in allo-HSCT complications, so as to offer new strategies for the prevention and treatment of allo-HSCT complications.},
}
@article {pmid40522628,
year = {2025},
author = {Urrutia-Carter, J and Madison, JD and Frederick, JA and Muletz Wolz, CR},
title = {Skin defenses and host-environment microbiome interactions in spotted salamanders.},
journal = {Integrative and comparative biology},
volume = {},
number = {},
pages = {},
doi = {10.1093/icb/icaf098},
pmid = {40522628},
issn = {1557-7023},
abstract = {Emerging infectious diseases have been of particular interest as a major threat to global biodiversity. In amphibians, two fungal sister taxa, Batrachochytrium dendrobatidis (Bd) and Batrachochytrium salamandrivorans (Bsal) along with the viral pathogen ranavirus have affected global populations. Factors such as host traits, abiotic and biotic environmental conditions, and pathogen prevalence contribute to species specific disease susceptibility. The eastern United States is home to the Appalachian Mountain system, known as a "hotspot" for salamander biodiversity. Bd and ranavirus are present throughout the Appalachians, and a Bsal emergence could be imminent. Throughout the Appalachians are the spotted salamanders, Ambystoma maculatum, a mostly terrestrial salamander that participates in mass breeding migration to ponds and vernal pools in the late spring. Previous experimental studies have shown that spotted salamanders appear to be resistant to Bd and Bsal infection, but the mechanisms behind Bd-defense remains unknown. Spotted salamanders emerging from their overwintering habitats were hypothesized to have potent anti-Bd function expressed in their mucus and in their skin microbiomes, as a countermeasure to annual Bd re-emergence. We used non-invasive sampling at two pools during the spotted salamander annual breeding event to (I) determine pathogen prevalence, (II) quantify the antifungal potential of salamander skin mucus, and (III) characterize the diversity and composition of the salamander skin microbiome and contrast it to that of the corresponding environmental microbiome. We did not detect any Bd, Bsal, or ranavirus in the salamanders. The salamander mucus did not inhibit Bd growth in vitro and anti-Bd bacteria were at low relative abundance in the microbiome. The salamander microbiome sourced a proportion of bacteria from the environment and appeared to select rare taxa from their respective pools, however their functional relevance in pathogen defense is unclear. Our results suggest that the spotted salamander mucosal secretions and skin microbiome are not the mechanisms of defense against Bd. Rather, elements not captured by the mucosome (e.g., immune cell gene expression) may confer resistance. This study contributes to the understanding of salamander intraspecies variation in disease susceptibility.},
}
@article {pmid40522380,
year = {2025},
author = {Saito, T and Karasawa, H and Ouchi, K and Ono, T and Kajiwara, T and Kohyama, A and Ikeda-Ohtsubo, W and Fukuda, S and Fujishima, F and Ozawa, Y and Suzuki, H and Watanabe, K and Ishioka, C and Kamei, T and Ohnuma, S and Abe, T and Unno, M},
title = {Characteristics of gut microbiota in high-methylated colorectal cancer.},
journal = {International journal of clinical oncology},
volume = {},
number = {},
pages = {},
pmid = {40522380},
issn = {1437-7772},
support = {JP22ek0210133//Japan Agency for Medical Research and Development (AMED)/ ; JP23zf0127001//Japan Agency for Medical Research and Development (AMED)/ ; JP23fk0108655//Japan Society for the Promotion of Science (JSPS) KAKENHI/ ; 24K11819//Japan Society for the Promotion of Science (JSPS) KAKENHI/ ; },
abstract = {BACKGROUND: Epigenetic alterations, including DNA methylation, significantly contribute to colorectal cancer (CRC); the gut microbiota is also involved. However, studies on the possible role of microbiota in DNA methylation are limited. This study investigates the association between gut microbiota composition and high-methylated CRC (HMCC).<br><br>METHODS: Fecal and tumor tissue samples were collected from 86 patients with sporadic CRC. HMCC was defined based on the methylation status of 16 CpG sites of tumor-derived genomic DNA. 16S rRNA gene sequencing was performed to reveal the composition of the gut microbiota. The load of Fusobacterium nucleatum (F. nucleatum) in tumor tissues was assessed using quantitative polymerase chain reaction (qPCR).<br><br>RESULTS: HMCC was identified in 21 patients, whereas 65 were classified as having low-methylated CRC (LMCC). HMCC was significantly associated with proximal location, large diameter, undifferentiated histology, and high frequency of BRAF mutation. In gut microbial analyses, the relative abundances of 84 bacteria, including F. nucleatum, were significantly different between HMCC and LMCC. The load of F. nucleatum in CRC specimens was significantly correlated with its relative abundance in fecal samples and tended to be enriched in HMCC tissues.<br><br>CONCLUSIONS: This study characterizes the gut microbiota profile in HMCC and suggests that bacteria, such as F. nucleatum, may contribute to HMCC pathogenesis through DNA methylation. Further studies are needed to determine whether the microbiome acts as a promoter or bystander in HMCC development.},
}
@article {pmid40522235,
year = {2025},
author = {Allam, AA and Rudayni, HA and Ahmed, NA and Alkhayl, FFA and Lamsabhi, AM and Kamel, EM},
title = {β-Glucuronidase Inhibition in Drug Development: Emerging Strategies for Mitigating Drug-Induced Toxicity and Enhancing Therapeutic Outcomes.},
journal = {Drug development research},
volume = {86},
number = {4},
pages = {e70118},
doi = {10.1002/ddr.70118},
pmid = {40522235},
issn = {1098-2299},
support = {//This study was supported and funded by the Deanship of Scientific Research at Imam Mohammad Ibn Saud Islamic University (IMSIU) (grant number IMSIU-DDRSP2501)./ ; },
mesh = {Humans ; *Glucuronidase/antagonists &amp; inhibitors/metabolism ; Animals ; *Drug Development ; Gastrointestinal Microbiome/drug effects ; *Enzyme Inhibitors/pharmacology ; *Drug-Related Side Effects and Adverse Reactions/prevention &amp; control ; Structure-Activity Relationship ; Glycoproteins ; },
abstract = {β-glucuronidase (βG) is a critical enzyme involved in the hydrolysis of glucuronide conjugates, significantly influencing drug metabolism, detoxification processes, and enterohepatic circulation. Although essential for maintaining physiological homeostasis, dysregulated βG activity has been implicated in diverse pathological conditions, including drug-induced toxicity, inflammation, and hormone-dependent cancers. Specifically, microbial βG expressed by gut microbiota can reactivate glucuronide-conjugated drugs, leading to adverse reactions through increased drug toxicity and reduced therapeutic efficacy. Consequently, inhibition of βG has emerged as an attractive therapeutic approach to reduce chemotherapy-induced toxicity, gastrointestinal complications, and metabolic disorders. This review systematically examines recent progress in the discovery, characterization, and optimization of βG inhibitors, focusing on natural products, synthetic molecules, and microbiome-targeted agents. Structure-activity relationship analyses reveal crucial functional groups and chemical modifications necessary for enhancing inhibitor potency, selectivity, and bioavailability. In addition, contemporary advances in βG inhibitor evaluation through enzyme kinetics, molecular docking simulations, high-throughput screening, and preclinical animal models are discussed, alongside essential pharmacokinetic parameters, including absorption, distribution, metabolism, excretion, and potential drug-drug interactions. Furthermore, emerging approaches such as microbiome modulation, CRISPR-based enzyme engineering, and combination therapies are explored. Despite promising preclinical outcomes, significant challenges remain regarding clinical translation, such as selectivity, bioavailability, and regulatory compliance. Ultimately, this review highlights future opportunities in precision medicine, emphasizing personalized βG inhibitor development to optimize therapeutic safety and effectiveness across various disease states.},
}
@article {pmid40522148,
year = {2025},
author = {Fejes, R and Séneca, J and Pjevac, P and Lutnik, M and Weisshaar, S and Pilat, N and Steiner, R and Wagner, KH and Woodman, RJ and Bondonno, CP and Hodgson, JM and Berry, D and Wolzt, M and Neubauer, O},
title = {Increased Nitrate Intake From Beetroot Juice Over 4 Weeks Changes the Composition of the Oral, But Not the Intestinal Microbiome.},
journal = {Molecular nutrition &amp; food research},
volume = {},
number = {},
pages = {e70156},
doi = {10.1002/mnfr.70156},
pmid = {40522148},
issn = {1613-4133},
support = {//Austrian Science Fund (FWF)/ ; KLI 858//Clinical Research (KLIF) program/ ; },
abstract = {Inorganic dietary nitrate, metabolized through an endogenous pathway involving nitrate reducing bacteria, improves cardiovascular health, but its effects on the oral and intestinal microbiomes of older adults with treated hypertension are unknown. Our study investigated the effects of nitrate from beetroot juice on the oral and intestinal microbiomes of this population. A randomized, double-blind, placebo-controlled crossover trial was conducted with 15 participants (age range: 56-71 years), who consumed nitrate-rich or nitrate-depleted (placebo) beetroot juice for 4 weeks. The oral microbiome analysis revealed an increase in Neisseria and a decrease in Veillonella relative abundance (for both, PERMANOVA p < 0.001), with no significant changes in the intestinal microbiome composition. Our findings suggest that an increased dietary nitrate intake from a vegetable source may selectively modulate the oral microbiome and promote an increased abundance of nitrate-reducing species, which was previously associated with improved cardiovascular health outcomes.},
}
@article {pmid40522116,
year = {2025},
author = {Li, W and Wang, M and Xu, K and He, J and Feng, X and Ma, G and Li, Y and Lai, H and Tang, A and He, C and He, Y and Jia, K and Liao, X and Yu, H and Tian, T and Liu, X},
title = {Coarse Grain Preference, Gut Microbiota Features, in Relation to Hypertriglyceridemia in Constipation Patients: A Cross-Sectional Study.},
journal = {Molecular nutrition &amp; food research},
volume = {},
number = {},
pages = {e70155},
doi = {10.1002/mnfr.70155},
pmid = {40522116},
issn = {1613-4133},
support = {82173504//National Natural Science Foundation of China/ ; 82011530197//National Natural Science Foundation of China/ ; TY0191118//BYHEALTH&#xa0;Nutrition and Health Research Foundation/ ; },
abstract = {Coarse grain (CG) benefits blood lipids involving gut microbiota regulations. Little is known about the relation between CG preference and blood lipids in constipation patients, and related gut microbiota features. Gut microbial genera and dietary information of 249 functional constipation participants are characterized by 16S rRNA sequencing and a food frequency questionnaire. CG preference was defined as a higher CG intake frequency than refined grain (RG) intake frequency. Compared with RG, CG preference was associated with a lower serum triglyceride (TG) (p = 0.015) and a lower risk of hypertriglyceridemia (HTG). The reallocations from RG to CG at frequencies of 3, 5, and 10 times per week were associated with reductions in the risk of HTG by 48%, 67%, and 89%, respectively. A machine learning based model using gut microbiota features well identified the likelihood of HTG, with the area under the curve achieving 0.79 (95% CI, 0.65-0.91). Furthermore, the microbiome risk score profiling HTG was negatively correlated with CG preference (r = -0.150, p = 0.021). Preferring coarse grain as a staple food was associated with lower HTG risk and differential gut microbiota features in constipation patients.},
}
@article {pmid40522112,
year = {2025},
author = {Li, L and Jin, Y and Li, T and Lv, B and Yuan, D and Li, X and Yuan, J},
title = {Flavonoid Polyphenols as Therapeutic Agents for Fatty Liver Disease: Mechanisms, Microbiome Interactions, and Metabolic Insights.},
journal = {Molecular nutrition &amp; food research},
volume = {},
number = {},
pages = {e70144},
doi = {10.1002/mnfr.70144},
pmid = {40522112},
issn = {1613-4133},
support = {202102AE090031//Major Science and Technology Project of Yunnan Province/ ; ZYXYB202410//Innovative Scientific Research Project of" key support and characteristic discipline of Yunnan first-class discipline- traditional Chinese Medicine"/ ; },
abstract = {Fatty liver disease (FLD), encompassing non-alcoholic fatty liver disease (NAFLD) and alcoholic fatty liver disease (AFLD), has become a major global health concern, primarily driven by unhealthy diets and lifestyle changes. Recently, flavonoids, which account for approximately 60% of polyphenolic compounds, have garnered attention for their antioxidant, anti-inflammatory, and immunomodulatory properties in combating metabolic diseases. This review summarizes recent advancements in the therapeutic potential of flavonoid polyphenols for treating FLD, with a focus on their bioactivity and mechanisms of action, interactions with the gut microbiome, and metabolic effects. The review discusses the bioactivity and biomarkers of flavonoids in treating FLD, their similar and differing roles in NAFLD and AFLD, regulation of gut microbiota, and synergistic mechanisms with other polyphenolic compounds. This review provides insights into the potential applications of flavonoids in treating fatty liver disease and suggests future research directions.},
}
@article {pmid40522093,
year = {2025},
author = {Dolo, O and Coulibaly, F and Somboro, AM and Sun, S and Diarra, M and Maiga, A and Bore, S and Fofana, DB and Marcelin, A-G and Diakite, B and Kassogue, Y and Holl, JL and Calvez, V and Traoré, CB and Murphy, R and Fodor, AA and Maiga, M and Maiga, AI},
title = {The human gut microbiome and its metabolic pathway dynamics before and during HIV antiretroviral therapy.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0220524},
doi = {10.1128/spectrum.02205-24},
pmid = {40522093},
issn = {2165-0497},
abstract = {The human gut microbiome consists of highly complex microbial populations that play important roles in disease pathogenesis. Changes in the gut microbiome are associated with HIV infection. However, it is unclear whether gut microbiome dysbiosis is causally linked to disease or whether it simply reflects disease-induced changes in the host immune and metabolic systems. This study aims to describe and compare intestinal microbial compositions and derived metabolic pathways in people living with HIV (PL-HIV) from prior to antiretroviral therapy (ART) to 6 and 12 months after ART initiation, compared to HIV-negative individuals. Whole-genome microbiome sequencing coupled with bioinformatics analysis was used to characterize participants' intestinal microbial structures and derived metabolic pathways. Pre- and post-ART gut microbiota characterization of PL-HIV revealed substantial dysbiosis compared to HIV-negative people. An enrichment of pro-inflammatory microorganisms was the hallmark of dysbiosis in the PL-HIV pre-ART, with a decline in Proteobacteria at 6 months of ART, continuing until 12 months of ART. Lower proportions of Bacteroidetes were noted pre-ART, but they increased slightly at 6 months of ART before decreasing again at 12 months of ART. Additionally, we reported metabolic changes that are particularly important for health and are associated with dysbiosis both before and post-ART. Alteration of the pyruvate fermentation to the isobutanol metabolic pathway persisted in PL-HIV after 12 months of ART, and this mechanism was correlated with a decrease in Ruminococcus bromii species. ART initiation appears to lead to changes in several crucial metabolic pathways and may not entirely restore the dysbiosis of the gut microbiota caused by HIV.IMPORTANCEResearchers are facing a major challenge in the treatment of HIV infection due to the continuous use of antiretroviral (ARV) molecules. However, regularly monitoring these molecules is necessary because they are not without consequences. They have toxicity and side effects and could also destabilize the intestinal microbiota, which could harm the metabolic pathways essential to good health. This study reveals that ARV treatment only partially restores gut microbiota dysbiosis and alters metabolic pathways due to pathogenic taxa. This provides additional insights into the relationship between antiretroviral therapy and the microbiome, potentially leading to new prevention and treatment strategies such as probiotic/prebiotic or microbiota transplants.},
}
@article {pmid40522089,
year = {2025},
author = {Hubert, J and Xiong, Q and Glowska-Patyniak, E and Furtak, EV and Klimov, PB},
title = {Analysis of the tripartite interactions between two bacterial symbionts, a novel Solitalea-like bacterium (Bacteroidota) and Cardinium, and the stored product mite Tyrophagus putrescentiae based on gene expression data.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0060925},
doi = {10.1128/spectrum.00609-25},
pmid = {40522089},
issn = {2165-0497},
abstract = {UNLABELLED: The intracellular parasite Cardinium influences the bacterial microbiome composition of arthropod hosts; however, the mechanisms involved remain poorly understood. We sought to evaluate the interactions between Cardinium (cTPut) and SOL in Tyrophagus putrescentiae cultures based on relative abundance and gene expression data. First, we assembled the genome of Candidatus Krakonobacterium acarorum (formerly the Soliltalea-like symbiont SOL), a novel lineage of the Bacteroidota symbiont of mites. The assemblage SOL genome (1.2 Mb) contained complete pathways for the biosynthesis of lipoic acids, pantothenate, and menaquinone from futalosine. SOL is considered a facultative inhabitant (with prevalences ranging from 36% to 80% among individuals) of the gut (from 10[2] to 10[4] copies/mite) that is not detected in eggs, suggesting an extracellular location in the gut of mites. Second, gene expression was analyzed in SOL-inhabited cultures, including two cultures with cTPut and two cultures without cTPut. Correlation-based evidence for competition between cTPut and SOL was found mainly in the expression of transporter proteins. The presence of cTPut decreased interactions between SOL and the mite host; however, SOL is under greater control by mites in the presence of cTPut than in the absence of cTPut. Mite KEGG gene expression levels in the peroxisome, autophagy, sphingolipid, apoptosis, PI3K-Akt, and lysozyme pathways were more strongly correlated with SOL gene expression in cultures without cTPut than in those with cTPut. In contrast, mite KEGG gene expression levels in the proteasome, NF-κB, TNF, calcium, and Rap1 signaling pathways were more strongly correlated with SOL in the presence of cTPut. The explanation for these results is that cTPut mostly interacts with the mite host, resulting in changes in the host's immunity-related/regulatory pathways, indirectly affecting the symbiont SOL.<br><br>IMPORTANCE: Here, we describe the novel Bacteroidetes symbiont (SOL) of mites. The analysis of gene expression in meta-transcriptomic samples from cultures with and without the intracellular parasite Cardinium revealed the effect of Cardinium on SOL as a model facultative symbiont of mites. Our findings suggest that there is competition between these two symbionts for nutrients. In addition, Cardinium can influence other bacterial symbionts via mite host immunity-related and regulatory pathways. Tyrophagus putrescentiae is a cosmopolitan pest mite that contaminates the home environment, including stored food and feed, with allergens. The interactions between intracellular bacteria and other members of the microbiome influence host physiology and indirectly affect allergen production.},
}
@article {pmid40521991,
year = {2025},
author = {Kulkarni, AS and Carrara, GMP and Jin, J and Laro, J and Peramuna, T and McCall, LI and Garg, N},
title = {Mass spectrometry-based metabolomics approaches to interrogate host-microbiome interactions in mammalian systems.},
journal = {Natural product reports},
volume = {},
number = {},
pages = {},
pmid = {40521991},
issn = {1460-4752},
abstract = {Covering: 2015 to 2025Chemical crosstalk is universal to all life, niche-specific, and essential to thrive. This crosstalk is mediated by a large diversity of molecules, including metal ions, small molecules, polysaccharides, nucleic acids, lipids, and proteins. Among these, specialized small molecules referred to as natural products (NPs) play an important role in microbe-drug/environment interactions, microbe-microbe, and microbe-host interactions. Microbial communication using NPs allows microbes to sense quorum, form biofilms, eliminate competition, establish symbiosis, evade immune attack, and respond to stress. In most cases, the elucidation of small molecule mediators and effectors of microbe-host interactions presents a major challenge due to the relatively low abundance of microbial metabolites in a milieu of host, microbe, and environmental metabolites. Advances in analytical instrumentation, such as mass spectrometers, and both experimental as well as computational methods to analyze data, coupled with the use of model organisms, have enabled fundamental discoveries of mechanisms of small molecule-mediated host-microbe interactions. The focus of this review is to detail the approaches applied in the last decade to disentangle microbiome-derived NPs in human and murine model systems. Select recent findings from diverse biological ecosystems are discussed to inform relevant parallels and potential strategies for research in human health.},
}
@article {pmid40521878,
year = {2025},
author = {Roos, M and Bunga, S and Tan, A and Maissy, E and Skola, D and Richter, A and Whittaker, DS and Desplats, P and Zarrinpar, A and Conrad, R and Kuersten, S},
title = {Optimizing mouse metatranscriptome profiling by selective removal of redundant nucleic acid sequences.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0016725},
doi = {10.1128/msystems.00167-25},
pmid = {40521878},
issn = {2379-5077},
abstract = {Metatranscriptome (MetaT) sequencing is a critical tool for profiling the dynamic metabolic functions of microbiomes. In addition to taxonomic information, MetaT also provides real-time gene expression data of both host and microbial populations, thus permitting authentic quantification of the functional (enzymatic) output of the microbiome and its host. The main challenge to effective and accurate MetaT analysis is the removal of highly abundant rRNA transcripts from these complex mixtures of microbes, which can number in the thousands of individual species. Regardless of the methodology for rRNA depletion, the design of rRNA removal probes based solely upon the taxonomic content of the microbiome typically requires very large numbers of individual probes, making this approach complex to commercially manufacture, costly, and frequently technically infeasible. In previous work (A. Tan, S. Murugapiran, A. Mikalauskas, J. Koble, et al., BMC Microbiol 23:299, 2023, https://doi.org/10.1186/s12866-023-03037-y), we designed a set of depletion probes for human stool samples using a design strategy based solely on sequence abundance, completely agnostic of the microbiomal species present. Here, we show that human-based probes are less effective when used with mouse cecal samples. However, adapting additional rRNA depletion probes specifically to cecal content provides both greater efficiency and consistency for MetaT analysis of mouse samples.IMPORTANCESequencing total RNA from microbiome samples is seriously impaired by the overwhelming proportion of rRNA to mRNA content. As much as 99% of sequencing reads can be assigned to the rRNA content, thus removal of these abundant transcripts is critical to metatranscriptome (MetaT) analysis. The use of Ribo Zero Plus rRNA depletion probes designed for human gut microbiomes proved to be less effective and more inconsistent across mouse cecal donor samples, a common experimental system for microbiome studies. In the present work, we have extended and refined a taxonomically neutral probe design method for mouse cecal content. The additional probes were carefully chosen to limit the number needed for effective depletion to reduce both the cost and risk of introducing bias to MetaT analysis. Our results demonstrate this method as efficient and consistent for rRNA removal in mouse cecal samples, thus providing a significant increase in the number of mRNA-rich sequencing reads for MetaT analysis.},
}
@article {pmid40521525,
year = {2025},
author = {Huang, YX and Tang, Q and Fu, SH and Zhong, HJ and Liu, Z and Zhong, QY and Wang, YH and Luo, YD and Li, XY and Chen, S and Zhu, HP},
title = {Comparison of Efavirenz and Dolutegravir on Gut Microbiome and Gut Barrier Functions.},
journal = {ACS omega},
volume = {10},
number = {22},
pages = {23099-23110},
pmid = {40521525},
issn = {2470-1343},
abstract = {Dolutegravir (DTG) is increasingly replacing efavirenz (EFV) as the recommended first-line antiretroviral therapy (cART) component due to its superior tolerance. However, both EFV-based and DTG-based cART regimens are associated with metabolic and neuropsychiatric disorders through mechanisms that remain poorly understood. In this study, the abundance of Lactobacillus was significantly reduced, along with elevated soluble CD14 levels, in HIV-1-infected individuals receiving EFV-based cART compared to those on DTG-based cART. Additionally, EFV treatment in mice resulted in the destruction of intestinal crypts, loss of goblet cells, decreased expression of intestinal ZO-1, and more severe damage to gut barrier integrity compared to the DTG and normal control groups. Furthermore, we identified a significant reduction in Lactobacillus in EFV-treated mice. Our results suggest that EFV and DTG may directly lead to gut dysbiosis and compromised gut barrier integrity, which could be targeted to prevent the side effects associated with EFV and DTG.},
}
@article {pmid40521400,
year = {2025},
author = {Niess, JH and Kaymak, T},
title = {Eosinophilic Esophagitis Pathogenesis: All Clear?.},
journal = {Inflammatory intestinal diseases},
volume = {10},
number = {1},
pages = {135-150},
pmid = {40521400},
issn = {2296-9365},
abstract = {BACKGROUND: Eosinophilic esophagitis (EoE) is a food- and aeroallergen-driven, type 2-mediated chronic inflammation that develops in genetically predisposed individuals with an impaired esophageal epithelial barrier. How pollutants, including detergents, the esophageal microbiome, immunity, and genetics trigger the multifaceted pathophysiology of EoE is not clear.<br><br>SUMMARY: This review summarizes and discusses recent findings concerning the possible contribution of the environment/exposome, the esophageal microbiome, genetics, immunity, and epithelial barrier integrity to developing esophageal type 2 inflammation and fibrosis in EoE. After summarizing the current literature, we formulate research questions that we consider relevant to EoE.<br><br>KEY MESSAGES: The anticipated progress in preclinical EoE animal models, primary cell culture technologies, sequencing technologies, and clinical trials, driven by academic research and the pharmaceutical industry, is poised to revolutionize our understanding of EoE. These advancements may uncover novel pathways that can be targeted for EoE treatment, inspiring hope for improved patient quality of life.},
}
@article {pmid40521100,
year = {2025},
author = {Kobelt, T and Klose, J and Mukherjee, R and Lippmann, M and Szafranski, SP and Stiesch, M and Zimmermann, S},
title = {Identification of anaerobic bacterial strains by pyrolysis-gas chromatography-ion mobility spectrometry.},
journal = {Frontiers in bioengineering and biotechnology},
volume = {13},
number = {},
pages = {1582565},
pmid = {40521100},
issn = {2296-4185},
abstract = {The rapid identification of bacterial pathogens is critical for the early diagnosis of severe clinical conditions, such as sepsis or implant-associated infections, and for the initiation of timely, targeted therapies. This need is particularly acute within the complex oral microbiome, where diverse opportunistic pathogens contribute to a range of local and systemic diseases. While techniques such as phenotypic systems and MALDI-TOF-MS offer faster results, they remain limited by costs, and operational constraints. To address these challenges and cater to the need for rapid identification of bacteria, we present a system for identification and classification of anaerobic bacteria as a first example. This system combines a pyrolyzer, a gas chromatograph and a highly sensitive ion mobility spectrometer. The ion mobility spectrometer has been optimized for coupling with the gas chromatograph and offers simultaneously recording of ion mobility spectra in both ion polarities during one gas chromatographic separation by using two drift tubes arranged in axial configuration. Feasibility has been demonstrated by building a database of fingerprints of eleven isolated reference samples of anaerobic bacteria with clinical relevance. Preliminary experiments have demonstrated that pattern recognition algorithms can predict the genus of isolated bacteria with a precision of up to 97%.},
}
@article {pmid40521029,
year = {2025},
author = {Chu, X and Li, S and Wang, Y and Guo, D and Zhao, N and Han, Y and Xing, Q},
title = {Alteration in gut microbiota accompanied by increased intestinal permeability and Tfh/Tfr imbalance in patients with active SLE.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1565416},
pmid = {40521029},
issn = {2235-2988},
mesh = {Humans ; *Lupus Erythematosus, Systemic/immunology/microbiology/pathology ; *Gastrointestinal Microbiome/immunology ; Female ; Male ; Adult ; Haptoglobins ; *T-Lymphocytes, Regulatory/immunology ; Feces/microbiology ; Middle Aged ; Permeability ; Protein Precursors ; RNA, Ribosomal, 16S/genetics ; Cholera Toxin ; Cytokines/metabolism ; *T Follicular Helper Cells/immunology ; Intestinal Mucosa/microbiology ; Interleukin-2 ; Interleukin-21 ; Interleukins ; Intestinal Barrier Function ; },
abstract = {BACKGROUND: Increased intestinal permeability and altered intestinal microbiota may influence cytokine regulatory immunity in systemic lupus erythematosus (SLE). This study aimed to elucidate the relationship between intestinal flora alters and follicular helper T cells (Tfh), regulatory T cells (Treg) cells, and cytokines in SLE.<br><br>METHODS: In total, 23 patients with active SLE (SLE-A group), 18 patients with stable SLE (SLE-nA group), and 24 healthy controls (HC group) were enrolled. Tfh, follicular T regulatory (Tfr), and Treg cells were measured by flow cytometry, and fecal samples were analyzed using 16S rRNA gene sequencing. The relationship between the gut microbiome and the SLE disease activity index (SLEDAI-2k), zonulin (an indicator of intestinal permeability), IL-2, IL-6, and IL-21 levels was analyzed.<br><br>RESULTS: Decreased Treg cells and imbalanced Tfh/Tfr were associated with elevated disease activity in SLE-A group. The increase in zonulin levels in SLE-A group indicated worsened intestinal mucosal barrier damage, potentially linked with the increase in the dominant microflora Escherichia-Shigella. Furthermore, the increase in zonulin was correlated with a severe imbalance in Tfh/Tfr. Moreover, decreased IL-2 levels were associated with a decrease in Ruminococcus and may modulate the reduction in Treg cells during disease progression. Zonulin also exhibited a negative correlation with IL-2.<br><br>CONCLUSION: Zonulin may be involved in the Tfh/Tfr immune imbalance in patients with SLE, and Faecalibacterium and Ruminococcus may contribute to disease development by regulating Treg cells and Tfh/Tfr imbalance. Taken together, these findings may provide new insights into the role of cytokines in the treatment of SLE.},
}
@article {pmid40521024,
year = {2025},
author = {Biesel, EA and Sundheimer, J and Badr, MT and Posadas-Cantera, S and Chikhladze, S and Fichtner-Feigl, S and Wittel, UA},
title = {Microbiological colonization of the pancreatic tumor affects postoperative complications and outcome after pancreatic surgery.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1521952},
pmid = {40521024},
issn = {2235-2988},
mesh = {Humans ; *Pancreatic Neoplasms/surgery/microbiology ; Male ; Female ; Aged ; Middle Aged ; *Postoperative Complications/microbiology/epidemiology ; Prospective Studies ; *Bacteria/classification/isolation &amp; purification ; *Pancreas/microbiology/surgery ; Aged, 80 and over ; Carcinoma, Pancreatic Ductal/surgery/microbiology ; Microbiota ; Adult ; Pancreatectomy/adverse effects ; Fungi/isolation &amp; purification/classification ; },
abstract = {BACKGROUND: The patient´s microbiome has become a focal point in cancer research. Even for pancreatic cancer, alterations in the microbiome appear to influence cancer formation and progression. The aim of our single-center analysis was the examination of microbiological colonization of pancreas tissue at the time of surgery and its potential influence on complications and outcome.<br><br>METHODS: We prospectively evaluated patients undergoing pancreatic surgery over a three-year period from June 2018 to June 2021. We focused on the microbiological colonization of pancreatic tissue which was acquired during pancreatic surgery. Tissue samples were cultivated at our institute of microbiology. Patients&#xb4; characteristics, complications and postoperative outcome were analyzed using a prospectively maintained SPSS database.<br><br>RESULTS: Between June 2018 and June 2021, we collected pancreatic tissue samples of a total of 178 patients undergoing pancreas resections, mostly due to ductal adenocarcinoma (PDAC; 50.6%). We could cultivate bacterial or fungal species in pancreatic tissue samples of 50 of our patients (28.1%). The majority of cases were characterized by the presence of a single microbial species, but 20 patients (11.2%) showed colonization with up to four different species. Among the bacterial species detected were Enterococcus faecium, Enterococcus faecalis, Escherichia coli, Staphylococcus aureus, Enterobacter cloacae and Klebsiella pneumonia. We found significantly more microbiological culture growth in patients with a preoperative biliary stent (74.0% vs. 15.6%, p < 0.001). Concerning postoperative complications, we found no difference concerning pancreatic fistula, but colonization with E. coli was associated with a significantly higher rate of postpancreatectomy hemorrhage (30.0% vs. 8.9%, p = 0.032). Interestingly, survival of PDAC patients seems to be negatively affected by positive microbiological findings at the time of surgery, but without reaching statistical significance (p = 0.770).<br><br>CONCLUSION: In this first analysis of our patient cohort, we could show a microbiological colonization of pancreatic tumor tissue in almost a third of our patients. There seems to be only a minor impact on postoperative complications, but long-term outcome seems to be worse in patients with a positive pancreas microbiome. Further observation is needed to evaluate the influence of the tumor microbiome on the long-term oncological outcome in PDAC patients.},
}
@article {pmid40520965,
year = {2025},
author = {Lorenzini, G and Nali, C},
title = {Plant protection, the Cinderella of the one health strategy?.},
journal = {One health (Amsterdam, Netherlands)},
volume = {20},
number = {},
pages = {101080},
pmid = {40520965},
issn = {2352-7714},
abstract = {Plant and microbiome health are fundamental to life on Earth, human well-being, and planetary health, yet their importance is often underestimated. Human and animal health depend on plant health for food security (nutritious food production, economic growth), food safety (contamination risks), ecosystem services (air quality, mental health benefits), and mitigating antimicrobial resistance (from agricultural antibiotic use). Plant health specialists are crucial for plant health, food security, and achieving the Sustainable Development Goals within a One Health framework. Plant diseases and pests can significantly impact food production, economic stability, and public health. To address these challenges, we need to integrate plant health into the One Health framework. This requires collaboration between plant scientists, veterinarians, human health experts, and environmental scientists. By working together, we can develop more sustainable and holistic approaches to agriculture and public health.},
}
@article {pmid40520922,
year = {2025},
author = {Martell, M and Quarnstrom, CF and Khoruts, A and Vezys, V and Staley, C and Shmidt, E},
title = {Chronic Intestinal Inflammation and Microbial Dysbiosis Are Associated With Female Reproductive Outcomes in a Mouse Model of Inflammatory Bowel Disease.},
journal = {Gastro hep advances},
volume = {4},
number = {7},
pages = {100670},
pmid = {40520922},
issn = {2772-5723},
abstract = {BACKGROUND AND AIMS: The mechanism for increased infertility and adverse pregnancy outcomes in women with active inflammatory bowel disease is unknown. We aimed to create a murine model of chronic gut inflammation to study the pathogenesis of reproductive outcomes in inflammatory bowel disease.<br><br>METHODS: Chronic intestinal inflammation was induced with dextran sodium sulfate (DSS) in specific-pathogen-free (SPF) female mice. SPF mice not treated with DSS served as controls. Daily estrous cycle monitoring was performed. Age-matched groups were cohabitated with SPF males for mating purposes. Pup weights, litter sizes, reproductive hormone serologies, peripheral and mucosal immune changes, and 16S rRNA gene taxonomic profiling of the fecal microbiome were measured and characterized.<br><br>RESULTS: DSS treatment led to weight loss, increased disease activity index scores, and reduced colon lengths. Compared to SPF controls, DSS mice spent less time in the estrus phase of the reproductive cycle (P < .05) and had decreased litter sizes and pup weights (P < .05). DSS-treated mice had lower anti-m&#xfc;llerian hormone and luteinizing hormone (P < .05) concentrations and higher estradiol (P < .05) concentrations. Among DSS mice, Turicibacter abundance correlated positively with the proportion of circulating neutrophils and proinflammatory cytokines and serum estradiol (Spearman &#x3c1; = 0.538-0.650, P < .001-.002). Lactobacillus and Prevotellaceae positively correlated with pup weights, litter size, estrus phase duration, luteinizing hormone, and immune cell changes from the colon and peripheral blood (&#x3c1; = 0.475-0.695, P < .01).<br><br>CONCLUSION: Chronic bowel inflammation induces gut dysbiosis and likely contributes to adverse reproductive outcomes through endocrine imbalances. Further investigation with human studies is needed.},
}
@article {pmid40520912,
year = {2025},
author = {Duan, Y and Siegenthaler, A and Skidmore, AK and Heurich, M and Abdullah, H and Chariton, AA and Laros, I and Rousseau, M and de Groot, GA},
title = {Landscape-scale variation in the canopy mycobiome in temperate beech and spruce forest stands explained by leaf water content and elevation.},
journal = {European journal of forest research},
volume = {144},
number = {3},
pages = {443-455},
pmid = {40520912},
issn = {1612-4669},
abstract = {UNLABELLED: Fungi represent a significant portion of Earth's biological diversity and are essential for ecosystem functions like organic matter decomposition and nutrient cycling. While fungi associated with plant roots have been extensively studied, our understanding of fungi in the forest canopies remains limited. To investigate the landscape-scale variation in the canopy mycobiome of temperate beech and spruce forest stands in the Bavarian Forest National Park (Germany), we examined the influence of geophysical conditions and host traits. We found that elevation significantly influenced fungal diversity and composition, with distinct effects observed in both beech and spruce stands. Moreover, canopy water content, a key indicator of tree vitality, was also strongly associated with changes in the canopy fungi community, suggesting a potential link between forest water stress and the forest canopy mycobiome. Our differential abundance analysis further identified a total of 41 fungal families as potential bioindicators: 17 families in beech stands and 9 in spruce stands were significantly associated with elevation, while 9 families in beech stands and 6 in spruce stands were linked to variations in leaf water content. These findings enhance our understanding of the spatial patterns of forest canopy microbial biodiversity and species distributions.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s10342-025-01768-3.},
}
@article {pmid40520768,
year = {2025},
author = {Feng, Z and Burgermeister, E and Philips, A and Zuo, T and Wen, W},
title = {The gut virome in association with the bacteriome in gastrointestinal diseases and beyond: roles, mechanisms, and clinical applications.},
journal = {Precision clinical medicine},
volume = {8},
number = {2},
pages = {pbaf010},
pmid = {40520768},
issn = {2516-1571},
abstract = {The gut virome, an essential component of the intestinal microbiome, constitutes ∼0.1% of the total microbial biomass but contains a far greater number of particles than bacteria, with phages making up 90%-95% of this virome. This review systematically examines the developmental patterns of the gut virome, focusing on factors influencing its composition, including diet, environment, host genetics, and immunity. Additionally, it explores the gut virome's associations with various diseases, its interactions with gut bacteria and the immune system, and its emerging clinical applications.},
}
@article {pmid40520642,
year = {2025},
author = {Sinisterra Loaiza, LI and Fernández-Edreira, D and Liñares-Blanco, J and Cepeda, A and Cardelle-Cobas, A and Fernandez-Lozano, C},
title = {Fecal microbiome analysis in patients with metabolic syndrome and type 2 diabetes.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e19108},
pmid = {40520642},
issn = {2167-8359},
mesh = {Humans ; *Diabetes Mellitus, Type 2/microbiology ; *Metabolic Syndrome/microbiology ; Male ; Female ; *Feces/microbiology ; Middle Aged ; *Gastrointestinal Microbiome ; Adult ; Aged ; Spain ; RNA, Ribosomal, 16S/genetics ; Cohort Studies ; },
abstract = {BACKGROUND: Metabolic syndrome (MS) and type 2 diabetes (T2D) are metabolically related diseases with rising global prevalence and increasingly evident links to the intestinal microbiota. Research suggests that imbalances in microbiota composition may play a crucial role in their pathogenesis. Specific population cohorts, such as the one in Galicia, Spain, offer the opportunity to analyze microbiota patterns within a distinct geographical and genetic context. This study was performed to investigate the relationship between the intestinal microbiota and MS and T2D.<br><br>METHODS: A cohort of 79 volunteers was analyzed over a 2-year study period. Recruitment posed significant challenges because of strict inclusion criteria (918PTE0540; PCI2018-093284), which required participants to be free from chronic medications and have a moderate to high risk of developing T2D. Volunteers were classified based on their serum glucose levels, body mass index, and the presence or absence of MS. To analyze the microbiota composition, amplicon sequencing of 16S rRNA genes was performed on stool samples. Alpha diversity was assessed using the Chao and Shannon indices, while beta diversity was evaluated using permutational analysis of variance with Bray-Curtis and Chao distances. Differential abundance analysis was conducted using the LinDA method.<br><br>RESULTS: In patients with MS, we observed a higher Firmicutes/Bacteroidetes ratio and an increased prevalence of Blautia compared to healthy patients. than in healthy individuals. Other enriched taxa in patients with MS included Tyzerella, Streptococcus, and Ruminococcus callidus. In patients with T2D, we observed a higher Bacteroidetes/Firmicutes ratio and a decrease in the phylum Actinobacteria compared with healthy individuals. Taxa such as Dorea, Prevotella, Dialister invisus, Fusicatenibacter, and Coprococcus were associated with T2D, while beneficial taxa such as Eubacterium, Ligilactobacillus, and Acidaminococcus were more prevalent in healthy or prediabetic individuals.<br><br>CONCLUSIONS: This study reveals notable differences in the intestinal microbiota composition among patients with MS and T2D. Changes in microbial composition, particularly the Firmicutes/Bacteroidetes ratio, may serve as indicators of underlying pathology. At more specific taxonomic levels, several enriched taxa were identified in patients with MS, including Blautia, Tyzzerella, Dorea, Streptococcus, and Ruminococcus callidus. Additionally, species such as Dorea longicatena and Dialister invisus were enriched in prediabetic and diabetic patients, whereas beneficial genera (Eubacterium, Acidaminococcus, Bifidobacterium, and Ligilactobacillus) were more prevalent in healthy and prediabetic individuals than in those with T2D.},
}
@article {pmid40520523,
year = {2025},
author = {Zaki, EA and Afifi, SM and Ammar, NM and Kadry, MO},
title = {Assembled human microbiome and metabolome in chronic kidney disease: Dysbiosis a double-edged sword interlinking Circ-YAP1, Circ-APOE &amp; Circ-SLC8A1.},
journal = {Toxicology reports},
volume = {14},
number = {},
pages = {102058},
pmid = {40520523},
issn = {2214-7500},
abstract = {Dysbiosis is an alteration in microbiota diversity previously elucidated in patients with chronic kidney disease (CKD). Relationship between dysbiosis and CKD is bidirectional; Uremic milieu disturbs the human microbiota on the other hand, gut metabolites influence CKD development. As a result, we outline the possible contribution of microbiota in the pathophysiology, diagnosis and monitoring of CKD. A growing body of research indicates that changes in circular RNAs (circ-RNAs) were observed in CKD with pathogenic implications, including modifying intracellular signaling, exaggerating oxidative stress, cellular apoptosis and inflammation. Additionally, Circ-RNAs exhibit promising role in clinical settings for monitoring, diagnosis, prognostication, and treatment of CKD. Herein blood samples were collected from 60 Egyptian patients with CKD as well as 60 healthy volunteers who served as controls. Following clinical evaluations, OPLS-DA and PCA GC-MS analysis were performed to detect metabolite perturbations. The levels of toxic uremic metabolites, such as urea, hexanedioic acid, ribonic acid, dodecanoic acid, pyrimidine, 1H-indole, 1H-indole-3-acetic acid, butanoic acid, L-cystine, and benzaldehyde linked to renal fibrosis were found to be elevated. Conversely, Reno-protective metabolites, such as short-chain fatty acids; 1H-indole were found to be negatively correlated with indole propionic acid, acetic acid, 2-propenoic acid, tryptophan, tyrosine, and glucitol (AUC 0.65) derived from the gut flora. CKD patients clarified an alteration both gene and protein expression of circRNAs (Circ-YAP1, circ-APOE, and circ-SLC8A1)/mTOR. Moreover, these biomarkers had a significant correlation with clinical investigations such as Creatinine, Glomerular filtration rate (GFR) and albumin/Creatinine (A/C) ratio. These results shed some light on the metabolic biomarkers that are associated with CKD and novel insights into metabolomics/microbiota/Circ-YAP1/circ-APOE/circ-SLC8A1/mTOR interlinked with disease prognosis/diagnosis that could be translated into clinically relevance.},
}
@article {pmid40520420,
year = {2025},
author = {Blankenberger, A and Lesmana, E and Yang, L and Comba, IY and Edwinson, A and Breen-Lyles, M and Keehn, A and Patel, R and Chen, J and Mars, RA and Kashyap, P and Farrugia, G and Grover, M},
title = {Longitudinal Changes in the Gut Microbiome of Patients With Irritable Bowel Syndrome After Campylobacter Infection are Associated With Proteolytic Activity.},
journal = {Gastro hep advances},
volume = {4},
number = {8},
pages = {100683},
pmid = {40520420},
issn = {2772-5723},
}
@article {pmid40520381,
year = {2025},
author = {Ashraf, H and Rezasoltani, S and Feizabadi, MM and Jasemi, S and Aghdaei, HA and Bakudezfouli, Z and Ijaz, UZ and Sechi, LA},
title = {On exploring cross-sectional stability and persistence of microbiome in a multiple body site colorectal cancer dataset.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1449642},
pmid = {40520381},
issn = {1664-302X},
abstract = {There are several ways to recover signature microbiome of a disease pathology. One way is to look at the core microbiome, which comprises microbial species prevalent across majority of the samples. At a finer level, certain subcommunities may exhibit stable signature across the sampling space. There can also be similarity of differential patterns across different body sites. In view of above, and leveraging recent advancements in analytical strategies, we revisit a multi-factorial Iranian ColoRectal Cancer (CRC) dataset, and explore stable and persistent patterns in the microbiome. For this purpose, 16S rRNA gene is amplified from saliva and stool samples of CRC patients using healthy controls as a baseline (n = 80). The dataset is supplemented with demographical and nutritional data of the study participants that were collected through filled questionnaire. Our results indicate that certain microbial species i.e., Actinobacteriota, Bifidobacterium, Prevotella and Fusobacterium are consistently present in the CRC patients suggesting their potential as diagnostic biomarkers of disease. Additionally, we identified a group of microbes such as Akkermansia, Selenomonas, Clostridia_UCG-014, Lautropia, Granulicatella, Bifidobacterium, and Gemella that exhibit similar differential response across body sites irrespective of where they are found, whether in saliva or stool samples. This suggest that a part of saliva microbiome can act as a proxy for stool microbiome giving further credence to oral-gut axis. Overall, our findings underscore the importance of exploring stable microbial biomarkers in multifactorial CRC dataset by marginalizing out variabilities, with the potential for improved diagnosis and treatment strategies.},
}
@article {pmid40520375,
year = {2025},
author = {Jin, L and Zhang, P and Sun, K and Wang, H},
title = {Gut microbiota dynamics and their impact on body condition in nestlings of the yellow-rumped flycatchers, Ficedula zanthopygia.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1595357},
pmid = {40520375},
issn = {1664-302X},
abstract = {Investigating the gut microbiome during host development is essential for understanding its influence on host health and fitness. While host body condition is a crucial fitness-related trait and a strong predictor of viability in numerous animal species, its relationship with gut bacteria remains underexplored, particularly in non-model organisms. This study examines the gut microbiome of the altricial wild bird species, yellow-rumped flycatchers (Ficedula zanthopygia), by analyzing nestling feces through 16S rRNA sequencing at four developmental stages: Day 3, Day 6, Day 9 and Day 12 post-hatching. We explored the temporal dynamics of the gut microbiome and its correlation with body condition, a key indicator of fitness. Our results demonstrate signinficant shifts in microbial community composition and diversity throughout development. Notably, Day 3 nestlings displayed lower alpha diversity compared to later stages, while microbial diversity stabilized from Days 6 to 12. Both the age of the nestlings and the environmental conditions of the nest box significantly shaped the gut microbial community structure. A contemporaneous relationship was observed, where the scaled-mass index (SMI) at Day 6 positively correlating with microbial diversity at that time. Additionally, a time-lagged effect emerged, linking SMI at Day 9 to microbial diversity at Day 6. These findings highlight the vital role of the gut microbiome in the development of nestlings, particularly emphasizing Day 6 as a critical period due to its stable microbial diversity and association with SMI. This study underscores the influence of gut bacteria on host fitness in developing birds.},
}
@article {pmid40520172,
year = {2025},
author = {Hao, F and Zeng, M and Cao, B and Liang, X and Hao, Z and Ye, K and Jiao, X and Feng, W and Zheng, X},
title = {7-α-O-Methylmorroniside ameliorated brain injury in 5×FAD mice by regulating the gut microbiome and NMDAR2B.},
journal = {Frontiers in pharmacology},
volume = {16},
number = {},
pages = {1545566},
pmid = {40520172},
issn = {1663-9812},
abstract = {Alzheimer's disease (AD) is a neurodegenerative disorder characterized by cognitive decline. 7-α-O-Methylmorroniside (MorA), an iridoid glycoside extracted from Cornus officinalis Sieb. et Zucc., has been shown to have neuroprotective effects, but the mechanism of its anti-AD effect has not been clarified. In the present study, we investigated the mechanism by which MorA ameliorated brain injury in 5×FAD mice by using gut microbiota (GM) combined with in vitro and in vivo pharmacological experiments. Behavioral tests revealed that MorA could enhance learning and memory ability and improve cognitive impairment. The results of pathology, flow cytometry and biochemical indexes showed that MorA could reduce the levels of neuronal apoptosis, oxidative stress, Aβ1-40, Aβ1-42, p-Tau, and inflammatory factors in the mouse brain tissues, and improve brain damage. 16S rDNA sequencing showed that MorA increased the abundance of the beneficial bacterium Lactobacillus and decreased the abundance of the inflammation-associated Muribaculaceae and Prevotellaceae, and that these differential bacteria were closely associated with brain biochemical indicators. In addition, pathway enrichment analysis, Western blot and molecular docking results showed that the ameliorative effect of MorA on brain injury in 5×FAD mice was closely related to NMDAR2B. Next, an inhibitor of NMDAR2B was added to Aβ25-35-induced N9 and PC12 cells to further investigate whether the effect of MorA on AD was mediated through NMDAR2B. In conclusion, MorA ameliorated brain injury in 5×FAD mice by restoring GM homeostasis and inhibiting NMDAR2B.},
}
@article {pmid40519728,
year = {2025},
author = {Liu, F and Sun, Y and Wang, J and Zhan, J},
title = {Study on the pathogenesis of idiopathic pediatric acute pancreatitis by combining intestinal microbiome and metabolome.},
journal = {Translational pediatrics},
volume = {14},
number = {5},
pages = {855-870},
pmid = {40519728},
issn = {2224-4344},
abstract = {BACKGROUND: Idiopathic pediatric acute pancreatitis (IPAP) represents a significant health threat to children and adolescents, yet its underlying pathogenesis remains poorly understood, necessitating further research to elucidate its mechanisms. This study aims to explore the roles of intestinal microbiota, short-chain fatty acids (SCFAs), and serum metabolites in the pathogenesis of IPAP, as well as to assess the therapeutic potential of acetic acid intervention in this condition.<br><br>METHODS: Fecal and serum samples from 22 cases of IPAP (excluding biliary origin) and 10 healthy controls were collected and analyzed. Intestinal microbial was characterized using 16S ribosomal RNA (16S rRNA) sequencing, while SCFAs and serum metabolites were quantified by liquid chromatography-tandem mass spectrometry (LC-MS/MS). Omics analysis was employed to identify microbial-metabolite regulation and regulatory networks and potential disease biomarkers. To evaluate the therapeutic efficacy of acetic acid in acute pancreatitis (AP), AP was induced in animal models by intraperitoneal injection of caerulein (50 &#xb5;g/kg; once daily for seven days), followed by oral administration of acetic acid (10 mL/kg, once daily) in 4-, 6-, and 8-week models. Pancreatic and ileum tissues were examined for histopathological changes, serum enzymes levels, and intestinal barrier integrity.<br><br>RESULTS: The results of 16S rRNA sequencing revealed significant differences in the composition and abundance of intestinal microbial communities between the control (Con) and IPAP groups. Pathogenic bacteria, such as f_Tannerellaceae and c_Bacteroidia, as well as certain symbiotic bacteria, were significantly enriched in the IPAP group. SCFAs metabolome analysis indicated that acetic acid, as a key intermediate metabolite, may play a regulatory role in the pathogenesis of IPAP. The construction of a microbial-metabolite regulatory network demonstrated that microorganisms such as g_Monoglobus and g_Morganella were closely associated with SCFAs, including acetic acid, suggesting that the development of IPAP is influenced by upstream and downstream regulatory mechanisms. Furthermore, significant associations were identified between serum metabolites and gut microbes. For instance, (4E,15E)-bilirubin and creatinine showed significant positive correlations with g_Bacteroides (P<0.01). Similarly, 1,2-ethanediol monoricinoleate was significantly positively correlated with g_Hungatella (P<0.01), while pubescenol and tecastemizole were significantly positively correlated with g_Parabacteroides (P<0.01). Animal experiments demonstrated that pancreatic and intestinal tissue damage was alleviated to varying degrees following treatment. Compared to the disease model group, the acetic acid treatment group exhibited significantly reduced serum levels of D-lactic acid, amylase, and lipase, along with a significantly increased positive staining surface density of intestinal barrier proteins (occludin, claudin-1, and ZO-1).<br><br>CONCLUSIONS: Intestinal flora, SCFAs and serum metabolites were significantly altered in IPAP, and the interaction regulated the development of IPAP. Acetic acid can effectively intervene the occurrence of IPAP.},
}
@article {pmid40519668,
year = {2025},
author = {Miller, SJ and Zhang, F and Taylor, SL and Shoubridge, AP and Flynn, E and Vasil, E and Woodman, RJ and Papanicolas, LE and Rogers, GB},
title = {Oropharyngeal detection of specific gut-derived Enterobacterales is associated with increased respiratory infection risk in older adults.},
journal = {Frontiers in aging},
volume = {6},
number = {},
pages = {1566034},
pmid = {40519668},
issn = {2673-6217},
abstract = {Respiratory tract infections (RTI) are a major contributor to morbidity and mortality in later life. RTI risk factors in older populations, including declining general health, altered airway physiology, and increased pharmaceutical exposures, also contribute to changes in the oropharyngeal (OP) microbiota. We sought to investigate whether such changes predict future incidence of RTI. OP microbiota characteristics were measured in 190 residents of long-term aged care. Fifty-four participants (28.4%) experienced one or more study-defined RTIs during the 12-month follow-up period, of which 28 (14.7%) occurred within 90 days of sample collection. OP microbiota composition was significantly associated with days to RTI event (F = 1.74, R[2] = 1.02%, p = 0.04). Detection of Enterobacterales species (Enterobacter cloacae, Escherichia coli, Klebsiella oxytoca, Klebsiella pneumoniae, Klebsiella variicola, and Proteus mirabilis) were independently associated with RTI risk after covariate adjustment (subdistribution HR: 4.84; 95% CI: 1.65-14.19; p = 0.002). Strain-level analysis performed on metagenomes from contemporaneous OP and stool samples identified co-carriage of indistinguishable Enterobacterales strains in those with Enterobacterales-positive OP samples, suggesting intra-participant strain acquisition. We report OP carriage of Enterobacterales species to be a marker of future RTI risk in long-term aged care residents, reflecting the independent influence of common ageing-associated risk exposures.},
}
@article {pmid40519640,
year = {2025},
author = {You, W and Ji, J and Wen, D and Wang, C and Sun, X and Zhao, P},
title = {Unlocking therapeutic potential of amlexanox in MASH with insights into bile acid metabolism and microbiome.},
journal = {Npj gut and liver},
volume = {2},
number = {},
pages = {},
pmid = {40519640},
issn = {3004-9806},
abstract = {Metabolic dysfunction-associated steatohepatitis (MASH) has become a global health issue associated with obesity and diabetes. It is becoming a leading cause of end-stage liver diseases such as cirrhosis and hepatocellular carcinoma (HCC). Despite its increasing prevalence, effective pharmacotherapies for MASH remain limited, underscoring the urgent need for novel interventions. Amlexanox, an inhibitor of noncanonical IκB kinases, has demonstrated potential in restoring insulin sensitivity and glucose homeostasis in obese mice and human patients, as shown in our earlier studies. Here, we aimed to assess the therapeutic potential of amlexanox in dyslipidemia-associated diseases, particularly MASH and HCC, and to elucidate the underlying mechanism. We employed GAN diet-fed Ldlr [-/-] mice, which simultaneously develop obesity, MASH, and atherosclerosis, to recapitulate human metabolic syndrome and associated complications. Amlexanox was administrated orally to these mice after disease onset to examine its therapeutic efficacy. Our study demonstrates that even a low dose of amlexanox significantly reversed MASH and nearly completely prevented the progression from MASH to HCC. Both phenotypic and transcriptomic studies revealed that amlexanox markedly improved MASH-related dyslipidemia, hepatic steatosis, inflammation, liver injury, and hepatic fibrosis. Furthermore, multi-omics analysis revealed that amlexanox enhances hepatic bile acid synthesis and promotes fecal bile acid excretion. Notably, amlexanox reprogrammed gut microbiota, robustly increasing the abundance of Akkermansia muciniphila, a probiotic known to improve metabolic dysfunction. These findings uncover the multifaceted therapeutic potential of amlexanox in treating MASH and atherosclerosis by targeting bile acid metabolism, gut microbiota, hepatic inflammation, and fibrosis. Our study highlights amlexanox as a promising candidate for clinical applications.},
}
@article {pmid40519637,
year = {2025},
author = {Clarke, G and Cryan, JF and O'Mahony, SM},
title = {The Gut Microbiome and Emotional Distress During Pregnancy: Shaking the Foundations of Future Mental Health?.},
journal = {Biological psychiatry global open science},
volume = {5},
number = {4},
pages = {100518},
pmid = {40519637},
issn = {2667-1743},
}
@article {pmid40519530,
year = {2025},
author = {Smith, S and Bongrand, C and Lawhorn, S and Ruby, EG and Septer, AN},
title = {Application of hsp60 amplicon sequencing to characterize microbial communities associated with juvenile and adult Euprymna scolopes squid.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf085},
pmid = {40519530},
issn = {2730-6151},
abstract = {The symbiotic relationship between Vibrio (Aliivibrio) fischeri and the Hawaiian bobtail squid, Euprymna scolopes, serves as a key model for understanding host-microbe interactions. Traditional culture-based methods have primarily isolated V. fischeri from the light organs of wild-caught squid, yet culture-independent analyses of this symbiotic microbiome remain limited. This study aims to enhance species-level resolution of bacterial communities associated with E. scolopes using hsp60 amplicon sequencing. We validated our hsp60 sequencing approach using pure cultures and mixed bacterial populations, demonstrating its ability to distinguish V. fischeri from other closely related vibrios and the possibility of using this approach for strain-level diversity with further optimization. This approach was applied to whole-animal juvenile squid exposed to either seawater or a clonal V. fischeri inoculum, as well as ventate samples and light organ cores from wild-caught adults. V. fischeri accounted for the majority of the identifiable taxa for whole-animal juvenile samples and comprised 94%-99% of amplicon sequence variants (ASVs) for adult light organ core samples, confirming that V. fischeri is the dominant, if not sole, symbiont typically associated with E. scolopes light organs. In one ventate sample, V. fischeri comprised 82% of reads, indicating the potential for non-invasive community assessments using this approach. Analysis of non-V. fischeri ASVs revealed that Bradyrhizobium spp. and other members of the Rhodobacterales order are conserved across juvenile and adult samples. These findings provide insight into the presence of additional microbial associations with the squid host tissue outside of the light organ that have not been previously detected through traditional culture methods.},
}
@article {pmid40519460,
year = {2025},
author = {Suvvari, TK and Vallurupalli, V and Koneru, KS and Ingawale, S and Yegurla, RR},
title = {The Lasting Imprint of Antibiotics on Gut Microbiota: Exploring Long-Term Consequences and Therapeutic Interventions.},
journal = {Cureus},
volume = {17},
number = {5},
pages = {e84114},
pmid = {40519460},
issn = {2168-8184},
abstract = {The widespread use of antibiotics has significantly impacted gut microbiota, often leading to long-term dysbiosis with profound health consequences. Antibiotics not only target pathogenic bacteria but also disrupt beneficial microbial communities, reducing diversity and increasing susceptibility to metabolic disorders, immune dysfunction, and opportunistic infections like Clostridioides difficile. The antibiotic-induced microbiota alterations can persist for weeks or even months post-treatment, contributing to ongoing health challenges. Restorative strategies, including probiotics, prebiotics, fecal microbiota transplantation, and dietary modifications, offer potential solutions to mitigate these effects. A balanced approach to antibiotic use, coupled with targeted interventions, is essential to preserving gut microbial health and minimizing long-term complications. Further research is needed to optimize therapeutic strategies and enhance patient outcomes. So, this editorial aims to examine the long-term consequences of antibiotic-induced gut microbiota disruption, highlight clinical and subclinical implications, and evaluate emerging therapeutic interventions aimed at microbiota restoration.},
}
@article {pmid40519172,
year = {2025},
author = {Coşkuner, G and Alkay, Z and Arioglu-Tuncil, S and Alvarez Gonzales, MA and Lindemann, SR and Tunçil, YE},
title = {In vitro fecal microbiota modulation properties of some dried apricots (Prunus armeniaca L.).},
journal = {Journal of the science of food and agriculture},
volume = {},
number = {},
pages = {},
doi = {10.1002/jsfa.70003},
pmid = {40519172},
issn = {1097-0010},
abstract = {BACKGROUND: The aim of this study was to evaluate and compare the gut microbiome modulatory effects of dietary fibers (DFs) of different Turkish apricot (Prunus armeniaca L.) varieties dried using different techniques. Three different sun-dried apricots belonging to Şekerpare, Iğdır Şalağı, and Hasanbey varieties from Erzincan region; and sun-dried, and sulfurized apricots belonging to Şekerpare variety from Malatya region were obtained. Neutral and acidic monosaccharide compositions were analyzed using gas chromatography-mass spectroscopy (GC-MS) and spectrophotometry, respectively. In vitro fecal fermentation analyses were applied and changes in microbiota composition and short-chain fatty acids were determined using 16S rRNA sequencing technique and GC, respectively.<br><br>RESULTS: Dried apricot DFs were dominated with pectin- and cellulose/hemicellulose-related monosaccharide units, and the DF compositions showed only slight differences from variety to variety. Dried apricot DFs were found to influence the &#x3b2;- and &#x3b1;-diversities of microbial communities in variety and drying techniques independent-ways. Although the degrees of promotions were slightly impacted by the apricot-variety and drying technology, dried apricot DFs were generally capable of promoting the beneficial microbial taxa, including Coprococcus eutactus, Lachnospiraceae, and Ruminococcus flavefaciens related operational taxonomic units (OTUs).<br><br>CONCLUSION: Overall, this study demonstrates that dried apricots can modulate colonic microbiota composition and function, with the effect being subtly impacted by variety, location, and drying techniques. These findings also suggest that gut microbiome modulation ability of DFs of dried appricot could be an important contribution factor to its health promoting properties. Thus, dried apricots have potential to be utilized for the development of functional foods aimed at promoting colonic health. &#xa9; 2025 Society of Chemical Industry.},
}
@article {pmid40518985,
year = {2025},
author = {Saeed, MH and Kujawska, M and Ellen, K and Acuna-Gonzalez, A and Bernabeu Lorenzo, M and Carmen Collado, M and Mommers, M and van Best, N and Hall, LJ and Neuhaus, K},
title = {Comprehensive analysis of Enterococcus spp. from two European healthy infant cohorts shows stable genomic traits including antimicrobial resistance (AMR).},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2516699},
doi = {10.1080/19490976.2025.2516699},
pmid = {40518985},
issn = {1949-0984},
mesh = {Humans ; *Enterococcus/genetics/drug effects/isolation &amp; purification/classification/pathogenicity ; Infant ; *Anti-Bacterial Agents/pharmacology ; Feces/microbiology ; Genome, Bacterial ; Gastrointestinal Microbiome ; *Drug Resistance, Bacterial/genetics ; Netherlands ; Spain ; Virulence Factors/genetics ; Cohort Studies ; Infant, Newborn ; Female ; Male ; Europe ; },
abstract = {Enterococcus spp. some of which are pathogenic, are common gut microbiota members, including also infants. Infants may be more susceptible to Enterococcus due to their developing gut ecosystems. It is unclear whether antibiotic resistance genes (ARGs) and certain genomic traits in enterococci are restricted to the human subpopulation or more widespread. Furthermore, the correlation between these traits and geographic variation is poorly understood. Therefore, we sequenced 100 strains isolated from full-term healthy infants' fecal samples from two geographically distant European cohorts (MAMI in Spain and LucKi from the Netherlands) to explore the diversity of Enterococcus spp. within the infant's gut microbiome and assess cohort-specific traits such as ARGs. Most isolates were E. faecalis and E. gallinarum, with a total of 11 species identified. We found a rich reservoir of ARGs, plasmids, prophages and virulence factors in the infant strains, with minimal cohort-specific differences in resistome profiles. In addition, Epx, a pore-forming toxin associated with pathogenicity, was found in E. hirae strains. While metabolic profiles were similar across cohorts, E. faecalis strains harbored more virulence genes and prophages compared to other species. An analysis of public Enterococcus genomes revealed that multi-drug resistant (MDR) strains exist without any significant geographic or temporal pattern. Phenotypic resistance analysis indicated that 28% of MAMI strains were gentamicin resistant, compared to 5% of the strains from the LucKi cohort, though LucKi isolates were also resistant to other antibiotics. We also selected ten E. faecalis isolates with varying virulence gene repertoires for phenotypic virulence testing in Caenorhabditis elegans and found them killing at various rates, however no clear pattern emerged in correlation with any specific genetic determinant. Overall, our results suggest that Enterococcus spp. including ARGs, are highly mobile across Europe and beyond. Their adaptability likely facilitates long-distance dissemination, with strains being acquired early in life from community environments.},
}
@article {pmid40518732,
year = {2025},
author = {Mota de Almeida, FJ and Rakhimova, O and Romani Vestman, N and Lee, NM and Brundin, M},
title = {In situ imaging and microbiome analysis of calculus-like deposits at the root apex: A case report of refractory apical periodontitis.},
journal = {International endodontic journal},
volume = {},
number = {},
pages = {},
doi = {10.1111/iej.14268},
pmid = {40518732},
issn = {1365-2591},
support = {7003589//Region of V&#xe4;sterbotten (Sweden)/ ; 977100//Region of V&#xe4;sterbotten (Sweden)/ ; RV-967705//Region of V&#xe4;sterbotten (Sweden)/ ; },
abstract = {AIM: This case report explored the application of next-generation sequencing (NGS) and fluorescence in situ hybridization (FISH) to visualize and characterize microbial populations in a refractory endodontic infection with apical calculus-like deposits, a rarely reported phenomenon.<br><br>SUMMARY: Histopathologic analysis revealed bacterial biofilms and calcifications on the root surface, with Gram-positive bacteria predominant in both hard and soft tissues. Microbial sequencing showed Pseudomonadota dominated hard tissues, whereas Bacillota were prevalent in soft tissues, with distinct genera like Lactibacterium and Streptococcus identified. FISH imaging confirmed spatially distributed bacterial taxa, including Actinomycetota and Chloroflexota, within the biofilm, aligning with NGS findings. Notably, Bacteroidota was exclusive to soft tissues, whereas Chloroflexota was detected only in hard tissues. The presence of extensive calculus-like deposits on the root surface provided new insights into the microbial complexity of persistent endodontic infections and their management.<br><br>KEY LEARNING POINTS: The combination of NGS and FISH provided unprecedented insights into the microbial composition of refractory endodontic infections, revealing a diverse and spatially organized ecosystem. Distinct microbial compositions in hard and soft tissues emphasize the importance of targeted therapeutic strategies for endodontic infections. The presence of unique bacterial taxa and biofilms in calculus-like deposits offers new avenues for research into the pathogenesis and persistence of endodontic infections.},
}
@article {pmid40518644,
year = {2025},
author = {Souza, JGS and Bertolini, M and Liu, J and Nagay, BE and Martins, R and Costa, RC and Brunson, JC and Shibli, J and Figueiredo, LC and Dongari-Bagtzoglou, A and Feres, M and Barão, VAR and Bor, B},
title = {Exploring the Impact of Biotic and Abiotic Surfaces on Protein Binding Modulation and Bacteria Attachment: Integrating Biological and Mathematical Approaches.},
journal = {ACS nano},
volume = {},
number = {},
pages = {},
doi = {10.1021/acsnano.5c06573},
pmid = {40518644},
issn = {1936-086X},
abstract = {The oral environment is composed of a diverse array of proteins, and any substrate inserted into this habitat promptly becomes subjected to protein adsorption and bacterial colonization. However, the predictive and modulatory nature of implant surfaces coated with salivary pellicle proteomes in microbial adhesion has not been explored using high-throughput techniques. Thus, using human saliva for salivary pellicle adsorption and microbial accumulation, we compared adsorption and community formation on titanium (Ti) biomaterials (implant devices) and dental surfaces (enamel and dentine). The proteomic profile was evaluated by liquid chromatography coupled with tandem mass spectrometry, and the microbiome was assessed using 16S RNA sequencing. Linear discriminant analysis (LDA) and canonical correlation analysis (CCA) were used to quantify variation in analyte amounts and identify likely biomarkers. Substrates were analyzed regarding their physical, chemical, and topographical properties. Our results showed that the salivary pellicle proteomes on Ti exhibited differences in composition and protein intensities compared with dental surfaces. These differences in proteomes affected the biological processes at the level of microbiome accumulation. Geometric analysis showed greater similarity between Ti and enamel proteomes, while dentine differed markedly. Ti harbors a microbiome community that differs from that of dental surfaces. Canonical correlation analysis (CCA) pinpointed proteins that promoted or inhibited the adherence of specific microbes. Apolipoprotein E showed a strong negative correlation (>0.8) with Streptococcus parasanguinis. Higher levels of the protein on dental surfaces were associated with reduced microbial adhesion, whereas its absence on Ti surfaces facilitated increased bacterial adhesion. These findings provide valuable insights into the initial biological responses after the insertion of implanted devices, which can be leveraged by biomedical engineering to develop biomaterials with enhanced outcomes and prevent microbial accumulation.},
}
@article {pmid40518557,
year = {2025},
author = {Oppenheimer, M and Tao, J and Moidunny, S and Roy, S},
title = {Anxiety-like behavior during protracted morphine withdrawal is driven by gut microbial dysbiosis and attenuated with probiotic treatment.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2517838},
doi = {10.1080/19490976.2025.2517838},
pmid = {40518557},
issn = {1949-0984},
mesh = {Animals ; *Probiotics/administration &amp; dosage/therapeutic use ; *Dysbiosis/microbiology ; *Gastrointestinal Microbiome/drug effects ; *Substance Withdrawal Syndrome/microbiology/psychology ; Mice ; *Anxiety/microbiology/etiology ; *Morphine/adverse effects ; Male ; Mice, Inbred C57BL ; Fecal Microbiota Transplantation ; Disease Models, Animal ; Behavior, Animal ; Morphine Dependence ; },
abstract = {The development of anxiety during protracted opioid withdrawal heightens the risk of relapse into the cycle of addiction. Understanding the mechanisms driving anxiety during opioid withdrawal could facilitate the development of therapeutics to prevent negative affect and promote continued abstinence. Our lab has previously established the gut microbiome as a driver of various side effects of opioid use, including analgesic tolerance and somatic withdrawal symptoms. We therefore hypothesized that the gut microbiome contributes to the development of anxiety-like behavior during protracted opioid withdrawal. In this study, we first established a mouse model of protracted morphine withdrawal, characterized by anxiety-like behavior and gut microbial dysbiosis. Next, we used fecal microbiota transplantation (FMT) to show that gut dysbiosis alone is sufficient to induce anxiety-like behavior. We further demonstrated that probiotic therapy during morphine withdrawal attenuated the onset of anxiety-like behavior, highlighting its therapeutic potential. Lastly, we examined transcriptional changes in the amygdala of morphine-withdrawn mice treated with probiotics to explore mechanisms by which the gut-brain axis mediates anxiety-like behavior. Our results support the use of probiotics as a promising therapeutic strategy to prevent gut dysbiosis and associated anxiety during opioid withdrawal, with potential implications for improving treatment outcomes in opioid recovery programs.},
}
@article {pmid40518272,
year = {2025},
author = {},
title = {Correction: Lost microbes of COVID-19: Bifidobacterium, Faecalibacterium depletion and decreased microbiome diversity associated with SARS-CoV-2 infection severity.},
journal = {BMJ open gastroenterology},
volume = {12},
number = {1},
pages = {},
doi = {10.1136/bmjgast-2022-000871corr1},
pmid = {40518272},
issn = {2054-4774},
}
@article {pmid40518243,
year = {2025},
author = {Kolp, M and Marcello, M and Holt, A and Rossi, K and Zurawski, C and Cancelliere, K and Telemeco, S and Swift, JF and Purple, K and Faulkner, C},
title = {Evidence of canine intestinal parasites and associated fecal bacteria among urban and rural dog parks in central Appalachia U.S.},
journal = {Veterinary parasitology, regional studies and reports},
volume = {62},
number = {},
pages = {101280},
doi = {10.1016/j.vprsr.2025.101280},
pmid = {40518243},
issn = {2405-9390},
mesh = {Animals ; Dogs ; *Dog Diseases/parasitology/epidemiology/microbiology ; *Feces/microbiology/parasitology ; Parks, Recreational ; Kentucky/epidemiology ; Rural Population ; RNA, Ribosomal, 16S/genetics ; Appalachian Region/epidemiology ; *Intestinal Diseases, Parasitic/veterinary/epidemiology/parasitology ; *Bacteria/isolation &amp; purification/classification/genetics ; Tennessee/epidemiology ; Ancylostoma/isolation &amp; purification ; Trichuris/isolation &amp; purification ; Toxocara canis/isolation &amp; purification ; Gastrointestinal Microbiome ; },
abstract = {Public dog parks provide opportunities for exercise and socialization, benefiting both dogs and their owners. However, dog parks can serve as reservoirs for gastrointestinal (GI) parasitic helminths, posing risks to canine and public health. This study investigated the presence of three common GI parasites, hookworm (Ancylostoma spp.), roundworm (Toxocara canis), and whipworm (Trichuris vulpis), in abandoned fecal samples from nine dog parks in Central Appalachia, comparing rural and urban environments. We also examined the relationship between parasite presence and fecal bacterial community composition using 16S rRNA sequencing. A total of 346 fecal samples were collected during 43 visits to parks in Tennessee and Kentucky. Centrifugal flotation (1.2 spg) revealed evidence of parasitic infection in 26.9 % of samples, with a higher percentage found in samples from rural parks (40.7 % of 135 samples) compared to urban parks (18.0 % of 211 samples; p < 0.0001). Hookworm was the most common parasite identified (18.8 %), with greater numbers of eggs in rural parks. Mixed infections were observed in 6.9 % of samples and found more often in rural dog parks. 16S rRNA sequencing indicated that bacterial diversity and community composition were influenced by park location and parasite presence. Rural parks exhibited more diverse bacterial communities and higher proportions of Actinomycetota, while urban parks showed higher levels of Fusobacteriota. Parasite-positive samples had greater bacterial diversity and were associated with specific taxa, such as Clostridia, linked to GI issues. Our findings highlight the increased potential of GI parasitic helminth contamination in rural dog parks and highlight the potential for parasites to alter canine gut microbiomes. These results emphasize the need for public health education on routine anthelmintic treatments to reduce zoonotic risks. The study further underscores the importance of a One Health approach to managing parasite transmission in communal canine spaces. Future work should explore the mechanisms underlying GI parasite-microbiome interactions and extend these findings to other geographic regions.},
}
@article {pmid40518048,
year = {2025},
author = {Snelson, M and Biesiekierski, JR and Chen, S and Sultan, N and Cardoso, BR},
title = {The effects of nut intake on gut microbiome composition and gut function in adults: a systematic review and meta-analysis.},
journal = {Advances in nutrition (Bethesda, Md.)},
volume = {},
number = {},
pages = {100465},
doi = {10.1016/j.advnut.2025.100465},
pmid = {40518048},
issn = {2156-5376},
abstract = {The reduced risk of chronic diseases such as cardiovascular disease and type 2 diabetes associated with nut consumption may occur via modulation of the gut microbiota, although this has not been comprehensively assessed. This systematic review of clinical trials aims to assess the effects of nuts on gut microbiota composition and metabolites in adults. Further, it examines the effects of nuts on gut function and symptoms in adults. The systematic review was conducted following PRISMA guidelines and registered in PROSPERO (CRD42023451282). Outcomes included microbiota diversity, specific bacterial abundances, gastrointestinal symptoms, intestinal permeability, faecal pH, faecal moisture, and short-chain fatty acid (SCFAs) concentrations. We performed meta-analyses to assess the overall effect of nuts on faecal moisture, pH, intestinal permeability and SCFA concentrations. Amongst the 28 intervention trials included in this review, almonds were the most commonly studied (12 trials), while other nuts, such as walnuts, peanuts, pistachios and Brazil nuts, were also examined. Nineteen articles reported the effects of almond, walnut, peanut or mixed nuts on the microbiota composition. Additionally, 6 trials used interventions involving a mixture of different nuts. A total of 19 trials assessed the community structure of the gut microbiota through the assessment of α-and β-diversity metrics, with most finding no significant differences following nut intervention. Regarding taxonomic changes, the majority of studies reported no significant changes across nut interventions. However, several studies noted increases in Clostridium and Roseburia, with mixed results for Bifidobacterium abundance following almond or walnut intervention. Five studies assessed faecal SCFA concentrations, with positive effects of nut interventions on propionate. There were no effects of nut interventions on faecal pH and intestinal permeability, with an unfavourable effect on faecal moisture. In summary, the available evidence indicates that nuts have modest effects on gut health, but the substantial heterogeneity between studies may hinder further conclusions. REGISTRATION NUMBER: PROSPERO CRD42023451282.},
}
@article {pmid40517966,
year = {2025},
author = {Zheng, X and Jiang, H and Cui, R and Cai, A and He, B and Tao, A and Wang, S},
title = {From Itchy Skin to Wheezing: Potential biomarkers and targeted drugs for Atopic Dermatitis and Asthma in Children.},
journal = {Respiratory medicine},
volume = {},
number = {},
pages = {108212},
doi = {10.1016/j.rmed.2025.108212},
pmid = {40517966},
issn = {1532-3064},
abstract = {Atopic dermatitis (AD) and allergic asthma (AA) are interconnected allergic diseases that frequently co-occur in early childhood, representing a critical sequence in the "atopic march". The rising global prevalence of these conditions, driven by environmental factors and epigenetic changes, underscores an urgent clinical need to understand their shared pathogenesis and disrupt disease progression. Evidence implicates multifaceted mechanisms in AD-to-AA progression, including skin barrier dysfunction, type 2 inflammation, microbiome dysbiosis, and systemic immune priming. These pathways not only elucidate the disease continuum but also offer actionable biomarkers for early prediction and targeted interventions. This review synthesizes the epidemiology, mechanistic insights, and translational implications of AD-to-AA progression, advocating for a paradigm shift toward early-risk stratification and precision medicine. By bridging mechanistic discoveries with clinical practice, we aim to guide optimized management and primary prevention, ultimately reducing the global allergy burden.},
}
@article {pmid40517941,
year = {2025},
author = {Singh, A and Bansal, J and Bharti, A and Joshi, M and Saravanan, C and Jain, CK},
title = {Integrative role of diet and gut microbiome dynamics for the Interventive therapeutics of Spinocerebellar ataxia type 3: The Current Update.},
journal = {Neuroscience},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.neuroscience.2025.06.024},
pmid = {40517941},
issn = {1873-7544},
abstract = {Neurodegenerative disorders such as Alzheimer's and Parkinson's have captured researchers' attention regarding their connection to gut microbiota and dietary factors. Research has shown that changes in our regular dietary consumption can profoundly influence the composition of the gut microbiota, which possesses the capacity to influence brain functioning through a number of mechanisms, suggesting that dietary modifications may serve as promising therapeutic intervention for managing and potentially mitigating the progression of several neurodegenerative diseases. Spinocerebellar Ataxia Type 3 (SCA3), a neurodegenerative disorder stems from an unstable CAG trinucleotide repeat expansion within the ATXN3 gene's coding regions. This leads to the production of polyglutamine, contributing to a range of symptoms. However, the therapeutic potential of targeting gut microbiome alterations through dietary interventions for SCA3 has not been extensively investigated. This review is the first to systematically integrate existing evidence on how dietary interventions and gut microbiome dynamics may be leveraged for the therapeutic management of SCA3. Specifically, we explore how dietary components including fermented foods, probiotics, fiber-rich diets, herbal compounds and pharmacological agents, including dietary and natural HDAC inhibitors can influence gut microbiota and modulate neuroinflammation, oxidative stress, and protein aggregation, which are common hallmarks in neurodegenerative diseases. This paper elucidates the gut microbiota's ability to affect neurological health and its significance in the management of SCA3, hence facilitating future research aimed at treating SCA3 patients by dietary modifications that modify particular gut flora.},
}
@article {pmid40517909,
year = {2025},
author = {Mai, X and Wu, J and Tian, Z and Liu, L and Zhuang, X and Liu, Z and Wan, R and Li, B and Shi, Y and Li, B and Wang, X},
title = {Microbial-Purine Metabolic Crosstalk Regulates Colitis-Related Intestinal Fibrosis: A Multi-Omics and Cohort Analysis Approach.},
journal = {The Journal of nutritional biochemistry},
volume = {},
number = {},
pages = {109984},
doi = {10.1016/j.jnutbio.2025.109984},
pmid = {40517909},
issn = {1873-4847},
abstract = {INTRODUCTION: Intestinal fibrosis (IF) is a severe complication of inflammatory bowel disease (IBD), often requiring surgical interventions. The modulating role of the microbial-metabolic link in IF remains unclear. We aimed to identify disturbances in microbiome-metabolome interactions during IF progression and recognize potential metabolic biomarkers.<br><br>METHODS: Compositional and functional signatures, along with murine IF progression, were determined through 16S rRNA sequencing and widely targeted metabolomics. Overall, 109 patients with IBD and 111 healthy controls (HCs) were enrolled and clinically evaluated. Correlations analyses were performed to reveal the relationship between microbial-purine metabolic alterations and disease markers.<br><br>RESULTS: Gut microbiome analysis identified structural disruptions, including a reduction in uric acid (UA)-decomposed microbes and an increase in hyperuricemia-associated taxa (P < 0.05), which contributed to impaired purine metabolism (P < 0.05). Metabolomic profiling further indicated reprogramming of purine metabolism in fibrogenesis, as evidenced by elevated UA levels in fecal, colonic, and serum samples that correlated with inflammatory and fibrotic markers. In IBD patients, compared to HCs, serum UA (342.55&#xb1;95.69 vs 294.78&#xb1;66.58 &#x3bc;mol/L) and UA/creatinine (UA/Cr) levels (5.17&#xb1;1.57 vs 4.40&#xb1;1.28) were greatly increased (P < 0.001) and positively correlated with the clinical and endoscopic activities, especially in CD patients. Serial measurements demonstrated elevated UA during stenosis formation. UA/Cr may be an independent risk factor (P&#x202f;=&#x202f;0.006) for stenosis prognosis.<br><br>CONCLUSIONS: Abnormal purine metabolism may regulate IF, as reflected in purine metabolism-related microbes and metabolites. Elevated serum UA and UA/Cr levels are promising biomarkers for detecting disease activity and predicting stenosis in IBD.},
}
@article {pmid40517616,
year = {2025},
author = {Olowe, OS and Johnson, T and Adeola, O},
title = {Red seaweed Chondracanthus chamissoi supplementation improved the growth performance of broiler chickens partially through effects on intestinal morphology and cecal microbiota.},
journal = {Poultry science},
volume = {104},
number = {9},
pages = {105402},
doi = {10.1016/j.psj.2025.105402},
pmid = {40517616},
issn = {1525-3171},
abstract = {Marine macroalgae has the potential to improve growth performance in broiler chickens due to the presence of bioactive compounds. This study examined the effects of a red seaweed (SW) powder, from Chondracanthus chamissoi, on the growth performance, intestinal morphology, and cecal microbiota of broiler chickens. A total of 256 male Cobb-500 broiler chicks were housed in battery cages and allocated on d 0 post hatching to 4 diets for 21 days in a randomized complete block design consisting of 8 replicate cages and 8 birds per replicate. The 4 diets included a corn-soybean-based diet (basal diet), or the basal diet supplemented with 0.5 %, 1 %, or 1.5 % SW. Body weight (BW) and feed intake (FI) were recorded weekly. On d 7, 14, and 21 post hatching, SW diets linearly increased the BW gain of birds (P < 0.01), but the gain-to-feed ratio (G: F) was not affected by the treatments except from day 0 to 7 (P < 0.05). Dietary SW linearly increased the feed intake throughout the experiment (P < 0.05). Dietary SW increased (P < 0.05) the ileal villus height to crypt depth ratio (VH: CD) and showed a tendency (P = 0.08) to linearly increase ileal villus height (VH). Additionally, dietary SW increased both jejunal VH and the VH: CD ratio (P < 0.05). No differences were observed in alpha diversity metrics; however, beta diversity analysis showed variations in the composition of the microbial community. Differential abundance showed that Bifidobacterium, and Butyricicoccus were abundant taxa in the SW diets. In conclusion, graded inclusions of SW improved the growth performance of broiler chickens when fed for 21 days, by altering the intestinal morphology and microbiota. However, the nutrient digestibility was not improved by seaweed.},
}
@article {pmid40517504,
year = {2025},
author = {Tang, X and Liu, Y and Yang, W and Wu, Y and Yong, T and Liu, W and Lv, F and Hussain, K and Wang, Y and Gao, X and Zhang, Y},
title = {Macroplastics in soybean cultivation: Neutral on plant growth but disruptive to nitrogen-fixing microbiome.},
journal = {Ecotoxicology and environmental safety},
volume = {301},
number = {},
pages = {118499},
doi = {10.1016/j.ecoenv.2025.118499},
pmid = {40517504},
issn = {1090-2414},
abstract = {Macroplastics are an emerging yet underexplored pollutant in agricultural soils, with the potential to disrupt nitrogen (N) cycling through physical interference and microbial community shifts. While extensive studies have focused on microplastics, the effects of larger plastic debris (>2 cm) on soil-plant systems in legume cropping systems remain poorly understood. We conducted a 71-d mesocosm study utilizing [15]N isotopic tracing and metagenomic sequencing to demonstrate how macroplastics influence soybean growth and soil-soybean continuum N cycling. Soybean growth was not affected under macroplastics exposure (up to 200 kg ha[-][1]). However, macroplastics increased soil NO3[-] and NH4[+] concentrations, and elevated urease and ammonia monooxygenase activities, suggesting enhanced N availability. Paradoxically, macroplastics significantly disrupted the N-fixing microbial community, reducing the abundance of key bacteria such as Azorhizobium and Bradyrhizobium. Nitrogen fixation pathways (in log10-transformed TPM+1) were markedly suppressed in soils treated with 200 kg ha[-1] macroplastics compared to untreated soils (p < 0.001). Our findings highlight the potential risks of macroplastics posing to N cycling and microbial health in agricultural soils. This study addresses a critical knowledge gap by shifting the focus from micro- to macroplastic impacts on biogeochemical cycling.},
}
@article {pmid40517386,
year = {2025},
author = {Ingham, AC and Ng, DYK and Iversen, S and Liu, CM and Dinh, KM and Holtfreter, S and Edslev, SM and Johannesen, TB and Rendboe, AK and Christiansen, MT and Ng, KL and Skov, R and Samietz, S and Radke, D and Weiss, S and Völker, U and Bröker, BM and Erikstrup, LT and Erikstrup, C and Price, LB and Andersen, PS and Stegger, M},
title = {Staphylococci in high resolution: Capturing diversity within the human nasal microbiota.},
journal = {Cell reports},
volume = {44},
number = {6},
pages = {115854},
doi = {10.1016/j.celrep.2025.115854},
pmid = {40517386},
issn = {2211-1247},
abstract = {Staphylococci include both nasal commensals and opportunistic pathogens, globally responsible for a large proportion of infection-related deaths, especially in S. aureus carriers. To understand staphylococcal temporal dynamics within the nasal microbiota, we employed Staphylococcus-targeted sequencing in two cohorts from Denmark and Germany. We identified two major staphylococcal community state types (sCSTs)-one dominated by S. aureus and one dominated by S. epidermidis-and eight subgroups defined by co-colonizing coagulase-negative staphylococci. The distribution of sCSTs was similar between the two cohorts. Predominance of either S. aureus or S. epidermidis was highly persistent over time, whereas co-colonizing staphylococcal species were transient with varying stability among the sCST subgroups. Detection of S. aureus by culture was positively associated with absolute abundance by qPCR. S. aureus domination was diminished when Dolosigranulum and Corynebacterium co-occurred. Our findings could inform efforts to reduce S. aureus nasal colonization and infection.},
}
@article {pmid40517372,
year = {2025},
author = {Sharma, A and Sharma, G and Im, SH},
title = {Gut microbiota in regulatory T cell generation and function: mechanisms and health implications.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2516702},
doi = {10.1080/19490976.2025.2516702},
pmid = {40517372},
issn = {1949-0984},
mesh = {*T-Lymphocytes, Regulatory/immunology ; Humans ; *Gastrointestinal Microbiome/immunology ; Animals ; Immune Tolerance ; Dysbiosis/immunology/microbiology ; Homeostasis ; },
abstract = {The establishment and maintenance of immune homeostasis rely on a dynamic, bidirectional exchange of information between commensal microorganisms and the host immune system. At the center of this process are CD4[+]Foxp3[+] regulatory T cells (Tregs), which have emerged as pivotal mediators to ensure immunological equilibrium. This review explores the sophisticated mechanisms by which the gut microbiota modulates the differentiation, expansion, and functional specialization of Tregs, orchestrating intestinal immune tolerance to support host-microbiota mutualism. We discuss the role of microbial-derived structural components and metabolites in shaping the immunoregulatory fitness of Tregs. Additionally, we explore the impact of gut microbial dysbiosis, where disrupted microbial-immune crosstalk compromises immune tolerance, contributing to the development of inflammatory and autoimmune disorders. Finally, we highlight the potential of microbiota-based strategies to recalibrate intestinal immunity and restore immune tolerance.},
}
@article {pmid40517367,
year = {2025},
author = {Xi, S and Lin, T and Haiyan, Z and Shiyue, Z and Qi, Q and Qiangqiang, X and Mingzhi, Z and Liu, L},
title = {Propionate ameliorates neural degeneration by modulating mitochondrial fission and fusion in nerve cells.},
journal = {Neurological research},
volume = {},
number = {},
pages = {1-10},
doi = {10.1080/01616412.2025.2520019},
pmid = {40517367},
issn = {1743-1328},
abstract = {BACKGROUND: Sporadic global cognitive decline is on the rise, and current drugs exhibit limited efficacy. Propionate, an SCFAs of the human microbiome, exhibits robust neuroprotective effects.<br><br>METHODS: We used CCK8 to evaluate neuronal proliferation, DCFH-DA fluorescence probe to quantify ROS production, ELISA to detect IL-1&#x3b2; and IL-6 release, MitoTracker to assess mitochondrial membrane potential, real-time quantitative PCR, and western blotting to analyze DRP1 and anti-Mfn2 protein expression. We also established an in vitro blood-brain barrier model and AD mouse model.<br><br>RESULTS: Propionate normalized the mitochondrial membrane potential in glutamate-treated HT22 cells, reversed growth suppression, ROS accumulation, and elevated IL-1 and IL-6 release. Propionate also decreases Drp1 expression and elevates Mfn2 expression via GRP41 receptor binding. In vitro blood-brain barrier models illustrated the potential of propionate to ameliorate glutamate-induced blood-brain barrier damage. In vivo, propionate notably improved the learning and memory capabilities of AD mice and mitigated AD-induced mitochondrial defects.<br><br>CONCLUSION: Supplementation with propionate provides neuroprotection against neurodegenerative diseases. Propionate supplementation may provide a novel strategy for early intervention of neurological disorders.},
}
@article {pmid40517181,
year = {2025},
author = {Marya, A and Porntaveetus, T and Okazaki, K and Jamilian, A},
title = {A comparative review of the oral microbiome in clear aligners and fixed orthodontic appliances.},
journal = {Evidence-based dentistry},
volume = {},
number = {},
pages = {},
pmid = {40517181},
issn = {1476-5446},
abstract = {A COMMENTARY ON: Lucchese A, Marcolina M, Mancini N et al. A comparison of the alterations of oral microbiome with fixed orthodontic therapy and clear aligners: a systematic review. J Oral Microbiol 2025; 17: 2372751.<br><br>DATA SOURCES: The review searched multiple electronic databases (PubMed, Cochrane Library, Embase, Web of Science, Scopus, Ovid, Dentistry and Oral Sciences Source) and gray literature (OpenGray) up to May 30, 2023.<br><br>STUDY SELECTION: The selection of the studies was processed according to PRISMA guidelines. Two reviewers independently screened titles and abstracts, with disagreements resolved by a third reviewer. Full-text articles were then assessed for eligibility based on pre-defined inclusion/exclusion criteria (RCTs, nRCTs, cohort studies; at least two time points for analysis; minimum 10 patients; clear aligners vs. fixed appliances or comparison between them; patients with good systemic health not taking medications).<br><br>DATA EXTRACTION AND SYNTHESIS: Data extraction from the included studies was carried out by two reviewers in consultation with a third reviewer to define the variables for extraction and resolve any disagreements. Extracted data included study characteristics (author, year, design, sample size, patient age), intervention details, sample collection methods (saliva, plaque), microbial analysis methods (16S rRNA sequencing, PCR, BANA test), and microbiological outcomes. A qualitative synthesis was performed due to the heterogeneity of the included studies, precluding meta-analysis.<br><br>RESULTS: A total of 484 articles were identified, with 9 studies that met the inclusion and exclusion criteria: eight non-randomized controlled trials and one randomized controlled trial. Sample sizes ranged from 10 to 77 participants. Various microbial analysis methods were employed, including 16S rRNA gene sequencing (5 studies), PCR (3 studies), and the BANA test (1 study). Following the application of rating scales, 1 article was classified as having a low risk of bias, 6 as having a moderate risk, and 2 as having a serious risk of bias.<br><br>CONCLUSIONS: The review suggests that clear aligners may be associated with a less detrimental impact on the oral microbiome compared to fixed appliances, possibly due to improved oral hygiene. Both therapies alter the oral microbiome; however, the changes caused by aligners are more conducive to better oral health compared to fixed appliances.},
}
@article {pmid40517042,
year = {2025},
author = {Rudgers, JA and Gehring, CA and Taylor, DL and Taylor, MD and Chung, YA},
title = {Integration of plant-soil feedbacks with resilience theory for climate change.},
journal = {Trends in ecology &amp; evolution},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tree.2025.05.001},
pmid = {40517042},
issn = {1872-8383},
abstract = {The resilience of ecosystems to climate disruption requires internal feedbacks that support the stability of ecosystem structure and function. Such feedbacks may include sustained interactions between plants and soil [plant-soil feedback (PSF)]. Theoretically, PSF could either boost or degrade ecosystem resilience. Three criteria must be met to attribute resilience to PSF: (i) The presence or amount of PSF must be manipulated; (ii) the ecosystem must face climate disruption after PSF is manipulated; and (iii) PSF must alter the resistance or recovery of ecosystem structure or function to disruption. Several case studies suggest that PSF may support (or degrade) resilience, but no study has yet met all criteria. Doing so could yield novel insights into how aboveground-belowground interactions shape ecosystem resilience to climate change.},
}
@article {pmid40516914,
year = {2025},
author = {Gripshover, TC and Treves, RS and Hardesty, JE},
title = {Identification of pre-clinical biomarkers of MASLD vs MetALD and the impact of diet.},
journal = {The American journal of pathology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ajpath.2025.05.013},
pmid = {40516914},
issn = {1525-2191},
abstract = {Recent diagnostic advancements have characterized MASLD and increased alcohol intake (MetALD) if alcohol consumption is ≥20 or 30 grams/day, females and males, respectively. Available treatments may affect dietary behavior or treat organ pathology but have limited effectiveness. There is a pre-clinical need for an animal model of MetALD that can assess concurrent diet and alcohol consumption on organ pathology to establish treatment strategies. Male, C57BL/6J mice were randomly assigned to six dietary groups for 13 weeks containing: ±chow diet (CD), ±high-fat diet (HFD), and water (H2O) or 10% (v/v) ethanol (EtOH). Glucose tolerance testing was performed at week 10. Physiological measures were assessed and cecal 16S rRNA and liver mRNA sequencing were performed. HFD+EtOH (MetALD) mice had exacerbated dyslipidemia and gut dysbiosis relative to HFD+H2O (MASLD) mice. CD+HFD+EtOH mice had reduced GLP-1 relative to HFD+EtOH mice. MASLD and MetALD mice had altered transcription factor regulatory networks which were altered with CD access. Kupffer cell markers are lower in HFD+EtOH mice relative to other groups. Diet and EtOH have distinct physiological effects in this MetALD model. Mice provided CD+HFD had worsened metabolic syndrome, but improved liver injury and microbiome diversity as compared to HFD mice. Hepatic gene markers and microbiome changes of MASLD were identified. This pre-clinical model helps identify novel therapeutics to treat MASLD and MetALD.},
}
@article {pmid40516734,
year = {2025},
author = {Lan, M and Gao, X and Li, L and Zhao, Y and Song, Q and Qin, X and Qin, D and Stanley, D and Hao, X and Zhu, J and Ding, X and Wu, G},
title = {Methyl3-indolyacetate produced by a gut bacterium of the tephritid gall fly is implicated in controlling Crofton weed by reducing its lignin synthesis.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {144974},
doi = {10.1016/j.ijbiomac.2025.144974},
pmid = {40516734},
issn = {1879-0003},
abstract = {Eupatorium adenophorum, an invasive species of global concern, imposes substantial ecological and economic burdens across its introduced range. This study investigates the tripartite interaction between E. adenophorum, its obligate phytophagous insect Procecidochares utilis, and the insect's enteric microbiota. We isolated Kluyvera ascorbata SZLYS-22, a gut-associated bacterium from P. utilis larvae, demonstrating potent herbicidal activity against the host plant. Bioactivity-guided characterization identified methyl indole-3-acetate (MeIAA) as the principal phytotoxin, exhibiting concentration-dependent inhibition of seed germination and induction of systemic morphological aberrations including stem spiralization, petiole epinasty, and eventual plant mortality. Histological examination revealed MeIAA-induced cytological disorganization in vascular tissues, manifesting as cellular pleomorphism and expanded intercellular lacunae. Transcriptomic profiling revealed significant down-regulation of phenylpropanoid pathway genes (PAL, 4CL, LiP), corroborated by enzymatic assays showing lignin reduction versus control. Paradoxical up-regulation of C4H expression suggests compensatory feedback mechanisms insufficient to maintain lignification. These findings establish MeIAA as a novel bioherbicide disrupting lignocellulosic integrity through targeted pathway modulation. Furthermore, this work elucidates the evolutionary arms race between E. adenophorum and P. utilis, highlighting the underappreciated role of insect-associated microbiota in mediating plant-insect interactions. The results provide a framework for developing microbiome-informed biocontrol strategies.},
}
@article {pmid40516585,
year = {2025},
author = {Kacerovsky, M and Vrbacky, F and Matulova, J and Bolehovska, R and Kukla, R and Pavlikova, L and Holeckova, M and Lubusky, M and Musilova, I and Jacobsson, B and Libra, A},
title = {Late preterm PROM (&gt;33 weeks): the risk of intra-amniotic inflammation and fetal inflammation is influenced by the cervical microbial ecosystem and cervical inflammation.},
journal = {American journal of obstetrics and gynecology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ajog.2025.06.017},
pmid = {40516585},
issn = {1097-6868},
abstract = {BACKGROUND: Approximately 25-30% of pregnancies with late preterm prelabor rupture of membranes (PROM) are complicated by the development of fetal inflammatory response syndrome (FIRS), which is characterized by elevated levels of interleukin-6 in fetal blood. FIRS represents a serious condition that can induce temporary or persistent changes in multiple essential fetal organs. Most importantly, FIRS may impact infant neurodevelopment and increase the risk of neuropsychiatric disorders.<br><br>OBJECTIVE: To characterize the cervical microbial ecosystem and cervical fluid interleukin-6 levels in late preterm PROM with respect to i) intra-amniotic inflammation and/or microbial invasion of the amniotic cavity, and ii) the development of FIRS.<br><br>STUDY DESIGN: This retrospective cohort study included women with singleton pregnancies complicated by late preterm PROM, in whom amniocentesis was performed at admission to assess intra-amniotic environment. Cervical fluid samples were collected using Dacron swabs upon admission. The samples were used for DNA isolation with sequencing of 16S rRNA gene and analysis of interleukin-6 levels. The cervical microbiota was classified based on the relative abundance of Lactobacillus species. Interleukin-6 levels in cervical fluid were measured using electrochemiluminescence. FIRS was defined as the concentration of interleukin-6 > 11.0 pg/mL in umbilical cord blood.<br><br>RESULTS: A total of 114 women with late preterm PROM were included in this study. In total, 378 microbial taxa were identified in the cervical samples. Dominant abundance (&#x2265;50%) of L. iners and the depletion (<50%) of L. spp. were the most prevalent cervical ecosystems in women with intra-amniotic infection [63% (5/8)] and microbial invasion of the amniotic cavity without inflammation [82% (9/11)], respectively. Women whose fetuses developed FIRS had a lower prevalence of L. crispatus dominant cervical microbiota [2% (1/42) vs. 43% (31/72); p < 0.0001] and higher prevalences of L. iners dominant [38% (16/42) vs. 19% (14/92); p = 0.05] and L. spp. depleted cervical microbiotas [55% (23/42) vs. 32% (23/72); p = 0.02], compared to those whose fetuses did not develop FIRS. In the group of women with amniotic fluid negative for inflammation and microorganisms, FIRS was associated with a lower prevalence of L. crispatus dominant microbiota [0% (0/25) vs. 46% (29/63); p < 0.0001] and a higher prevalence of L. iners dominant microbiota [44% (11/25) vs. 20% (13/63); p = 0.04]. Cervical IL-6 levels were highest in women with intra-amniotic infection. The presence of FIRS was associated with elevated IL-6 levels.<br><br>CONCLUSION: Intra-amniotic and fetal inflammatory complications were influenced by the cervical microbial ecosystem and local inflammation. The absence of a high relative abundance of L. crispatus in the cervical microbial ecosystem was associated with an increased risk of the development of FIRS, irrespectively on the inflammatory status of amniotic fluid at admission.},
}
@article {pmid40516571,
year = {2025},
author = {Eubank, TA and Jo, J and Alam, MJ and Begum, K and McPherson, JK and Le, TM and Horvath, TD and Haidacher, SJ and Poggio, EC and Lin, R and Yue, CS and Ducharme, MP and Koudssi, G and Mercier, J and Alder, JD and Silverman, MH and Garey, KW and , },
title = {Efficacy, safety, pharmacokinetics, and associated microbiome changes of ibezapolstat compared with vancomycin in adults with Clostridioides difficile infection: a phase 2b, randomised, double-blind, active-controlled, multicentre study.},
journal = {The Lancet. Microbe},
volume = {},
number = {},
pages = {101126},
doi = {10.1016/j.lanmic.2025.101126},
pmid = {40516571},
issn = {2666-5247},
abstract = {BACKGROUND: Clostridioides difficile infection is a common health-care-associated and community-acquired disease with few antibiotic treatment options. We aimed to assess the safety, efficacy, pharmacokinetics, and associated microbiome changes of ibezapolstat, an antibiotic that inhibits the PolC-type DNA polymerase III α subunit C, versus vancomycin for the treatment of C difficile infection in adults.<br><br>METHODS: This was a phase 2b, randomised, double-blind, active-controlled study conducted at 15 centres, primarily outpatient clinics and hospitals, in the USA. Adults aged 18-90 years, with signs and symptoms of C difficile infection and a positive toxin stool test were recruited. Participants were randomly assigned (1:1) with block assignment by study site using an interactive web response system to receive oral ibezapolstat (450 mg twice daily) or oral vancomycin (125 mg every 6 h) for 10 days. Masking was achieved by over-encapsulation of both study drugs (ibezapolstat and vancomycin) and placebo into identically sized capsules. Participants were excluded if they had received more than 24 h of treatment with oral vancomycin, fidaxomicin, or metronidazole for the current episode of C difficile infection before the first dose of study drug or any other antibacterial therapy within 48 h, had had more than three episodes of C difficile infection in the previous 12 months, or had had more than one previous episode in the past 3 months (excluding the current episode). The primary efficacy endpoint was initial clinical cure maintained for at least 48 h after the end of treatment. All individuals with C difficile infection who met inclusion and exclusion criteria, were randomly assigned, and were administered at least one dose of study drug were included in the efficacy analysis. The safety and tolerability of ibezapolstat was assessed in all individuals who were administered at least one dose of study drug. This study is registered with ClinicalTrials.gov, NCT04247542.<br><br>FINDINGS: Between March 12, 2021, and Oct 27, 2023, 39 individuals were assessed for eligibility, 32 of whom were recruited and randomly assigned to ibezapolstat (n=18) or vancomycin (n=14). Two participants were excluded from the efficacy analysis: one participant in the ibezapolstat group withdrew consent before receiving the study drug and another was identified after random assignment as having an exclusion criterion. The primary efficacy analysis included 16 participants in the ibezapolstat group and 14 in the vancomycin group; 24 (80%) participants were female and six (20%) were male. 15 (94%) of 16 participants in the ibezapolstat group had initial clinical cure compared with 14 (100%) of 14 participants in the vancomycin group (treatment difference -6&#xb7;3% [95% CI -30&#xb7;7 to 19&#xb7;4]; p=1&#xb7;0). Ibezapolstat was well tolerated with a safety profile similar to vancomycin. No drug-related serious adverse events, drug-related treatment withdrawal, or treatment-related deaths occurred in either group.<br><br>INTERPRETATION: Ibezapolstat is a Gram-positive selective spectrum antibiotic that shows potential in the treatment of initial C difficile infection and prevention of recurrence. Further clinical development is warranted.<br><br>FUNDING: Acurx Pharmaceuticals.},
}
@article {pmid40516493,
year = {2025},
author = {Semwal, P and Shivhare, R and Majhi, B and Mishra, SK and Misra, S and Misra, A and Srivastava, S and Chauhan, PS},
title = {Endophytic bacterial's phenylalanine and trans-cinnamic acid as exogenous precursors involved in the modulating colchicine biosynthesis pathway in Gloriosa superba.},
journal = {Plant physiology and biochemistry : PPB},
volume = {227},
number = {},
pages = {110151},
doi = {10.1016/j.plaphy.2025.110151},
pmid = {40516493},
issn = {1873-2690},
abstract = {Unlocking the hidden power of endophytes reveals a novel pathway for boosting colchicine biosynthesis in Gloriosa superba. Metabolite analysis of endophyte culture filtrates identifies essential precursors i.e., phenyl ethyl alcohol, phenylalanine, trans-cinnamic acid, and benzoic acid participating in colchicine biosynthesis. Bacilli-treated Gloriosa superba plants demonstrated a remarkable increase in plant growth and colchicine content over untreated plants. Moreover, enhanced nutrient uptake (Fe, Zn, Cu, Mn) further induced the enzymatic activities critical for colchicine biosynthesis genes such as PAL, NMT, CYP450, and OMT. The metagenomic analysis associated with Bacilli-treated G. superba plants further revealed a shift in Bacillus species, and the functional pathway confirmed the upregulation of precursors in colchicine biosynthesis. Our study highlights the significant role of endophytic Bacilli on plant growth, enhanced nutrient uptake, and shifts in the endophytic microbiome to induce colchicine biosynthesis in G. Superba. It offers a detailed understanding of the endophyte's potential for deciphering its role in enhancing growth and active metabolite composition. It provides valuable insights for sustainable agriculture and unlocking new possibilities for pharmaceutical applications.},
}
@article {pmid40516324,
year = {2025},
author = {Xu, R and Li, T and Wang, Z and Wang, H and Sun, M and Xie, J and Tong, L and Peng, W and Wang, Y},
title = {Association among lean mass, gut microbiome alterations and bone mineral density in high-altitude.},
journal = {Clinical nutrition (Edinburgh, Scotland)},
volume = {51},
number = {},
pages = {18-27},
doi = {10.1016/j.clnu.2025.05.018},
pmid = {40516324},
issn = {1532-1983},
abstract = {BACKGROUND: Body composition, particularly lean body mass, plays a pivotal role in skeletal health and has been increasingly linked to the gut microbiota (GM). However, evidence from vulnerable high-altitude populations remains scarce.<br><br>OBJECTIVE: This study aimed to evaluate the association between body composition and bone mineral density (BMD) at high altitudes and explore the potential role of GM.<br><br>METHODS: A total of 820 Tibetan participants were recruited. BMD at the lumbar spine (L1-L4) and total hip was measured using dual-energy X-ray absorptiometry (DXA). Multivariate linear regression was applied to evaluate the associations between body composition indices and BMD. Participants were stratified into low lean mass index (LLMI) and high lean mass index (HLMI) subgroups using restricted cubic splines (RCS) and body mass index. Stool samples from a subset of participants (n = 383) were analyzed to determine the relative abundances of KEGG Orthology groups.<br><br>RESULTS: LMI was positively associated with hip BMD at high altitude [&#x3b2; (95 % CI) = 0.005 (0.003,0.007), P < 0.05], whereas no significant association was observed with spine BMD. This correlation varied significantly by altitude (Pinter< 0.05). A similar positive relationship was observed between microbial diversity (Shannon index) and hip_BMD [hip: &#x3b2; (95 % CI) = 0.605 (0.165, 1.044), P < 0.05]. Compared to the HLMI group, LLMI participants exhibited greater microbial diversity (P < 0.05), higher Faecalibacteriums abundance, and lower levels of Prevotella copri (P< 0.05). Functional metagenomic analysis identified differential enrichment of microbial pathways, including riboflavin metabolism, terpenoid backbone biosynthesis, alanine, aspartate, and glutamate metabolism (P < 0.05).<br><br>CONCLUSION: These findings highlight the correlation between LMI and hip BMD among high-altitude Tibetan adults, offering a potential mechanism for the interplay between GM profiles and bone health in high-altitude populations.},
}
@article {pmid40516193,
year = {2025},
author = {Roy, S and More, M and Trivedi, A and Saha, P and Bose, D and Das, S and Mahmud, ZH and Hanifi, SMMA and Chatterjee, S},
title = {Aging and climate change-induced heat stress synergistically increase susceptibility to Vibrio vulnificus infection via an altered gut microbiome-immune axis.},
journal = {The Science of the total environment},
volume = {989},
number = {},
pages = {179881},
doi = {10.1016/j.scitotenv.2025.179881},
pmid = {40516193},
issn = {1879-1026},
abstract = {Climate change is exacerbating heatwaves, significantly increasing public health risks, including heightened vulnerability to Vibrio vulnificus infections, especially among older adults. While heat stress alone impairs immune regulation and compromises gut integrity, the combined effects of aging and climate-induced heat stress on infectious severity remain insufficiently explored. Using young (12-week-old) and aged (24-month-old) mouse models, we examined how aging and periodic heat stress synergistically influence susceptibility to Vibrio vulnificus by assessing gut microbiome alterations, immune responses, and antibiotic resistance gene dynamics. Heat stress markedly impaired intestinal barrier function, induced significant microbiome shifts, elevated systemic inflammation, and promoted enrichment of antibiotic resistance genes particularly those conferring tetracycline resistance with effects significantly amplified in aged mice. Upon Vibrio vulnificus infection, aged heat-stressed mice demonstrated elevated inflammatory responses, severe intestinal damage, and pronounced immune dysregulation compared to younger counterparts. Gut depletion and probiotic recolonization models further validated microbiota involvement, showing that Roseburia intestinalis significantly reduced heat stress-exacerbated CD4[+] T-cell immunosenescence in aged mice. Collectively, this study provides robust experimental evidence highlighting the critical interplay between aging and climate-driven heat stress in intensifying infectious disease severity via microbiome-immune axis disruptions, underscoring the need for microbiota-targeted strategies in climate-vulnerable populations.},
}
@article {pmid40516145,
year = {2025},
author = {Velasco, WV and Grimaldo, MT and Karimi, N and Clowers, MJ and Krishna, A and Wu, R and Ejaz, R and Yuan, B and Aguila, SD and Bouchelkia, I and Barragan, JEM and Larsen, KE and Rezai, Y and Khalaj, F and Mitra, K and Rodriguez, CR and Millares, R and de Anda, AB and Castro-Pando, S and Karandikar, UC and Petrosino, JF and McAllister, F and Kadara, H and Ostrin, EJ and Fahrmann, JF and Hoffman, KL and Moghaddam, SJ},
title = {Comparative effects of combustible cigarette versus electronic cigarette exposures on KRAS mutant lung cancer promotion.},
journal = {Neoplasia (New York, N.Y.)},
volume = {67},
number = {},
pages = {101185},
doi = {10.1016/j.neo.2025.101185},
pmid = {40516145},
issn = {1476-5586},
abstract = {Despite the emerging public health concern related to the use of electronic cigarette vapors (ECV), its impact on lung cancer is poorly understood. We assessed the effect of ECV on lung tumorigenesis in a mouse model of lung adenocarcinoma. Mice were exposed to either room air, combustible cigarette smoke (CCS), or ECV 2 hours daily for 8 weeks at which lung samples were harvested and studied for different outcomes. We found that CCS, but not ECV, led to a significant increase in tumor burden. Immunophenotyping of both CCS- and ECV-exposed lungs displayed pronounced pro-tumor immunosuppressive phenotypes, characterized by significantly decreased CD4+ IFNγ+ and CD8+ GZMB+ T cells along with an elevated CD4+ FOXP3+ regulatory T cells. However, differential changes in myeloid cells were observed between CCS and ECV-exposed lungs. A microbiome profiling of matched stool and lung samples showed differences in the relative abundance of lung Pseudomonadotas, while gut Bacillota, particularly Turicibacter, and Ileibacterium were increased by CCS and ECV. We conclude that both CCS and ECV exposure under the applied regimen lead to a protumor immune suppressive lung microenvironment although with different magnitudes and slightly different phenotypes that might explain their differential effects on tumor burden warranting further studies.},
}
@article {pmid40516101,
year = {2025},
author = {Saqr, A and Cheng, S and Al-Kofahi, M and Staley, C and Jacobson, PA},
title = {Microbiome-Informed Dosing: Exploring Gut Microbial Communities Impact on Mycophenolate Enterohepatic Circulation and Therapeutic Target Achievement.},
journal = {Clinical pharmacology and therapeutics},
volume = {},
number = {},
pages = {},
doi = {10.1002/cpt.3740},
pmid = {40516101},
issn = {1532-6535},
abstract = {Pharmacomicrobiomics is an emerging field due to important microbiome effects on pharmacokinetics and clinical outcomes. However, the application of this knowledge remains limited. Mycophenolic acid (MPA) is the primary active metabolite of the immunosuppressant, mycophenolate mofetil (MMF). MPA undergoes glucuronidation to form MPA glucuronide (MPAG) which is deglucuronidated by bacterial β-glucuronidases and reformed as MPA through enterohepatic circulation (EHC). We studied the stool microbiome effect on the pharmacokinetics of MPA, its metabolites, and EHC in hematopoietic cell transplant (HCT) recipients using a semi-mechanistic population pharmacokinetic model. Microbiome communities were identified using correlation network analysis, and their impact on pharmacokinetics was assessed using full fixed-effects modeling. Simulations were then conducted to evaluate MMF dosing regimens and to assess the impact of community abundance on EHC and MPA therapeutic target achievement. High abundance of Bacteroides uniformis-dominant and Bacteroides vulgatus-dominant communities was associated with higher EHC and an increase in MPA exposure. Low abundance of these communities was associated with a 52-80% and 4-83% lower EHC and MPA exposure, respectively. Simulations showed 70% of individuals with low abundance of these communities achieved the therapeutic target at the typical HCT MMF dose of 1,000 mg Q8 hours IV; however, ≥ 95% were within the therapeutic target at 1,250 mg Q8 hours or 1,750 mg Q12 hours. EHC accounted for 34% of the MPA area under the curve. Elimination of EHC reduced troughs by 100%. This work quantifies the microbiome's effect on pharmacokinetics, paving the way for future microbiome-informed dosing to optimize therapeutic target attainment.},
}
@article {pmid40515945,
year = {2025},
author = {Gong, W and Li, Q and Lai, Y and Yang, D and Xu, X and Liao, H and Wang, H and Cai, F and Li, H},
title = {Rice endophytic fungal community and its potential role on rice grains Cd accumulation.},
journal = {World journal of microbiology &amp; biotechnology},
volume = {41},
number = {6},
pages = {201},
pmid = {40515945},
issn = {1573-0972},
support = {202403AP140035//Yunnan International Joint Laboratory of Research and Development of Crop Safety Production on Heavy Metal Pollution Areas/ ; 42267059//Natural Science Foundation of China/ ; 202501AS070148//Yunnan Fundamental Research Projects/ ; KUST-AN2023006Y//Medical Joint Special Project of Kunming University of Science and Technology-The First People's Hospital of Anning/ ; },
mesh = {*Oryza/microbiology/metabolism/growth &amp; development ; *Cadmium/metabolism/analysis ; *Endophytes/metabolism/classification/isolation &amp; purification/genetics ; *Fungi/classification/isolation &amp; purification/metabolism/genetics ; Soil Pollutants/metabolism/analysis ; Soil Microbiology ; Mycobiome ; Plant Roots/microbiology ; Soil/chemistry ; Biodiversity ; Edible Grain/microbiology/metabolism ; High-Throughput Nucleotide Sequencing ; },
abstract = {Rice is a cadmium (Cd) high-accumulator, therefore, the soils Cd contamination may cause food security problems. Endophytes played a crucial role on host plants' heavy metal accumulation. However, the endophytic fungal community of rice and its role on rice grains Cd accumulation is still unclear. In this study, the endophytic fungal community of rice at different growth stages from different Cd-contaminated sites (LC and HC, contains lower and higher concentration of Cd, respectively) were investigated by high-throughput sequencing method. In addition, the culturable fungal endophytes were isolated and Cd tolerance assessments were also conducted for some of the isolates. The results showed that the soils Cd concentration and rice tissue showed greater effect on the endophytic fungal community than that of the rice growth stage. The dominant endophytic fungi changed with the soils Cd concentration, and higher Cd concentration reduced the species diversity (Shannon index) and evenness (Evenness index) of endophytic fungi, especially in the roots. In addition, the correlation analysis of dominant endophytic fungi with environmental factors showed that Alternaria, Fusarium and Saccharomyces had a significant positive correlation with Cd concentration. While, the linear discriminant analysis effect size (LEfSe) analysis showed that Stellatospora, Westerdykella, Sarocladium, Spencerozyma and Penicillium were the biomarkers (the relative abundance significantly increased) in multiple tissues from higher Cd-contaminated site. The endophytic fungi from site HC possessed higher ration of Cd tolerant isolates, and the tolerant isolates belong to Sarocladium, Alternaria, Fusarium, etc. Notably, the co-occurrence networks showed that higher Cd concentration increased modularity and number of communities of rice endophytes, especially in the roots, while decreased the positive correlation among different endophytic groups (genus level) in different tissues. These results suggested that rice may respond to higher Cd stress through enriching Cd tolerant endophytic fungi. While, the endophytic fungal community affected rice Cd tolerance by improving its microbiome stability, diversifying microbial survival strategies and maintaining the ecological balance.},
}
@article {pmid40515809,
year = {2025},
author = {Zhang, Z and Yang, Z and Lin, S and Jiang, S and Zhou, X and Li, J and Lu, W and Zhang, J},
title = {Probiotic-induced enrichment of Adlercreutzia equolifaciens increases gut microbiome wellness index and maps to lower host blood glucose levels.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2520407},
doi = {10.1080/19490976.2025.2520407},
pmid = {40515809},
issn = {1949-0984},
mesh = {Humans ; *Probiotics/administration &amp; dosage/pharmacology ; *Gastrointestinal Microbiome/drug effects ; Male ; Female ; *Blood Glucose/analysis/metabolism ; Adult ; Middle Aged ; Metagenomics ; Feces/microbiology ; Bacteria/classification/genetics/isolation &amp; purification ; Young Adult ; },
abstract = {The gut microbiome is essential for maintaining host health, influencing gut function and metabolic regulation. While probiotics are widely used to manage gut health, evidence of their specific effects in healthy individuals remains limited. Most studies focus on diseased populations, with little attention to early interventions in individuals without major diseases. In this study, we investigated the effects of probiotics on gut health in participants free from significant health conditions. Fifty-four participants were randomly assigned to receive either a placebo or composite probiotics for 60 d. Shotgun metagenomics revealed that individuals with lower baseline Gut Microbiome Wellness Index 2 (GMWI) exhibited more decisive responses to probiotic intervention, characterized by an increased abundance of beneficial commensal bacteria, including Adlercreutzia equolifaciens. Probiotic intake significantly improved the function of the gut microbiome, reducing antibiotic resistance genes and virulence factors while enhancing carbohydrate-active enzymes. Notably, A. equolifaciens promoted the production of palmitoyl serinol, a metabolite associated with improved GMWI and preventive benefits in blood glucose. In a population-based experiment, these findings were validated in a follow-up single-strain probiotic intervention with Lacticaseibacillus casei Zhang. Our study highlights the potential of probiotics as an early intervention strategy for maintaining gut health in individuals without significant health conditions.},
}
@article {pmid40515794,
year = {2025},
author = {Hassan, ASI and Henawy, AR and Saied, YA and Garas, KA and Shahat, OM and Halema, AA},
title = {Direct-fed Microbials (DFM) and Poultry Genomics: A Synergistic Approach to Sustainable Antibiotic Free Farming.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {40515794},
issn = {1867-1314},
abstract = {Improper usage of antibiotics in poultry production is a great threat to the ecosystem because their residues can enter into the food chain or leach into soil or water systems and increase antibiotic resistance risks. Hence, direct-fed microbials (DFMs) have gained recognition as a sustainable and viable alternative to antibiotics in poultry production, capitalizing on the relationship between microbial genetics, host genomics, and gut microbiota. This review delves into the genetic and host genomic mechanisms through DFMs effects including the enhancement of nutrient metabolism, modulation of gut microbiota and strengthening of the host immunity. The revolution of multi-omics has participated in the identification of probiotic strains with desirable traits and revealed their impact on host gene expression, particularly in genes related to intestinal health, such as tight junction proteins and mucins. Furthermore, the review summarizes the benefits of using DFMs in poultry production, the factors affecting their efficacy and their challenges and limitations. Future research integrating host and microbial genomics, along with precision microbiome engineering, holds promise for maximizing the potential of DFMs in advancing sustainable poultry farming practices.},
}
@article {pmid40515785,
year = {2025},
author = {Flegler, WA and Behrens, F and Sturmhöfel, AT and Sonntag, M and Schmitt, L and Rang, K and Deeken, HF and Sun, Y and Maack, GC and Büscher, W and Baer, M and Lispki, A},
title = {Long read 16S amplicon analyses and improved cultivation techniques as joined approach for the identification of viable bacterial populations in silage.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxaf151},
pmid = {40515785},
issn = {1365-2672},
abstract = {AIMS: Lactic acid bacteria (LAB) are crucial for the quality and preservation of silage. Exploration and isolation of the key microbiome are important for improving fermentation processes. While cultivation-dependent methods enable the isolation of LAB, they often overlook organisms with challenging cultivation requirements. Next-generation sequencing provides cultivation-independent microbiome insights. In contrast to commonly used methods, long-read sequencing platforms like the Pacific Biosciences (PacBio) single-molecule real-time (SMRT) platform offer species-level resolution. This study aims to investigate the benefits of a combined cultivation-dependent and -independent approach for silage microbiome analyses.<br><br>METHODS AND RESULTS: The common isolation medium for LAB was supplemented with sterile pressed juice from plant material improving the cultivation conditions. PacBio amplicon sequencing provided an almost complete and cultivation-independent picture of the bacterial community. The use of mock communities and a live/dead discriminating treatment of the samples revealed that the analysis can be misleading if appropriate controls are not performed.<br><br>CONCLUSION: Growth of plant-associated microorganisms can be supported by a plant juice containing isolation medium, allowing isolation of the dominant LAB from silage. Microbial dynamics can be represented using long-read sequencing. However, the use of controls such as a live/dead discrimination and mock communities is essential for the reliability of the data.},
}
@article {pmid40515726,
year = {2025},
author = {Melby, MK and Mylabathula, S and Azad, MB and Turner, S and Geva-Zatorsky, N and Tropini, C and Manus, MB and Blaser, M and Nichter, M},
title = {Public Health Microbiome Curriculum: Looking Below the Tip of the Iceberg for Approaches to Population Health.},
journal = {Microbial biotechnology},
volume = {18},
number = {6},
pages = {e70160},
pmid = {40515726},
issn = {1751-7915},
support = {//Canadian Institute for Advanced Research/ ; },
mesh = {Humans ; *Public Health/education ; *Microbiota ; *Curriculum ; *Population Health ; Anti-Bacterial Agents/therapeutic use ; Breast Feeding ; },
abstract = {We discuss the opportunity for public health microbiome curricula to bridge the gaps in knowledge that exist between microbiome researchers and the lay public. We propose equipping public health professionals, important facilitators of public outreach and behaviour change, with three public health curriculum modules focused on breastfeeding, antibiotics and diet. These modules shift the focus from microbes as pathogens to potential partners in promoting health across the life course. Current public health messages cover only the 'tip of the iceberg' in exploring mechanisms, and this microbiome curriculum dives below the surface to provide fresh perspectives. These microbiome insights allow us to move beyond a focus on microbes as pathogens to understand the numerous collaborative roles played by the microbiome in producing health, and the upstream factors influencing the microbiome, thereby offering mechanistic insights that can be harnessed for public health education.},
}
@article {pmid40515692,
year = {2025},
author = {Soffritti, I and D'Accolti, M and Bini, F and Mazziga, E and Volta, A and Bisi, M and Mazzacane, S and Caselli, E},
title = {Probiotic-Based Approaches for Sustainable Control of Infectious Risk in Mass Transport: Current Data and Future Perspectives.},
journal = {Microbial biotechnology},
volume = {18},
number = {6},
pages = {e70177},
pmid = {40515692},
issn = {1751-7915},
mesh = {*Probiotics/administration &amp; dosage ; Humans ; *Sanitation/methods ; *Infection Control/methods ; Transportation ; Disinfection/methods ; },
abstract = {The built environments of high-traffic areas can play a significant role in the transmission of microorganisms and associated infections, sometimes favouring the selection of multidrug-resistant (MDR) organisms due to the excessive use of conventional disinfectants. Probiotic-based sanitation (PBS) was suggested as a novel alternative approach to control the infectious risk in crowded community environments due to its effectiveness in reducing fungal, bacterial, and viral pathogens in sanitary settings. PBS may thus trigger a paradigm shift from chemical to biological strategies in cleaning environments with high human occupancy, offering an ecological and economically sustainable alternative to conventional chemical disinfection. Providing robust data supporting the results reported so far, it has the potential to optimise bioburden control and infection prevention in mass transportation spaces. This review brings together existing research on PBS in mass transportation areas, pinpoints areas of lack of information, and explores its potential future uses, including the creation of probiotic-based materials for sustainable biocontrol in high-traffic areas.},
}
@article {pmid40515627,
year = {2025},
author = {Hasan, MR and Thapa, A and Kabir, AH},
title = {Iron retention coupled with trade-offs in localized symbiotic effects confers tolerance to combined iron deficiency and drought in soybean.},
journal = {Journal of experimental botany},
volume = {},
number = {},
pages = {},
doi = {10.1093/jxb/eraf263},
pmid = {40515627},
issn = {1460-2431},
abstract = {Iron (Fe) and water availability are closely interlinked, with deficiencies in both adversely affecting soybean growth. However, the strategies employed by soybean to tolerate such conditions remain poorly understood. This study elucidates the interactions of host factors, and microbial associations using multi-omics approaches in Clark (tolerant) and Arisoy (sensitive) genotypes exposed to Fe deficiency and drought. Clark exhibited resilience to stress through sustained osmotic regulation, nutrient uptake, and photosynthetic activity, in contrast to Arisoy. Particularly, Fe retention in Clark, accompanied by the upregulation of ferritin-like proteins, may mitigate oxidative stress by reducing Fenton reactions. Furthermore, higher jasmonic and salicylic acid levels in Clark may contribute to its enhanced stress adaptation compared to Arisoy. RNA-seq analysis revealed 818 and 500 upregulated, along with 931 and 361 downregulated genes, in the roots of Clark and Arisoy, respectively, under stress. We observed the upregulation of symbiotic genes, such as Chalcone-flavonone isomerase 1 and SWEET10, accompanied by increased rhizosphere siderophore and root flavonoid in Clark. This indicates a significant role of microbes in mediating differential stress tolerance in soybean. Particularly, the combined stress led to distinct root and nodule microbiome dynamics, with Clark recruiting beneficial microbes such as Variovorax and Paecilomyces, whereas Arisoy exhibited the opposite pattern. In addition, Clark maintained nodule Bradyrhizobium and tissue nitrogen status, supported by ammonium retention and induction of Ammonium transporter 1 in the roots. Furthermore, in vitro compatibility between V. paradoxus and P. lilacinus suggests a synergistic interaction, with their localized signals benefiting Clark. Remarkably, enriched microbiomes significantly improved growth parameters, accompanied by elevated rhizosphere siderophore in sensitive genotypes under stress. This study is the first to uncover mechanisms of dual stress tolerance in soybean that may offer promising targets for breeding programs and microbiome-based biofertilizer strategies to improve combined stress tolerance in soybean and other legumes.},
}
@article {pmid40515620,
year = {2025},
author = {González, CT and Martin, C and Crane, M and Gutierrez, K and Thomas, J and Remisoski, L and Okros, M and Fu, Y and Guzior, DV and Finkhouse, D and Bridges, C and Mielke, J and Querido, G and Padillo, L and Girgis, R and McClelland, M and Conrad, D and Li, X and Quinn, RA},
title = {Microenvironmental Effects of a Non-Antibiotic Therapy for a Chronic Polymicrobial Infection Alter Microbial Physiology, Competition, and Virulence.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf125},
pmid = {40515620},
issn = {1751-7370},
abstract = {People with cystic fibrosis (pwCF) have reduced mucociliary clearance in their airways, leading to the build-up of thick, sticky mucus susceptible to opportunistic infection. A new treatment, comprised of three small molecule drugs called Elexacaftor/Tezacaftor/Ivacaftor (ETI), has improved mucociliary clearance and lung function in pwCF, but how this therapy alters lung infections is poorly understood. This study experimentally modeled the biochemical changes in airway mucus caused by ETI to determine its effect on the CF lung microbiome structure and function. We prepared Artificial Sputum Medium (ASM) with reduced primary carbon sources (amino acids, deoxyribonucleic acid DNA, and mucin) to mimic the effects of ETI on mucus biochemistry due to improved mucociliary clearance and reduced pulmonary inflammation. The control and modified ASM were inoculated with pure CF pathogens or mixed-species communities and then grown in oxic and anoxic conditions, followed by multi-omics data analysis. Although oxygen strongly altered the community structure, the nutrient depletions in ASM had little effect. Instead, the reduced carbon sources altered the physiology of the collective community and its individual pathogens. This included modified growth kinetics in addition to altered nitrogen and nucleotide metabolism. Under reduced amino acid concentrations, a known effect of ETI on the sputum metabolome, the production of both Pseudomonas aeruginosa's quinolones and rhamnolipids was significantly reduced. This indirect effect of ETI translates to reduced killing of competing pathogens and reduced toxicity to epithelial cells isolated from the airways of explanted human lung tissues. These findings indicate that ETI may provide further benefit to pwCF by reducing the competition and virulence of its principal pathogen and highlight how microenvironmental effects can have powerful impacts on polymicrobial infections.},
}
@article {pmid40515619,
year = {2025},
author = {Ochiai, KK and Goshima, G},
title = {Ruegeria strains promote growth and morphogenesis of the giant coenocytic alga Bryopsis.},
journal = {Journal of experimental botany},
volume = {},
number = {},
pages = {},
doi = {10.1093/jxb/eraf262},
pmid = {40515619},
issn = {1460-2431},
abstract = {An evolutionarily intriguing life form among extant organisms is the giant coenocyte, exemplified by green macroalgae in the order Bryopsidales. In these algae, cell separation does not follow nuclear division, resulting in a body composed of a single multinucleated cell. How a single cell grows to over 10 cm and undergoes characteristic morphogenesis without cell division or differentiation remains poorly understood. Macroalgae are known to associate with numerous microbes, and in some cases, these interactions influence algal cell division and differentiation. Here, we show that specific bacterial strains can promote the growth and morphogenesis of the coenocytic macroalga Bryopsis. Among >100 bacterial isolates obtained from Bryopsis, four strains belonging to the genus Ruegeria were found to accelerate the growth of the main axis and induce side-branch formation when co-cultured with the alga. The same effects were observed using conditioned seawater in which Ruegeria had been pre-cultured and subsequently removed. Seasonal microbiome analysis revealed that cultured Bryopsis associates with hundreds of bacterial species, exhibiting seasonal variations in community composition. However, Ruegeria was one of the few bacterial genera consistently associated with the cultured strain, suggesting a symbiotic relationship. Notably, although Ruegeria was not detected in Bryopsis strains isolated from other regions, its effects on growth and morphogenesis were observed in co-culture experiments. These findings suggest that Bryopsis, like multicellular macroalgae, utilises associated bacteria for growth and development without strict specificity.},
}
@article {pmid40515551,
year = {2025},
author = {Roussel, C and Lessard-Lord, J and Nallabelli, N and Muller, C and Flamand, N and Silvestri, C and Di Marzo, V},
title = {Human Gut Microbes Produce EPA- and DHA-Derived Oxylipins, but not N-Acyl-Ethanolamines, From Fish Oil.},
journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology},
volume = {39},
number = {12},
pages = {e70713},
doi = {10.1096/fj.202500752RR},
pmid = {40515551},
issn = {1530-6860},
support = {//Canadian Government | Natural Sciences and Engineering Research Council of Canada (NSERC)/ ; //Canadian Government | CIHR | Institute of Nutrition, Metabolism and Diabetes (INMD)/ ; //Canadian Government | Social Sciences and Humanities Research Council of Canada (SSHRC)/ ; },
mesh = {Humans ; *Eicosapentaenoic Acid/metabolism ; *Docosahexaenoic Acids/metabolism ; *Gastrointestinal Microbiome/physiology ; *Fish Oils/metabolism ; *Ethanolamines/metabolism ; *Oxylipins/metabolism ; Feces/microbiology ; Male ; Female ; },
abstract = {We recently reported that human fecal microbiota colonized in a simulator of the human intestinal microbiome ecosystem (SHIME) process dietary oil from Buglossoides arvensis (Ahiflower), rich in the n-3 polyunsaturated fatty acid (PUFA) stearidonic acid, to the endocannabinoid (eCB)-like N-stearidonoyl-ethanolamine. Here, we assess if human fecal microbiota collected in summer and winter and inoculated in the SHIME (simulating four different intestinal sections; ileum, and ascending, transverse and descending colon) and then treated with fish oil (FO) rich in triglyceride-esterified docosahexaenoic and eicosapentaenoic acids (DHA and EPA, respectively) result in the formation of the corresponding anti-inflammatory and anticancer n-3 PUFA metabolites, including N-acylethanolamines and oxylipins. Effluents were collected every day and analyzed by LC-MS/MS for PUFA metabolites and bacterial and short-chain fatty acids (SCFA) composition during an initial 7-day treatment with vehicle and then a further 7-day treatment with FO (DHA and EPA in equal amounts, 910 mg/day each). A time-dependent increase of DHA and EPA was observed, particularly with the summer microbiota in all intestinal sections except for the duodenum, which does not contain gut microbiota. The formation of 17-hydroxy-docosahexaenoic acid from DHA, and 15-hydroxy- and 18-hydroxy-eicosapentaenoic acid from EPA was observed within the summer samples. However, no accumulation of N-docosahexaenoyl-ethanolamine or N-eicosapentaenoyl-ethanolamine, nor any other N-acyl-ethanolamines, was detected in any intestinal section and season. These data suggest that a human fecal microbiome cultivated in a SHIME processes DHA and EPA-containing triglycerides to oxylipins with known activity on the host, but not necessarily to N-acyl-ethanolamines.},
}
@article {pmid40515459,
year = {2025},
author = {Camilleri, M},
title = {Review: Human Intestinal Barrier-Optimal Measurement and Effects of Diet in the Absence of Overt Inflammation or Ulceration.},
journal = {Alimentary pharmacology &amp; therapeutics},
volume = {},
number = {},
pages = {},
doi = {10.1111/apt.70225},
pmid = {40515459},
issn = {1365-2036},
abstract = {BACKGROUND: The intestinal barrier protects humans from potentially deleterious ingested material. It consists of several components: commensal organisms, mucus, and transepithelial pathways, and immune functions.<br><br>AIMS: To review, with major focus on human studies, the methods to measure intestinal barrier function in&#xa0;vivo and the impaired intestinal barrier function in non-inflammatory conditions, and the deleterious or beneficial effects of dietary components on the intestinal barrier.<br><br>METHODS: PUBMED literature search was intentionally focused, when possible, on human studies conducted in&#xa0;vivo.<br><br>RESULTS: Although many gastrointestinal, rheumatological, and degenerative neurological diseases are attributed to impaired intestinal barrier function, often termed "leaky gut," methods of accurate measurement of intestinal barrier function in&#xa0;vivo in humans are still being developed. In&#xa0;vivo measurements provide an overall assessment of barrier function at a whole organ level, whereas ex&#xa0;vivo or in&#xa0;vitro measurements using mucosal biopsies address mechanistic information at the cellular level. Several dietary components are detrimental to the barrier, including ethanol, fat, sugars, gliadin, food additives, emulsifiers, and microbial transglutaminase. Conversely, dietary components improving barrier function include fibre and metabolites such as short-chain fatty acids, anthocyanins, polyphenols, vitamins (such as A and D), zinc, specific amino acids (such as glutamine) and probiotics.<br><br>CONCLUSIONS: Currently, data are not exclusively from human studies, and research is needed to corroborate observations in animals or further validate in humans. There are several practical dietary approaches that can be instituted for restoration of the intestinal barrier in humans.},
}
@article {pmid40514749,
year = {2025},
author = {Seiblitz, IGL and Capel, KCC and Oliveira, RR and Zilberberg, C and Cordeiro, CAMM and Francini, CLB and Zanotti, AA and Ciotti, AM and Kitahara, MV},
title = {Composition and rhythmic variations in the microbiome of Southwestern Atlantic corals.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {71},
pmid = {40514749},
issn = {2524-6372},
support = {Finance Code 001//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior- Brasil (CAPES)/ ; 2022/09789-5//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2020/15945-4//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2021/06866-6//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 305274/2021-0//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; },
abstract = {BACKGROUND: Diel and tidal rhythms can regulate the metabolism, physiology, behavior, and gene expression patterns of different organisms, with evidence of an integration on the circadian behavior of host species and their microbial community. Corals host a diverse and dynamic microbial community, with variable diversity and abundance across geographic and temporal scales. Within scleractinian corals, those that host endosymbiotic algae (i.e., zooxanthellate) display a diel variation in the oxygen levels, an oscillation in their internal environment that has the potential to influence its microbiome abundance and/or composition. Here we investigate in situ daily fluctuations on the microbial community of two zooxanthellate (Madracis decactis and Mussismilia hispida) and two azooxanthellate coral species (Tubastraea coccinea and T. tagusensis) along a 72-hour period.<br><br>RESULTS: Day and night alpha diversity values were similar for all species, with Ma. decactis hosting a significantly more diverse community. Similarly, there was no fluctuation in the microbiome composition at the Amplicon Sequence Variants (ASV) level between day and night within species, but all species were significantly different from each other. Interestingly, Mu. hispida, an endemic species to the Southwestern Atlantic, had a high proportion of unidentified microbial taxa at genus level, suggesting a species-specific microbiome community composed by unidentified taxa. Significant rhythmicity in the abundance of individual ASVs was observed for one ASV (genus Pseudoalteromonas) in T. tagusensis and one (genus Woeseia) in Ma. decactis, with 24 and 12-hour fluctuations, respectively. In addition, DESeq2 recovered 13 ASVs (four in Ma. decactis, two in Mu. hispida, six in T. coccinea, and one in T. tagusensis) with different abundances between day and night.<br><br>CONCLUSIONS: Results show divergent microbial communities when comparing zooxanthellate and azooxanthellate species, with few significant changes within a 24-hour period. Future studies should focus on metabolic pathways to better understand how the microbiome community can adjust to environmental changes within the coral host in short time scales.},
}
@article {pmid40514740,
year = {2025},
author = {Martin, I and Elsheshtawy, A and Clokie, BGJ and MacKenzie, S and Bateman, KS and Bass, D and Stentiford, GD and Albalat, A},
title = {Microbiome dynamics associated with Hematodinium sp. infection in Norway lobster (Nephrops norvegicus).},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {62},
pmid = {40514740},
issn = {2524-4671},
abstract = {BACKGROUND: The parasite Hematodinium sp. causes morbidity and seasonal mortality events in more than 40 decapod species globally and therefore, it is now recognised as a significant threat to the future sustainability of shellfish fisheries and aquaculture worldwide. Among these, Norway lobster (Nephrops norvegicus), an important representative of the marine benthos and supporting the most valuable shellfish fishery in the UK, experience yearly seasonal Hematodinium sp. patent infections. Currently, little is known about the N. norvegicus microbiome and potential role during Hematodinium sp.<br><br>INFECTION: Therefore, in this study we investigated the microbiome dynamics of N. norvegicus associated with Hematodinium sp. infection and disease progression in the haemolymph and gut. N. norvegicus were sampled from the Clyde Sea Area, Scotland during the peak of the Hematodinium sp. patent infection. The presence and intensity of Hematodinium sp. infection were determined using the body colour method (BCM), pleopod method (PM), histology (heart, gonads, hepatopancreas, gills and muscle) and molecular tools (PCR).<br><br>RESULTS: Marked shifts in the bacterial richness of the haemolymph and significant alterations in the overall bacterial community composition of both tissues were observed in infected lobsters. These changes, observed even at subpatent levels of infection (only positive by PCR), indicate a prompt and persistent microbiome shift associated with Hematodinium sp.<br><br>INFECTION: Furthermore, smaller healthy animals (25.2&#x2009;&#xb1;&#x2009;1.20&#xa0;mm CL) known to be particularly susceptible to high severity infection displayed a decreased microbiome richness in the haemolymph suggesting a potential link between the host microbiome and susceptibility to disease progression, a possibility that merits further research.<br><br>CONCLUSIONS: This study offers the first insights into the pathobiome of N. norvegicus due to Hematodinium sp. infection and disease that in turn provides a foundation for further studies on the pathogenesis of this important parasitic disease.},
}
@article {pmid40514722,
year = {2025},
author = {Zhang, M and Xiao, Y and Song, Q and Li, Z},
title = {Antarctic ice-free terrestrial microbial functional redundancy in core ecological functions and microhabitat-specific microbial taxa and adaptive strategy.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {70},
pmid = {40514722},
issn = {2524-6372},
support = {2022YFC280410//National Key Research and Development Program of China/ ; },
abstract = {BACKGROUND: Although ice-free terrestrial ecosystems in Antarctica cover only limited areas, they harbor diverse and metabolically active microbial communities. These ecosystems encompass distinct microhabitats such as mosses, lichens, and soils, each offering unique ecological niches. However, how different microbial taxa respond to microhabitat heterogeneity, ecological strategies such as functional redundancy and specialization contribute to adaptation in extreme environments remains underexplored. To address these questions, we employed high-throughput 16 S rRNA gene and ITS sequencing in combination with GeoChip-based functional gene profiling to assess the structure and functional potential of microbial communities across moss, lichen and soil microhabitats in Antarctic ice-free terrestrial ecosystem.<br><br>RESULTS: Microhabitat type has a greater influence on microbial community structure and function in the ice-free Antarctic terrestrial ecosystem than geographical location. Though all prokaryotic communities were dominated by Pseudomonadota, Nostoc and Endobacter were significantly enriched in the moss and lichen microhabitats, respectively. Meanwhile, all fungal communities were primarily dominated by Ascomycota and Basidiomycota, with Byssoloma and Usnea showing significant enrichment in the moss and lichen microhabitats, respectively. Despite these taxonomic differences, the three microhabitats show similar core ecological functions with widespread microbial functional redundancy. Nevertheless, clear microhabitat-specific functional specialization was suggested. For example, moss microhabitat was enriched in Pyoverdin_pvcC and Zeaxanthin_glucosyltransferase, sdhA, lichen microhabitat harbored higher levels of nhaA, nikC, vacuolar_iron_transport, mttB, glucoamylase, pel_Cdeg, pme_Cdeg, rgh, rgl, while soil microhabitat was enriched in 5f1_ppn and isopullulanase. Notably, genes involved in carotenoid biosynthesis were significantly more abundant in moss and lichen microhabitats than in soil microhabitat, indicating the adaptive capacity of symbiotic microorganisms to mitigate ultraviolet radiation and oxidative stress to protect their hosts.<br><br>CONCLUSIONS: Microbial communities associated with distinct microhabitats (i.e. mosses, lichens, and soils) in Antarctic ice-free terrestrial ecosystem exhibit both functional redundancy in core ecological functions and microhabitat-specific specialization in key microbial taxa and adaptive strategy.},
}
@article {pmid40514640,
year = {2025},
author = {Almulla, AF and Maes, M},
title = {Peripheral Immune-Inflammatory Pathways in Major Depressive Disorder, Bipolar Disorder, and Schizophrenia: Exploring Their Potential as Treatment Targets.},
journal = {CNS drugs},
volume = {},
number = {},
pages = {},
pmid = {40514640},
issn = {1179-1934},
support = {RA66/016//FF66 grant and a Sompoch Endowment Fund (Faculty of Medicine), MDCU/ ; BG-RRP-2.004-0007-&#x421;01//Strategic Research and Innovation Program for the Development of MU - PLOVDIV-(SRIPD-MUP)", Creation of a network of research higher schools, National plan for recovery and sustainability, European Union - NextGenerationEU/ ; },
abstract = {Major depressive disorder (MDD), bipolar disorder (BD), and schizophrenia (SCZ) are major mental disorders linked to substantial morbidity. Traditional monoamine-based pharmacotherapies frequently produce inadequate outcomes for many patients. The elevated levels of treatment resistance require the exploration of new pharmacological targets. Evidence indicates that peripheral immune-inflammatory dysregulation, characterized by an imbalance between immunological responses and compensatory immune-regulatory systems (IRS/CIRS), together with increased oxidative and nitrosative stress (O&amp;NS), significantly contributes to the pathogenesis of these disorders. This review examines IRS/CIRS/O&amp;NS pathways as new drug targets and highlights novel pharmacological trials. Antiinflammatory drugs have been repurposed as augmentation strategies for the treatment of MDD/BD and SCZ, including nonsteroidal antiinflammatory medications, such as cyclooxygenase-2 (COX-2) inhibitors; cytokine-targeting biologics, such as tumor necrosis factor-α monoclonal antibodies; and minocycline, an antibiotic that attenuates neuroinflammation. N-acetylcysteine, curcumin, and omega-3 polyunsaturated fatty acids demonstrate some efficacy as augmentation therapies in MDD, likely by diminishing IRS activation and O&amp;NS. Strategies aimed at the gut-brain axis and gut dysbiosis, including fecal microbiota transplantation, are under investigation for their capacity to restore immunological homeostasis by improving gut barrier integrity and microbiome composition. This review examines new potential therapeutic targets arising from recent discoveries in neuro-immune interactions and oxidative stress, including particular lymphocyte surface markers, the CIRS, and intracellular network molecules in both affective and psychotic disorders. The evidence underscores the clinical importance of immune-targeted augmentation treatments in psychiatric disorders and supports the ongoing development of these novel pharmacotherapies within a precision medicine paradigm.},
}
@article {pmid40514563,
year = {2025},
author = {Coley-O'Rourke, EJ and Lum, GR and Pronovost, GN and Yu, LW and Özcan, E and Yu, KB and McDermott, J and Chakhoyan, A and Goldman, E and Vuong, HE and Paramo, J and McCune, S and Sejane, K and Renwick, S and Bode, L and Chu, A and Calkins, KL and Hsiao, EY},
title = {Murine maternal microbiome modifies adverse effects of protein undernutrition on offspring neurobehaviour.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {40514563},
issn = {2058-5276},
support = {1R01HD111079//U.S. Department of Health &amp; Human Services | NIH | Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD)/ ; Graduate Research Fellowship//National Science Foundation (NSF)/ ; },
abstract = {Protein undernutrition results in impaired growth and neurobehavioural development in children. However, the impact of timing, environmental factors and maternal versus neonatal influences are unclear. Here, using a mouse model of fetal growth restriction where maternal protein intake is limited during pregnancy, we show that adult offspring exhibit cognitive and anxiety-like behavioural abnormalities. Cross-fostering newborn mice to dams previously exposed to either low protein or standard diet reveals that behavioural impairments in adult offspring require diet-induced conditioning of both fetal development and maternal peripartum physiology. Maternal gut microbiome diversity is reduced, maternal immune, milk, and serum metabolomic profiles are altered, and widespread changes in fetal brain transcriptomic and metabolomic profiles are observed, including subsets of microbiome-dependent metabolites. Finally, we show that dam treatment with a cocktail of ten diet- and microbiome-dependent metabolites results in differential effects on fetal development and postnatal behaviour. Our study highlights the impact of prenatal maternal protein undernutrition on offspring neurobehavioural trajectories and the role of the maternal microbiome.},
}
@article {pmid40514454,
year = {2025},
author = {Veloso Soares, SP and Jarquín-Díaz, VH and Veiga, MM and Karl, S and Czirják, G&#xc1; and Weyrich, A and Metzger, S and East, ML and Hofer, H and Heitlinger, E and Benhaiem, S and Ferreira, SCM},
title = {Mucosal immune responses and intestinal microbiome associations in wild spotted hyenas (Crocuta crocuta).},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {924},
pmid = {40514454},
issn = {2399-3642},
support = {GRAKO 2046//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; DFG-Grako 2046//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; DFG-Grako 2046//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; GRK 2046//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; GRK 2046//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; GRK 2046//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; GRK 2046//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; GRK 2046//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/immunology ; *Hyaenidae/microbiology/immunology ; *Immunity, Mucosal ; Feces/microbiology/chemistry ; Female ; Male ; Tanzania ; Bacteria/classification/genetics ; },
abstract = {Little is known about host-gut microbiome interactions within natural populations at the intestinal mucosa, the primary interface. We investigate associations between the intestinal microbiome and mucosal immune measures while controlling for host, social and ecological factors in 199 samples of 158 wild spotted hyenas (Crocuta crocuta) in the Serengeti National Park, Tanzania. We profile the microbiome composition using a multi-amplicon approach and measure faecal immunoglobulin A and mucin. Probabilistic models indicate that both immune measures predicted microbiome similarity among individuals in an age-dependent manner. These associations are the strongest within bacteria, intermediate within parasites, and weakest within fungi communities. Machine learning models accurately predicted both immune measures and identify the taxa driving these associations: symbiotic bacteria reported in humans and laboratory mice, unclassified bacteria, parasitic hookworms and fungi. These findings improve our understanding of the gut microbiome, its drivers, and interactions in wild populations under natural selection.},
}
@article {pmid40514374,
year = {2025},
author = {Xu, L and Yan, J and Yin, T and Pan, Y and Chen, M and Wang, X and Wu, L and Ding, H},
title = {Di (2-ethylhexyl) Phthalate decrease pregnancy rate via disrupting the microbe-gut-hypothalamic-pituitary-ovarian axis in mice.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {107},
pmid = {40514374},
issn = {2055-5008},
support = {BK20230153//Natural Science Foundation of Jiangsu Province, China/ ; ZKX14035//Nanjing Medical Science and Technique Development Foundation/ ; },
mesh = {Animals ; Female ; *Gastrointestinal Microbiome/drug effects ; *Diethylhexyl Phthalate/toxicity ; Mice ; Pregnancy ; *Ovary/drug effects ; *Hypothalamo-Hypophyseal System/drug effects ; Gonadotropin-Releasing Hormone/metabolism ; Endocrine Disruptors/toxicity ; Astrocytes/drug effects/metabolism ; Bacteria/classification/genetics/drug effects ; },
abstract = {Di (2-ethylhexyl) Phthalate (DEHP), a widely used plasticizer and endocrine disruptor, poses risks to human health, particularly reproductive function. Using a mouse model, we investigated how DEHP exposure impacts the hypothalamic-pituitary-ovarian (HPO) axis through gut microbiome disruption. DEHP decreased pregnancy rates by impairing ovarian function, activating hypothalamic astrocytes, and increasing neuregulin 1 (NRG1) expression. NRG1 binding to astrocyte ErbB2 receptors elevated prostaglandin E2 (PGE2) and gonadotropin-releasing hormone (GnRH), disrupting HPO axis homeostasis. Additionally, DEHP altered gut microbiota, destabilized microbial networks, and impacted β-glucuronidase-related taxa, leading to hormone fluctuations and reduced fertility. This study highlights gut microbiome perturbations as a novel mechanism linking DEHP exposure to reproductive dysfunction. Our study provides novel insights concerning perturbations of the gut microbiome and HPO axis and their functions as a potential new mechanism by which DEHP exposes interferes with the reproductive function-related human health.},
}
@article {pmid40514168,
year = {2025},
author = {Ebrahimi, F and Maleki, H and Ebrahimi, M and Beiki, AH},
title = {A novel approach to finding the compositional differences and biomarkers in gut microbiota in type 2 diabetic patients via meta-analysis, data-mining, and multivariate analysis.},
journal = {Endocrinologia, diabetes y nutricion},
volume = {72},
number = {6},
pages = {501561},
doi = {10.1016/j.endien.2025.501561},
pmid = {40514168},
issn = {2530-0180},
mesh = {*Diabetes Mellitus, Type 2/microbiology ; Humans ; *Gastrointestinal Microbiome ; *Data Mining ; Biomarkers/analysis ; Multivariate Analysis ; Male ; Middle Aged ; Female ; },
abstract = {Type 2 diabetes mellitus (T2DM)-one of the fastest globally spreading diseases-is a chronic metabolic disorder characterized by elevated blood glucose levels. It has been suggested that the composition of gut microbiota plays key roles in the prevalence of T2DM. In this study, a novel approach of large-scale data mining and multivariate analysis of the gut microbiome of T2DM patients and healthy controls was conducted to find the key compositional differences in their microbiota and potential biomarkers of the disease.<br><br>METHODS: First, suitable datasets were identified (9 in total with 946 samples), analyzed, and their operational taxonomic units (OTUs) were computed by identical parameters to increase accuracy. The following OTUs were merged and compared based on their health status, and compositional differences detected. For biomarker identification, the OTUs were subjected to 9 different attribute weighting models. Additionally, OTUs were independently analyzed by multivariate algorithms (LEfSe test) to verify the realized biomarkers.<br><br>RESULTS: Overall, 23 genera and 4 phyla were identified as possible biomarkers. At genus level, the decrease of Bacteroides, Methanobrevibacter, Paraprevotella, and [Eubacterium] hallii group in T2DM and the increase of Prevotella, Megamonas, Megasphaera, Ligilactobacillus, and Lachnoclostridium were selected as biomarkers; and at phylum level, the increase of Synergistota and the decrease of Euryarchaeota, Desulfobacterota (Thermodesulfobacteriota), and Ptescibacteria.<br><br>CONCLUSION: This is the first study ever conducted to find the microbial compositional differences and biomarkers in T2DM using data mining models applied on a widespread metagenome dataset and verified by multivariate analysis.},
}
@article {pmid40513921,
year = {2025},
author = {Zhang, X and Sheng, N and Wang, Z and Cao, Y and Jiang, X and Yan, H and Cheng, F and Geng, T and Wei, K and Zhang, L and Gao, M and Zhou, G and Chen, P},
title = {Exploring the mechanism of Carbonized Typhae Pollen in treating blood stasis syndrome through metabolic profiling: the synergistic effect of hemostasis without blood stasis.},
journal = {Journal of ethnopharmacology},
volume = {},
number = {},
pages = {120124},
doi = {10.1016/j.jep.2025.120124},
pmid = {40513921},
issn = {1872-7573},
abstract = {Removing blood stasis and stopping bleeding traditional Chinese medicines (RBSB-TCM) formed a unique class of TCM, characterized by vasodilating, removing stasis and hemostatic effects. Carbonized Typhae Pollen (CTP), derived from Typhae Pollen (TP) through carbonization, has emerged as a particularly valuable therapeutic agent. It has been widely used in clinical practice to treat hemorrhagic disorders caused by blood stasis syndrome (BSS). However, the potential mechanism for CTP to achieve the dual synergistic effect of promoting blood flow and hemostasis remains unclear.<br><br>AIM OF THE STUDY: From the standpoint of metabolite profiles, this study attempts to investigate the fundamental mechanism of CTP in the elimination of blood stasis and the cessation of bleeding.<br><br>MATERIALS AND METHODS: First, chemical constituents, absorbed constituents and metabolites in rats following oral administration of CTP were identified by ultra-high performance liquid chromatography coupled with the quadrupole time-of-flight mass spectrometry (UHPLC-Q-TOF-MS) method combined with MetabolitePilot 2.0.4 software. Subsequently, the pharmacological effects of CTP were systematically investigated using rat models with BSS and zebrafish with cerebral hemorrhage. Specifically, the impact on coagulation function and histopathology in rats, as well as the effect on cerebral hemorrhage in zebrafish, were thoroughly evaluated. Untargeted metabolomics based on rat plasma was applied to analyze the metabolic profile changes, revealing the potential action mechanism. The underlying mechanism was furtherly confirmed by gut microbiome analysis and systemic molecular biology experiments.<br><br>RESULTS: 34 prototype chemicals and 71 metabolites from the liver, heart, spleen, lung, kidney, small intestine, uterus, and serum were found. CTP improved the abnormal coagulation system, promoted blood circulation, and reduced pathological damage caused by BSS. Plasma metabolomics revealed that BSS significantly altered bile acid (BA) metabolism and arachidonic acid (AA) metabolism. Gut microbiome analysis and fecal microbiota transplantation (FMT) experiments further demonstrated that CTP modulated the gut microbiota. This modulation promoted BA production and activated endothelial nitric oxide synthase (eNOS), leading to increased nitric oxide (NO) levels. These changes contributed to the therapeutic effect of CTP in removing blood stasis. Systemic molecular biology experiments showed that CTP activated key components of the AA metabolic pathway. It promoted PLC&#x3b3;1 phosphorylation, increased intracellular Ca[2+] levels, and upregulated COX-2 expression. In addition, CTP enhanced the production of AA-related metabolites, including 6-keto-prostaglandin F1&#x3b1; (6-keto-PGF1&#x3b1;), prostaglandin E2 (PGE2), and thromboxane B2 (TXB2). It also increased the transcription of AA metabolism-related genes, such as PLC&#x3b3;1, PTGS2a, PTGS2b, PTGIS, PTGES, TXBAS, and vWF.<br><br>CONCLUSIONS: CTP could promote the generation of AA metabolites through PLC&#x3b3;1/Ca[2+]/COX-2 to stop bleeding, while also enhancing eNOS activity and NO synthesis through gut microbiota-bile acid axis to remove blood stasis. These two effect were balanced to achieve hemostasis without blood stasis.},
}
@article {pmid40513864,
year = {2025},
author = {Li, Y and Fan, Q and Dong, H and Chang, S and Liu, W},
title = {Screening of potential probiotic Bifidobacteria from intestinal tract and its application in fermented milk.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2024-25960},
pmid = {40513864},
issn = {1525-3198},
abstract = {Bifidobacteria, a significant component of human gut microbiota, play a crucial role in maintaining human health. Studies have shown that the composition of gut microbiome is closely related to the geographical environment, ethnicity, and dietary structure of the host. Currently, most of the mainstream probiotics on the market are based on the gut microbiota characteristics of Western populations, which may not be completely suitable for the gut environment of Chinese people. Therefore, the isolation and screening of Bifidobacteria with probiotic functions in the intestinal tract is critically important to meet the demands of the Chinese market. In the present study, 216 Bifidobacterial strains were isolated and identified from 35 fecal samples collected from the city of Hohhot, Inner Mongolia, China. Further investigations were conducted to determine the probiotic potential of these strains. Among the screened strains, Bifidobacterium longum ssp. longum IMAU12449 was identified as the most promising probiotic strain. The survival rate of strain IMAU12449 was highest in the simulated artificial gastrointestinal fluid. The survival rate of strain IMAU12449 in artificial gastric fluid for 3 h was 62.38%, and the survival rate was 40.30% in the artificial intestinal fluid for 8 h. Furthermore, the strain exhibited excellent cell autoaggregation (72.79%) and surface hydrophobicity (45.66%). Strain IMAU12449 also exhibited a strong inhibitory effect on common pathogens. Safety evaluation revealed that the strain possessed 2 potential antibiotic resistance genes and no virulence factors. This strain exhibited γ-hemolysis in vitro. The advantages of a stable viable count, moderate acidity, and absence of whey precipitation were observed in fermented cow and soy milk processed by strain IMAU12449 combined with commercial starters. After storage at 4°C for 21 d, the viable cell count remained above 10[7] cfu/mL. In conclusion, a Bifidobacterial strain, IMAU12449, with favorable probiotic properties was identified in this study. This strain has demonstrated significant potential for application in fermented milk, and further research should be conducted to elucidate its role in promoting health.},
}
@article {pmid40513821,
year = {2025},
author = {Yokus, B and Maccioni, L and Fu, L and Haskó, G and Nagy, LE and Gao, B and Pacher, P},
title = {The Link Between Alcohol Consumption and Kidney Injury.},
journal = {The American journal of pathology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ajpath.2025.05.011},
pmid = {40513821},
issn = {1525-2191},
abstract = {Alcohol consumption contributes to systemic organ dysfunction, but its direct effect on kidney health is unclear. Epidemiological studies show inconsistent findings due to reliance on conventional markers like serum creatinine (sCr) and blood urea nitrogen (BUN), which are insensitive to early chronic kidney disease (CKD) and influenced by factors such as muscle mass, diet, and hydration status. Experimental studies indicate that alcohol may directly exacerbate renal damage through mitochondrial dysfunction, oxidative stress, and inflammation. Furthermore, indirect effects from alcohol-induced altered intestinal permeability and microbiome, liver injury, microcirculatory/cardiac dysfunction and muscle damage may also facilitate kidney damage. Notably, alcohol-related liver disease can lead to hepatorenal syndrome, a severe form of kidney dysfunction driven by circulatory disturbances and systemic inflammation. This overview explores the adverse effects of alcohol misuse on kidney health and disease, emphasizing the need for comprehensive epidemiological studies with more sensitive kidney injury biomarkers. It also highlights the importance of using clinically relevant preclinical models to clarify the underlying mechanisms of alcohol-related kidney injury and to enhance our understanding of its long-term clinical consequences.},
}
@article {pmid40513460,
year = {2025},
author = {Piercy, E and Sun, X and Ellis, PR and Taylor, M and Guo, M},
title = {Temporal dynamics of microbial communities in anaerobic digestion: Influence of temperature and feedstock composition on reactor performance and stability.},
journal = {Water research},
volume = {284},
number = {},
pages = {123974},
doi = {10.1016/j.watres.2025.123974},
pmid = {40513460},
issn = {1879-2448},
abstract = {This study presents a novel multi-disciplinary approach, integrating explainable machine-learning with detailed chemical and biological analysis using microbial fermentation food wastewater to identify critical parameters influencing AD microbiome diversity and reactor performance over time. Our research addresses knowledge gaps on the resource recovery potential from food fermentation wastewater which remains largely unexplored. Eighteen continuous bioreactors were operated under varying temperature and process configuration (single vs. two stages) using wastewater stream derived from real-world microbial protein manufacturing. Detailed chemical analysis fingerprinted the fermentation-wastewater throughout the AD process including sugars, sugar alcohols and volatile fatty acids (VFAs). Significant elevations in Methanomassiliicoccus were correlated to high butyric acid concentrations (p < 0.05) and decreased biogas production, further elucidating the role of this newly discovered methanogen in AD. Machine-learning models predicting reactor performance achieved high accuracy based on operational parameters and microbial taxonomy (14.03 root mean squared error and 0.86 R[2]). Operational parameters were found to have the most substantial influence on chemical oxygen demand removal. Oscillibacter and Clostridium sensu stricto were highlighted as key factors impacting specific biogas yield for the first time. By integrating detailed chemical and biological fingerprinting with explainable machine learning models this research presents a novel approach to advance whole-systems AD understanding, offering insights of potential new biomarkers (Oscillibacter and Clostridium sensu stricto) for industrial applications of sustainable waste-to-energy systems.},
}
@article {pmid40513117,
year = {2025},
author = {Vogtmann, E and Yano, Y and Shi, J and Wan, Y and Purandare, V and McLean, J and Li, S and Knight, R and Kahle, L and Hullings, AG and Hua, X and Graubard, BI and Gillison, ML and Caporaso, JG and Bokulich, NA and Blaser, MJ and Freedman, ND and Chaturvedi, AK and Abnet, CC},
title = {The oral microbiome and all-cause mortality in aUS population representative prospective cohort.},
journal = {The Journal of infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/infdis/jiaf321},
pmid = {40513117},
issn = {1537-6613},
abstract = {No large studies have evaluated whether the human oral microbiome is directly associated with mortality. We evaluated prospective associations between the oral microbiome, measured using 16S rRNA gene sequencing, from participants aged 20-69 years in the 2009-2012 cycles of the National Health and Nutrition Examination Survey (NHANES) and all-cause mortality (N=7,721, representing ∼194 million individuals). Alpha diversity was inversely associated with mortality, and some significant associations were observed with the beta diversity matrices. Higher relative abundances of Granulicatella and Lactobacillus were associated with increased risk, while Bacteroides was associated with decreased all-cause mortality at the genus level. Results suggest oral bacterial communities may be important contributors to health and disease.},
}
@article {pmid40512801,
year = {2025},
author = {Probst, SI and Felder, FD and Poltorak, V and Mewalal, R and Blaby, IK and Robinson, SL},
title = {Enzymatic carbon-fluorine bond cleavage by human gut microbes.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {24},
pages = {e2504122122},
doi = {10.1073/pnas.2504122122},
pmid = {40512801},
issn = {1091-6490},
support = {2022-YIG-090//Helmut Horten Stiftung (Helmut Horten Foundation)/ ; PZPGP2_209124//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (SNF)/ ; PZPGP2_209124//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (SNF)/ ; N/A//Peter und Traudl Engelhorn Stiftung (Peter and Traudl Engelhorn Foundation)/ ; 230-2024//Uniscientia Foundation/ ; 23-2-ETH-047//Eidgen&#xf6;ssische Technische Hochschule Z&#xfc;rich (ETH)/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Carbon/metabolism/chemistry ; *Fluorine/metabolism/chemistry ; Halogenation ; *Bacterial Proteins/metabolism/chemistry/genetics ; *Hydrolases/metabolism/chemistry ; Molecular Dynamics Simulation ; },
abstract = {Fluorinated compounds are used for agrochemical, pharmaceutical, and numerous industrial applications, resulting in global contamination. In many molecules, fluorine is incorporated to enhance the half-life and improve bioavailability. Fluorinated compounds enter the human body through food, water, and xenobiotics including pharmaceuticals, exposing gut microbes to these substances. The human gut microbiota is known for its xenobiotic biotransformation capabilities, but it was not previously known whether gut microbial enzymes could break carbon-fluorine bonds, potentially altering the toxicity of these compounds. Here, through the development of a rapid, miniaturized fluoride detection assay for whole-cell screening, we identified active gut microbial defluorinases. We biochemically characterized enzymes from diverse human gut microbial classes including Clostridia, Bacilli, and Coriobacteriia, with the capacity to hydrolyze (di)fluorinated organic acids and a fluorinated amino acid. Whole-protein alanine scanning, molecular dynamics simulations, and chimeric protein design enabled the identification of a disordered C-terminal protein segment involved in defluorination activity. Domain swapping exclusively of the C-terminus conferred defluorination activity to a nondefluorinating dehalogenase. To advance our understanding of the structural and sequence differences between defluorinating and nondefluorinating dehalogenases, we trained machine learning models which identified protein termini as important features. Models trained on 41-amino acid segments from protein C termini alone predicted defluorination activity with 83% accuracy (compared to 95% accuracy based on full-length protein features). This work is relevant for therapeutic interventions and environmental and human health by uncovering specificity-determining signatures of fluorine biochemistry from the gut microbiome.},
}
@article {pmid40512576,
year = {2025},
author = {Jogani, VG and Mohamed Elfadil, O and Edakkanambeth Varayil, J and Mundi, MS},
title = {Exploring the role of glucagon-like peptide-1 receptor agonists in critical illness: mechanisms, benefits, and clinical implications.},
journal = {Current opinion in critical care},
volume = {},
number = {},
pages = {},
doi = {10.1097/MCC.0000000000001294},
pmid = {40512576},
issn = {1531-7072},
abstract = {PURPOSE OF REVIEW: This review aims to synthesize current evidence on the expanding role of glucagon-like peptide-1 (GLP-1) receptor agonists (RAs) beyond glycemic control, particularly in the context of critical illness. With growing recognition of their anti-inflammatory, immunomodulatory, and organ-protective properties, GLP-1RAs show promise in managing complications such as sepsis, acute respiratory distress syndrome (ARDS), acute kidney injury, and multiorgan dysfunction. This review explores their mechanisms across vital systems - including cardiovascular, pulmonary, renal, hepatic, neuropsychiatric, and gut-lung-microbiome axes - highlighting preclinical and clinical data. By consolidating emerging findings, this review aims to inform future translational research and support the integration of GLP-1RAs into critical care strategies.<br><br>RECENT FINDINGS: Recent evidence highlights GLP-1RAs as promising adjuncts in critical illness due to their multiorgan protective effects. In cardiovascular systems, GLP-1RAs improve endothelial function, reduce ischemia-reperfusion injury, and modulate autonomic tone. In the CNS, they provide neuroprotection by reducing neuroinflammation and pyroptosis. In the lungs, they attenuate ARDS by decreasing cytokine production, enhancing surfactant secretion, and restoring alveolar-capillary integrity. Renally, they reduce acute injury and preserve filtration function. In the gut, GLP-1RAs modulate the microbiome, enhance barrier integrity, and lower systemic inflammation via the gut-lung axis. Additionally, they reduce hepatic inflammation and support pancreatic beta-cell survival, improving insulin sensitivity and metabolic stability in critical care.<br><br>SUMMARY: GLP-1 receptor agonists hold promise as multiorgan protective agents in critical illness, offering benefits beyond glucose control. Their anti-inflammatory, metabolic, and vaso-protective properties may be harnessed to prevent or attenuate organ failure, support recovery, and improve long-term outcomes in critically ill patients. Further clinical trials are warranted to define their safety, efficacy, and optimal application across ICU populations.},
}
@article {pmid40512497,
year = {2025},
author = {Qi, W and Kong, M and Meng, X and Sun, Z and Mei, Z and Pu, Y and Zhou, X and Wang, Q and Qiu, JG and Jiang, BH and Shen, J and Yuan, C and Ji, JS and Wang, X and Kan, H and Zheng, Y},
title = {The Role of Gut Microbiota in the Association Between Air Pollution and Cognitive Function in Older Adults.},
journal = {Environmental health perspectives},
volume = {},
number = {},
pages = {},
doi = {10.1289/EHP16515},
pmid = {40512497},
issn = {1552-9924},
abstract = {BACKGROUND: Growing evidence links air pollution to cognitive dysfunction in older adults. The gut microbiome and circulating metabolites present an important yet unexplored pathway, given their crucial role in the gut-brain axis.<br><br>OBJECTIVES: We aimed to explore the potential roles of gut bacteria, fungi, microbial functional potentials, and circuiting metabolites in the association of residential PM2.5 and O3 exposures with cognitive dysfunction.<br><br>METHODS: We analyzed gut microbiome data from 1,027 older adults using metagenome and internal transcribed spacer sequencing to profile bacterial and fungal taxa, functional pathways, and enzyme abundances. Targeted metabolomics quantified 195 circulating metabolites, such as amino acids and organic acids. Annual average ambient PM2.5 and O3 exposures were estimated using satellite-based models. Cognitive outcomes, including mild cognitive impairment and cognitive decline, were assessed using the Mini-mental State Examination and Hasegawa dementia scale. Statistical analyses included Microbiome Multivariable Association with Linear Models (with a false discovery rate threshold of 0.25) for microbial associations and multivariate regression for metabolites and cognitive outcomes.<br><br>RESULTS: Higher PM2.5 and O3 exposures were associated with disturbances in microbial composition, altered taxonomic profiles (e.g., decreased abundances of Blautia obeum and Gordonibacter pamelaeae), and disrupted functional pathways, particularly those regulating 2-oxoglutarate. These findings were partially replicated in an independent population. Higher air pollution levels were associated with increased circulating levels of 2-oxoglutarate and L-glutamine (key metabolites in neurodegenerative progression), which were further linked to higher odds of concurrent mild cognitive impairment (OR: 1.39-1.56) and an increased 2-year risk of cognitive decline (OR: 1.26-1.37). These associations were partially mediated by air pollution-related changes in microbial anaerobic energy metabolism pathways, especially involving 2-oxoglutarate metabolism and the enzyme aspartate transaminase.<br><br>CONCLUSIONS: Our findings highlight the role of the gut microbiome and microbial metabolites in mediating the detrimental impact of air pollution on cognitive health in older adults, providing new insights into the underlying etiology for future hypothesis generation. https://doi.org/10.1289/EHP16515.},
}
@article {pmid40512444,
year = {2025},
author = {Abbasi, A and Sheykhsaran, E and Hosseinzadeh, N and Bazdar, M and Hamehjani, M and Aghapour, B and Shojaee-Aliabadi, S},
title = {Novel Approaches in Establishing Chemical Food Safety Based on the Detoxification Capacity of Probiotics and Postbiotics: A Critical Review.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {40512444},
issn = {1867-1314},
abstract = {Environmental and chemical contaminants from industrial and agricultural sources increasingly threaten food safety worldwide. These contaminants, including bacterial toxins (e.g., botulinum toxin), mycotoxins (e.g., aflatoxin, ochratoxin), pesticides, heavy metals, and microplastics, pose significant health and economic risks. Emerging evidence highlights that chronic exposure to such xenobiotics disrupts gut microbiota structure and function, adversely affecting host health. While traditional physicochemical detoxification methods exist, they often require impractical conditions. Biological detoxification via probiotics and their metabolites (postbiotics) has gained attention as a practical and cost-effective alternative. Numerous studies concur that probiotics can bind, biotransform, or sequester xenobiotics, thereby mitigating toxicity and restoring microbiota balance. However, variations in strain efficacy, binding mechanisms, and in vivo performance indicate areas needing further exploration. This review critically synthesizes current knowledge on probiotic-mediated detoxification mechanisms, their interaction with xenobiotics and the gut microbiome, and host responses, highlighting consensus, discrepancies, and gaps to inform future research and applications.},
}
@article {pmid40512087,
year = {2025},
author = {Sahoo, B and Goyal, R and Dutta, S and Joshi, P and Sanyal, K},
title = {Candida albicans: Insights into the Biology and Experimental Innovations of a Commonly Isolated Human Fungal Pathogen.},
journal = {ACS infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1021/acsinfecdis.5c00079},
pmid = {40512087},
issn = {2373-8227},
abstract = {Candida albicans is an opportunistic pathogen associated with healthy humans. It is the major causative agent for superficial and invasive candidiasis in immunocompromised individuals globally. Lack of awareness toward fungal infections, poor disease management, and increasing drug resistance have contributed to the burden of C. albicans-associated diseases. C. albicans displays polymorphism, assisting in host interaction, virulence, and sustenance of the pathogen. Well-known polymorphic forms of C. albicans include yeast, hyphal, pseudohyphal, white, opaque, gray, GUT, and chlamydospores. While the predominant mode of propagation is via mitosis, the organism also displays a parasexual cycle. The pathogen's parasexual mating and genome plasticity introduce variants in the population, leading to adaptability and drug resistance. This organism can adopt robust pathogenic modules capable of destroying host tissues and forming drug-resistant biofilms. On the other hand, its ability to maintain an amicable interaction with the host immune system, coexisting microbiome, and adaptability to the host microenvironment makes it a successful commensal. Over the years, C. albicans has emerged as a useful model for understanding basic cell biology and drug resistance in fungal pathogens. Advancements in genetic manipulation tools have accelerated our understanding of these biological processes and eased the drug development process. This review provides comprehensive information about C. albicans and the tools available to investigate it. Studying its life cycle, disease epidemiology, mechanisms of infection, and host immune responses is crucial for developing effective therapeutic interventions.},
}
@article {pmid40512059,
year = {2025},
author = {Sadiq, S and Shen, ZY and Jiao, X and Zhang, N and Wang, L and Xu, T and Wu, P and Khan, I},
title = {Metabolome-microbiome modulations induced by ZIF8@ZIF67 supplementation in the midgut of Bombyx mori.},
journal = {Insect molecular biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/imb.13008},
pmid = {40512059},
issn = {1365-2583},
support = {32372948//National Natural Science Foundation of China/ ; BE2022355//Jiangsu Provincial Key Research and Development Program/ ; KYCX24_4142//Research Innovation Project of Postgraduate Students in Jiangsu Province/ ; //China Agriculture Research System of MOF and MARA/ ; },
abstract = {Bombyx mori is an economically crucial lepidopteran insect, and its health is closely related to the gut microbiota and metabolic status. Our previous research confirmed that metal-organic frameworks nanocomposite ZIF8@ZIF67 supplementation can significantly enhance silkworm survival rates upon bacterial challenges without adversely affecting its growth or cocoon weight. To elucidate the mechanism, this study integrated non-targeted metabolomics and 16S rRNA sequencing to dissect ZIF8@ZIF67-driven midgut modulations. The results showed that ZIF8@ZIF67 supplementation led to significant metabolic shifts in the midgut of B. mori, with 96 metabolites up-regulated and 54 down-regulated in the negative ion model, and 117 up-regulated and 43 down-regulated in the positive ion model. Key pathways included glutathione metabolism, purine/pyrimidine metabolism, and histidine metabolism, which are involved in antioxidant defence, nucleotide and protein synthesis for growth and immunity regulation. Furthermore, the gut microbiota composition of B. mori was significantly altered after ZIF8@ZIF67 supplementation, with a marked increase in the relative abundance of Mammaliicoccus and Enterococcus. Lastly, the correlation between metabolites and microbiomes was analysed, including Enterococcus and 1-methylhistidine (r = 0.8895, p = 0.0001), Akkermansia and N-acetyl-d-galactosamine (r = 0.8674, p = 0.0003). These findings demonstrated that ZIF8@ZIF67 could optimise silkworm health by orchestrating metabolite-microbe interactions to enhance nutrient assimilation and oxidative stress resilience, while simultaneously activating pathways essential for growth regulation and immune function.},
}
@article {pmid40511943,
year = {2025},
author = {Wang, B and Liang, Y and Lian, K and Zhang, C and Han, M and Wang, M and Shao, H and McMinn, A and Wang, H},
title = {Correlation with viruses enhances network complexity and stability of co-occurrence prokaryotes across the oceans.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0053925},
doi = {10.1128/msystems.00539-25},
pmid = {40511943},
issn = {2379-5077},
abstract = {UNLABELLED: Viruses play critical roles in shaping microbial distribution, organization, and ecological functions. However, the mechanisms behind the association and structuring of microbiomes with viruses still remain largely unknown. To understand how viruses affect the assembly of marine microbiomes, the network complexity and stability of prokaryotic microbiomes with/without viruses were analyzed and compared using the Tara Ocean Project data set, including samples collected from the Indian Ocean (IO), South Pacific Ocean (SPO), North Pacific Ocean (NPO), Mediterranean Sea, and South Atlantic Ocean. The network complexity of prokaryotic communities was substantially different across oceans, being high in the IO and low in the SPO and NPO. Network complexity and stability of marine prokaryotic microbial communities were enhanced by the influence of viruses: microbiomes associated with viruses were more complex, had a high modularity, and were robust with low fragmentation and vulnerability and higher compositional stability than prokaryotic microbiomes without an association with viruses. Results presented here shed light on how the associations with viruses influenced microbial assembly and their co-occurrence pattern and stability across the oceans. Overall, given such changed environmental characteristics across the oceans, stable and resilient microbiome networks imply that biotic associations with viruses play a critical role in maintaining the integrity and resilience of marine microbiomes and their ecological functions.<br><br>IMPORTANCE: This study represents the first detailed research on the effects of viruses on the organization of marine prokaryotic microbiomes at the global scale. Biotic factors and environmental heterogeneity directly and indirectly affect microbiome and viral co-occurrence with varied strength. Network complexity and stability of marine microbial communities were enhanced by the influence of viruses. Thus, given such dynamic environmental gradients in the ocean, stable and persistent microbiome networks suggest that biotic associations with viruses play a critical role in maintaining the integrity and resilience of marine microbiomes and influencing the function of marine ecosystems.},
}
@article {pmid40511937,
year = {2025},
author = {Knotek, AAU and Kristich, CJ},
title = {The cell wall hydrolase MltG is essential to maintain cell wall homeostasis of Enterococcus faecalis.},
journal = {Journal of bacteriology},
volume = {},
number = {},
pages = {e0005625},
doi = {10.1128/jb.00056-25},
pmid = {40511937},
issn = {1098-5530},
abstract = {UNLABELLED: Infections caused by enterococci are increasingly prevalent and difficult to treat due to multidrug resistance. Enterococcus faecalis exhibits intrinsic resistance toward cephalosporins, which inhibit the final step of peptidoglycan (PG) synthesis. Intrinsic resistance requires multiple factors in the PG synthesis pathway and at least two cell-wall-stress signal transduction systems; however, the complete molecular mechanism of enterococcal cephalosporin resistance remains to be elucidated. MltG, a predicted PG hydrolase, is thought to process nascent strands of PG, suggesting that MltG might play an important role in enterococcal cell wall homeostasis and potentially cephalosporin resistance. Here, we demonstrate that enterococcal MltG cleaves nascent PG. An E. faecalis mutant lacking MltG exhibits several related phenotypes in the absence of exogenous stress: a marked growth defect, a loss of cell wall integrity, a reduction in PG synthesis, and activation of two cell-wall-stress signal transduction systems that drive elevated cephalosporin resistance. Together, these results are consistent with the model that MltG promotes proper cell wall homeostasis in E. faecalis, and further reveal that the enzymatic activity of MltG is not necessary for it to perform this function-instead, the LysM (putative PG-binding) domain of MltG plays the critical role. Nevertheless, the enzymatic activity of MltG does impact cephalosporin resistance, because a catalytically inactive MltG variant leads to elevated resistance. Collectively, our findings represent the first description of MltG function in E. faecalis and point to at least two distinct roles for MltG in PG homeostasis and cephalosporin resistance.<br><br>IMPORTANCE: Enterococcus faecalis is an opportunistic pathogen that colonizes the human gut microbiome. Infections caused by E. faecalis are increasingly prevalent and difficult to treat due to the multidrug resistance exhibited toward common clinical antibiotics. A thorough understanding of the mechanisms used by E. faecalis to maintain cell wall homeostasis will serve as a foundation for future development of new therapeutics that disable enterococcal resistance to cell-wall-active antibiotics and may reveal new vulnerabilities that could be exploited by novel antimicrobials. Here, we demonstrate that the MltG peptidoglycan hydrolase is essential for enterococcal cell wall homeostasis, but that the enzymatic activity of MltG is not required for this role. Instead, the enzymatic activity of MltG impacts intrinsic resistance toward cephalosporins.},
}
@article {pmid40511923,
year = {2025},
author = {Cho, Y-J and Shin, SY and Yang, J and Kim, HK and Rintarhat, P and Park, M and Sung, M and Lagree, K and Underhill, DM and Lee, D-W and Choi, S and Choi, CH and Yang, C-S and Jung, WH},
title = {Live Malassezia strains from the mucosa of patients with ulcerative colitis: pathogenic potential and environmental adaptations.},
journal = {mBio},
volume = {},
number = {},
pages = {e0140025},
doi = {10.1128/mbio.01400-25},
pmid = {40511923},
issn = {2150-7511},
abstract = {UNLABELLED: The human gut contains a diverse range of microorganisms, including bacteria, viruses, protozoa, and fungi. Although research has predominantly focused on bacterial populations, emerging evidence highlights the significant role of the gut mycobiota, particularly in the context of inflammatory bowel disease (IBD), including ulcerative colitis (UC) and Crohn's disease. This study investigates the intestinal mucosal mycobiota of UC patients, aiming to isolate and characterize live Malassezia fungal strains from the gut mucosa. Our analysis confirmed the presence of Malassezia in the intestinal mucosal layer of UC patients, with live Malassezia globosa strains being successfully isolated. As Malassezia is generally associated with the skin, the genomic and transcriptomic profiles and virulence of the M. globosa gut isolates were compared with those of the skin isolates. While both gut and skin isolates of M. globosa shared high genomic similarity, transcriptomic analysis revealed distinct responses to oxygen levels, suggesting niche-specific adaptation. Compared with the skin isolates, the gut isolates exhibited higher virulence in a dextran sulfate sodium-induced mouse colitis model, resulting in more severe disease, reduced survival rates, and elevated proinflammatory cytokine levels in the host. Our findings highlight the potential role of M. globosa in the pathogenesis of IBD and underscore the importance of niche-specific adaptations in fungal virulence.<br><br>IMPORTANCE: Malassezia fungi predominantly reside on human skin and are associated with several skin diseases, such as seborrheic dermatitis. They have also been implicated in various other diseases, including inflammatory bowel disease (IBD). While Malassezia DNA has been detected in many fungal microbiome studies using fecal samples, no previous research had isolated live Malassezia strains from the gut or confirmed that live Malassezia cells reside within the gut environment. In this study, we successfully isolated live Malassezia globosa strains from the gut mucosal surface of ulcerative colitis patients and compared them to M. globosa skin isolates. Our results revealed significant differences in pathogenicity between the gut and skin isolates and suggest the important role of M. globosa in the gut and its involvement in IBD.},
}
@article {pmid40511703,
year = {2025},
author = {Li, Q and Cha, Y and Zhan, Y and Miao, X and He, G and Lv, P and Wang, L and Li, W and Chen, C},
title = {Atomic Ce-Induced Adaptive Synergism for Self-Optimized Multi-Enzymatic Nanozyme Design for Soil Amendment.},
journal = {Small (Weinheim an der Bergstrasse, Germany)},
volume = {},
number = {},
pages = {e2503939},
doi = {10.1002/smll.202503939},
pmid = {40511703},
issn = {1613-6829},
support = {82204558//National Natural Science Foundation of China/ ; YDZJ202401074ZYTS//Natural Science Foundation of Jilin Province/ ; },
abstract = {Single-atom nanozymes (SAzymes) offer exceptional promise as next-generation substitutes for natural enzymes due to its superior catalytic performance. However, single active sites of SAzymes have predominantly been limited to mimicking a monofunctional enzymatic activity, which hinders their adaptability in complex biological systems. Herein, an innovative Ce-induced adaptive synergism is reported, which allows Ce single-atom to activate Ni-Fe dual-site adaptive synergy for boosting multi-enzymatic activities of Ce-modified nanozyme (Ce-MOF), along with finely tuned reactive oxygen species (ROS) production. In-situ spectroscopic studies and theoretical calculations reveal that Ce induces spin-state polarization of Ni and Fe centers, promoting the generation of bound Ni/Fe = O intermediates that modulate ROS pathways depending on substrate and pH. This adaptive synergism enables continuous structural adaptation of the dual-metal active sites, enhancing both catalytic efficiency and selectivity. Functionally, Ce-MOF exhibits potent antifungal activity against Fusarium solani in vitro without the introduction of exogenous O2 or H2O2. Meanwhile, soil experiments demonstrate effective inhibition of phytopathogen colonization and a notable recovery of beneficial microbial communities via selective production of ROS. Furthermore, the amended soil treated with Ce-MOF flourishes Panax ginseng growth and provides a promising solution for sustainable plant cultivation via rhizosphere microbiome regulation.},
}
@article {pmid40511381,
year = {2025},
author = {Guo, H and Zhou, X and Li, Z and Zhi, J and Fu, C and Liu, X and Wu, Y and Liu, F and Feng, N},
title = {Exploring the systemic impacts of urinary tract infection-specific antibiotic treatments on the gut microbiome, metabolome, and intestinal morphology in rats.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e19486},
pmid = {40511381},
issn = {2167-8359},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Anti-Bacterial Agents/pharmacology/adverse effects ; Rats ; *Metabolome/drug effects ; *Urinary Tract Infections/drug therapy/microbiology ; *Intestinal Mucosa/drug effects/pathology ; *Intestines/drug effects/pathology ; Male ; Rats, Sprague-Dawley ; },
abstract = {The gut microbiota is a dynamic ecosystem that plays a crucial role in host metabolism, immune system regulation, and protection against pathogens. An imbalanced gut microbiota has been associated with various diseases such as inflammatory bowel disease, metabolic disorders, and autoimmune diseases. Antibiotic therapy can disrupt the balance of the microbiome, making it essential to understand the specific effects of these antibiotics on gut microbiota and related host function. This study aims to systematically investigate the impact of UTI-specific antibiotic treatment on the gut microbiota of rats. By analyzing changes in microbial composition and their effects on host metabolism and intestinal structure, we seek to provide new insights into the broader consequences of antibiotic intervention on host-microbiota interactions. The research findings indicate that antibiotic treatment leads to a significant disruption in microbial diversity and metabolic characteristics, as well as notable histological changes in the intestinal mucosa. These results highlight the need for cautious use of antibiotics, considering their extensive effects beyond antimicrobial activity. Future research should focus on strategies to mitigate these impacts, potentially through targeted antibiotic therapies or probiotics, to better balance treatment efficacy with health preservation.},
}
@article {pmid40511069,
year = {2025},
author = {Lakkoju, S and Bolisetty, D and Kumar, R},
title = {Sweet Shield: Enhancing Oral Health with Bioactive HETAFU Candies in Adults - A Dose-Dependent Study.},
journal = {Journal of pharmacy &amp; bioallied sciences},
volume = {17},
number = {Suppl 1},
pages = {S133-S136},
pmid = {40511069},
issn = {0976-4879},
abstract = {Functional foods incorporating probiotics, essential oils, and DHA, PhosphatidylSerine have been explored as innovative approaches to improving oral health. This study evaluates the effects of consuming two versus five HETAFU candies daily on oral microbial levels over eight weeks. To compare the impact of moderate (two candies/day) and higher (five candies/day) HETAFU candy consumption on oral microbial populations, focusing on Streptococcus mutans, Lactobacillus, Actinomycetes, and Candida. A total of 200 participants were randomly divided into two groups: Group 1 consumed two candies daily, and Group 2 consumed five candies daily. Microbial levels were measured at baseline, 2 weeks, 4 weeks, and 8 weeks using microbiological techniques. Statistical analysis included Z scores and P values to determine the significance of microbial changes between groups. Both groups showed significant reductions in Streptococcus mutans and Candida, with a concurrent decrease in Lactobacillus and Actinomycetes levels over time. However, Group 2 demonstrated greater microbial shifts, indicating enhanced modulation of the oral microbiome with higher candy consumption. Higher consumption of HETAFU candies (five/day) provides superior benefits in reducing pathogenic microbes and promoting beneficial bacteria compared to moderate consumption (two/day). This suggests a dose-dependent relationship, with increased intake offering additional protective effects against oral microbial imbalances. Functional foods like HETAFU candies represent a promising adjunct to oral hygiene practices.},
}
@article {pmid40511019,
year = {2025},
author = {Tiwari, M and Acharya, N and Mahakarkar, M},
title = {Navigating the Vaginal Milieu During Perimenopause: A Narrative Review of Physiological Changes and Clinical Implications.},
journal = {Journal of pharmacy &amp; bioallied sciences},
volume = {17},
number = {Suppl 1},
pages = {S92-S95},
pmid = {40511019},
issn = {0976-4879},
abstract = {Perimenopause represents a transitional phase in a woman's life, marked by significant hormonal and physiological changes that profoundly impact the vaginal milieu. These changes can lead to a variety of symptoms, collectively known as genitourinary syndrome of menopause, affecting a woman's sexual health, quality of life, and overall well-being. This narrative review aims to explore the underlying physiological alterations in the vaginal environment during perimenopause, their clinical implications, and current therapeutic approaches. By highlighting the challenges and emerging strategies in managing these changes, this review provides insights into personalized treatment options for improving women's health during this crucial period.},
}
@article {pmid40510906,
year = {2025},
author = {Okamoto, H and Li, S and Nakamura, Y},
title = {The Role of Skin Dysbiosis and Quorum Sensing in Atopic Dermatitis.},
journal = {JID innovations : skin science from molecules to population health},
volume = {5},
number = {4},
pages = {100377},
pmid = {40510906},
issn = {2667-0267},
abstract = {The skin microbiome plays a crucial role in the pathogenesis of atopic dermatitis (AD), a chronic inflammatory skin disorder strongly associated with microbial dysbiosis, particularly Staphylococcus aureus colonization. However, the mechanisms linking S aureus to AD remain insufficiently understood. This review explores the impact of the quorum-sensing (QS) system, particularly the accessory gene regulator Agr, in AD development and progression. By examining key microbial-host interactions, we provide insights into how QS influences skin inflammation and dysbiosis. Furthermore, we discuss the potential of microbiome-targeted therapeutic strategies to mitigate or prevent AD, highlighting their implications for future research and clinical applications.},
}
@article {pmid40510813,
year = {2025},
author = {Li, H and Chen, J and Fenger, M and Jiang, Y},
title = {Editorial: Statistical approaches, applications, and software for longitudinal microbiome data analysis and microbiome multi-omics data integration.},
journal = {Frontiers in genetics},
volume = {16},
number = {},
pages = {1624791},
pmid = {40510813},
issn = {1664-8021},
}
@article {pmid40510800,
year = {2025},
author = {Peng, X and Han, N and Gong, Y and He, L and Xu, Y and Xiao, D and Zhang, T and Qiang, Y and Li, X and Zhang, W and Zhang, J},
title = {Characterization of the salivary microbiome in healthy individuals under fatigue status.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1506723},
pmid = {40510800},
issn = {2235-2988},
mesh = {Humans ; *Saliva/microbiology ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Male ; Adult ; Female ; *Fatigue/microbiology ; Healthy Volunteers ; Biomarkers/analysis ; *Bacteria/classification/genetics/isolation &amp; purification ; DNA, Bacterial/genetics ; Young Adult ; High-Throughput Nucleotide Sequencing ; Computational Biology ; Sequence Analysis, DNA ; Middle Aged ; },
abstract = {BACKGROUND &amp; AIMS: Limited understanding exists regarding the characteristics and biological significance of the salivary microbiome in healthy individuals experiencing physiological fatigue. This study aimed to delineate the structural and functional alterations in the salivary microbiome of healthy individuals undergoing physiological fatigue compared to energetic controls, and to explore its potential as a biomarker for fatigue status.<br><br>METHODS: A cohort of 7 healthy individuals experiencing acute physiological fatigue (induced by prolonged study and confirmed via electroencephalography; Fatigue group, FTG) and 63 energetic healthy controls (Energetic group, ENG) were enrolled. Saliva samples were collected, from which microbial DNA was extracted. The V3-V4 hypervariable region of the 16S rRNA gene was subsequently sequenced using high-throughput technology. Bioinformatics analyses encompassed assessment of alpha and beta diversity, identification of differential taxa using Linear discriminant analysis Effect Size (LEfSe) with multi-method cross-validation, construction of microbial co-occurrence networks, and screening of fatigue-associated biomarker genera via the Boruta-SHAP algorithm. Microbial community phenotypes and potential functional pathways were predicted using BugBase and PICRUSt2, respectively.<br><br>RESULTS: The FTG group exhibited significantly diminished alpha diversity (Simpson index, p=0.01071) relative to the ENG group. Beta diversity analysis demonstrated significant dissimilarities in microbial community structure between the groups (p<0.05). Taxonomic profiling revealed a significant enrichment in the relative abundance of potential periodontopathogenic genera, including Streptococcus and Filifactor, within the FTG group, concomitantly with a significant depletion of health-associated genera such as Rothia and Neisseria. A predictive model constructed using the Boruta-SHAP algorithm, based on 15 key genera, effectively discriminated between fatigue and non-fatigue states, achieving an area under the receiver operating characteristic curve (AUC) of 0.948. Phenotypic predictions indicated a significant increase in the proportion of bacteria harboring Mobile Genetic Elements (MGEs) (p=0.048), alongside significant reductions in the proportion of aerobic bacteria (p=0.006) and biofilm-forming capacity (p=0.002) in the FTG group. Functional pathway analysis (PICRUSt2) revealed an enrichment of pathways such as "Neuroactive ligand-receptor interaction" in the FTG group, whereas pathways pertinent to energy metabolism (e.g., Citrate cycle (TCA cycle), Oxidative phosphorylation) and amino acid metabolism (e.g., Phenylalanine metabolism, Histidine metabolism) were significantly enriched in the ENG group.<br><br>CONCLUSION: This study provides novel evidence that physiological fatigue induces significant structural and functional alterations in the salivary microbiome of healthy individuals. These perturbations include diminished microbial diversity, disrupted community architecture, enrichment of potential opportunistic pathogens, and marked shifts in key metabolic pathways, particularly those governing neuroactivity and energy metabolism. These findings suggest that the salivary microbiome may be implicated in the physiological regulation of fatigue, potentially via an "oral-microbiome-brain axis," and underscore its potential as a source of non-invasive biomarkers for assessing fatigue status. Further mechanistic investigations are warranted to elucidate these interactions.},
}
@article {pmid40510677,
year = {2025},
author = {Zhang, Z and Guan, S and Chen, L and Jiang, F and Dong, H and Chen, Z and Lv, L and Song, H and Sun, W and He, D and Jiang, S and Tian, F},
title = {Association between oral microbiome diversity and kidney stones: a cross-sectional study.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1600961},
pmid = {40510677},
issn = {1664-302X},
abstract = {BACKGROUND: Kidney stones are a common urologic disorder that imposes a significant burden on global public health. This study aimed to determine the association between oral microbiome diversity and kidney stones.<br><br>METHODS: The data for this study came from the National Health and Nutrition Examination Survey 2009-2012 survey cycle. Use of alpha diversity to assess oral microbiome diversity. Multivariate logistic regression modeling was used to assess the association between different alpha-diversity indicators and kidney stones. Subgroup analyses and interaction tests were used to assess the stability of the association between alpha-diversity and kidney stones. Restricted cubic spline plots were used to assess non-linear associations and dose-response relationships.<br><br>RESULTS: The study included 5,870 eligible participants with a mean age of 43.74 years at baseline. After adjusting for all covariates, the observed oral microbiome diversity was significantly negatively associated with the risk of kidney stones (P < 0.05). Subgroup analyses showed that oral microbiome diversity was negatively associated with the risk of kidney stones in certain populations, particularly among those aged 40-60 years, men, obese, with moderate to high cardiovascular health scores, smokers, and those without hypertension. Restricted cubic spline analysis suggested a significant non-linear negative correlation between the Shannon and Simpson diversity indices and the risk of kidney stones (p for non-linear < 0.05). Since our study was a cross-sectional design, the main limitation was the inability to prove causality.<br><br>CONCLUSIONS: In this study, we found an inverse relationship between oral microbiome diversity and kidney stone risk observed in alpha diversity. This reveals the complexity of host-microbiome interactions, and further mechanistic studies are necessary to elucidate these complex roles in the future.},
}
@article {pmid40510676,
year = {2025},
author = {Bruins-van Sonsbeek, LGR and Verschuren, MCM and Kaal, S and Lindenburg, PW and Rodenburg, KCW and Clauss, M and Speksnijder, AGCL and Rutten, VPMG and Bonnet, BFJ and Wittink, F},
title = {Rhinoceromics: a multi-amplicon study with clinical markers to transferrin saturation levels in ex-situ black rhinoceros (Diceros bicornis michaeli).},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1515939},
pmid = {40510676},
issn = {1664-302X},
abstract = {Iron overload disorder (IOD) is a common condition in ex-situ black rhinoceroses (Diceros bicornis), although it has not been reported in the wild. This study aimed to gain a deeper understanding of the relationship between 25-hydroxy vitamin D [25(OH)D], inflammatory markers, insulin levels, the gut microbiome, dietary components, and transferrin saturation (TS) in ex-situ black rhinoceroses. Blood and fecal samples from 11 black rhinoceroses at five different European zoological institutions were monitored over a 1-year period. Inflammatory markers such as interleukin 6 (IL-6), serum amyloid A (SAA), interferon γ (IFN-γ), and tumor necrosis factor α (TNF-α) were analyzed. Our study corroborates the findings of previous research, which demonstrated that insulin, inflammatory markers, and TS% are higher in ex-situ black rhinoceroses compared to published wild ranges. Our data show no correlations between insulin, 25(OH)D, TS%, inflammatory markers, or short-chain fatty acids (SFCAs). Serum 25(OH)D exhibited significantly higher levels in summer than in winter. Transferrin saturation was influenced by age, which is consistent with previous studies. The microbiome did not differ significantly among individuals, institutions, sex, or season, unlike the mycobiome, which exhibited significant differences across institutions. The impact of the mycobiome differences on the physiology of the animals could not be determined from this study.},
}
@article {pmid40510675,
year = {2025},
author = {Qiao, H and Zeng, Q and Martin, F and Wang, Q},
title = {Impact of the soil layer on the soil microbial diversity and composition of Pinus yunnanensis at the Ailao Mountains subtropical forest.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1558906},
pmid = {40510675},
issn = {1664-302X},
abstract = {Microbial communities residing in forest soils play crucial roles in decomposing organic matter and recycling nutrients, making these ecosystems one of the most diverse habitats on Earth. However, the composition and function of these complex and diverse microbiomes across different soil layers remain largely unknown. In this study, we collected soil samples from various layers and analysed the bacterial and fungal community compositions in experimental forest ecosystems using sequencing techniques. Our findings revealed that the soil layer was the primary factor influencing microbial communities, whereas sampling season had only a marginal effect. The most prevalent bacterial phyla and fungal classes were Acidobacteria, Actinobacteria, Armatimonadetes, Bacteroidetes, Firmicutes, Planctomycetes, Proteobacteria, Verrucomicrobia, and Agaricomycetes. Owing to the heterogeneity of the soil layer environment, we observed distinct patterns in the bacterial and fungal microbiomes across different layers. Moreover, the soil layer affected the network complexity, with fungi exhibiting higher complexity in the upper layer, whereas bacteria showed the opposite trend. Additionally, the dominant bacterial and fungal taxa across all soil layers belonged predominantly to Acidobacteria and Agaricomycetes, respectively. These findings underscore the significance of soil layers in shaping soil microbial communities and highlight the composition and co-occurrence patterns of the microbial communities within these layers.},
}
@article {pmid40510674,
year = {2025},
author = {Chen, J and Su, R and He, Y and Chen, J},
title = {Intermittent fasting inhibits the development of colorectal cancer in APC [Min/+] mice through gut microbiota and its related metabolites.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1563224},
pmid = {40510674},
issn = {1664-302X},
abstract = {BACKGROUND AND OBJECTIVES: Intermittent fasting is an emerging dietary approach, but its specific role in colorectal cancer (CRC) is not yet clear. In this study, we investigated the relationship between intermittent fasting and colorectal development in mice.<br><br>METHODS: First, APC [Min/+] mouse models (a spontaneous model of colorectal cancer) were subjected to intermittent fasting intervention (2 days/week) with regular monitoring of body weight changes. Subsequently, 16S rRNA sequencing and untargeted metabolomics were employed to analyze alterations in fecal microbial community structure and metabolic profiles following the fasting intervention. Tumor development was quantitatively assessed by enumerating CRC lesions using HE staining, while histopathological evaluation was performed to determine the degree of neoplastic progression. Concurrently, western blotting was conducted to examine the expression levels of intestinal barrier function-related proteins. Finally, in vitro validation experiments, including colony formation assay and transwell invasion assay, were performed to investigate the effects of the key microbial metabolite isovaleric acid on the proliferative and invasive capacities of CRC cells.<br><br>RESULTS: Intermittent fasting significantly reduced tumor incidence by approximately 50% compared to the control group (1.25 &#xb1; 0.38 vs 2.50 &#xb1; 0.38 tumors/mouse, P = 0.017) and markedly attenuated tumor progression. 16S rRNA sequencing analysis revealed significant enrichment of two key bacterial genera, Alistipes (P = 0.030) and Odoribacter (P = 0.030), along with a significant reduction in fecal isovaleric acid levels (P < 0.05) in the intermittent fasting group. Furthermore, intermittent fasting effectively controlled body weight gain (P < 0.05) and significantly improved intestinal barrier function (P < 0.05). In vitro experiments further demonstrated that isovaleric acid directly promoted CRC cell proliferation (P < 0.05) and enhanced their invasive capacity (P < 0.05).<br><br>CONCLUSION: Intermittent fasting suppresses CRC development in mice through its effects on gut microbiota and related metabolites.},
}
@article {pmid40510672,
year = {2025},
author = {Yang, M and Wang, J and Qi, Y and Gao, P and Li, L and Guo, J and Zhao, Y and Liu, J and Chen, Z and Zhao, J and Yu, L},
title = {Plant developmental stage drives the assembly and functional adaptability of endophytic microbial communities.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1492141},
pmid = {40510672},
issn = {1664-302X},
abstract = {INTRODUCTION: The seeds of Amorphophallus muelleri represent a unique category of herbaceous seeds that arise from triploid apomixis. They necessitate an exceptionally protracted maturation phase of 8 months, followed by a dormancy period of 4 months, before they can germinate and give rise to fully formed new plants. Currently, the connection between endophytic microbial communities in A. muelleri seeds and the host plant's development is largely unexplored.<br><br>METHODS: Herein, we analyzed the temporal dynamics of the endophytic bacterial and fungal communities from seed germination to seedling establishment (seven stages) through amplicon sequencing.<br><br>RESULTS AND DISCUSSION: The results showed that plant developmental stage explained the large variation in endophytic bacterial and fungal communities in A. muelleri and that multiple microbial attributes (e.g., &#x3b1;, &#x3b2;-diversity, community composition, and bacterial and fungal ecological networks) are driven by the developmental state of A. muelleri. Metagenomic analyses further indicated that the four stages after rooting have higher microbial functional diversity. Microbial functional genes involved in cell wall/membrane/envelope biogenesis, inorganic ion transport and metabolism, and carbon degradation were abundant in A. muelleri seeds from Stage 1 to Stage 3 (before rooting). From Stage 4 to Stage 7 (after rooting), microbial functional genes involved in the carbon, nitrogen and phosphorus cycles, starch and sucrose metabolism, and energy production and conversion were more abundant. Coincidentally, more abundant Proteobacteria, and Basidiomycota taxa related to carbon degradation were found in stages 1-3, while more Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium and Stenotrophomonas taxa associated with nitrogen cycling and plant growth promotion were observed in stages 4-7. These findings have greatly improved our basic understanding of the assembly and functional adaptability of the endophytic microbiome during A. muelleri plant development and are helpful for the mining, development and utilization of functional microbial resources.},
}
@article {pmid40510587,
year = {2025},
author = {Xie, Y and Cao, Q and Huang, Z and Zou, X},
title = {Gut Microbiota in Lactose Intolerance: A Mendelian Randomization Study on Microbial Mechanisms and Potential Links to Tumor Inflammatory Microenvironments.},
journal = {Mediators of inflammation},
volume = {2025},
number = {},
pages = {8181816},
pmid = {40510587},
issn = {1466-1861},
mesh = {*Gastrointestinal Microbiome/genetics/physiology ; Humans ; *Mendelian Randomization Analysis/methods ; *Lactose Intolerance/microbiology/genetics ; Genome-Wide Association Study ; Polymorphism, Single Nucleotide/genetics ; *Inflammation/microbiology ; },
abstract = {Background: Previous observational studies have suggested an association between the composition of the intestinal microbiome and lactose intolerance (LI). However, the causal direction remains unclear. This study utilized Mendelian randomization (MR) to rigorously evaluate the potential causal link between the gut microbiome and LI. Methods: Genome-wide association studies (GWASs) summary statistics for gut microbiota and LI were sourced from previously published GWAS studies. Multiple methods, such as Simple mode, MR-Egger regression, weighted median, inverse variance-weighted (IVW), and weighted model, were used to determine the causal relationship between gut microbiota and LI. To validate the primary findings from the MR analyses, several sensitivity analyses were conducted. Furthermore, a reverse MR analysis was executed on bacterial taxa previously identified to have a potential causal link with LI risk, aiming to evaluate the possibility of reverse causation. Results: The IVW results revealed that the genus Lachnospiraceae UCG008 (OR = 0.584, 95%CI 0.356-0.958, p=0.0330), genus Eubacterium hallii group (OR = 0.467, 95% CI 0.242-0.899, p=0.023), and genus Ruminococcus gauvreauii group (OR = 0.506, 95% CI 0.2653-0.968, p=0.039) have a protective effect against LI. In contrast, the genus Holdemania (OR = 1.86, 95% CI 1.105-3.131, p=0.0194) displayed a predisposing effect. Sensitivity analyses did not detect any outlier single-nucleotide polymorphisms (SNPs). Further analyses reinforced the association between specific gut microbiota compositions and LI. No evidence suggested reverse causality between LI and the bacterial taxa identified in the reverse MR analysis. Conclusions: From a genetic standpoint, this MR study indicates a causal relationship between variations in gut microbiota composition and LI. This not only underscores the potential of gut microbiota-centric treatments for LI but also provides a foundation for exploring the role of gut microbiota in LI development. Further study of the mechanism of Lachnospiraceae in the treatment of IL is conducive to the discovery of new therapeutic targets for IL.},
}
@article {pmid40510495,
year = {2025},
author = {Bankole, T and Li, Y},
title = {The early-life gut microbiome in common pediatric diseases: roles and therapeutic implications.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1597206},
pmid = {40510495},
issn = {2296-861X},
abstract = {The early-life gut microbiome has been increasingly recognized as a contributing factor for pediatric health and diseases. Studies have reported that the human gut microbiota colonization commences at birth and progresses over the course of the first three years of life, until it reaches a mature and stable diversity and composition. During this critical window, the gut microbiome is vulnerably subjected to environmental factors, leading to transient microbial reprogramming and functional changes. The dynamic early-life intestinal microbiota is frequently manipulated by environmental factors, which impact the composition and function of the gut microflora, hence confer to short-and/or long-term health outcomes extending to adulthood. Evidence has shown that the imbalanced gut microbial community early in life is associated with several childhood diseases and disorders, such as inflammatory bowel diseases, allergies, attention-deficit/hyperactivity disorder and pediatric obesity. Manipulating the early-life intestinal microbes can either ameliorate or impair host's immunological and metabolic responses, impacting overall health conditions later in life. This narrative review article discusses the recent understanding and implications of the early-life gut microbiome in common pediatric diseases and potential intervention approaches.},
}
@article {pmid40510389,
year = {2025},
author = {Morishima, S and Abe, A and Okamoto, S and Kapoor, MP and Matsuura, S and Kuriya, K and Ozeki, M and Nishio, M and Miura, H and Inoue, R},
title = {Partially hydrolyzed guar gum ingestion suppresses atopic dermatitis-like symptoms through prebiotic effect in mice.},
journal = {Journal of clinical biochemistry and nutrition},
volume = {76},
number = {3},
pages = {280-288},
pmid = {40510389},
issn = {0912-0009},
abstract = {Growing knowledge reveals the association between the gut microbiome and skin, rendering the gut microbiome an appealing potential therapeutic target for atopic dermatitis (AD). In this study, we assessed the effect of partially hydrolyzed guar gum (PHGG) on AD-like symptoms induced by topical 1-Chloro-2,4-dinitrobenzene (DNCB) in BALB/c mice. Four weeks of PHGG feeding prevented the loss of epidermal barrier integrity and epithelial hyperplasia in the AD lesion (p<0.05, effect size >0.80), indicating a reduction in AD-like symptoms. According to the postulated mechanism, PHGG ingestion modulates the gut microbiome resulting in enhanced butyrate production (p<0.05). Butyrate suppresses Th2 function in gut immunity, which is believed to have significance in systemic immune regulation. The lowering of blood Th2 cytokines (IL-4 and IL-10, p<0.05) in the PHGG-fed group confirmed the existence of such a pathway, and butyrate can possibly be considered to have an indirect involvement in the suppression of Th2 immune response in the AD lesions. These findings encourage support for an association between gut microbiome and skin through the immune system, implying that daily PHGG ingestion may be beneficial for suppressing AD symptoms across the gut-immune-skin axis.},
}
@article {pmid40510115,
year = {2025},
author = {Dang, Y and Xu, X and Ma, J and Zhou, M and Xu, C and Huang, X and Xu, F and Wang, Z and Shi, H and Zhang, S},
title = {Gut microbiome signatures predict 5-ASA efficacy in ulcerative colitis.},
journal = {iScience},
volume = {28},
number = {6},
pages = {112568},
pmid = {40510115},
issn = {2589-0042},
abstract = {Ulcerative colitis (UC) prevalence is rising globally, yet fewer than 50% of patients achieve mucosal healing (MH) with first-line 5-aminosalicylic acid (5-ASA) therapy. We aimed to identify microbial signatures that could predict the treatment efficacy of 5-ASA. Active UC patients on standardized 5-ASA treatment were prospectively enrolled. Shotgun metagenomic sequencing was performed to identify the taxonomic and functional profiles before and after treatment. Six species were enriched in the effective group and 3 species in the ineffective group at baseline. Faecalibacterium prausnitzii, Blautia massiliensis, and Phascolarctobacterium faecium were consistently depleted in the ineffective group at both time points. A random forest model based on these three species predicted ineffective 5-ASA treatment with area under the curve (AUC) = 0.80 (validation in the Inflammatory Bowel Disease Multi'omics Database [IBDMDB]: AUC = 0.82, specificity = 0.88, negative predictive value [NPV] = 0.70, and positive predictive value [PPV] = 0.80). Gut microbiome signatures have potential to serve as non-invasive predictors for ineffective 5-ASA treatment in UC.},
}
@article {pmid40509837,
year = {2025},
author = {Han, D and Ciren, Y and Li, Q and Li, J},
title = {[Changes of intestinal microflora in patients with colorectal benign and malignant tumors in high altitude area and comparison with the normal population in low altitude area].},
journal = {Beijing da xue xue bao. Yi xue ban = Journal of Peking University. Health sciences},
volume = {57},
number = {3},
pages = {578-583},
pmid = {40509837},
issn = {1671-167X},
mesh = {Humans ; *Altitude ; *Colorectal Neoplasms/microbiology ; *Gastrointestinal Microbiome ; Feces/microbiology ; Male ; Female ; Middle Aged ; Tibet ; RNA, Ribosomal, 16S/genetics ; Colonoscopy ; Adult ; Aged ; Adenoma/microbiology ; },
abstract = {OBJECTIVE: To analyze the changes of intestinal flora in patients with benign and malignant colorectal tumors in high altitude areas and to compare them with the normal population in low altitude areas.<br><br>METHODS: The clinical data of 61 patients who underwent colonoscopy in the People' s Hospital of Tibet Autonomous Region from 2020 to 2022 were collected as the high altitude group. According to the colonoscopy results, they were divided into control group (29 cases), non-adenomatous polyp group (12 cases), adenoma group (10 cases), colorectal cancer group (10 cases). 17 patients who had negative colonoscopy results in the Peking University Third Hospital during the same period were collected as the low altitude control group. Before bowel preparation for colonoscopy, the fecal samples were collected. Then the DNA of bacteria in the fecal samples was extracted. The V3-V4 variable region of the 16S rRNA gene was PCR amplified and high-throughput sequenced. The species diversity of fecal flora was analyzed.<br><br>RESULTS: Alpha diversity analysis showed that the species diversity of samples from the high altitude colorectal cancer group differed statistically from that of the high altitude non-adenomatous polyp group and the low altitude control group, and the species diversity of colorectal samples from the high altitude colorectal cancer group was higher than that of the other two groups. While beta diversity showed no significant difference among the five groups. Differences were found in phylum level analysis that the abundance of Actinobacteriota in the low altitude control group was significantly lower than those in each group of the high altitude area, while the abundance of Actinobacteriota in the colorectal cancer group was significantly lower than those in the other 3 groups of the high altitude area. Differences were found in genus level analysis that the abundance of Bacteroides, Phascclarctobacterium and Lachnoclostridium in the low altitude control group was significantly higher than those of all the groups in the high altitude area; the abundance of Blautia and Collinsella in the high altitude control group was the highest. Lactobacillus was not detected in the low altitude control group, while there was a highly significant difference (P < 0.05) in the level of Lactobacillus in the four groups of high altitude area, and the abundance of Lactobacillus was significantly higher in the control group than those of the other three groups. In the four groups of samples at high altitude, the abundance of Bifidobacterium decreased significantly, while the abundance of Christensenellaceae_R-7_group increased significantly.<br><br>CONCLUSION: Compared with the high and low altitude controls, the diversity and abundance of intestinal flora in patients with colorectal benign and malignant tumors at high altitudes are different. And the abundance of species are also diffe-rent at the phylum and genus levels, suggesting that altitude factors may have some influence on intestinal flora.},
}
@article {pmid40509691,
year = {2025},
author = {Dermietzel, A and Tosun, B and Nguyen, M and Wessel, K and Rauer, L and Neumann, AU and Hirsch, T and , and Traidl-Hoffmann, C and Reiger, M and Hülpüsch, C and Kueckelhaus, M},
title = {Skin microbiome analysis of a junctional epidermolysis bullosa patient treated with genetically modified stem cells.},
journal = {Journal der Deutschen Dermatologischen Gesellschaft = Journal of the German Society of Dermatology : JDDG},
volume = {},
number = {},
pages = {},
doi = {10.1111/ddg.15776},
pmid = {40509691},
issn = {1610-0387},
abstract = {BACKGROUND AND OBJECTIVE: Junctional epidermolysis bullosa (JEB) is a subtype of epidermolysis bullosa caused by mutations in the LAMB3 gene. We treated a patient with JEB using genetically corrected autologous epidermal cultures retrovirally transduced with the functional LAMB3 gene sequence. The objective of this study was to analyze the skin microbiome of this patient, with a particular focus on transgenic skin, and to compare the findings to the skin microbiome of healthy controls and patients with atopic dermatitis and well-documented microbial dysbiosis.<br><br>PATIENTS AND METHODS: Skin microbiome analysis was performed on a JEB patient 72&#xa0;months after combined gene and stem cell therapy. Skin swabs from age-matched healthy controls and atopic dermatitis patients were included from the ProRaD study of CK-CARE.<br><br>RESULTS: The transgenic skin had comparably high relative and absolute Staphylococcus (S.) aureus abundance to blistering and non-blistering skin of the JEB patient, while the total bacterial load was lower. In blistering skin of the JEB patient, higher bacterial load was driven by S. aureus.<br><br>CONCLUSIONS: Our investigation confirms a unique microbiome composition in JEB, characterized by S. aureus driven bacterial overgrowth. The dysbiosis was not reversed in transgenic, non-blistering skin areas. However, the transgenic skin demonstrates stability in an environment of bacterial dysbiosis.},
}
@article {pmid40509652,
year = {2025},
author = {Dempsey, E and Walsh, AM and Yadav, S and Wilson, J and Sheedy, FJ and Corr, SC},
title = {Protective Properties of the White Button Mushroom, Agaricus bisporus, in a Mouse Model of Colitis.},
journal = {Molecular nutrition &amp; food research},
volume = {},
number = {},
pages = {e70133},
doi = {10.1002/mnfr.70133},
pmid = {40509652},
issn = {1613-4133},
support = {EPSPD/2022/130//Irish Research Council Enterprise Partnership Scheme (Postdoctoral)/ ; 19/FFP/6499//Science Foundation Ireland Frontiers for the Future Programme/ ; },
abstract = {Previous work demonstrated the promising immunomodulatory potential of a naturally derived whole mushroom powder (WMP) from the white button mushroom, Agaricus bisporus. Here, we further investigate the protective properties of WMP in a mouse model of colitis. An in vitro digested WMP (IVD-WMP) reduced permeability of intestinal epithelial Caco-2 and HT-29-MTX cell monolayers to FITC dextran. In vivo, WMP orally administered to mice as a pretreatment before induction of dextran sulfate sodium (DSS)-induced colitis. Though statistically significant decreases in disease scores were not reported, we observed an antiinflammatory and antioxidative stress profile in the colon. Additionally, 16S ribosomal RNA (16S rRNA) microbiome analysis revealed differences in bacterial abundance associated with WMP pretreatment, including a decrease in Allobaculum species associated with inflammatory bowel disease. In a DSS-colitis recovery model, WMP promoted recovery as evidenced by improved weight gain, reduced stool scores, reduced IL-1β levels, and myeloperoxidase (MPO) activity in colonic tissue. This work demonstrates the health benefits associated with the consumption of the white button mushroom, including support of intestinal barrier integrity combined with antioxidant and antiinflammatory activity.},
}
@article {pmid40509476,
year = {2025},
author = {Bemis, DH and Camphausen, CE and Liu, E and Dantus, JJ and Navarro, JA and Dykstra, KL and Paltrowitz, LA and Dzhelmach, M and Joerg, M and Tamelessio, P and Belenky, P},
title = {Nutrient Availability and Pathogen Clearance Impact Microbiome Composition in a Gnotobiotic Kimchi Model.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {11},
pages = {},
doi = {10.3390/foods14111948},
pmid = {40509476},
issn = {2304-8158},
abstract = {Kimchi is a fermented Korean food typically made with napa cabbage, garlic, radish, ginger, and chili pepper. It is becoming increasingly popular due to its flavor, high fiber content, and purported probiotic benefits. The microbial ecology of the fermentation community has been extensively studied, though what's less understood is how its microbial community changes when nutrients or pathogens are introduced. To study this, we used gnotobiotic cabbage media inoculated with a kimchi starter culture as a model system. These inoculated samples were exposed to E. coli or Bacillus cereus, with or without added nutrients in the form of tryptic soy broth (TSB). We tracked pH, colony-forming units (CFUs), and community composition over time. We also used Oxford Nanopore sequencing to analyze the 16S rRNA gene (V4-V9), followed by use of the Emu algorithm for taxonomic assignments. As expected, LABs suppressed pathogens, but this effect was weaker early on in the nutrient-rich condition. Pathogen exposure changed the overall community-Lactobacillus species became more common, and Leuconostoc mesenteroides less so. Interestingly, adding nutrients alone caused similar microbial shifts to those seen with pathogen exposure. This could suggest that nutrient levels have a larger impact on the final microbiome structure than direct microbial competition. Together, these findings suggest that monitoring total microbial composition, and not just the presence of pathogens, may be important for ensuring kimchi fermentation reproducibility.},
}
@article {pmid40509473,
year = {2025},
author = {Gao, Y and Liu, Y and Ma, T and Liang, Q and Sun, J and Wu, X and Song, Y and Nie, H and Huang, J and Mu, G},
title = {Fermented Dairy Products as Precision Modulators of Gut Microbiota and Host Health: Mechanistic Insights, Clinical Evidence, and Future Directions.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {11},
pages = {},
doi = {10.3390/foods14111946},
pmid = {40509473},
issn = {2304-8158},
support = {32302032//National Natural Science Foundation of China/ ; 2022YFD2101503//National Key Research and Development Program/ ; 2020GXNSFBA297083//Natural Science Foundation of Guangxi, China/ ; },
abstract = {Dairy products-encompassing yogurt, kefir, cheese, and cultured milk beverages-are emerging as versatile, food-based modulators of gut microbiota and host physiology. This review synthesizes mechanistic insights demonstrating how live starter cultures and their fermentation-derived metabolites (short-chain fatty acids, bioactive peptides, and exopolysaccharides) act synergistically to enhance microbial diversity, reinforce epithelial barrier integrity via upregulation of tight-junction proteins, and modulate immune signaling. Clinical evidence supports significant improvements in metabolic parameters (fasting glucose, lipid profiles, blood pressure) and reductions in systemic inflammation across metabolic syndrome, hypertension, and IBS cohorts. We highlight critical modulatory factors-including strain specificity, host enterotypes and FUT2 genotype, fermentation parameters, and matrix composition-that govern probiotic engraftment, postbiotic yield, and therapeutic efficacy. Despite promising short-term outcomes, current studies are limited by heterogeneous designs and brief intervention periods, underscoring the need for long-term, adaptive trials and integrative multi-omics to establish durability and causality. Looking forward, precision nutrition frameworks that harness baseline microbiota profiling, host genetics, and data-driven fermentation design will enable bespoke fermented dairy formulations, transforming these traditional foods into next-generation functional matrices for targeted prevention and management of metabolic, inflammatory, and neuroimmune disorders.},
}
@article {pmid40509138,
year = {2025},
author = {Zhu, K and Jiang, M and Yan, M and Huang, Y and Yang, T and Zhu, C},
title = {Characteristics and Functions of Different Intestinal Segments in Juvenile Greater Amberjack (Seriola dumerili).},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {11},
pages = {},
doi = {10.3390/ani15111672},
pmid = {40509138},
issn = {2076-2615},
abstract = {The greater amberjack (Seriola dumerili), a key species in marine aquaculture, relies heavily on its intestine for nutrient absorption and immune function. However, the structural and functional specialization of its intestinal segments remains poorly understood. In this study, we divided the intestine of S. dumerili into foregut, midgut, and hindgut, and conducted a multi-omics analysis integrating histological staining (H&amp;E/AB-PAS), digestive enzyme assays, transcriptome sequencing, and 16S rRNA microbiota profiling to characterize structural, functional, molecular, and microbial differences across intestinal segments. Histological examinations revealed that brush border microvillus length, muscle layer thickness, and folding height were significantly greater in the foregut and hindgut compared to the midgut, while mucus and goblet cell density was higher in the foregut and midgut. Digestive enzyme assays showed that lipase activity peaked in the foregut, α-amylase in the midgut, and protease in the midgut and hindgut. Alkaline phosphatase (AKP) and acid phosphatase (ACP) activities were highest in the foregut and midgut. Immune-related enzyme activities (SOD (Superoxide dismutase), GSH-Px (Glutathione peroxidase), T-AOC (Total Antioxidant Capacity)) were elevated and MDA levels were lower in the midgut, indicating its role as the primary immune site. Transcriptome analysis identified segment-specific expression of nutrient transporters, such as slc6a19b (hindgut, protein), apoa1b (foregut, lipid), and slc37a4 (midgut, carbohydrate). Microbiome analysis revealed Ruminococcus dominance in the foregut (lipid digestion) and Prevotella, Bifidobacterium, and Lactobacillus enrichment in the midgut (carbohydrate metabolism and immunity). These findings highlight functional zonation in S. dumerili: the foregut specializes in lipid digestion, the midgut in carbohydrate metabolism and immunity, and the hindgut in protein digestion. This study provides foundational insights for optimizing aquaculture practices and advancing research in nutrition, immunology, and disease modeling in S. dumerili.},
}
@article {pmid40509108,
year = {2025},
author = {Rhim, H and Aguilar, MG and Boykin, KL and Zapanta, K and Krumbeck, JA and Mitchell, MA},
title = {A Preliminary Investigation of the Gastrointestinal Bacterial Microbiomes of Barred Owls (Strix varia) Admitted to a Wildlife Hospital.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {11},
pages = {},
doi = {10.3390/ani15111643},
pmid = {40509108},
issn = {2076-2615},
support = {PG007872//Louisiana State University/ ; Foundation//Fluker Farms/ ; },
abstract = {Research on the gut microbiome, which includes microbial communities and genetic material in the gastrointestinal tract, has revealed essential roles beyond digestion, such as immune regulation, metabolism, and homeostasis. However, studies on birds-key ecosystem members-remain limited. Injured wild birds admitted to wildlife hospitals often receive antibiotics that can alter gut microbiota, leading to dysbiosis and promoting antimicrobial-resistant (AMR) bacteria. This study examined how hospitalization and antibiotics influence the cloacal microbiota of barred owls admitted for fracture repair. A total of 17 cloacal swab samples were analyzed using next-generation sequencing targeting 16S rRNA and AMR genes. Across all samples, Bacillota (Firmicutes), Actinomycetota (Actinobacteria), and Pseudomonadota (Proteobacteria) were the most abundant phyla. In non-antibiotic-treated owls, alpha and beta diversity showed no significant changes between admission and release; however, antibiotic-treated owls exhibited significant diversity shifts in these parameters at release. AMR genes were detected in most samples at admission, with some increasing significantly during hospitalization, suggesting an impact of antibiotic exposure. These findings provide insights into how antibiotics used in wildlife rehabilitation affect host microbiota and contribute to AMR gene dissemination.},
}
@article {pmid40509083,
year = {2025},
author = {Florit-Ruiz, A and Rago, L and Rojas, A and Guzelkhanova, B and Pont-Beltran, A and Lamelas, A and Solaz-Fuster, MC and Martinez-Blanch, JF and López, ME and García-Lainez, G and Rosier, BT and Day, R and Rubio, T and Batchelor, R and Nixon, SL},
title = {Postbiotic Lactiplantibacillus plantarum CECT 9161 Influences the Canine Oral Metagenome and Reduces Plaque Biofilm Formation.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {11},
pages = {},
doi = {10.3390/ani15111615},
pmid = {40509083},
issn = {2076-2615},
support = {N/A//Archer Daniels Midland (United States)/ ; },
abstract = {Periodontal diseases are highly prevalent in dogs and intricately interconnected with the composition and functional attributes of the oral microbiota. The demand for non-invasive interventions to support oral health presents an opportunity for functional ingredients. The novel postbiotic heat-treated (HT) Lactiplantibacillus plantarum CECT 9161 inhibited growth and biofilm formation of oral microorganisms in vitro. The in vitro growth of saliva-derived biofilms was also inhibited and revealed microbiome modulation. Two doses of the postbiotic (LOW: 5 mg dog/day, HIGH: 25 mg/dog/day) were assessed in a placebo-controlled, double-blinded, 57-day clinical trial involving 60 dogs. Associations were found between the postbiotic, reduced plaque formation, and modulation of the oral microbiome, including increased abundance of genes involved in denitrification, heme and catechol biosynthesis, and oxidative stress reduction. The results suggest that HT Lactiplantibacillus plantarum CECT 9161 may support oral health in dogs by modifying the microbiome of supragingival plaque and reducing plaque formation.},
}
@article {pmid40509068,
year = {2025},
author = {Xiong, Y and Tang, C and Wang, X and Wang, Y and Yang, F},
title = {Unlocking the Potential of Paper Mulberry Powder in Cherry Valley Ducks: Impacts on Growth, Serum Biochemistry, and Cecum Microbiome.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {11},
pages = {},
doi = {10.3390/ani15111602},
pmid = {40509068},
issn = {2076-2615},
support = {32201473//National Natural Science Foundation of China/ ; },
abstract = {This study investigates the effects of incorporating paper mulberry (Broussonetia papyrifera L.) powder into the diets of Cherry Valley ducks on growth performance, serum biochemistry, and the gut microbiome. A total of 350 14-day-old male Cherry Valley ducks were randomly assigned to five groups receiving diets with 0%, 4%, 6%, 8%, and 10% paper mulberry powder for 42 days. Growth performance, meat quality, serum immunity, and cecal microbial composition were assessed. The results showed no significant differences in average daily feed intake and feed conversion ratio among treatments, with the 6% paper mulberry group showing the highest average daily gain (79.73 g) (p < 0.05). Meat quality parameters, including color, drip loss, cooking loss, and shear force, were not significantly affected by paper mulberry powder supplementation, while the 8% paper mulberry group showed the highest pH24 value (5.47) (p < 0.05). Serum biochemistry revealed increased total protein (G0, G4, G6, G8, and G10: 41.50, 44.47, 45.58, 45.67, and 45.85 g/L, respectively), albumin (G0, G4, G6, G8, and G10: 18.61, 19.56, 20.29, 20.2, and 20.39 g/L, respectively), total cholesterol (G0, G4, G6, G8, and G10: 5.31, 4.96, 5.37, 5.53, and 5.59 mmol/L, respectively), and high-density lipoprotein cholesterol (HDL) in ducks fed 6%, 8%, and 10% paper mulberry powder, with lower alanine aminotransferase (ALT), aspartate aminotransferase (AST), and total bilirubin (TBI) in the 8% and 10% groups (p < 0.05). Cecal microbial diversity was enhanced with paper mulberry powder, particularly in the 6% group, which showed increased Bacteroides abundance (p < 0.05). Supplementing duck diets with 6% paper mulberry powder increased average daily gain, without adversely affecting meat quality and health, suggesting its potential as a sustainable feed ingredient in the duck meat industry.},
}
@article {pmid40509060,
year = {2025},
author = {Ghafoor, D and Hayakijkosol, O and Ewels, C and Kinobe, R},
title = {Characterisation of the Gastrointestinal Microbiome of Green Sea Turtles (Chelonia mydas): A Systematic Review.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {11},
pages = {},
doi = {10.3390/ani15111594},
pmid = {40509060},
issn = {2076-2615},
abstract = {The gut microbiome of sea turtles is essential for their ecological resilience and adaptation to environmental stressors. We hypothesised that different gut microbial profiles existed between green sea turtles kept in captivity and those in the wild. The aim of this systematic review was to determine dominant bacterial phyla in the gut microbiomes of wild and captive green sea turtles. Comparison of the top four bacterial phyla revealed that Bacillota was the most abundant phylum in captive turtles (40.9-87.5%), but it only ranked second (3.5-57.8%) in wild turtles. Bacteroidota had comparable relative abundance in captive (8.7-45.6%) and wild (3.6-43.1%) populations. By contrast, the relative abundance of Pseudomonadota was higher in wild turtles (6.2-68.1%) compared to the captive population (0.1-6.6%). Verrucomicrobiota was less prevalent in wild and captive populations, with relative abundances ranging from 0.28 to 5.4% and 2.3 to 7.2%, respectively. These findings highlight a putative gut microbial shift between wild and captive green sea turtle populations. This shift may be shaped by variations in environmental factors in captivity or the wild. Nonetheless, the significance of these putative changes is still unknown; the potential to use microbial shifts to guide management, rehabilitation, and conservation of green sea turtles is promising, but remains limited.},
}
@article {pmid40509032,
year = {2025},
author = {Martins, P and Pimentel, T and Ribeiro, N and Calado, R},
title = {Acute Effect of Short-Term Benzocaine Anesthesia on the Skin Mucus Microbiome of Atlantic salmon (Salmo salar).},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {11},
pages = {},
doi = {10.3390/ani15111566},
pmid = {40509032},
issn = {2076-2615},
support = {UIDP/50017/2020+UIDB/50017/2020+LA/P/0094/2020//Centro de Estudos Ambientais e Marinhos/ ; },
abstract = {Routine aquaculture practices such as capture, transportation, and handling can disrupt the relationship between commensal and opportunistic bacteria in the fish skin microbiome. Anesthetic baths are a common welfare practice in aquaculture to reduce stress during handling. However, to date, no studies assessed the effect of anesthetics on bacterial communities in fish skin mucus. This study is the first to evaluate the influence of benzocaine, a widely used anesthetic, on the skin mucus bacterial microbiome of Atlantic salmon reared in a recirculating aquaculture system (RAS). Using Illumina high-throughput 16S rRNA gene sequencing, we found that bacterial richness and diversity were significantly reduced in skin mucus samples from fish with anesthesia (ANE) when compared with those without anesthesia (CTR). The predominant bacterial classes in both groups were Gammaproteobacteria (54.1-62.6%) and Betaproteobacteria (22.6-22.9%). However, significant dissimilarities in beta diversity were observed between the bacterial community structure of salmon skin mucus samples from ANE and CTR. These findings demonstrate that benzocaine exposure alters skin mucus microbiome of Atlantic salmon potentially leading to dysbiosis. This study also provides baseline information on the bacterial communities of Atlantic salmon skin mucus microbiome in an RAS. As no temporal resampling was performed, the duration and persistence of these changes remain unknown and warrant further investigation.},
}
@article {pmid40509031,
year = {2025},
author = {Ávila-Cervantes, R and González-Pech, P and Sandoval-Castro, C and Torres-Acosta, F and Ramos-Zapata, J and Galicia-Jiménez, M and Pacheco-Arjona, R},
title = {Effects of Grazing in a Low Deciduous Forest on Rumen Microbiota and Volatile Fatty Acid Production in Lambs.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {11},
pages = {},
doi = {10.3390/ani15111565},
pmid = {40509031},
issn = {2076-2615},
abstract = {The aim of the present study was to evaluate the effect of grazing the low deciduous forest (LDF) vegetation on the diversity of the rumen microbiome in growing lambs and its relationship with volatile fatty acid (VFA) profiles. After a 35-day indoor acclimatization (stabilization period), the lambs were assigned to two groups: housed (CG, n = 4) and grazing (EG, n = 4). The grazing lambs had a 14-day habituation period in the LDF (4 h/day) and a further 30 grazing days when fodder intake was observed. Ruminal samples were collected at the end of the stabilization, on day 14 post-stabilization (14DPS), and on day 44 post-stabilization (44DPS). The ruminal butyrate concentration showed a progressive decrease of approximately 23% over the time (p = 0.0130). The qualitative composition (p = 0.001) and relative proportions of bacteria (p = 0.004) in EG-44DPS exhibited a greater diversity, with 107 total genera and 19 unique, significant abundances in 13 genera with a higher presence of Bacteroidales_RF16_group, Lachnospiraceae_ND3007_group, and WCHB1-41. Moreover, significant functional profiles are associated with key metabolic pathways in bacteria and are interconnected by the need to generate energy and biosynthetic precursors and to manage available nitrogen and carbon. Finally, eight bacterial genera were identified as biomarkers correlated with the increase in VFA in EG-44DPS.},
}
@article {pmid40508333,
year = {2025},
author = {Aleksieienko, I and Fernandes Hertel, M and Reilhan, J and de Castro, M and Légeret, B and Caixeta Oliveira, H and Reiter, IM and Santaella, C},
title = {Soil-Gradient-Derived Bacterial Synthetic Communities Enhance Drought Tolerance in Quercus pubescens and Sorbus domestica Seedlings.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {11},
pages = {},
doi = {10.3390/plants14111659},
pmid = {40508333},
issn = {2223-7747},
support = {101094587//HORIZON EUROPE INFRA-2022-TECH project 'PHENET'/ ; 88887.712065/2022-00//Coordena&#xe7;&#xe3;o de Aperfeicoamento de Pessoal de N&#xed;vel Superior/ ; ANR-20-EBI5-0008-07//Agence Nationale de la Recherche/ ; ANR-20-EBI5-0008-07//2019-2020 BiodivERsA+ joint call, BiodivClim ERA-Net COFUND, Funda&#xe7;&#xe3;o Arauc&#xe1;ria/Secretaria de Estado da Ci&#xea;ncia, Tecnologia e Ensino Superior do Paran&#xe1; (NAPI Biodiversidade), FAPESP (BR), ANR (FR), Federal Ministry of Education and Research (DE)/ ; Sv 946/10 - 41880PL//CAPES-COFECUB/ ; },
abstract = {Climate-change-induced drought threatens forest restoration by limiting seedling establishment. To address this, we developed synthetic bacterial communities (SynComs) tailored to support drought tolerance in two Mediterranean tree species, Quercus pubescens and Sorbus domestica. Bacteria were isolated from forest soil exposed to long-term drought, sampling across soil depths and root-associated compartments. We selected strains with key plant-beneficial traits, including exopolysaccharide (EPS) production, hormone synthesis (auxin, ABA), siderophore release, and osmotic tolerance. SynComs were assembled based on functional complementarity and ecological origin. Biofilm assays showed that even weak individual producers could enhance community-level performance. After initial screening on Arabidopsis thaliana, the most and least effective SynComs were tested on Q. pubescens and S. domestica seedlings. Compared to controls, the best-performing SynComs reduced the proportion of drought-symptomatic seedlings by 47% in Q. pubescens and 71% in S. domestica, outperforming single-strain inoculants. Notably, EPS-rich SynCom B aligned with the conservative root traits of Q. pubescens, while hormone-rich SynCom F matched the acquisitive strategy of S. domestica. Predictive modeling identified bacterial identity and symptom timing as key predictors of drought resilience. Our results highlight the value of matching microbial traits with plant strategies and drought context for climate-smart forest restoration.},
}
@article {pmid40508300,
year = {2025},
author = {Bashizi, TF and Kim, MJ and Lim, K and Lee, G and Tagele, SB and Shin, JH},
title = {Application of a Synthetic Microbial Community to Enhance Pepper Resistance Against Phytophthora capsici.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {11},
pages = {},
doi = {10.3390/plants14111625},
pmid = {40508300},
issn = {2223-7747},
support = {2021R1A6C101A416//Korea Basic Science Institute/ ; },
abstract = {Pepper (Capsicum annuum) production faces significant challenges from soil-borne pathogens, particularly Phytophthora capsici, which induces root rot and damping-off diseases. Management of this pathogen remains challenging owing to the scarcity of resistant cultivars and the ineffectiveness of chemical control methods. A single strain has been used to prevent pathogenic disease, and this approach limits the exploration of consortia comprising different genera. In this study, we isolated five bacterial strains (Bacillus sp. T3, Flavobacterium anhuiense T4, Cytobacillus firmus T8, Streptomyces roseicoloratus T14, and Pseudomonas frederiksbergensis A6) from the rhizosphere of healthy pepper plants. We then applied this 5-isolate synthetic microbial community (SynCom) to Capsicum annuum to evaluate its efficacy in improving pepper resilience against P. capsici. The SynCom members exhibited phosphate solubilization, indole-3-acetic acid production, catalase activity, siderophore synthesis, and strong antagonism against P. capsici. The SynCom reduced disease severity and enhanced the growth of pepper plants. Furthermore, the beneficial genera such as Bacillus, Fusicolla, and Trichoderma, significantly increased in the rhizosphere of pepper after the application of the SynCom. Microbial functional prediction analysis revealed that these microbial shifts were associated with nitrogen cycling and pathogen suppression. Our SynCom approach demonstrates the effectiveness of microbial consortia in promoting the growth of pathogen-infected plants by reprogramming the microbial community in the rhizosphere.},
}
@article {pmid40508259,
year = {2025},
author = {Gorvel, S and Walter, B and Taylor, JD and Unsworth, RKF},
title = {Functional Roles of the Seagrass (Zostera marina) Holobiont Change with Plant Development.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {11},
pages = {},
doi = {10.3390/plants14111584},
pmid = {40508259},
issn = {2223-7747},
abstract = {Seagrass meadows play a critical role in biogeochemical cycling, especially in nitrogen and sulphur processes, driven by their associated microbiome. This study provides a novel functional analysis of microbial communities in seagrass (Zostera marina) rhizosphere and endosphere, comparing seedlings and mature plants. While nitrogen-fixing bacteria are more abundant in seedlings, mature plants exhibit greater microbial diversity and stability. Sediment samples show higher microbial diversity than roots, suggesting distinct niche environments in seagrass roots. Key microbial taxa (sulphur-oxidizing and nitrogen-cycling bacteria) were observed across developmental stages, with rapid establishment in seedlings aiding survival in sulphide-rich, anoxic sediments. Chromatiales, which oxidize sulphur, are hypothesized to support juvenile plant growth by mitigating sulphide toxicity, a key stressor in early development. Additionally, sulfate-reducing bacteria (SRB), though potentially harmful due to H2S production, may also aid in nitrogen fixation by producing ammonium. The study underscores the dynamic relationship between seagrass and its microbiome, especially the differences in microbial community structure and function between juvenile and mature plants. The study emphasizes the need for a deeper understanding of microbial roles within the seagrass holobiont to aid with Blue Carbon stores and to improve restoration success, particularly for juvenile plants struggling to establish effective microbiomes.},
}
@article {pmid40508212,
year = {2025},
author = {Arias-Carrión, O and Guerra-Crespo, M and Padilla-Godínez, FJ and Soto-Rojas, LO and Manjarrez, E},
title = {α-Synuclein Pathology in Synucleinopathies: Mechanisms, Biomarkers, and Therapeutic Challenges.},
journal = {International journal of molecular sciences},
volume = {26},
number = {11},
pages = {},
doi = {10.3390/ijms26115405},
pmid = {40508212},
issn = {1422-0067},
mesh = {Humans ; *alpha-Synuclein/metabolism/chemistry/genetics ; Biomarkers/metabolism ; *Synucleinopathies/metabolism/pathology/therapy/diagnosis ; Animals ; Parkinson Disease/metabolism/pathology ; Protein Aggregation, Pathological/metabolism ; },
abstract = {Parkinson's disease and related synucleinopathies, including dementia with Lewy bodies and multiple system atrophy, are characterised by the pathological aggregation of the α-synuclein (aSyn) protein in neuronal and glial cells, leading to cellular dysfunction and neurodegeneration. This review synthesizes knowledge of aSyn biology, including its structure, aggregation mechanisms, cellular interactions, and systemic influences. We highlight the structural diversity of aSyn aggregates, ranging from oligomers to fibrils, their strain-like properties, and their prion-like propagation. While the role of prion-like mechanisms in disease progression remains a topic of ongoing debate, these processes may contribute to the clinical heterogeneity of synucleinopathies. Dysregulation of protein clearance pathways, including chaperone-mediated autophagy and the ubiquitin-proteasome system, exacerbates aSyn accumulation, while post-translational modifications influence its toxicity and aggregation propensity. Emerging evidence suggests that immune responses and alterations in the gut microbiome are key modulators of aSyn pathology, linking peripheral processes-particularly those of intestinal origin-to central neurodegeneration. Advances in biomarker development, such as cerebrospinal fluid assays, post-translationally modified aSyn, and real-time quaking-induced conversion technology, hold promise for early diagnosis and disease monitoring. Furthermore, positron emission tomography imaging and conformation-specific antibodies offer innovative tools for visualising and targeting aSyn pathology in vivo. Despite significant progress, challenges remain in accurately modelling human synucleinopathies, as existing animal and cellular models capture only specific aspects of the disease. This review underscores the need for more reliable aSyn biomarkers to facilitate the development of effective treatments. Achieving this goal requires an interdisciplinary approach integrating genetic, epigenetic, and environmental insights.},
}
@article {pmid40508173,
year = {2025},
author = {Giebeler, L and Ehrhardt, C and Häder, A and Lauf, T and Deinhardt-Emmer, S and Löffler, B},
title = {Colonizing Bacteria Aggravate Inflammation, Cytotoxicity and Immune Defense During Influenza A Virus Infection.},
journal = {International journal of molecular sciences},
volume = {26},
number = {11},
pages = {},
doi = {10.3390/ijms26115364},
pmid = {40508173},
issn = {1422-0067},
support = {LPI-BT1 and BT2//BMBF/ ; EXC 2051-Project-ID 390713860 and SFB 1278/2, D02//Deutsche Forschungsgemeinschaft/ ; },
mesh = {Humans ; *Influenza A virus/immunology ; *Inflammation/microbiology/immunology ; Macrophages/immunology/microbiology ; Staphylococcus aureus/immunology ; Animals ; *Influenza, Human/immunology/microbiology/virology ; Epithelial Cells/microbiology/virology/immunology ; Staphylococcus epidermidis/immunology ; Cytokines/metabolism ; Coinfection/microbiology/immunology ; *Orthomyxoviridae Infections/immunology/microbiology ; A549 Cells ; },
abstract = {A diverse bacterial community colonizes the respiratory system, including commensals such as Staphylococcus epidermidis (S. epidermidis) and Streptococcus salivarius (S. salivarius), as well as facultative pathogens like Staphylococcus aureus (S. aureus). This study aimed to establish a colonized cell culture model to investigate the impact of these bacteria on influenza A virus (IAV) infection. Respiratory epithelial cells were exposed to S. epidermidis, S. salivarius, or S. aureus, using either live or heat-inactivated bacteria, followed by IAV infection. Cell integrity was assessed microscopically, cytotoxicity was measured via LDH assay, and inflammatory responses were analyzed through cytokine expression. Additionally, macrophage function was examined in response to bacterial colonization and IAV infection. While commensals maintained epithelial integrity for 48 h, S. aureus induced severe cell damage and death. The most pronounced epithelial destruction was caused by coinfection with S. aureus and IAV. Notably, commensals did not confer protection against IAV but instead enhanced epithelial inflammation. These effects were dependent on live bacteria, as inactivated bacteria had no impact. However, prior exposure to S. epidermidis and S. salivarius improved macrophage-mediated immune responses against IAV. These findings suggest that while individual commensals do not directly protect epithelial cells, they may contribute to immune training and enhance lung defense mechanisms.},
}
@article {pmid40508160,
year = {2025},
author = {Renesteen, E and Boyajian, JL and Islam, P and Kassab, A and Abosalha, A and Makhlouf, S and Santos, M and Chen, H and Shum-Tim, C and Prakash, S},
title = {Microbiome Engineering for Biotherapeutic in Alzheimer's Disease Through the Gut-Brain Axis: Potentials and Limitations.},
journal = {International journal of molecular sciences},
volume = {26},
number = {11},
pages = {},
doi = {10.3390/ijms26115351},
pmid = {40508160},
issn = {1422-0067},
support = {252743//CIHR/ ; //Indonesia Endowment Fund for Education from the Ministry of Finance of the Republic of Indonesia/ ; 335999//Fonds de Recherche du Qu&#xe9;bec - Sant&#xe9; (FRQS)/ ; 2020-245622//Islamic Development Bank Scholarship/ ; //The Ministry of Higher Education of the Arab Republic of Egypt/ ; 504933//Canadian Graduate Scholarship-Masters from the Natural Sciences and Engineering Research Council (NSERC)/ ; 351337//Fonds de Recherche du Qu&#xe9;bec - Sant&#xe9; (FRQS)/ ; },
mesh = {Humans ; *Alzheimer Disease/therapy/microbiology/metabolism ; *Gastrointestinal Microbiome ; *Brain/metabolism ; Probiotics/therapeutic use ; Animals ; Prebiotics/administration &amp; dosage ; *Brain-Gut Axis ; *Biological Therapy/methods ; },
abstract = {Alzheimer's disease (AD) is a neurodegenerative condition characterized by considerable cognitive decline and functional impairment, primarily due to the progressive alteration of neurons, microglia, and astrocytes. Pathological manifestations of AD include the loss of synaptic plasticity, reduction in synaptic strength by amyloid-beta, aggregation, and neurotoxicity from tau protein post-translational modifications, all contributing to the disruption of neural networks. Despite its current pharmacological treatment for AD, different approaches to treat such disease are being developed, from a microbiome perspective. The microbiome encompasses a diverse microorganism, including beneficial bacteria that create a positive impact to diminish AD pathogenesis. Growing evidence suggests that probiotic, prebiotic, synbiotic, and postbiotics can positively modulate the gut-brain axis, reducing systemic inflammation, restoring neurotransmitter balance, and improving gut health, thereby possibly mitigating AD pathogenesis. Moreover, there is paraprobiotics as the most recently developed biotherapeutic with beneficial effects. This review explores the correlation between AD and gut-brain axis as a novel biotherapeutic target. The underlying mechanism of the microbiota-gut-brain axis in AD is examined. Novel insights into the current applications as potential treatment and its limitations are highlighted.},
}
@article {pmid40508052,
year = {2025},
author = {Zheng, X and Liu, J and Wang, X},
title = {Quorum Signaling Molecules: Interactions Between Plants and Associated Pathogens.},
journal = {International journal of molecular sciences},
volume = {26},
number = {11},
pages = {},
doi = {10.3390/ijms26115235},
pmid = {40508052},
issn = {1422-0067},
support = {202201BC070004//The Science and Technology Major Project from Yunnan Province/ ; 32370138//The National Natural Science Foundation of China/ ; 32260029//The National Natural Science Foundation of China/ ; 202201AT070089//The Applied Basic Research Foundation of Yunnan Province/ ; 2023YFD1400013//The National Key Research and Development Program/ ; },
mesh = {*Quorum Sensing ; *Plants/microbiology/metabolism/parasitology ; Signal Transduction ; Fungi/pathogenicity/metabolism ; Animals ; Bacteria/pathogenicity/metabolism ; Nematoda/physiology ; *Host-Pathogen Interactions ; Plant Diseases/microbiology ; Microbiota ; },
abstract = {The morphogenesis and defense evolution of plants are intricately linked to soil microbial community dynamics, where beneficial and pathogenic bacteria regulate ecosystem stability through chemical signaling. A microbial communication mechanism known as quorum sensing (QS), which affects population density, virulence, and biofilm formation, substantially impacts plant development and immune responses. However, plants have developed strategies to detect and manipulate QS signals, enabling bidirectional interactions that influence both plant physiology and the balance of the microbiome. In this review, QS signals from bacteria, fungi, and nematodes are systematically examined, emphasizing their recognition by plant receptors, downstream signaling pathways, and the activation of defense responses. Most significantly, attention is given to the role of fungal and nematode QS molecules in modulating plant microbe interactions. By elucidating these communication networks, we highlight their potential applications in sustainable agriculture, offering novel insights into crop health management and ecosystem resilience.},
}
@article {pmid40508035,
year = {2025},
author = {Toto, F and Scanu, M and Gramegna, M and Putignani, L and Del Chierico, F},
title = {Impact of DNA Extraction and 16S rRNA Gene Amplification Strategy on Microbiota Profiling of Faecal Samples.},
journal = {International journal of molecular sciences},
volume = {26},
number = {11},
pages = {},
doi = {10.3390/ijms26115226},
pmid = {40508035},
issn = {1422-0067},
support = {Current Research funds//Italian Ministry of Health/ ; n.a.//Technogenetics S.p.A./ ; },
mesh = {*RNA, Ribosomal, 16S/genetics ; *Feces/microbiology ; Humans ; *DNA, Bacterial/genetics/isolation &amp; purification ; *Gastrointestinal Microbiome/genetics ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; *Microbiota/genetics ; Bacteria/genetics/classification ; Metagenome ; },
abstract = {High-throughput 16S rRNA metagenomic sequencing has advanced our understanding of the gut microbiome, but its reliability depends on upstream processes such as DNA extraction and bacterial library preparation. In this study, we evaluated the impact of three different DNA extraction methods (a manual method with an ad hoc-designed pre-extraction phase (PE-QIA), and two automated magnetic bead-based methods (T180H and TAT132H)) and two bacterial library preparation protocols (home brew and VeriFi) on the 16S rRNA-based metagenomic profiling of faecal samples. T180H and TAT132H produced significantly higher DNA concentrations than PE-QIA, whereas TAT132H yielded DNA of lower purity compared to the others. In the taxonomic analysis, PE-QIA provided a balanced recovery of Gram-positive and Gram-negative bacteria, TAT132H was enriched in Gram-positive taxa, and T180H was enriched in Gram-negative taxa. An analysis of Microbial Community Standard (MOCK) samples showed that PE-QIA and T180H were more accurate than TAT132H. Finally, the VeriFi method yielded higher amplicon concentrations and sequence counts than the home brew protocol, despite the high level of chimeras. In conclusion, a robust performance in terms of DNA yield, purity, and taxonomic representation was obtained by PE-QIA and T180H. Furthermore, it was found that the impact of PCR-based steps on gut microbiota profiling can be minimized by an accurate bioinformatic pipeline.},
}
@article {pmid40507956,
year = {2025},
author = {Baușic, AIG and Scurtu, F and Manu, A and Matasariu, DR and Brătilă, E},
title = {Gut Microbiota Dysbiosis in Endometriosis: A Potential Link to Inflammation and Disease Progression.},
journal = {International journal of molecular sciences},
volume = {26},
number = {11},
pages = {},
doi = {10.3390/ijms26115144},
pmid = {40507956},
issn = {1422-0067},
support = {"PUBLISH NOT PERISH" - 2025//Carol Davila University of Medicine and Pharmacy/ ; },
mesh = {Humans ; Female ; *Endometriosis/microbiology/pathology ; *Dysbiosis/microbiology/complications ; *Gastrointestinal Microbiome ; Adult ; Disease Progression ; *Inflammation/microbiology ; Biomarkers ; Feces/microbiology ; },
abstract = {Endometriosis is a complex gynaecological disorder characterised by the presence of endometrial-like tissue outside the uterus, leading to chronic inflammation, pain, and infertility. Recent research suggests that gut microbiota may play a crucial role in the pathogenesis and progression of endometriosis by modulating immune responses and oestrogen metabolism. This study investigates the intestinal microbiota composition in women with endometriosis and its potential as a disease diagnosis and severity biomarker. Stool samples from nine patients diagnosed with endometriosis were analysed using the GI Effects[®] Comprehensive Stool Profile test. The tests revealed significant dysbiosis, particularly an altered Firmicutes/Bacteroidetes ratio and increased levels of Bacteroidetes. Inflammatory markers, including β-glucuronidase and secretory IgA, were also elevated, suggesting a potential link between gut microbiota and systemic inflammation in endometriosis. While our findings align with previous studies, further research with larger cohorts is necessary to validate these observations. Understanding the role of the microbiome in endometriosis could open new avenues for noninvasive diagnostic tools in endometriosis and microbiota-targeted therapies.},
}
@article {pmid40507947,
year = {2025},
author = {Cheng, CF and Nguyen, TKN and Shen, SC and Chen, BY and Wu, YB and Liang, HJ and Wu, CH},
title = {Synbiotic Supplementation Attenuates Doxorubicin-Induced Oxidative Stress and Inflammation in the Gut-Heart Axis of Chemotherapy-Treated Mice.},
journal = {International journal of molecular sciences},
volume = {26},
number = {11},
pages = {},
doi = {10.3390/ijms26115136},
pmid = {40507947},
issn = {1422-0067},
support = {N/A//This study was partly funded by Industry-Academic Cooperation Project from ARJIL Pharmaceu-ticals LLC, TTY Biopharm Co., Ltd., and Shiun Chao Biopharm Co., Ltd./ ; },
mesh = {Animals ; *Doxorubicin/adverse effects ; *Synbiotics/administration &amp; dosage ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Oxidative Stress/drug effects ; Male ; *Inflammation/chemically induced/metabolism ; Mice, Inbred ICR ; *Heart/drug effects ; Dietary Supplements ; Probiotics ; },
abstract = {The gut microbiome supports immune health and influences gut and heart functions through the gut-heart axis. Synbiotics (SBT), combining probiotics and prebiotics, help restore microbiome balance. Chemotherapy often disrupts this balance, leading to adverse effects on the gut and heart. This study explores the potential of SBT supplementation in reducing heart and gut inflammation caused by doxorubicin (DOX) chemotherapy. The gut microbiome plays a vital role in immune health, and metabolites produced by gut bacteria contribute to physiological functions through the gut-heart axis. Chemotherapy drugs often disrupt these processes, leading to adverse effects on internal organs. Using 24 ICR male mice divided into four groups, the experiment assessed the impact of SBT on DOX-induced damage. Results indicated that DOX treatment significantly worsened survival rates, physical performance, heart function, and gut microbiome stability. However, co-treatment with SBT improved these markers, suggesting that SBT may help mitigate chemotherapy-induced side effects in cancer patients.},
}
@article {pmid40507919,
year = {2025},
author = {Belvončíková, P and Macáková, K and Tóthová, N and Babál, P and Tarabčáková, L and Gardlík, R},
title = {Investigating the Role of Gut Microbiota in the Pathogenesis and Progression of Rheumatoid Arthritis in a Collagen-Induced Arthritis Mouse Model.},
journal = {International journal of molecular sciences},
volume = {26},
number = {11},
pages = {},
doi = {10.3390/ijms26115099},
pmid = {40507919},
issn = {1422-0067},
support = {APVV-21-0370//Slovak Research and Development Agency/ ; VEGA 1/0706/25//Ministry of Education, Science, Research and Sport of the Slovak Republic/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; *Arthritis, Rheumatoid/microbiology/pathology/therapy/etiology ; *Arthritis, Experimental/microbiology/pathology/therapy ; Mice ; Disease Models, Animal ; RNA, Ribosomal, 16S/genetics ; Disease Progression ; Humans ; Mice, Inbred DBA ; Male ; Fecal Microbiota Transplantation ; Female ; },
abstract = {Rheumatoid arthritis (RA) is a chronic systemic autoimmune disorder whose precise etiology remains unclear, though growing evidence implicates gut microbiota in its pathogenesis. This study aimed to investigate the role of gut microbiota in the onset and progression of RA by employing fecal microbiota transplantation (FMT) in a collagen-induced arthritis (CIA) mouse model using DBA/1J and Aire[-]/[-] strains. Mice received FMT from healthy donors, treatment-naïve RA patients, or treated RA patients in relapse, followed by assessment of microbiota composition via 16S rRNA sequencing, arthritis severity scoring, histological evaluations, and systemic inflammatory markers. The findings revealed distinct microbiota clustering patterns post-FMT across experimental groups, highlighting strain-specific colonization effects. Notably, genera such as Bifidobacterium and Paraprevotella correlated positively with arthritis severity in DBA/1J mice, whereas Corynebacterium, Enterorhabdus, and Odoribacter exhibited negative correlations, suggesting potential protective roles. Despite these microbial differences, minor variations in arthritis scores, paw inflammation, or systemic inflammation were observed among FMT groups. This indicates that although gut microbiota alterations are associated with RA pathogenesis, further investigation with larger cohorts and comprehensive sequencing approaches is essential to elucidate the therapeutic potential of microbiome modulation in autoimmune diseases.},
}
@article {pmid40507861,
year = {2025},
author = {Bircher, A and Katkeviciute, E and Morsy, Y and Lang, S and Montalban-Arques, A and Scharl, M},
title = {Roseburia intestinalis Modulates Immune Responses by Inducing M1 Macrophage Polarization.},
journal = {International journal of molecular sciences},
volume = {26},
number = {11},
pages = {},
doi = {10.3390/ijms26115049},
pmid = {40507861},
issn = {1422-0067},
support = {KFS-5372-08-2021-R//Swiss Cancer Research Foundation/ ; NA//Fondazione San Salvatore/ ; NA//Holcim Foundation/ ; },
mesh = {*Macrophages/immunology/microbiology/metabolism ; Humans ; Animals ; Colorectal Neoplasms/immunology/microbiology ; *Clostridiales/immunology ; Mice ; Gastrointestinal Microbiome/immunology ; *Macrophage Activation/immunology ; Cytokines/metabolism ; Cell Line, Tumor ; Coculture Techniques ; },
abstract = {In recent years, the gut microbiome has been recognized as one influential factor in cancer development. Particularly in colorectal cancer (CRC), several studies observed a major imbalance of the intestinal microbiota, marked by a reduction in beneficial bacterial species, such as Roseburia intestinalis, and an increase in opportunistic pathobionts, like Peptostreptococcus stomatis. We previously observed that specific Eubacteriales, including R. intestinalis, were significantly reduced in CRC patients and have a potent anti-tumor immune effect when applied as oral monotherapy in mice. Here, we investigate the molecular mechanism of R. intestinalis on various cell types in vitro, highlighting its potential therapeutic value in CRC. Co-culture experiments with macrophages demonstrated that R. intestinalis exposure induced an increase in the M1 phenotype and decreased the M2 phenotype, suggesting macrophage-polarizing properties of these bacteria. R. intestinalis also triggered a gene expression profile resembling M1 macrophages and led to distinct chemokine and cytokine secretion in cancer cells, suggesting an immune-activating environment. However, we did not observe direct cytotoxic effects in cancer cells. Our research provides insights into the potential of R. intestinalis to activate immune responses, supporting further investigation into its therapeutic role in CRC. These findings underscore the need for deeper studies on the bacterium's impact on CRC pathogenesis and treatment.},
}
@article {pmid40507844,
year = {2025},
author = {Usman, S and You, Y and Waseem, A},
title = {Exploring the Healing Powers of Histatins: From Oral Health to Therapeutics.},
journal = {International journal of molecular sciences},
volume = {26},
number = {11},
pages = {},
doi = {10.3390/ijms26115019},
pmid = {40507844},
issn = {1422-0067},
mesh = {Humans ; *Histatins/chemistry/metabolism/therapeutic use/genetics/pharmacology ; *Wound Healing ; *Oral Health ; Animals ; },
abstract = {Histatin peptides are a family of small histidine-rich cationic polypeptides produced by two genes, HTN1 and HTN3. They are found in salivary secretions from the parotid, sublingual, and submandibular salivary glands. These peptides undergo proteolytic cleavages to produce different histatin fragments which play multiple roles including wound healing, maintenance of enamel, and regulation of balance in the oral microbiome. In this review, we explored the expression, structural characteristics, and metal-ion-binding capacities of these peptides and how their functions are modulated by their structure. We also provide here an insight into the potential use of histatins as biomarkers and therapeutic peptides in the management of oral and non-oral diseases including cancer. Potential gaps in the current understanding of histatins that warrant further research have also been highlighted.},
}
@article {pmid40507838,
year = {2025},
author = {Yuzbashian, E and Fernando, DN and Jacobs, RL and Lesker, TR and Strowig, T and Ussar, S and Chan, CB},
title = {A Comparison of the Effects of Milk, Yogurt, and Cheese on Insulin Sensitivity, Hepatic Steatosis, and Gut Microbiota in Diet-Induced Obese Male Mice.},
journal = {International journal of molecular sciences},
volume = {26},
number = {11},
pages = {},
doi = {10.3390/ijms26115026},
pmid = {40507838},
issn = {1422-0067},
mesh = {Animals ; *Gastrointestinal Microbiome ; *Yogurt ; Male ; Mice ; *Milk ; Diet, High-Fat/adverse effects ; *Insulin Resistance ; *Cheese ; *Obesity/metabolism/etiology/microbiology ; Mice, Inbred C57BL ; Liver/metabolism ; *Fatty Liver/metabolism/etiology ; Mice, Obese ; Lipid Metabolism ; },
abstract = {The effects of low-fat dairy products on insulin resistance (IR), hepatic steatosis, and gut microbiota composition in high-fat diet (HFD)-fed obese mice were examined. C57BL/6 male mice (n = 16/group) were fed a high-fat diet (HFD, 45% fat) or HFD supplemented with either fat-free milk (MILK), fat-free yogurt (YOG), or reduced-fat (19% milk fat) cheddar cheese (CHE) at 10% of the total energy intake for 8 weeks. Body weight, fat mass, liver lipids, and metabolic enzymes were evaluated. Compared with HFD, MILK reduced homeostatic assessment of insulin resistance along with increased hepatic insulin signaling and decreased hepatic gluconeogenic enzymes. YOG and MILK decreased hepatic triacylglycerol content and lipid droplet size, while CHE had no effect. In the liver, MILK and YOG downregulated de novo lipogenesis enzymes. In MILK, fat oxidation capacity was elevated. Compared with HFD, liver lipidomic analysis in MILK and YOG revealed unique profiles of decreased proinflammatory lipid species, including ceramides. Dairy feeding elicited an increase in beneficial bacteria, such as Streptococcus in YOG and Anaero-tignum in MILK, as shown by 16S rRNA sequencing of gut microbiota. In conclusion, the ability of milk and yogurt to reduce hepatic steatosis in HFD mice may be explained, at least in part, by the regulation of the gut microbiome and liver lipidome.},
}
@article {pmid40507833,
year = {2025},
author = {Bratborska, AW and Głuszak, P and Joks, M and Kaźmierska, J and Pazdrowski, J and Polańska, A and Jain, S and Yadav, H and Masternak, MM and Dańczak-Pazdrowska, A},
title = {Skin Microbiome and Radiation-Induced Skin Injury: Unraveling the Relationship, Mechanisms, and Therapeutic Implications.},
journal = {International journal of molecular sciences},
volume = {26},
number = {11},
pages = {},
doi = {10.3390/ijms26115022},
pmid = {40507833},
issn = {1422-0067},
mesh = {Humans ; *Skin/microbiology/radiation effects/pathology ; *Microbiota/radiation effects ; Animals ; *Radiodermatitis/microbiology/therapy/etiology ; Dysbiosis/microbiology ; *Radiation Injuries/microbiology ; Radiotherapy/adverse effects ; Skin Microbiome ; },
abstract = {Radiotherapy (RT) is a treatment method commonly used in oncology. A vast majority of patients undergoing RT suffer from radiation-induced skin injury (RISI), which results from complex biochemical reactions in the irradiated skin. Current strategies for preventing and managing RISI are insufficient for achieving full skin regeneration. Multiple studies have shown that alterations in the skin microbiome correlate with the development and severity of RISI. These studies suggest that dysbiosis is a crucial factor in promoting radiation-associated dermatitis. Targeting the skin microbiota presents a potential therapeutic approach that could significantly improve the quality of life for patients undergoing RT. This review aims to present current findings on the interplay between the skin microbiome and radiation-induced skin damage as well as to discuss potential therapeutic strategies for preventing and mitigating this condition.},
}
@article {pmid40507816,
year = {2025},
author = {AlDawsari, M and Al-Ansari, MM and AlMalki, RH and Rahman, AMA and Al-Alwan, M},
title = {The MDA-MB-231 Breast Cancer Cell Secretomes Modify Metabolomes of Pseudomonas aeruginosa Breast Microbiome.},
journal = {International journal of molecular sciences},
volume = {26},
number = {11},
pages = {},
doi = {10.3390/ijms26115003},
pmid = {40507816},
issn = {1422-0067},
support = {RAC#2240005 and 2220015//King Faisal Specialist Hospital &amp; Research Centre/ ; },
mesh = {Humans ; *Pseudomonas aeruginosa/metabolism/drug effects/growth &amp; development ; Female ; Cell Line, Tumor ; *Metabolome/drug effects ; *Breast Neoplasms/microbiology/metabolism ; *Microbiota ; Culture Media, Conditioned/pharmacology ; *Breast/microbiology ; },
abstract = {Breast cancer (BC) is globally becoming a great challenge, being both the most diagnosed cancer and the leading cause of death in women. In addition to cancer cells, many bacteria co-inhabit BC, which differ in type and number from the resident microbiota found in healthy breast tissue. While many reports have demonstrated the ability of different bacteria to dysregulate BC's metabolites, the reciprocal effect of these metabolites on the bacterial microbiota has not yet been investigated. Herein, we assess the effect of conditioned media (CM) from a triple-negative BC cell line (MDA-MB-231) on the metabolic profile of Pseudomonas aeruginosa (P. aeruginosa), an important breast resident Gram-negative bacteria that influence oncogenesis. Optical density and scanning electron microscopes were used to assess the impact of MDA-MB-231-CM (BC-CM) on P. aeruginosa growth and morphological changes, respectively. In addition, liquid chromatography-high-resolution mass spectrometry was used to identify metabolic changes in P. aeruginosa and their secretomes in response to the BC-CM. The BC-CM significantly suppressed the growth of P. aeruginosa in the log phase and induced concentration-dependent cytopathological changes in their cell walls. The metabolites of P. aeruginosa were dysregulated considerably depending on the time of exposure to the BC-CM. When treated with the BC-CM, P. aeruginosa induced the purine alkaloid spliceostatin (FR901464), a prominent antitumor metabolite. The BC-CM also promoted other P. aeruginosa metabolites such as amino acids, phosphoribosyl-AMP, 2-aminoacetophenone, pyochelin I, guanosine monophosphate, riboflavin, and terpenoids, which are capable of interfering with oncogenesis. Nine of the significantly identified metabolites from the 0-3 h comparison and four of those identified from the 0-6 h comparison have potential roles in influencing cancer cell behavior. Our findings demonstrate the ability of triple-negative BC-CM not only to alter the growth and morphology of P. aeruginosa but also to modulate their metabolic profile. A better understanding of the influence of BC on certain resident breast microbiomes, such as P. aeruginosa, may open a new therapeutic intervention opportunity for the treatment of cancer.},
}
@article {pmid40507815,
year = {2025},
author = {Kiriyama, Y and Tokumaru, H and Sadamoto, H and Nochi, H},
title = {Biological Actions of Bile Acids via Cell Surface Receptors.},
journal = {International journal of molecular sciences},
volume = {26},
number = {11},
pages = {},
doi = {10.3390/ijms26115004},
pmid = {40507815},
issn = {1422-0067},
mesh = {*Bile Acids and Salts/metabolism/chemistry ; Humans ; Animals ; Receptors, G-Protein-Coupled/metabolism/chemistry ; *Receptors, Cell Surface/metabolism/chemistry ; },
abstract = {Bile acids (BAs) are synthesized in the liver from cholesterol and are subsequently conjugated with glycine and taurine. In the intestine, bile acids undergo various modifications, such as deconjugation, dehydrogenation, oxidation, and epimerization by the gut microbiota. These bile acids are absorbed in the intestine and transported to the liver as well as the systemic circulation. BAs can activate many types of receptors, including nuclear receptors and cell surface receptors. By activating these receptors, BAs can exert various effects on the metabolic, immune, and nervous systems. Recently, the detailed structure of TGR5, the major plasma membrane receptor for BAs, was elucidated, revealing a putative second BA binding site along with the orthosteric binding site. Furthermore, BAs act as ligands for bitter taste receptors and the Leukemia inhibitory factor receptor. In addition, the Mas-related, G-protein-coupled receptor X4 interacts with receptor activity-modifying proteins. Thus, a variety of cell surface receptors are associated with BAs, and BAs are thought to have very complex activities. This review focuses on recent advances regarding cell surface receptors for bile acids and the biological actions they mediate.},
}
@article {pmid40507814,
year = {2025},
author = {Biazzo, M and Pinzauti, D and Podrini, C},
title = {SkinDuo[TM] as a Targeted Probiotic Therapy: Shifts in Skin Microbiota and Clinical Outcomes in Acne Patients.},
journal = {International journal of molecular sciences},
volume = {26},
number = {11},
pages = {},
doi = {10.3390/ijms26115000},
pmid = {40507814},
issn = {1422-0067},
support = {R&amp;I-2022-019L//Xjenza Malta/ ; },
mesh = {Humans ; *Probiotics/therapeutic use/administration &amp; dosage ; *Acne Vulgaris/microbiology/therapy/drug therapy ; *Skin/microbiology ; *Microbiota/drug effects ; Male ; Female ; Treatment Outcome ; RNA, Ribosomal, 16S/genetics ; Adult ; Young Adult ; Adolescent ; Propionibacterium acnes ; Skin Microbiome ; },
abstract = {Acne vulgaris is a common dermatological condition strongly associated with disruptions in the skin microbiota, specifically involving key species such as Cutibacterium acnes and Staphylococcus epidermidis. This study investigates the efficacy of SkinDuo[TM], a topical probiotic containing Lactiplantibacillus plantarum, in modulating the skin microbiota and improving clinical outcomes in patients with acne vulgaris. Over a 4-week to 8-week observational study period, microbial composition and diversity shifts were analyzed using full-length 16S rRNA sequencing. Patient responses were categorized into "good" responders (showing significant clinical improvement) and "no_change" responders (with minimal or no improvement). SkinDuo[TM] treatment resulted in lower post-treatment Cutibacterium acnes abundance in the "good" group compared to the "no_change" group. The "good" group maintained a stable level of alpha diversity following treatment. In contrast, the "no_change" group exhibited a marked reduction in microbial diversity. Beta diversity analysis revealed distinct clustering patterns associated with improved clinical outcomes. These findings suggest that the preservation of microbial richness and evenness may serve as a potential biomarker for positive response to probiotic therapy. This study highlights the potential of SkinDuo[TM] to restore microbial balance and alleviate acne symptoms, contributing to the growing body of evidence supporting microbiome-based therapeutic strategies in dermatology.},
}
@article {pmid40507757,
year = {2025},
author = {Cano-Mármol, RP and Fernández-Ruiz, VE and Martínez-Pascual, C and Ros-Madrid, I and Martín-Pozuelo, G and Oliva-Bolarín, A and Martínez-Sánchez, MA and Egea-Valenzuela, J and Núñez-Sánchez, M&#xc1; and Ramos-Molina, B and Ruiz-Alcaraz, AJ and Ferrer-Gómez, M},
title = {Corporal Composition and Gut Microbiome Modification Through Exclusion Dietary Intervention in Adult Patients with Crohn's Disease: Protocol for a Prospective, Interventional, Controlled, Randomized Clinical Trial.},
journal = {Journal of clinical medicine},
volume = {14},
number = {11},
pages = {},
doi = {10.3390/jcm14113998},
pmid = {40507757},
issn = {2077-0383},
abstract = {Background: Crohn's disease (CD) is an inflammatory bowel disease in which there is an alteration in the homeostasis and functionality of the intestinal mucosa accompanied by a dysbiosis of the commensal microbiota. The analysis of different dietary strategies to achieve CD remission and reduce gastrointestinal symptoms concludes that it is necessary to restrict the intake of ultra-processed products and to promote the consumption of those with anti-inflammatory effects that improve intestinal permeability and dysbiosis. Methods: Based on previous studies conducted in other cohorts, mainly pediatric, we propose an experimental, prospective, randomized study in patients with active CD who do not show improvement with conventional pharmacological treatment. The control group will receive standard nutritional recommendations while the intervention group will be prescribed an exclusion diet supplemented with enteral nutrition. Results: Patients in the intervention group are expected to exhibit increased lean body mass and reduced visceral fat, as measured by bioelectrical impedance analysis (BIA), alongside higher rates of clinical remission (CDAI), decreased inflammatory markers, and improved gut microbiota composition. Additionally, improvements in health-related quality of life are anticipated, as assessed by validated questionnaires. Conclusions: In the present project, we plan to conduct a detailed study to determine the potential of the exclusion diet for the treatment and remission of CD in adult patients, with the hypothesis that this nutritional intervention will be able to modify and improve intestinal dysbiosis, inflammatory status, and clinical and body composition markers in these patients.},
}
@article {pmid40507435,
year = {2025},
author = {Smolinska, S and Popescu, FD and Zemelka-Wiacek, M},
title = {A Review of the Influence of Prebiotics, Probiotics, Synbiotics, and Postbiotics on the Human Gut Microbiome and Intestinal Integrity.},
journal = {Journal of clinical medicine},
volume = {14},
number = {11},
pages = {},
doi = {10.3390/jcm14113673},
pmid = {40507435},
issn = {2077-0383},
abstract = {OBJECTIVE: This review aims to comprehensively evaluate the current evidence on the role of prebiotics, probiotics, synbiotics, and postbiotics-collectively referred to as "biotics"-in modulating the human gut microbiota and enhancing intestinal epithelial integrity.<br><br>FINDINGS: Biotics exert their beneficial effects through several mechanisms, including by promoting the growth of beneficial microbes, producing short-chain fatty acids (SCFAs), strengthening the gut barrier, and regulating immune responses. Prebiotics selectively stimulate beneficial bacteria, probiotics introduce live microorganisms with therapeutic functions, synbiotics combine the strengths of both, and postbiotics offer non-viable microbial components and metabolites that mimic probiotic benefits with enhanced safety profiles. Each type of biotic demonstrates unique and complementary effects across a range of conditions, such as inflammatory bowel disease, irritable bowel syndrome, obesity, constipation, and antibiotic-associated diarrhea.<br><br>IMPLICATIONS: As disruptions in the gut microbiota and intestinal barrier are increasingly linked to chronic and immune-mediated diseases, leveraging biotics offers promising avenues for personalized nutrition, preventive healthcare, and adjunct therapies. The integration of biotics into clinical and dietary strategies may significantly contribute to improving gastrointestinal and systemic health.},
}
@article {pmid40507352,
year = {2025},
author = {Gambichler, T and Weyer-Fahlbusch, SS and Overbeck, J and Abu Rached, N and Becker, JC and Susok, L},
title = {Impaired Overall Survival of Melanoma Patients Due to Antibiotic Use Prior to Immune Checkpoint Inhibitor Therapy: Systematic Review and Meta-Analysis.},
journal = {Cancers},
volume = {17},
number = {11},
pages = {},
doi = {10.3390/cancers17111872},
pmid = {40507352},
issn = {2072-6694},
abstract = {Background: The gut microbiome plays a pivotal role in shaping systemic immunity and modulating anti-tumor responses. Preclinical and clinical studies have shown that higher gut microbial diversity and the presence of specific commensal taxa correlate with improved responses to immune checkpoint inhibitors (ICI) in melanoma. Conversely, broad-spectrum antibiotics can induce dysbiosis, reducing T cell activation and cytokine production, and have been linked to diminished ICI efficacy in several cancer types. Methods: We conducted a systematic review and meta-analysis of seven retrospective cohorts (total n = 5213) comparing overall survival in cutaneous melanoma (CM) patients who did or did not receive systemic antibiotics within six weeks before ICI initiation. From each study, we extracted hazard ratios (HRs) for death, antibiotic-to-ICI interval, ICI regimen (PD-1 monotherapy vs. PD-1 + CTLA-4 combination), cohort size, and country. Pooled log-HRs were estimated under fixed-effect and random-effects (REML) models. Statistical heterogeneity was quantified by Cochran's Q and I[2] statistics, and τ[2]. We performed leave-one-out sensitivity analyses, generated a Baujat plot to identify influential studies, applied trim-and-fill to assess publication bias, and ran meta-regressions for regimen, antibiotic timing, sample size, and geography. Results: Under the fixed-effect model, antibiotic exposure corresponded to a pooled HR of 1.26 (95% CI 1.13-1.41; p < 0.001). The random-effects model yielded a pooled HR of 1.55 (95% CI 1.21-1.98; p = 0.0005) with substantial heterogeneity (Q = 25.1; I[2] = 76%). Prediction intervals (0.78-3.06) underscored between-study variability. Leave-one-out analyses produced HRs from 1.50 to 1.75, confirming robustness, and the Baujat plot highlighted two cohorts as primary heterogeneity drivers. Trim-and-fill adjusted the HR to 1.46 (95% CI 1.08-1.97). In subgroup analyses, combination therapy studies (k = 4) showed a pooled HR of ~1.9 (I[2] = 58%) versus ~1.3 (I[2] = 79%) for monotherapy. Meta-regression attributed the largest variance to the regimen (R[2] = 32%; β(monotherapy) = -0.35; p = 0.13). Conclusions: Pre-ICI antibiotic use in CM is consistently associated with a 26-55% increase in mortality risk, particularly with PD-1 + CTLA-4 combinations, reinforcing the mechanistic link between microbiome integrity and ICI success. Looking ahead, integrating prospective microbiome profiling into clinical trials will be critical to personalize ICI therapy, clarify causality, and identify microbial biomarkers for optimal treatment selection. Prospective, microbiome-integrated trials promise to refine melanoma immunotherapy by tailoring antibiotic stewardship and microbial interventions to enhance patient outcomes.},
}
@article {pmid40507344,
year = {2025},
author = {Gomes de Sousa, R and Guerreiro, CS and Santos, I and Cravo, M},
title = {The Knowledge Gap in Gut Microbiome Characterization in Early-Onset Colorectal Cancer Patients: A Systematic Scoping Review.},
journal = {Cancers},
volume = {17},
number = {11},
pages = {},
doi = {10.3390/cancers17111863},
pmid = {40507344},
issn = {2072-6694},
abstract = {BACKGROUND/OBJECTIVES: Over the past two decades, the incidence of early-onset colorectal cancer (EoCRC) has been increasing, although its underlying causes remain unclear. Gut microbiome is known to play a role in carcinogenesis of colorectal cancer. This scoping review aims to systematically map and synthetize current evidence on gut microbiome characterization in EoCRC (vs. late-onset colorectal cancer (LoCRC) and healthy individuals), describe the methodology used, and identify knowledge gaps to inform and guide future research.<br><br>METHODS: This systematic scoping review followed the Joanna Briggs Institute (JBI) methodology for scoping reviews. Searches were conducted in PubMed, Web of Science, and Scopus between January and February 2025. Two reviewers independently screened and selected the studies. One reviewer extracted the relevant information, using an adapted version of the JBI template.<br><br>RESULTS: Seven studies met eligibility criteria. Compared to healthy young adults, EoCRC patients had a predominance of lower &#x3b1; diversity, different &#x3b2; diversity, and greater abundance of Flavonifractor plautii, Akkermansia muciniphila, Bacteroides, and Fusobacteria. Comparisons with LoCRC showed that EoCRC had distinct &#x3b2; diversity and a higher abundance in Fusobacterium, Akkermansia, Bacteroides, and Actinomyces. Only three studies correlated the microbiota composition of EoCRC with clinicopathology features and suggested positive associations between Fusobacterium abundance, rectal tumors and lower survival and Akkermansia abundance with body mass index (BMI) &#x2265; 25 kg/m[2], rectal EoCRC, and better survival.<br><br>CONCLUSIONS: There is a lack of large, methodologically robust studies linking gut microbiota with clinicopathological, lifestyle, and tumor molecular features in EoCRC. Our review highlights critical knowledge gaps, the need for standardized methodologies, and key areas for future investigation.},
}
@article {pmid40507200,
year = {2025},
author = {Suzuki, Y and Ishioka, K and Nakamura, T and Miyazaki, N and Marubashi, S and Suzutani, T},
title = {Function of Yogurt Fermented with the Lactococcus lactis 11/19-B1 Strain in Improving the Lipid Profile and Intestinal Microbiome in Hemodialysis Patients.},
journal = {Nutrients},
volume = {17},
number = {11},
pages = {},
doi = {10.3390/nu17111931},
pmid = {40507200},
issn = {2072-6643},
mesh = {Humans ; *Yogurt/microbiology ; *Gastrointestinal Microbiome ; *Renal Dialysis ; Male ; Female ; Middle Aged ; Aged ; *Renal Insufficiency, Chronic/therapy/blood ; *Fermentation ; *Lipids/blood ; Indican/blood ; Methylamines/blood ; Dysbiosis ; Probiotics ; },
abstract = {BACKGROUND/OBJECTIVES: The number of chronic kidney disease (CKD) patients is increasing in Japan, and this population is at high risk of death from cardiovascular and cerebrovascular diseases. Therefore, prevention of arteriosclerosis as a common underlying cause of these diseases is required. In this study, we examined whether 11/19-B1 yogurt, which has been proven to reduce serum low-density lipoprotein (LDL) levels, can decrease the serum levels of indoxylsulfate and trimethylamine-N-oxide (TMAO), which are produced by intestinal microbiota and known to cause arteriosclerosis, through improving dysbiosis in hemodialysis patients.<br><br>METHODS: Nineteen dialysis patients consumed 50 g of 11/19-B1 yogurt daily for 8 weeks, and changes in serum lipid profile and uremic toxin levels, intestinal microbiome, as well as the frequency of bowel movement and stool characteristics were observed.<br><br>RESULTS: The results demonstrated that an intake of yogurt decreased serum LDL 99.3 to 88.5 (p = 0.049) and indoxylsulfate in seven of nine subjects with previously high concentrations, and improved stool characteristics as estimated by the Bristle stool score, although decreased HDL and no beneficial effect on serum TMAO was observed.<br><br>CONCLUSIONS: These results may suggest that the ingestion of 11/19-B1 yogurt provides a preventative effect against the progression of atherosclerosis and renal dysfunction.},
}
@article {pmid40507161,
year = {2025},
author = {Li, Y and Liao, X and Tang, S and Wang, Q and Lin, H and Yu, X and Xiao, Y and Tao, X and Zhong, T},
title = {Potential Therapeutic Targets for Androgenetic Alopecia (AGA) in Obese Individuals as Revealed by a Gut Microbiome Analysis: A Mendelian Randomization Study.},
journal = {Nutrients},
volume = {17},
number = {11},
pages = {},
doi = {10.3390/nu17111892},
pmid = {40507161},
issn = {2072-6643},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Alopecia/microbiology/genetics/therapy ; Mendelian Randomization Analysis ; *Obesity/complications/microbiology/genetics ; Genome-Wide Association Study ; Male ; Female ; Adult ; },
abstract = {Objective: This study aimed to investigate the role of the gut microbiome in androgenetic alopecia (AGA) among obese individuals using Mendelian randomization (MR), and to identify potential therapeutic targets for mitigating AGA in this population. Methods: Genomic data for 412 gut microbiomes, AGA, and obesity were obtained from genome-wide association studies (GWAS). Bidirectional MR was performed using inverse variance weighted (IVW) as the primary analysis method, complemented by sensitivity analyses. Potential therapeutic targets within the gut microbiome associated with AGA in obese individuals were identified. Results: Two gut microbiomes were identified as having a significant impact on obese individuals with AGA. Specifically, the abundance of the sulfoglycolysis pathway in gut bacteria was found to significantly increase the risk of both obesity and AGA. In contrast, the abundance of the de novo biosynthesis of the adenosine ribonucleotide pathway in gut bacteria was associated with a significant increase in the risk of obesity but a significant decrease in the risk of AGA. Conclusions: The abundance of gut bacterial pathways, including sulfoglycolysis and the de novo biosynthesis of adenosine ribonucleotides, can serve as potential therapeutic targets for managing obesity-associated AGA. These findings offer a novel research direction for the development of innovative diagnostic and treatment strategies for patients with obesity and AGA.},
}
@article {pmid40507159,
year = {2025},
author = {Watson, AE and Yusuf, N},
title = {The Influence of Dietary Factors on Melanoma Development and Progression: A Comprehensive Review.},
journal = {Nutrients},
volume = {17},
number = {11},
pages = {},
doi = {10.3390/nu17111891},
pmid = {40507159},
issn = {2072-6643},
mesh = {Humans ; *Melanoma/etiology/prevention &amp; control/pathology ; Gastrointestinal Microbiome ; *Diet/adverse effects ; Disease Progression ; *Skin Neoplasms/etiology/prevention &amp; control/pathology ; Antioxidants/administration &amp; dosage ; Risk Factors ; Oxidative Stress ; },
abstract = {Melanoma is an aggressive cutaneous malignancy with increasing global incidence and high metastatic potential. While ultraviolet (UV) radiation remains the primary environmental risk factor, emerging evidence suggests that dietary factors may influence melanoma risk, progression, and treatment outcomes. This comprehensive review examines the impact of dietary components, including fats, vitamins, minerals, antioxidants, bioactive compounds, and the gut microbiome, on melanoma pathogenesis. The current literature indicates that diets rich in polyunsaturated fatty acids (PUFAs), antioxidants, and plant-based bioactive compounds may confer protective effects against melanoma by modulating oxidative stress, inflammation, and immune response. Additionally, the gut microbiome plays a critical role in melanoma progression and immunotherapy response, with dietary patterns influencing microbial composition and, consequently, host immunity. Despite these promising associations, research remains limited, and findings across studies are inconsistent, preventing the establishment of definitive dietary guidelines for melanoma prevention and management. Future research should focus on large-scale prospective studies to elucidate the mechanisms underlying the dietary influences on melanoma and determine evidence-based nutritional strategies. Understanding the interplay between diet, immune modulation, and gut microbiome composition represents a promising avenue for advancing melanoma prevention and treatment strategies.},
}
@article {pmid40507144,
year = {2025},
author = {González, A and Fullaondo, A and Odriozola, A},
title = {In Search of Healthy Ageing: A Microbiome-Based Precision Nutrition Approach for Type 2 Diabetes Prevention.},
journal = {Nutrients},
volume = {17},
number = {11},
pages = {},
doi = {10.3390/nu17111877},
pmid = {40507144},
issn = {2072-6643},
support = {IT1547-22//Basque Government, Department of Education/ ; },
mesh = {Humans ; *Diabetes Mellitus, Type 2/prevention &amp; control/microbiology ; *Gastrointestinal Microbiome/physiology ; Aged ; Female ; Middle Aged ; Male ; *Healthy Aging ; *Precision Medicine/methods ; Spain ; Feces/microbiology ; Overweight/microbiology ; },
abstract = {Background/Objectives: Type 2 diabetes (T2D) is a leading cause of morbidity and mortality worldwide and in Spain, particularly in the elderly population, affecting healthy ageing. Nutritional strategies are key to its prevention. The gut microbiota is also implicated in T2D and can be modulated by nutrition. We hypothesize that precision nutrition through microbiota modulation may help prevent T2D. This article aims to (1) describe a gut microbiota bacterial profile associated with T2D prevention, (2) provide precision nutrition tools to optimize this profile, (3) analyze how overweight influences the microbiota composition and precision nutrition response, and (4) address the technical challenges of microbiome-based precision nutrition clinical implementation to prevent T2D. Methods: A review of gut microbiota associated with T2D prevention was conducted. 13 healthy Spanish participants over 62 with optimal blood glucose levels (7 normal weight and 6 overweight) underwent a 3-month precision nutrition intervention to optimize T2D-preventive gut microbiota using a bioinformatics food recommendation system, Phymofood (EP22382095). Fecal microbiota was analyzed pre- and post-intervention using full-length 16S rRNA gene amplification, MinION sequencing, and NCBI taxonomic classification. Results: 31 potentially preventive bacteria against T2D were selected. The intervention increased the relative abundance of beneficial genera (Butyrivibrio and Faecalibacterium) and species (Eshraghiella crossota, and Faecalibacterium prausnitzii). The overweight influenced microbiota composition and intervention response. Conclusions: A gut microbiota profile associated with T2D prevention was identified, and precision nutrition could increase the relative abundance of beneficial bacteria. Confounding factors such as overweight should be considered when designing microbiome-based precision nutrition interventions. These results contribute to a better understanding of the microbiota associated with T2D prevention and address technical challenges for clinical implementation in future healthy ageing strategies.},
}
@article {pmid40507096,
year = {2025},
author = {Lutsiv, T and Fitzgerald, VK and Neil, ES and McGinley, JN and Hussan, H and Thompson, HJ},
title = {Cooked Bean (Phaseolus vulgaris L.) Consumption Alters Bile Acid Metabolism in a Mouse Model of Diet-Induced Metabolic Dysfunction: Proof-of-Concept Investigation.},
journal = {Nutrients},
volume = {17},
number = {11},
pages = {},
doi = {10.3390/nu17111827},
pmid = {40507096},
issn = {2072-6643},
support = {58-3060-8-031//USDA ARS/ ; 2020-05206//National Institute for Food and Agriculture:/ ; },
mesh = {Animals ; *Bile Acids and Salts/metabolism ; Mice, Inbred C57BL ; *Phaseolus ; Mice ; Male ; Liver/metabolism ; Disease Models, Animal ; Feces/chemistry ; Cecum/microbiology/metabolism ; Gastrointestinal Microbiome ; Cooking ; Obesity/metabolism ; Metabolomics ; *Diet ; *Metabolic Diseases/etiology/metabolism ; Diet, High-Fat/adverse effects ; },
abstract = {Background/Objectives: Metabolic dysregulation underlies a myriad of chronic diseases, including metabolic dysfunction-associated steatotic liver disease (MASLD) and obesity, and bile acids emerge as an important mediator in their etiology. Weight control by improving diet quality is the standard of care in prevention and control of these metabolic diseases. Inclusion of pulses, such as common bean, is an affordable yet neglected approach to improving diet quality and metabolic outcomes. Thus, this study evaluated the possibility that common bean alters bile acid metabolism in a health-beneficial manner. Methods: Using biospecimens from several similarly designed studies, cecal content, feces, liver tissue, and plasma samples from C57BL/6 mice fed an obesogenic diet lacking (control) or containing cooked common bean were subjected to total bile acid analysis and untargeted metabolomics. RNA-seq, qPCR, and Western blot assays of liver tissue complemented the bile acid analyses. Microbial composition and predicted function in the cecal contents were evaluated using 16S rRNA gene amplicon and shotgun metagenomic sequencing. Results: Bean-fed mice had increased cecal bile acid content and excreted more bile acids per gram of feces. Consistent with these effects, increased synthesis of bile acids in the liver was observed. Microbial composition and capacity to metabolize bile acids were markedly altered by bean, with greater prominence of secondary bile acid metabolites in bean-fed mice, i.e., microbial metabolites of chenodeoxycholate/lithocholate increased while metabolites of hyocholate were reduced. Conclusions: In rendering mice resistant to obesogenic diet-induced MASLD and obesity, cooked bean consumption sequesters bile acids, increasing their hepatic synthesis and enhancing their diversity through microbial metabolism. Bean-induced changes in bile acid metabolism have potential to improve dyslipidemia.},
}
@article {pmid40507094,
year = {2025},
author = {Binda, S and Chow-Shi-Yée, M and El Salti, S and Auclair-Ouellet, N and Oula, ML and Carton, T and Leuillet, S and Tomassi, D and Hemmings, R and Kadoch, IJ},
title = {The Effect of Probiotics on Health in Pregnancy and Infants: A Randomized, Double-Blind, Placebo-Controlled Trial.},
journal = {Nutrients},
volume = {17},
number = {11},
pages = {},
doi = {10.3390/nu17111825},
pmid = {40507094},
issn = {2072-6643},
mesh = {Humans ; Female ; *Probiotics/administration &amp; dosage ; Pregnancy ; Double-Blind Method ; Adult ; Infant, Newborn ; Gastrointestinal Microbiome ; Infant ; Lacticaseibacillus rhamnosus ; Vagina/microbiology ; Dietary Supplements ; Bifidobacterium bifidum ; Young Adult ; },
abstract = {Background/Objectives: There is growing interest in the benefits of probiotic supplementation during pregnancy and lactation, but evidence supporting the beneficial effects for mother-infant dyads remains scarce. This study assessed the effects of probiotic supplementation on infection frequency and immunity in pregnant women and infants, and on microbiome establishment during the first month of life. Methods: At 28 weeks of gestation, 180 healthy pregnant women were randomized to receive either a placebo (n = 90) or a probiotic supplement (n = 90), Prenatis™, containing 5 billion CFU/day of Lacticaseibacillus rhamnosus Rosell[®]-11 and Bifidobacterium bifidum HA-132. Results: There was a significantly lower number of women with one or more infections during the study in the probiotics group (8 vs. 18, p = 0.05) and a trend for a lower number of infections during pregnancy (primary outcome) in the probiotics group (p = 0.07). Regarding infants, a lower number of days with infections during the first month of life was observed in the probiotics group (4.7 days on average vs. 10.5 days, p = 0.03). The vaginal microbiota composition during pregnancy and after childbirth showed no significant differences between groups while the infants' gut microbiome demonstrated a significantly higher abundance/prevalence of beneficial taxa in the probiotics group. The benefits conferred by probiotics were especially notable when considering birth by C-section. Probiotics promoted the vertical transmission of beneficial species and the induction of a highly interconnected microbiota, structured around key species. Conclusions: Probiotic supplementation during the third trimester of pregnancy and lactation is a valid strategy for conferring benefits to mothers and infants.},
}
@article {pmid40507071,
year = {2025},
author = {Bigman, G and Rusu, ME and Shelawala, N and Sorkin, JD and Beamer, BA and Ryan, AS},
title = {A Comprehensive Scoping Review on Diet and Nutrition in Relation to Long COVID-19 Symptoms and Recovery.},
journal = {Nutrients},
volume = {17},
number = {11},
pages = {},
doi = {10.3390/nu17111802},
pmid = {40507071},
issn = {2072-6643},
mesh = {Humans ; *COVID-19/complications/physiopathology/diet therapy ; *Nutritional Status ; *Diet ; SARS-CoV-2 ; Post-Acute COVID-19 Syndrome ; Adult ; },
abstract = {Background/Objectives: Long COVID-19 is characterized by persistent symptoms lasting three months or more following SARS-CoV-2 infection. Nutrition has emerged as a modifiable factor influencing recovery trajectories and symptom burden; however, existing evidence remains fragmented across diverse study designs and populations. This scoping review synthesized global evidence on the role of diet and nutrition in managing long COVID-19 symptoms and supporting recovery. Methods: Following PRISMA-ScR and Joanna Briggs Institute guidelines for scoping reviews, we searched major biomedical databases for studies published between 2020 and 2025. Eligible studies examined dietary intake, nutritional status, or nutrition-related interventions in adults with long COVID-19. Results: After duplicates were removed, 1808 records were screened, resulting in 50 studies that met the inclusion criteria-27 intervention studies and 23 observational studies. Nutritional exposures included micronutrients (e.g., vitamins D, K2), amino acids (e.g., L-arginine), multinutrient formulations, microbiota-targeted therapies (e.g., probiotics, synbiotics), nutritional status, diet quality, and whole-diet patterns (e.g., the Mediterranean diet). Approximately 76% of studies reported improvements in long COVID-19-related symptoms such as fatigue, mood disturbances, physical function, and markers of inflammation. Conclusions: Diet and nutrition may support long COVID-19 recovery by targeting inflammation and the gut microbiome to alleviate symptoms and improve functional outcomes. Well-powered trials of whole-diet approaches, combined with targeted supplementation, are needed to confirm their potential as scalable, accessible tools for post-COVID-19 recovery and management.},
}
@article {pmid40507067,
year = {2025},
author = {George, H and Permata, FS and D'Souza, CM and Adeghate, EA},
title = {Cultural and Molecular Factors Predisposed to Non-Alcoholic Fatty Liver Disease and Type 2 Diabetes Mellitus.},
journal = {Nutrients},
volume = {17},
number = {11},
pages = {},
doi = {10.3390/nu17111797},
pmid = {40507067},
issn = {2072-6643},
support = {G00003388; G00002809; G00003627, 31M374//United Arab Emirates University/ ; },
mesh = {Humans ; *Non-alcoholic Fatty Liver Disease/epidemiology/ethnology/genetics/etiology ; *Diabetes Mellitus, Type 2/ethnology/epidemiology/etiology ; Prevalence ; *Culture ; Insulin Resistance ; Genetic Predisposition to Disease ; },
abstract = {There is an exponential increase in the global prevalence of non-alcoholic fatty liver disease (NAFLD) in all populations. The objective of this review is to examine how different cultures and molecular entities influence the progression of NAFLD. Research databases, including PubMed, Scopus, the American Diabetes Association, the American Liver Foundation, and Diabetes UK, were used to retrieve information. Our data analysis showed that cultural norms shape the perceptions of health, illness, and mortality, thus influencing how individuals view themselves and express their experiences and may also affect decisions related to treatment and healthcare. Cultural competence, the ability to understand and navigate cultural differences, is essential for eliciting patient and practitioner perspectives and integrating this understanding into diagnostic and treatment plans. By acknowledging and respecting a patient's cultural background, healthcare providers can foster trust, improve care quality, enhance acceptance of diagnoses, and boost treatment adherence. Although cultural factors play a crucial role in the progression of NAFLD, the disease is also shaped by genetic predispositions, molecular mechanisms, and comorbidities. Molecular pathways involved in the development and progression of NAFLD include alterations in lipid metabolism, insulin signaling, insulin resistance, oxidative stress, defective gut microbiome, and inflammation. This study concludes that a combination of cultural preferences and molecular factors has contributed to the worldwide exponential rise in the prevalence of NAFLD, which in turn has led to an increase in the prevalence of comorbidities such as cardiovascular diseases, diabetes mellitus, and metabolic syndrome.},
}
@article {pmid40507042,
year = {2025},
author = {Kadiyska, T and Vassilev, D and Tourtourikov, I and Ciurinskiene, S and Madzharova, D and Savcheva, M and Stoynev, N and Mileva-Popova, R and Tafradjiiska-Hadjiolova, R and Mitev, V},
title = {Age-Dependent Gut Microbiome Dysbiosis in Autism Spectrum Disorder and the Role of Key Bacterial Ratios.},
journal = {Nutrients},
volume = {17},
number = {11},
pages = {},
doi = {10.3390/nu17111775},
pmid = {40507042},
issn = {2072-6643},
support = {D-116/29.05.2024//Medical University of Sofia/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Autism Spectrum Disorder/microbiology ; *Dysbiosis/microbiology ; Child ; Adolescent ; Child, Preschool ; Male ; Female ; Young Adult ; Age Factors ; Feces/microbiology ; Biomarkers ; Case-Control Studies ; },
abstract = {Background/Objectives: Autism spectrum disorder (ASD) has a wide-ranging impact on individuals' quality of life and development, and there is a critical need for greater awareness, early intervention, and comprehensive support strategies to effectively address the unique needs of those affected by ASD. Recent studies highlight the gut microbiome's potential role in modulating ASD symptoms via the gut-brain axis, but specific microbial biomarkers remain unclear. This study aims to investigate differences in gut microbiota composition between ASD patients and neurotypical controls in a novel approach, specifically assessing ratios of Firmicutes/Bacteroidetes (F/B), Actinobacteria/Proteobacteria (A/P), and Prevotella/Bacteroides (P/B) as potential biomarkers. Methods: We analyzed gut microbiome samples from 302 Bulgarian children and adolescents diagnosed with ASD (aged 2-19 years). Microbial ratios (F/B, A/P, and P/B) were calculated and compared against previously reported reference meta-analytic means from European neurotypical populations. The statistical significance of deviations was assessed using parametric (t-tests), non-parametric (Wilcoxon signed-rank tests), and proportion-based (binomial tests) methods. Effect sizes were quantified using Cohen's d. Significant differences between ASD cases and neurotypical reference values were observed across several age groups. Results: Notably, children with ASD demonstrated significantly lower F/B and A/P ratios, with the youngest cohort (0-4 years) exhibiting the greatest differences. Deviations in the P/B ratio varied across age groups, with a significant elevation in the oldest group (≥10 years). Collectively, ASD cases consistently exhibited microbiota profiles indicative of dysbiosis. Conclusions: Our findings support gut microbiome dysbiosis as a potential biomarker for ASD, highlighting significantly altered bacterial ratios compared to neurotypical controls. These microbiome shifts could reflect early-life disruptions influencing neurodevelopment. Future studies should adopt longitudinal and mechanistic approaches to elucidate causal relationships and evaluate therapeutic microbiome modulation strategies.},
}
@article {pmid40507003,
year = {2025},
author = {Karkala, A and Kotoulas, SC and Tzinas, A and Massa, E and Mouloudi, E and Gkakou, F and Pataka, A},
title = {The Lung Microbiome and Its Impact on Obstructive Sleep Apnea: A Diagnostic Frontier.},
journal = {Diagnostics (Basel, Switzerland)},
volume = {15},
number = {11},
pages = {},
doi = {10.3390/diagnostics15111431},
pmid = {40507003},
issn = {2075-4418},
abstract = {Obstructive sleep apnea (OSA), a prevalent disorder characterized by recurrent upper airway collapse, is increasingly recognized as a systemic inflammatory condition influenced by microbial dysregulation. Emerging evidence underscores the lung microbiome as a mediator in OSA pathophysiology, where dysbiotic shifts driven by intermittent hypoxia, oxidative stress and mechanical airway trauma amplify inflammatory cascades and perpetuate respiratory instability. This review synthesizes current knowledge on the bidirectional interplay between OSA and lung microbial communities. It aims to highlight how hypoxia-induced alterations in microbial ecology disrupt immune homeostasis, while inflammation-driven mucosal injury fosters pathogenic colonization. Clinical correlations between specific taxa like Streptococcus and Prevotella, and disease severity, suggest microbial signatures as novel biomarkers for OSA progression and treatment response. Furthermore, oxidative stress markers and pro-inflammatory cytokines emerge as potential diagnostic tools that bridge microbial dysbiosis with sleep-related outcomes. However, challenges persist in sampling standardization of the low-biomass lower airways, as well as in causative mechanisms linking microbial dysbiosis to OSA pathophysiology. By integrating microbial ecology with precision sleep medicine, this paradigm shift promises to transform OSA management from mechanical stabilization to holistic ecosystem restoration.},
}
@article {pmid40506791,
year = {2025},
author = {Cai, A and Shen, D and Xiong, Q and Li, S and Qiu, C and Li, L and Chen, Z and Lin, X and Yao, Q and Zhang, Y and Chen, R and Kou, L},
title = {The gut microbiome and metabolomic alterations underlying colitis-induced encephalopathy in mice: mechanistic insight.},
journal = {Behavioral and brain functions : BBF},
volume = {21},
number = {1},
pages = {17},
pmid = {40506791},
issn = {1744-9081},
support = {Y20210133//Wenzhou Science and Technology Bureau/ ; 2024ZYC-A10//Zhejiang Medical Association Clinical Medical Research special fund project/ ; 2023KY907//Zhejiang Medical and Health Science and Technology Program/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; Mice ; *Colitis/metabolism/complications/chemically induced/microbiology ; Male ; Hippocampus/metabolism ; *Metabolome/physiology ; *Brain Diseases/metabolism/microbiology/etiology ; Dextran Sulfate ; Colon/metabolism ; *Inflammatory Bowel Diseases/metabolism/complications/microbiology ; Disease Models, Animal ; Mice, Inbred C57BL ; Brain/metabolism ; Metabolomics ; Fatty Acids, Volatile/metabolism ; Brain-Gut Axis/physiology ; },
abstract = {BACKGROUND: In addition to classical gastrointestinal symptoms, patients with inflammatory bowel disease (IBD) often exhibit neurological manifestations, such as mood disorders and cognitive dysfunctions, which are frequently overlooked. However, the potential pathogenesis of IBD-related encephalopathy remains unclear, and few studies have explored the influence of interactions between the gut microbiota and the host gut-brain metabolome on the emergence of brain diseases in IBD mice. In this study, we conducted a comprehensive analysis of gut microbiome and metabolome alterations in dextran sulfate sodium salt (DSS)-induced IBD mice compared to control mice, focusing on colonic contents and hippocampal tissue. Our aim was to investigate the putative mechanisms underlying the microbiota-gut-brain axis in IBD-induced encephalopathy.<br><br>RESULTS: IBD mice showed depression-like behaviors and cognitive deficits. Metabolic profiling revealed distinct patterns in the colonic contents and hippocampal areas of IBD mice, marked by decreased energy metabolism, amino acid levels, short-chain fatty acids (SCFAs), and choline metabolism. These metabolic changes were negatively associated with the abundance of Bacteroides, Turicibacter, Ruminococcus, and Akkermansia, while Desulfovibrio and Lactobacillus showed positive correlations.<br><br>CONCLUSIONS: This study identifies unique microbial and gut-brain metabolite signatures associated with DSS-induced changes and offers new metabolic insights into the microbiota-gut-brain axis in IBD-related brain disorders. It highlights the potential of targeting gut microbiota to modulate host metabolism as a therapeutic approach for IBD-related neurological complications.},
}
@article {pmid40506747,
year = {2025},
author = {Pasche, JM and Sawlani, R and Buttrós, VH and Desaeger, J and Garrett, KA and Martins, SJ},
title = {Underground guardians: how collagen and chitin amendments shape soil microbiome structure and function for Meloidogyne enterolobii control.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {141},
pmid = {40506747},
issn = {2049-2618},
support = {2021-68013-33758//National Institute of Food and Agriculture/ ; },
mesh = {*Chitin/pharmacology ; Animals ; *Soil Microbiology ; *Tylenchoidea/drug effects/pathogenicity ; Solanum lycopersicum/parasitology/growth &amp; development/microbiology ; *Collagen/pharmacology ; Soil/chemistry ; *Microbiota/drug effects ; *Plant Diseases/parasitology/prevention &amp; control ; Bacteria/classification/genetics/isolation &amp; purification ; Fungi/classification/isolation &amp; purification/genetics ; Plant Roots/parasitology ; },
abstract = {BACKGROUND: The emergence of the guava root-knot nematode (Meloidogyne enterolobii) poses a significant threat to tomato yields globally. This study evaluated the impact of collagen and chitin soil amendments on soil microbial composition and function (fungal and bacterial communities) and their effects on tomato plant health and M. enterolobii infection under standard (5000 eggs plant[-1]) and high (50,000 eggs plant[-1]) inoculum pressure. Conducted in a greenhouse setting, the study investigated the effectiveness of these amendments in nurturing beneficial microbial communities across both native and agricultural soils.<br><br>RESULTS: Both collagen and chitin were effective in reducing nematode egg counts by up to 66% and 84% under standard and high inoculum pressure, respectively, and enhanced plant health parameters (biomass and chlorophyll content). Moreover, a microbiome shift led to an increase in bacterial (Kitasatospora, Bacillus, and Streptomyces) and fungal (Phialemonium) genera, known for their chitinase, collagenase, and plant-parasitic nematode control. Among the microbes, Streptomyces spp. were found among the core microbiome and associated with a lower disease incidence assessed through a phenotype-OTU network analysis (PhONA). Under standard inoculum, higher metabolite expression was observed with amino acids representing a majority among the metabolite groups.<br><br>CONCLUSIONS: The findings highlight the potential of collagen and chitin to mitigate M. enterolobii infection by fostering beneficial soil microbial communities. Video Abstract.},
}
@article {pmid40506735,
year = {2025},
author = {Kampouris, ID and Kuhl-Nagel, T and Behr, JH and Sommermann, L and Babin, D and Francioli, D and Zrenner, R and Kublik, S and Schloter, M and Ludewig, U and Smalla, K and Neumann, G and Grosch, R and Geistlinger, J},
title = {Selective recruitment of beneficial microbes in the rhizosphere of maize affected by microbial inoculants, farming practice, and seasonal variations.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {69},
pmid = {40506735},
issn = {2524-6372},
abstract = {BACKGROUND: Plant beneficial microorganisms as inoculants can improve crop performance, but factors affecting their impact on plant performance under field conditions remain unclear, thereby limiting their use in farming. Here, we investigated how farming practices (e.g., tillage and N-fertilization intensity) and growing seasons influenced the impact of a beneficial microorganism consortium (BMc: Trichoderma, Bacillus, and Pseudomonas strains) in maize and affected the rhizosphere competence of each BMc strain. In addition, we tested whether the consortium affects the resident rhizosphere microbiome and crop performance. In two growing seasons (2020 and 2021), we assessed how BMc inoculation affects maize growth, nutritional status, gene expression, and rhizosphere microbiome under different farming practices at the flowering stage.<br><br>RESULTS: Inoculated strains successfully colonized the maize rhizosphere independently of farming practice. BMc inoculation improved plant growth and iron uptake in 2020, regardless of farming practice. These effects co-occurred with lower precipitation levels in 2020 compared to 2021. BMc inoculation reduced the expression of several stress-related genes in maize in 2020 under drought. An increased iron uptake by the BMc-inoculated plants was observed in 2020 and was associated with the upregulation of the gene ZmNAS3, which is linked to iron uptake. Therefore, BMc inoculation mitigated the drought impact on maize. The microbial rhizosphere communities were altered by BMc inoculation in both years, but patterns of responder taxa differed between seasons. Metagenome analysis revealed that more genes (e.g., genes encoding biosurfactants and siderophores) were enriched in the rhizosphere of BMc-inoculated plants in 2020 than in 2021. Moreover, we identified bacterial and fungal taxa positively associated with maize iron uptake. The relative abundance of these iron uptake-associated bacterial and fungal taxa significantly increased due to BMc inoculation in 2020, while they showed overall higher relative abundances in 2021, independently of BMc inoculation. We mapped the sequences of these iron-associated taxa to publicly available genomes and verified the occurrence of various plant beneficial traits in several mapped genomes.<br><br>CONCLUSIONS: Overall, we show that the growing season determined the effect of BMc inoculation on maize plants by shaping microbiome composition and function in the maize rhizosphere more than farming practice. These findings highlight the importance of the complex interplay between microbial inoculants and the resident rhizosphere microorganisms under abiotic stress conditions.},
}
@article {pmid40506497,
year = {2025},
author = {Jung, DR and Choi, Y and Jeong, M and Singh, V and Jeon, SY and Seo, I and Park, NJ and Lee, YH and Park, JY and Han, HS and Shin, JH and Chong, GO},
title = {Metagenomic insight into the vaginal microbiome in women infected with HPV 16 and 18.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {105},
pmid = {40506497},
issn = {2055-5008},
mesh = {Female ; Humans ; *Vagina/microbiology/virology ; *Human papillomavirus 16/genetics/isolation &amp; purification ; *Papillomavirus Infections/virology/microbiology ; *Microbiota/genetics ; Metagenomics ; *Human papillomavirus 18/genetics/isolation &amp; purification ; *Bacteria/classification/genetics/isolation &amp; purification ; Uterine Cervical Neoplasms/virology/microbiology ; Metagenome ; Adult ; Middle Aged ; },
abstract = {Human papillomavirus (HPV) 16 and 18 (HPV 16/18) account for over 70% of cervical cancer (CC) cases, yet their interaction with the vaginal microbiome (VM) remains unclear. This study explored the association between high-risk HPV types (HR-HPVs), VM composition and bacterial function using shotgun metagenomic sequencing. In early-stage cervical lesions, the HPV 16/18 group showed reduced Lactobacillus-dominant community state types compared to other HR-HPVs, while invasive CC exhibited increased pathogenic bacteria, including Streptococcus agalactiae, Fannyhessea vaginae, and Sneathia vaginalis. The VM associated with HPV 16/18 was enriched in immune response and inflammation pathways, whereas other HR-HPVs were linked to cellular metabolism and hormonal signaling. Notably, HPV 16/18 exhibited stronger bacterial-fungal correlations, indicating shifts in the microbial community. Furthermore, 137 metagenome-assembled genomes provided insights into unique microbial genomic signatures. Our study links VM differences with HPV 16/18 oncogenic potential across cervical lesion stages, urging further research for better diagnostics and treatments.},
}
@article {pmid40506424,
year = {2025},
author = {Belluomo, I and Tarazi, M and Lao-Kaim, NP and Tai, YF and Spanel, P and Hanna, GB},
title = {Detection of Volatile Organic Compounds as an emerging strategy for Parkinson's disease diagnosis and monitoring.},
journal = {NPJ Parkinson's disease},
volume = {11},
number = {1},
pages = {161},
pmid = {40506424},
issn = {2373-8057},
abstract = {Growing evidence suggests that specific volatile organic compound (VOC) profiles may reflect key pathophysiological processes in Parkinson's disease (PD), including alterations in the microbiome, metabolism, and oxidative stress. Identifying reliable VOC biomarkers could enable non-invasive tests for early diagnosis, disease monitoring, and therapy evaluation. This review examines VOC analysis in biological matrices such as breath, skin, and stool, outlining current research and future applications in PD. We evaluate analytical techniques based on sensitivity, specificity, and clinical applicability. Additionally, we classify VOCs identified in previous studies alongside their proposed biological origins. Special attention is given to short-chain fatty acids, produced by the gut microbiome, a novel target in PD research. Our findings highlight the need for larger cohort studies and standardized protocols to advance VOC-based diagnostics in PD. Understanding the interplay between VOCs and PD may facilitate biomarker discovery, enhancing non-invasive diagnostic strategies and personalized disease management.},
}
@article {pmid40506319,
year = {2025},
author = {Chang, CM and Lam, LY and Lam, HYP and Kao, PY and Hsu, ST and Wu, WJ and Chang, KC and Huang, CY},
title = {Potential role of intratumoral Fusobacterium nucleatum and interleukin-1 beta in breast cancer cell growth.},
journal = {Journal of microbiology, immunology, and infection = Wei mian yu gan ran za zhi},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jmii.2025.05.008},
pmid = {40506319},
issn = {1995-9133},
abstract = {BACKGROUND: It has been shown that the human breast harbors a rich and diverse microbiome, with significant differences observed between tumor tissue and normal breast tissue. Recently, Fusobacterium nucleatum (F. nucleatum) has been shown to affect breast cancer growth, but the underlying mechanism remains enigmatic.<br><br>METHODS: Breast cancer tissues were obtained from clinical patients and analyzed for the microbiome composition using 16S rDNA sequencing and qPCR. Both serum and intratumoral cytokine levels were measured to assess their correlation with intratumoral F. nucleatum. Breast cancer cell lines and patient-derived cancer cells were infected with different strains of F. nucleatum, followed by different analyses. Additionally, peripheral blood mononuclear cells (PBMCs) were isolated from healthy individuals to investigate the immunoregulatory effect of F. nucleatum.<br><br>RESULTS: Our results identified a higher abundance of F. nucleatum in breast cancer tissue compared to adjacent normal breast tissue, which strongly correlated with intratumoral IL-1&#x3b2; levels. In vitro studies confirmed this correlation, demonstrating that infection of breast cancer cells with F. nucleatum promotes tumor growth. Further investigation suggested that F. nucleatum induces IL-1&#x3b2; secretion in both breast cancer cells and PBMCs, but only IL-1&#x3b2; secreted by breast cancer cells stimulates cancer cell growth. Inhibition of NLRP3 reversed the growth-promoting effect of F. nucleatum on breast cancer cells.<br><br>CONCLUSION: Our results demonstrate the role of F. nucleatum in stimulating breast cancer cell growth. Therefore, targeting intratumoral F. nucleatum could provide a promising therapeutic approach to combat breast cancer.},
}
@article {pmid40506211,
year = {2025},
author = {Plant, BJ and Einarsson, GG and Deasy, KF and Dahly, D and Singh, PK and Barry, PJ and Goss, CH and Fajac, I and Vagg, T and Durieu, I and Flanagan, E and O'Callaghan, G and Martin, C and Burgel, PR and Haworth, CS and Floto, RA and Downey, DG and Dupont, LJ and Jones, AM and Elborn, JS and Eustace, JA and Mall, MA and Tunney, MM},
title = {Cystic Fibrosis Microbiome-directed Antibiotic Therapy Trial in Exacerbations Results Stratified (CFMATTERS): Results of a multi-centre randomised controlled trial.},
journal = {The European respiratory journal},
volume = {},
number = {},
pages = {},
doi = {10.1183/13993003.02443-2024},
pmid = {40506211},
issn = {1399-3003},
abstract = {BACKGROUND: This study explores the effectiveness and safety of microbiome-directed-antimicrobial-therapy versus usual-antimicrobial-therapy in adult cystic fibrosis pulmonary exacerbations.<br><br>METHODS: A multi-centre two-arm parallel randomised control trial conducted across Europe/North-America enrolled 223 participants (January 2015 - August 2017). All participants were chronically colonised with Pseudomonas aeruginosa and were randomised 1:1 into two study-arms. The "usual-therapy group" received 2-weeks of IV ceftazidime 3g thrice-daily (for allergies: aztreonam 2g thrice-daily) and tobramycin 5-10mg&#xb7;kg[-1] once-daily. The "microbiome-directed group" received the same usual-therapy plus an additional antibiotic with greatest presumed activity against the 2nd, 3rd and 4th most abundant genera present in the sputum microbiome, selected by a Consensus Expert Treatment Panel. The primary outcome was change in percentage of predicted FEV1 (ppFEV1) at 14 days post initiation of antibiotics. Secondary outcomes examined ppFEV1 at 7 days, 28 days, and 3 months; time-to-next exacerbation; symptom burden at 7 days; Health Related Quality of Life (HRQoL) at 28 days; and number of exacerbations and IV antibiotic days at 12 months.<br><br>RESULTS: 149 participants had an eligible exacerbation (usual-therapy n=83, microbiome-directed therapy n=66). There was no difference between the groups for ppFEV1 at day 14 (-1.1%, 95%CI -3.9 to 1.7; p=0.46), or ppFEV1 measured at other time-points, or for time-to-next exacerbation (microbiome-directed versus usual-therapy Hazard Ratio 0.91 [95%CI 0.60 to 1.38; p=0.66]). The microbiome-directed group trended to have more IV days (median 42 versus 28; p=0.08) and more subsequent exacerbations (median 3 versus 2; p=0.044) the following year. There were no appreciable differences in symptom burden; however, HRQoL sub-scores were consistently worse in the microbiome-directed group (-4.3 points versus usual therapy (95%CI -8.3 to -0.3, p=0.033).<br><br>CONCLUSION: The addition of a third antibiotic based on sputum microbiome sequencing analysis did not result in improved clinical outcomes.},
}
@article {pmid40506032,
year = {2025},
author = {Wang, R and Yunxiang, X and Degen, A and Han, X and Zhao, X and Zhang, Q and Huang, Y and Bai, B and Yang, Y and Liu, S and Xue, Y and Hao, L},
title = {Milk Composition Changes and Alterations in Bacteria, Serum, and Gut Metabolome Over Time in Lactating Naks and Simmental Cows.},
journal = {Animal bioscience},
volume = {},
number = {},
pages = {},
doi = {10.5713/ab.25.0109},
pmid = {40506032},
issn = {2765-0189},
abstract = {OBJECTIVE: This study aimed to elucidate the mechanisms underlying milk composition divergence between naks (female yaks) and Simmental cows (S-cows) by integrating longitudinal multi-omics analyses of gut microbiota and metabolomes.<br><br>METHODS: We determined the gut microbiota and metabolites of both species over a 54-day period (day 26 to 80 of lactation), with ten naks and ten S-cows. Gut microbiota dynamics were assessed via 16S rRNA sequencing, while serum and fecal metabolomes were profiled using UHPLC-MS/MS. Statistical analyses included Wilcoxon rank-sum tests, LEfSe (LDA > 2, p < 0.05), and Spearman correlations (r > 0.70).<br><br>RESULTS: Milk yield was lesser (0.53-0.91 vs. 2.07-3.88 kg/d) but concentrations of fat (5.63-6.30% vs. 3.30-3.74%), protein (5.66-6.30% vs. 3.39-3.74%), and conjugated linoleic acid&#xff08;CLA&#xff09; (1.74-2.35% vs. 1.40-1.75%) were greater (p < 0.001) in nak than S-cow milk. Species-specific microbial signatures emerged. In naks, the g-Family-XIII-AD3011-group&#xa0;and&#xa0;g-norank-Ruminococcaceae were correlated with bile acid metabolism and CLA synthesis via 13-hydroxyoctadecadienoic acid transport. Additionally, the naks gut had a greater concentration of 13-hydroxyoctadecadienoic acid, a precursor of CLA, which may be transported to mammary cells via phosphatidylcholine and converted to CLA under the catalysis of fatty acid desaturase2(FADS2). S-cows harbored g-Succinivibrio and g-Eubacterium-ruminantium-group, which are linked to galactose utilization and mTOR-mediated amino acid allocation. Metabolomics revealed naks-enriched steroid biosynthesis and taurine pathways (FDR < 0.05), while S-cows exhibited a lactating network associated with greater milk yield.<br><br>CONCLUSIONS: Host-specific gut microbiota mediated nutrient allocation trade-offs. Naks optimized lipid-rich milk through bile acid and CLA metabolic networks, whereas S-cows enhanced yield via microbial-galactose synergies. This research underscores the pivotal role of the gut microbiome in mediating milk composition and suggests that microbiome manipulation could be a promising strategy to enhance milk quality in ruminants.},
}
@article {pmid40506009,
year = {2025},
author = {Si, Y and Ma, W and Zhang, Q and Zhang, Y and An, J and Zhang, M and Fu, Y and Yu, Y and Zhang, H and Fang, Y and Zhang, D},
title = {Investigating acupuncture therapy in depression: mechanisms of synaptic plasticity regulation.},
journal = {Neuroscience},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.neuroscience.2025.06.005},
pmid = {40506009},
issn = {1873-7544},
abstract = {Depression is a severe heterogeneous mental illness that is highly co-morbid with other mental and somatic disorders. It poses a significant healthcare burden on both individuals and society. Currently, the use of single-target antidepressants exhibits suboptimal efficacy with significant adverse effects. Acupuncture has been advocated as a practical and effective treatment for depression, due to its low adverse effects rate compared to antidepressant medication. Currently, several studies have shown that acupuncture treatment for depression primarily involves multiple therapeutic mechanisms, including the regulation of specific gene expression, neuropeptide and neurotransmitter release, increasing the expression of neurotrophic factors, suppressing hyperactivity of the hypothalamic-pituitary-adrenal (HPA) axis, attenuating inflammatory responses, and restoring gut microbiota balance. These therapeutic effects involve the regulation of critical signaling pathways, including the cAMP-responsive element binding protein (CREB) signaling pathway, mitogen-activated protein kinases (MAPK) signaling pathway, mechanistic target of rapamycin (mTOR) signaling pathway, and toll-like receptors (TLR) signaling pathway. Notably, depression-associated molecular mechanisms and signaling pathway dysregulations are closely linked to impaired neural and synaptic plasticity. Acupuncture synergistically modulates the neuro-immune-microbiome multidimensional network and integrates crosstalk among key pathways such as CREB, thereby systemically restoring synaptic plasticity. This multi-dimensional integrative mechanism likely underlies its therapeutic superiority over single-target antidepressants. This review aims to elucidate how acupuncture restores cerebral synaptic plasticity by rectifying depression-related systemic dysfunctions and signaling pathway abnormalities, which will advance our understanding of its regulatory potential in depression treatment and inform the development of precision therapeutic strategies.},
}
@article {pmid40505847,
year = {2025},
author = {Yadav, A and Tadas, M and Kale, M and Wankhede, N and Umekar, M and Kotagale, N and Taksande, B},
title = {Gut Microbiota and Behavioral Ontogeny in Autism Spectrum Disorder: A Pathway to Therapeutic Innovations.},
journal = {Physiology &amp; behavior},
volume = {},
number = {},
pages = {114989},
doi = {10.1016/j.physbeh.2025.114989},
pmid = {40505847},
issn = {1873-507X},
abstract = {Autism Spectrum Disorder (ASD) is a multifaceted neurodevelopmental condition characterized by deficits in social communication, repetitive behaviors, and restricted interests. Emerging evidence suggests that gut-brain axis a dynamic, bidirectional communication network between gut microbiota and central nervous system, is critical in shaping behavioral ontogeny in ASD. Dysbiosis of gut microbiota, commonly observed in individuals with ASD, has been associated with alterations in neurodevelopmental trajectories and symptom severity. Furthermore, disturbances in maternal microbiome during pregnancy are increasingly recognized as key factors influencing fetal brain development, potentially heightening risk of ASD and behavioral manifestations. Mechanistic research reveals that gut-derived metabolites modulate blood-brain barrier integrity, neuroinflammatory processes, and neuronal circuit formation, contributing to behavioral outcomes. These findings emphasize gut microbiota's profound influence on emergence and progression of ASD-related behaviors. Promising therapeutic strategies, including probiotics, prebiotics, fecal microbiota transplantation, and dietary interventions, have demonstrated potential in modulating the gut microbiome and improving behavioral symptoms in ASD. However, challenges such as individual variability in microbiome composition, limited clinical evidence, and an incomplete understanding of causative mechanisms remain significant barriers to clinical translation. This review explores the interplay between gut microbiota and ASD-associated behaviors, focusing on key mechanisms such as microbial regulation of neurotransmitter production, immune signaling, and neuroinflammation. It further highlights gut microbiota's potential as a modifiable factor influencing neurodevelopmental and behavioral outcomes in ASD. By advancing our understanding of gut-brain axis, we can pave the way for personalized and targeted interventions aimed at improving behavioral ontogeny and developmental trajectories in individuals with ASD.},
}
@article {pmid40505719,
year = {2025},
author = {Zhu, X and Xu, Y},
title = {Gut microbiome contributes to 6PPD-Quinone induced cognitive impairment through PI3K/Akt signaling.},
journal = {Toxicology},
volume = {},
number = {},
pages = {154217},
doi = {10.1016/j.tox.2025.154217},
pmid = {40505719},
issn = {1879-3185},
abstract = {Studies show that N-(1,3-dimethylbutyl)-N'-phenyl-p-phenylenediamine-quinone (6PPD-Q) accumulates in the central nervous system, but its role in cognitive impairment and underlying mechanisms remain unclear. Morris water maze assay revealed that 6-PPDQ significantly impairs cognitive function, particularly learning and memory. HE staining revealed alterations in the hippocampal DG and CA3 regions of exposed mice, including sparse cell arrangement, blurred boundaries, nuclear condensation, and a reduction in Nissl bodies. Fecal microbiota transplantation from 6-PPDQ-exposed mice to normal mice induced cognitive deficits and hippocampal pathological damage. Western Blot assay showed that 6-PPDQ exposure resulted in inhibition of PI3K/AKT signaling. Moreover, blunted PI3K/AKT signaling was observed in mice transplanted with 6-PPDQ-associated mice fecal microbiota. Further analysis of 16S rDNA assay identified a total of 30 differential bacteria at the genus level, including 8 upregulated bacteria such as g_Helicobacter and 22 downregulated bacteria such as g_Prevotellaceae_NK3B31_group. In conclusion, this study uncovers gut microbiome mediates 6PPD-Q-induced cognitive impairment through inhibiting of PI3K/Akt signaling, and provides a basis for further investigation into gut microbiome's protective effects on 6-PPDQ-induced nervous system injury.},
}
@article {pmid40505623,
year = {2025},
author = {Singh, BK and Hu, HW and Macdonald, CA and Xiong, C},
title = {Microbiome-facilitated plant nutrient acquisition.},
journal = {Cell host &amp; microbe},
volume = {33},
number = {6},
pages = {869-881},
doi = {10.1016/j.chom.2025.05.005},
pmid = {40505623},
issn = {1934-6069},
mesh = {*Microbiota/physiology ; *Plants/microbiology/metabolism ; *Nutrients/metabolism ; Ecosystem ; Bacteria/metabolism ; Symbiosis ; Biological Evolution ; },
abstract = {Plants and microbiomes have co-evolved for millennia. Through this co-evolution, microbiomes have become essential for plant nutrient acquisition, which involves plant signaling, microbial sensing, and acquiring and sharing nutrients. In this review, we synthesize recent advancements in the complex associations of molecular, physiological, and eco-evolutionary mechanisms that underpin microbe-facilitated plant nutrient uptake. Focusing on emerging insights in plant-microbial communication and metabolic pathways, we evaluate potential opportunities to harness plant microbiomes to sustainably supply nutrients in agricultural and natural ecosystems. However, further progress is constrained by key knowledge gaps. We propose an amended conceptual framework for advancement that includes a holistic understanding of eco-evolutionary relationships with explicit consideration of signaling and sensing mechanisms. Finally, we argue that advancing fundamental science by utilizing emerging analytical approaches in an integrated way is critical to develop effective microbiome-informed tools that can enhance plant nutrient acquisition and promote long-term food security and environmental sustainability.},
}
@article {pmid40505621,
year = {2025},
author = {Zhernakova, A and Yassour, M and Hall, LJ and Collado, MC},
title = {Unlocking the power of human milk and infant feeding: Understanding how nutrition and early microbiota interaction shapes health programming.},
journal = {Cell host &amp; microbe},
volume = {33},
number = {6},
pages = {820-835},
doi = {10.1016/j.chom.2025.05.014},
pmid = {40505621},
issn = {1934-6069},
mesh = {Humans ; *Milk, Human/chemistry/microbiology ; Infant ; *Gastrointestinal Microbiome/physiology ; *Infant Nutritional Physiological Phenomena ; Infant, Newborn ; Breast Feeding ; Oligosaccharides ; Weaning ; },
abstract = {Human milk represents a highly evolved bioactive system that promotes colonization by infant microbial pioneers, supports immune maturation, and fosters infant development. Beyond providing nutrition, human milk contains key bioactive components, such as microbes, metabolites, human milk oligosaccharides, immunoglobulins, lactoferrin, and antimicrobial peptides. These factors influence colonization of the infant gut microbiome and facilitate immune development and metabolic health, with implications for health outcomes and risk of non-communicable diseases. In this review, we highlight the impact of infant feeding, human milk constituents (especially bioactive compounds), and weaning on infant microbial trajectories. By understanding how early-life nutrition influences microbial colonization and nutrient sensing, i.e., "how we feed our microbes," we can develop targeted interventions and personalized diets to support proper gut maturation and disease prevention from infancy to adulthood, as well as explore the therapeutic potential of human milk bioactives beyond infancy, offering new strategies for disease prevention and treatment.},
}
@article {pmid40505620,
year = {2025},
author = {Kiessling, S and Liu, S and Haller, D and Thaiss, CA},
title = {Origins and functions of microbiome rhythms.},
journal = {Cell host &amp; microbe},
volume = {33},
number = {6},
pages = {808-819},
doi = {10.1016/j.chom.2025.05.017},
pmid = {40505620},
issn = {1934-6069},
mesh = {Humans ; *Circadian Rhythm/physiology ; *Gastrointestinal Microbiome/physiology ; Animals ; *Host Microbial Interactions ; *Microbiota/physiology ; },
abstract = {Daily oscillations in microbiota composition and function are emerging as an important element in host-microbiota interactions. Here, we summarize features of the microbiota that undergo diurnal rhythms, their development, their impact on the biology of the host, and their relevance to human health and disease. In particular, we focus on the intrinsic and extrinsic factors that regulate microbiota oscillations and the multifaceted roles that microbiota rhythmicity plays in host physiology, immunity, and metabolism. Given the pervasive impact of intestinal microorganisms on host health, understanding the origins and functions of microbiota rhythms is a critical aspect of the circadian biology of the meta-organism.},
}
@article {pmid40505619,
year = {2025},
author = {Bakkeren, E and Piskovsky, V and Foster, KR},
title = {Metabolic ecology of microbiomes: Nutrient competition, host benefits, and community engineering.},
journal = {Cell host &amp; microbe},
volume = {33},
number = {6},
pages = {790-807},
doi = {10.1016/j.chom.2025.05.013},
pmid = {40505619},
issn = {1934-6069},
mesh = {*Microbiota/physiology ; Humans ; *Nutrients/metabolism ; Animals ; *Bacteria/metabolism/genetics ; *Host Microbial Interactions ; Plants/microbiology ; },
abstract = {Many plants and animals, including humans, host diverse communities of microbes that provide many benefits. A key challenge in understanding microbiomes is that the species composition often differs among individuals, which can thwart generalization. Here, we argue that the key to identifying general principles for microbiome science lies in microbial metabolism. In the human microbiome and in other systems, every microbial species must find ways to harvest nutrients to thrive. The available nutrients in a microbiome interact with microbial metabolism to define which species have the potential to persist in a host. The resulting nutrient competition shapes other mechanisms, including bacterial warfare and cross-feeding, to define microbiome composition and properties. We discuss impacts on ecological stability, colonization resistance, nutrient provision for the host, and evolution. A focus on the metabolic ecology of microbiomes offers a powerful way to understand and engineer microbiomes in health, agriculture, and the environment.},
}
@article {pmid40505618,
year = {2025},
author = {Sanders, ME and Hill, C},
title = {The microbiome: An actor or stage for the beneficial action of probiotics, prebiotics, synbiotics, and postbiotics?.},
journal = {Cell host &amp; microbe},
volume = {33},
number = {6},
pages = {777-789},
doi = {10.1016/j.chom.2025.04.017},
pmid = {40505618},
issn = {1934-6069},
mesh = {*Probiotics/administration &amp; dosage ; *Prebiotics/administration &amp; dosage ; *Synbiotics/administration &amp; dosage ; Humans ; *Microbiota/physiology ; *Gastrointestinal Microbiome ; Animals ; },
abstract = {Probiotics, prebiotics, synbiotics, and postbiotics are required, by definition, to confer a health benefit on the host. It is often presumed the host microbiome plays a central role in the mechanism of action of these substances, collectively referred to here as "biotics." However, the definitions of both probiotics and postbiotics do not include an associated mechanism nor the involvement of the microbiome. The definitions of prebiotics and synbiotics require evidence of selective utilization by the host microbiome, but do not state that confirmatory evidence must be provided that this utilization causes the associated health benefit. In this perspective, we discuss evidence supporting a role for the microbiome in delivering these health benefits and whether or not measuring microbiome alterations can serve as important readouts of efficacy. We also discuss the possibility of expanding the biotics family with substances such as bacteriophage, fermented foods, and live dietary microbes.},
}
@article {pmid40505617,
year = {2025},
author = {Greathouse, KL and Choudhury, A},
title = {Precision nutrition and the gut microbiome: Harnessing AI to revolutionize cancer prevention and therapy.},
journal = {Cell host &amp; microbe},
volume = {33},
number = {6},
pages = {766-776},
doi = {10.1016/j.chom.2025.05.011},
pmid = {40505617},
issn = {1934-6069},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Neoplasms/prevention &amp; control/therapy/microbiology/diet therapy ; *Precision Medicine/methods ; *Artificial Intelligence ; Diet ; },
abstract = {The gut microbiome plays a pivotal role in human health, particularly in cancer prevention and treatment. Diet can significantly influence microbiome composition, but individual variability complicates intervention outcomes. We review the microbiome's influence on cancer development and therapy outcomes and evaluate dietary strategies that modulate microbial composition and metabolites. To address these complexities, we propose the digital gut twin: an artificial intelligence (AI)-driven, dynamically updated simulation that integrates nutrient databases, multi-omic microbiome profiles, host genomics, and clinical data to predict personalized responses to dietary interventions. While significant data and regulatory challenges exist that currently limit clinical implementation, emerging solutions-including pre-trained microbiome models, mechanistic simulators, automated knowledge graphs, and privacy-preserving training-provide a promising pathway toward establishing personalized diet-microbiome modulation as a core component of precision oncology.},
}
@article {pmid40505616,
year = {2025},
author = {Shenhav, L and Azad, MB and Silverman, MA},
title = {Human milk as a microbial pacemaker.},
journal = {Cell host &amp; microbe},
volume = {33},
number = {6},
pages = {762-765},
doi = {10.1016/j.chom.2025.05.018},
pmid = {40505616},
issn = {1934-6069},
mesh = {Humans ; *Milk, Human/microbiology ; *Gastrointestinal Microbiome/physiology ; Infant ; Weaning ; Child ; Female ; },
abstract = {A Nature Medicine paper by Sawhney et al.[1] presents a strain-resolved analysis of the gut microbiome from infancy through eight years of age, identifying weaning as an evolutionary trigger for microbial adaptation. Their findings refine the timeline of microbiome development and highlight human milk as a pacemaker of microbial succession.},
}
@article {pmid40505513,
year = {2025},
author = {Subramanian, M and Thaiss, CA},
title = {Microbial regulation of interoception.},
journal = {Current opinion in neurobiology},
volume = {93},
number = {},
pages = {103064},
doi = {10.1016/j.conb.2025.103064},
pmid = {40505513},
issn = {1873-6882},
abstract = {Interoceptive pathways communicate between the body and the brain to coordinate behavioral responses to changes in the internal milieu. An important contributor to the internal milieu of the body is the gastrointestinal microbiome. Here, we conceptualize the role of the microbiome and microbiome-derived metabolites in interoceptive processes that enable homeostasis maintenance. We highlight four key features that make the microbiome a valuable sensory source for interoceptive processes: its capacity to engage canonical sensory pathways, dynamic responsiveness to environmental perturbations, diurnal oscillations aligned with host circadian rhythms, and the selective gating of sensory information through the intestinal barrier. We further explore how microbiome-derived sensory information contributes to homeostasis, imparts valence to events and cues, and serves as a substrate for memory. Collectively, we present a framework for understanding interoceptive dysfunction through the lens of microbiome-host interactions.},
}
@article {pmid40504882,
year = {2025},
author = {Combrink, L and Spaan, JM and Perret, A and Maehara, T and Hyun, B and Parker, D and Johns, JL and Blouin, MS and Magnusson, K and Steinauer, ML},
title = {Does schistosome infection affect behavior through the gut-brain axis?.},
journal = {PLoS neglected tropical diseases},
volume = {19},
number = {6},
pages = {e0013088},
doi = {10.1371/journal.pntd.0013088},
pmid = {40504882},
issn = {1935-2735},
abstract = {Parasitic helminths infect over 2 billion people, primarily those living in poverty. Helminth infections typically establish in early childhood and persist through critical periods of growth and development, leading to cognitive deficits and/or behavioral changes. These deficits could result from the helminths themselves or due to dysbiosis of the gut microbiota and its influence on the gut-brain axis. Using two cohorts of 3-week-old female mice, we measured levels of anxiety, fear, compulsion, spatial learning, and spatial memory, between schistosome-infected and sham-exposed mice. Additionally, we compared their fecal microbiomes using 16S rRNA gene sequencing at two time points during the chronic stage of infection. Schistosome-infected mice showed higher levels of anxiety in the open field test, reduced spatial learning in the Morris water maze task, and enhanced memory retention in the novel object task. All mice performed equally on the marble bury task. Each cohort started with unique microbiota which showed marked changes in the beta diversity of their microbiota after exposure. In both cohorts, at 7- weeks post exposure, infected mice had more Alistipes sp. and Bacteroides thetaiotaomicron and less Turicibacter sp. and Ligilactobacillus sp. than uninfected mice. At 10 weeks, infected mice had more Alistipes sp. and fewer Muribaculaceae sp. Interestingly, taxon shifts in infected mice were those typically associated with protective effects on liver disease and IL-10 gut conditions, suggesting a possible protective role of the shifted microbiome. Our analyses did not indicate associations between behavioral measures and microbiome composition; however, this could be due to the strong impact of infection on the microbiome composition. Findings here uncover behavioral and cognitive impacts of schistosome infection and shed light on the complex interplay between schistosome infection, behavioral changes, and host microbiome composition, which could ultimately support future global health efforts.},
}
@article {pmid40504797,
year = {2025},
author = {Perraud, Q and Sperandio, V},
title = {Enterohemorrhagic E. coli (EHEC) and the microbiome.},
journal = {PLoS pathogens},
volume = {21},
number = {6},
pages = {e1013224},
pmid = {40504797},
issn = {1553-7374},
}
@article {pmid40504562,
year = {2025},
author = {Soleimani, RA and Milani, PG and Khani, N and Homayouni-Rad, A},
title = {The Overlooked Hazard: Clostridioides difficile in Preterm Infants and Immature Immune Systems-Harnessing Postbiotics for Safer Therapeutic Strategies.},
journal = {Letters in applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/lambio/ovaf083},
pmid = {40504562},
issn = {1472-765X},
abstract = {Clostridioides difficile is a potentially harmful bacterium that can affect preterm infants more seriously than full-term infants, largely due to their immature immune systems and underdeveloped gut microbiota. Although colonization with C. difficile is often harmless in healthy babies, preterm infants are more likely to develop infections, which can lead to serious health problems. This review looks at how an immature immune system and an imbalanced gut microbiome increase the risk of C. difficile infection (CDI) in early life. To reduce this risk, researchers are exploring postbiotics-non-living bacterial products or byproducts-as a safer alternative to traditional treatments like antibiotics. Postbiotics can help by strengthening the gut barrier, reducing inflammation, and supporting the growth of beneficial bacteria. They are also considered safe for use in vulnerable populations, including infants. This review discusses the types of postbiotics, their functions, and how they may help prevent or manage CDI. It also highlights their potential for use in infant formula as a preventative strategy. Overall, postbiotics may offer a promising new way to protect preterm infants from C. difficile and support healthier immune and gut development.},
}
@article {pmid40504523,
year = {2025},
author = {Stinson, LF and Geddes, DT},
title = {Typical skin and oral bacterial species present in human milk are not the result of contamination during the sampling process.},
journal = {Letters in applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/lambio/ovaf084},
pmid = {40504523},
issn = {1472-765X},
abstract = {Human milk has a low microbial biomass with a microbiome dominated by typical skin and oral taxa, raising concerns about contamination during sample collection. However, to date, no study has directly compared samples collected with and without aseptic technique, leaving questions related to potential contamination within the field. To address this, we compared the microbiota of hand-expressed milk samples collected from 23 mothers before and after cleansing of the hands and breast. Metataxonomic analysis showed that taxonomic profiles were largely unaffected by cleansing, with only Rothia mucilaginosa significantly more abundant in non-aseptically collected samples (P = 0.007). Although aseptically and non-aseptically collected samples were taxonomically similar, there was a higher level of bacterial richness (P = 0.003) and evenness (Shannon diversity, P = 0.0002) in non-aseptically collected samples, suggesting that multiple low-abundance taxa are introduced via skin contamination. These findings support the use of aseptic collection methods to minimise external contamination and accurately assess milk microbial diversity. Importantly, they also suggest that common skin and oral taxa detected in human milk are likely true members of the mammary microbiome.},
}
@article {pmid40504492,
year = {2025},
author = {Rosamond, KM and Esser, HJ and Assink, RB and Jaramillo-Ortiz, L and Rowe, M and Kirke, EC and Matson, KD},
title = {Host-microbiome interactions as moderators of host quality and biodiversity-disease relationships.},
journal = {Integrative and comparative biology},
volume = {},
number = {},
pages = {},
doi = {10.1093/icb/icaf091},
pmid = {40504492},
issn = {1557-7023},
abstract = {Biodiversity-disease studies typically focus on how changes in community composition (e.g., species richness, abundance, and functional or phylogenetic metrics of biodiversity) affect disease risk. In doing so, these studies tend to overlook intraspecific variation in the organisms comprising the community. Yet, intraspecific variation, which occurs to varying degrees both within and between communities, could also modulate biodiversity-disease relationships. One important driver of intraspecific variation is the microbiome. By directly and indirectly influencing health and susceptibility to infection and disease, microbiomes are integral to organismal functioning. Thus, the microbiome plays a crucial role in host quality. We define host quality as an integration of host traits related to parasite exposure, establishment, growth, and infectivity, which ultimately shape parasite fitness. The microbiome can impact host quality via a variety of mechanisms including host size and developmental stage, immune function, reproduction, nutrient acquisition, and behavior. However, the potential for such microbiome-driven changes in host quality to trigger cascading effects on community-level processes, specifically by altering parasite transmission dynamics and community competence, has not been well explored. Here, we examine and illustrate a pathway by which the microbiome may influence variation in organismal biology (i.e., host quality) of hosts in communities. Furthermore, we consider how major anthropogenic drivers of microbiome shifts, such as climate change, pollution, land use change, and domestication, might influence this pathway and thereby alter outcomes. Future studies bridging microbiome and disease ecology research will provide opportunities to unify these concepts across scales and between the plant and animal domains. To date, most microbiome research has focused on humans, crops, and laboratory animals. However, to better understand the potential for knock-on ecological effects of microbiomes, more attention must be paid to the microbiomes of wild plants and animals. Ultimately, more experimental and theoretical data are needed to clarify how the microbiome impacts host quality and disease dynamics, as well as how anthropogenic factors continuously reshape these relationships.},
}
@article {pmid40504464,
year = {2025},
author = {Chen, YR and Chen, LD and Zheng, LJ},
title = {Exploring the trimethylamine-degrading genes in the human gut microbiome.},
journal = {AMB Express},
volume = {15},
number = {1},
pages = {91},
pmid = {40504464},
issn = {2191-0855},
support = {32100082//National Natural Science Foundation of China/ ; 2023A03J0696//Science and Technology Program of Guangzhou/ ; },
abstract = {Trimethylamine (TMA), produced by gut microbes, is a precursor to a risk factor for cardiovascular diseases. Currently, TMA-degrading bacteria in the human gut have rarely been studied. This study combined TMA-enriched cultures (from 104 young male stool samples) with metagenomic profiling to identify key microbial players of TMA degradation. The results showed that the contribution of Enterococcus to methane metabolism was significantly higher in TMA-enriched culture samples. The 68.58% up-regulation of dmd-tmd (dimethylamine/trimethylamine dehydrogenase) in the TMA-enriched group indicated that the anaerobic dehydrogenase pathway participated in TMA metabolism. Notably, we first identified that taxa containing dmd-tmd belonged to Christensenella timonensis. The up-regulation of genes involved in methanogenesis (M00563) as well as the significant enrichment of M00563 (Reporter Score = 2.223) indicated that the methanogenesis pathway may play a role. We constructed gene databases for genes involved in the anaerobic dehydrogenase pathway (1526 sequences for dmd-tmd, 1319 sequences for mauA, and 326 sequences for mauB, respectively) and the aerobic oxidation pathway (2146 sequences for tmm, 1445 sequences for tdm, and 1519 sequences for dmm, respectively) based on genomes from the Integrated Microbial Genome (IMG) database, most of which belong to Pseudomonadota. Screening gut metagenomes with these databases revealed low sequence identity (< 70%), possibly because of the underrepresentation of gut-specific genomes from IMG. This study links Christensenella timonensis to TMA degradation, providing potential targets for microbiota modulation and a gene-centric framework to advance the characterization of gut microbial TMA metabolism.},
}
@article {pmid40504322,
year = {2025},
author = {Pachauri, A and Sharma, S},
title = {Unravelling the gut-skin axis: the role of gut microbiota in pathogenesis and management of psoriasis.},
journal = {Inflammopharmacology},
volume = {},
number = {},
pages = {},
pmid = {40504322},
issn = {1568-5608},
abstract = {Psoriasis is a chronic, multifactorial, inflammatory skin disease, increasingly recognized as a systemic disorder influenced by the gut-skin axis, which is a dynamic bidirectional communication between intestinal microbiome and cutaneous immune response. This narrative review explores the understanding of the gut-skin axis with the latest evidence on how gut dysbiosis occurs in psoriasis, characterized by reduced microbial diversity and its shifts, and how it contributes to pathogenesis and exacerbation of psoriasis. Notably, recent scientific literature evidence suggests that the alteration of gut microbiome in psoriasis includes a decreased level of beneficial species like Faecalibacterium prausnitzii and a rise in the level of proinflammatory bacterial species like Prevotella copri. Mechanistic insights reveal that gut-derived metabolites, impaired barrier functions, and immune signaling, particularly involving IL-23 and Th17 cells, play a pivotal role in this axis, linking intestinal health to cutaneous manifestations. Both animal and human trials underscore the therapeutic potential of interventions targeting the gut microbiota, including prebiotics, probiotics, dietary modifications, and FMT, demonstrating some promising but variable effects on disease severity and systemic inflammation. Despite these advances, translating the gut-skin axis into clinical practice presents a notable challenge due to limited scientific evidence, a lack of standardised microbiome profiling, and the absence of universally accepted biomarkers to monitor and stratify therapeutic outcomes. These limitations hinder the development of personalised care approaches and the integration of the gut-skin axis as a promising frontier in many autoimmune diseases, where the gut-skin axis and the intestinal microbiome play a crucial role.},
}
@article {pmid40504059,
year = {2025},
author = {Daana, S and Rokach, Y and Abedat, S and Nachman, D and Mohsen, H and Karram, S and Zandberg, Y and Tzach-Nachman, R and Cohen, J and Amir, O and Houri-Haddad, Y and Rabea Asleh, },
title = {Periodontitis Accelerates Progression of Heart Failure With Preserved Ejection Fraction in Mice.},
journal = {JACC. Basic to translational science},
volume = {},
number = {},
pages = {101270},
doi = {10.1016/j.jacbts.2025.03.002},
pmid = {40504059},
issn = {2452-302X},
abstract = {Chronic low-grade inflammation and nitric oxide (NO) depletion are important contributors to heart failure with preserved ejection fraction (HFpEF) pathophysiology. Periodontitis (PD) is a common inflammatory disease implicated in dysregulation of NO hemostasis. Epidemiological studies have shown an association between PD and increased risk of cardiovascular disease, including heart failure. However, a causative relationship between the 2 diseases has not yet been proven. In this study, we sought to investigate the direct effect of PD induction on HFpEF progression in a mouse model. Induction of PD in HFpEF mice resulted in significant oral microbial dysbiosis, accelerated progression of diastolic dysfunction by echocardiography, and increased myocardial inflammation and fibrosis. These deleterious effects seen with PD were shown to be mediated by increased systemic blood pressure, increased systemic inflammation, and NO depletion. Our study provides evidence of potential mechanistic links between PD and HFpEF progression and suggests PD as a new therapeutic target for HFpEF.},
}
@article {pmid40503970,
year = {2025},
author = {Erkert, L and Kabisch, M and Gamez-Belmonte, R and Gonzalez-Acera, M and Patankar, JV and Schödel, L and Hofmann, K and Wagner, Y and Plattner, C and Spath, EM and Distler, U and Tenzer, S and , and Neufert, C and Neurath, MF and Becker, C},
title = {Pharmacological inhibitors of the gamma-secretase enzyme complex disrupt epithelial cell function triggering colitis in mice.},
journal = {Journal of Crohn's &amp; colitis},
volume = {},
number = {},
pages = {},
doi = {10.1093/ecco-jcc/jjaf096},
pmid = {40503970},
issn = {1876-4479},
abstract = {BACKGROUND AND AIMS: Inhibiting γ-secretase mediated Notch signaling has been explored as a potential treatment for Alzheimer's disease and cancer. However, clinical trials have revealed that this approach can lead to side effects, such as gut inflammation. Notch signaling has been shown to be a key mediator of intestinal epithelial homeostasis. We aimed to investigate the molecular mechanisms of γ-secretase inhibition-associated colitis.<br><br>METHODS: Mice and small intestinal organoids were treated with &#x3b3;-secretase inhibitors and analyzed for IEC differentiation and inflammation-associated markers using different molecular and histological approaches, along with transcriptomic and proteomic analyses. To evaluate the role of the microbiome in colitis development, mice undergoing pharmacological &#x3b3;-secretase inhibition were treated with antibiotics. Additionally, inflammatory bowel disease (IBD) patient samples and control samples were analyzed to assess the expression of Notch signaling pathway components in IECs.<br><br>RESULTS: This study shows that pharmacological &#x3b3;-secretase inhibition induces inflammation in both the small and large intestine of mice, a phenotype that could be rescued upon microbiota depletion. Inhibiting the &#x3b3;-secretase induced structural disruption of the epithelium and inflammatory cytokine release. On a molecular level, epithelial organoids exhibited disrupted IEC differentiation and impaired proliferation, associated with defective Notch signaling. Finally, analysis of IBD patients revealed deregulation of Notch pathway components within IECs.<br><br>CONCLUSIONS: In conclusion, systemic use of &#x3b3;-secretase inhibitors disrupts epithelial cell function by impairing IEC differentiation and triggering gut inflammation in mice. These findings should be considered when designing future therapeutic interventions involving &#x3b3;-secretase inhibitors.},
}
@article {pmid40503883,
year = {2025},
author = {Pearson-Lund, AS and Williams, SD and Eaton, KR and Clark, AS and Holloway, NH and Ewen, KA and Muller, EM},
title = {Evaluating the effect of amoxicillin treatment on the microbiome of Orbicella faveolata with Caribbean yellow band disease.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0240724},
doi = {10.1128/aem.02407-24},
pmid = {40503883},
issn = {1098-5336},
abstract = {Host microbiomes play a key role in coral disease dynamics; thus, it is essential to characterize microbial communities of diseased tissues and identify how they are altered by potential treatments, especially as coral reef populations continue to decline globally. The abundance of Orbicella faveolata, a major reef-building Caribbean coral species, has significantly declined due to several stressors, including infectious disease. Caribbean yellow band disease (CYBD) often results in complete colony mortality. We applied an amoxicillin-laced Base2B ointment to CYBD lesion areas on O. faveolata within Buck Island Reef National Monument, St. Croix, USVI, trying to halt disease progression. Another CYBD lesion area on the same colony served as a paired untreated control. Microbiomes of the apparently healthy tissue adjacent to the treatment were characterized pretreatment and 2 days post-treatment, along with the paired untreated CYBD controls and nearby healthy colonies. Both microbiomes of untreated CYBD lesions and apparently healthy tissue on CYBD colonies had a significantly higher alpha diversity and significantly differed from those of nearby healthy colonies, suggesting potential systemic effects of CYBD. Amoxicillin treatment significantly changed the microbial community composition of tissues adjacent to the treatment site. The relative abundance of the bacterial family Vibrionaceae, a putative pathogen for CYBD and often associated with other coral diseases, was enriched post-treatment. However, the lesion progression rates of treated and untreated lesion areas were similar. Our results suggest that amoxicillin may disrupt the microbiome of adjacent tissue on O. faveolata, allowing for opportunistic Vibrio sp. bacteria to colonize, and may not be an effective treatment for CYBD.IMPORTANCEOrbicella faveolata, a primary reef-building coral species in the Caribbean, has been severely impacted by Caribbean yellow band disease. This disease causes tissue loss, which often culminates in the complete loss of the colony since recovery is rarely observed. The present study is significant because the development of an effective long-term treatment for Caribbean yellow band disease and understanding how the microbial partners contribute to pathogenesis are essential for conserving Caribbean coral reefs. While treatment with amoxicillin was not effective, our study uncovered valuable insights into the microbial composition of Caribbean yellow band disease in O. faveolata. In addition, this study highlights the possible unintended negative effects of treatment with amoxicillin and casts doubt on Vibrionaceae as the culprit of this disease.},
}
@article {pmid40503824,
year = {2025},
author = {Snelling, TJ and Condren, M and Huntington, JA and Warren, HE and Taylor-Pickard, J and Sinclair, LA},
title = {The rumen microbiota and metabolism of dairy cows are affected by the dietary rate of inclusion of Yucca schidigera extract.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0064125},
doi = {10.1128/spectrum.00641-25},
pmid = {40503824},
issn = {2165-0497},
abstract = {Natural plant compounds can be used to supplement livestock diets, improving feed efficiency, production, and health, while also reducing environmental impact. In the present study, a Yucca schidigera (Mohave Yucca) extract was added at four rates of inclusion (ROI) of 0, 5, 15, or 30 g/day to a ryegrass and maize silage-based diet and fed to dairy cows in a 4 × 4 Latin square experimental design. Each period was 28 days in duration, with sampling undertaken during the final week of each period. Solid phase digesta (SPD) and liquid phase digesta (LPD) samples were collected via a rumen cannula and analyzed for volatile fatty acids (VFAs), ammonia N, and microbiome using 16S rRNA gene sequencing. Total fecal and urine collection was undertaken over a 3-day period. Rumen microbial diversity was not affected by ROI (LPD: P = 0.180; SPD: P = 0.059). However, discriminant analysis found a decrease in Methanobrevibacter millerae (linear discriminant analysis, LDA = 2.15) and an increase in an unclassified species of Proteobacteria (LDA = 2.10) associated with ROI. Univariate analysis also revealed differential abundance of operational taxonomic units classified as Prevotellaceae and Fibrobacteraceae by ROI (P < 0.05). Maximum rumen ammonia N concentration decreased linearly from 228 to 109 mg/L with ROI (P = 0.044). Rumen VFA concentration was unaffected with the exception of propionate, which showed a linear increase with ROI (P = 0.010). The diurnal rumen pH range (maximum-minimum) also decreased with ROI (P = 0.004). Dry matter intake and milk yield were not affected (P > 0.05) by ROI; however, there was a linear increase in milk fat content from 38.9 to 42.0 g/kg with ROI (P < 0.05).IMPORTANCEDomestic livestock such as dairy cows are inefficient utilizers of dietary nitrogen. This increases feed costs and reduces animal production efficiency. Excreted nitrogenous compounds are also an environmental hazard, such as when they enter water courses as nitrate or are lost to the atmosphere as ammonia or nitrous oxide. Dietary protein is degraded in the rumen via the activity of the microbial population, mainly into ammonia, which may then be utilized by the microbial population to synthesize microbial protein or absorbed into the blood and potentially excreted. Manipulation of the diet or altering the microbial population may increase the utilization of dietary protein, increasing animal performance, decreasing feed costs, and reducing the environmental impact of milk production. This study examines the effect of Yucca schidigera extract on the rumen microbiome and nitrogen utilization in dairy cows.},
}
@article {pmid40503236,
year = {2025},
author = {Bartosik, T and Pjevac, P and Séneca, J and Morgenstern, C and Arnoldner, T and Gangl, K and Sinz, C and Campion, NJ and Tu, A and Stanek, V and Bangert, C and Schneider, S and Eckl-Dorna, J},
title = {Dupilumab treatment has no effect on the nasal microbiome in patients with NSAID-exacerbated respiratory disease: a longitudinal pilot study.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1508500},
pmid = {40503236},
issn = {1664-3224},
mesh = {Humans ; *Antibodies, Monoclonal, Humanized/therapeutic use ; Male ; Middle Aged ; *Microbiota/drug effects ; Pilot Projects ; Female ; Longitudinal Studies ; Aged ; Adult ; *Anti-Inflammatory Agents, Non-Steroidal/adverse effects ; Quality of Life ; RNA, Ribosomal, 16S/genetics ; Nasal Polyps/drug therapy/microbiology ; Treatment Outcome ; },
abstract = {BACKGROUND: Non-steroidal anti-inflammatory drugs-exacerbated respiratory disease (N-ERD) affects up to 10% of patients suffering from nasal polyps and has a severe impact on quality of life. Dupilumab, a monoclonal antibody targeting the IL-4 receptor α chain, leads to symptom relief and reduction in nasal type 2 mediator levels. Here, we investigated the impact of dupilumab treatment on the composition and diversity of the nasal microbiome.<br><br>METHODOLOGY: Nasal microbiome was analyzed by 16s rRNA gene amplicon sequencing in 28 patients before, 4, 12, and 24 weeks after dupilumab therapy.<br><br>RESULTS: After stringent decontamination and removal of patients whose samples contained less than 500 reads at &#x2265; one of the four visits, full datasets from 8 out of 28 patients remained for downstream analysis of microbiome data. All 8 patients showed significant reduction in TPS (total polyp score; p=0.0078) and an improvement in SNOT-22 (Sino-nasal outcome test-22, a quality of life questionnaire; p=0.0781) after dupilumab therapy. During 24 weeks of dupilumab therapy, there were no major changes in microbiome diversity or composition observed (Shannon index: V1-V4:p-adj=0.25, Chao 1 Index V1-V4:p-adj=0.31), and only 2 out of 8 patients showed a decrease in staphylococci abundance.<br><br>CONCLUSIONS: More than 70% of the samples did not pass quality control, this warrants further refinement of nasal microbiome sampling techniques and mandatory guidelines on stringent quality control for analysis of this low biomass data in future. Furthermore, dupilumab did not have an impact on microbiome diversity or composition.},
}
@article {pmid40502641,
year = {2025},
author = {Lu, L and Li, Y and Su, H and Ren, S and Liu, Y and Shao, G and Liu, W and Ji, G and Xu, H},
title = {Huangqin decoction inhibits colorectal inflammatory cancer transformation by improving gut microbiome-mediated metabolic dysfunction.},
journal = {Journal of pharmaceutical analysis},
volume = {15},
number = {5},
pages = {101138},
pmid = {40502641},
issn = {2214-0883},
abstract = {Colorectal inflammatory cancer transformation poses a major risk to patients with colitis. Patients with chronic intestinal inflammation have an approximately 2-3 folds increased risk of developing colorectal cancer (CRC). Unfortunately, there is currently no effective intervention available. Huangqin decoction (HQD), a well-known traditional Chinese medicine (TCM) formula, is frequently clinically prescribed for treating patients with colitis, and its active ingredients have effective antitumour efficacy. Nonetheless, the mechanism of HQD-mediated prevention of colorectal inflammatory cancer transformation remains unclear. A strategy integrating metagenomic, lipidomic, and messenger RNA (mRNA) sequencing analysis was used to investigate the regulatory effects of HQD on the gut microbiome, metabolism and potential mechanisms involved in colorectal inflammatory cancer transformation. Our study revealed that HQD suppressed colorectal inflammatory cancer transformation, which was associated with enhanced intestinal barrier function, decreased the inflammatory response, and regulation of the gut microbiome. Notably, cohousing experiments revealed that the transfer of the gut microbiome from HQD-treated mice largely inhibited the pathological transformation of colitis. Moreover, gut microbiome transfer from HQD-treated mice primarily resulted in the altered regulation of fatty acid metabolism, especially the remodeling of arachidonic acid metabolism, which was associated with the amelioration of pathological transformation. Arachidonic acid metabolism and the key metabolic enzyme arachidonic acid 12-lipoxygenase (ALOX12) were affected by HQD treatment, and no obvious protective effect of HQD was observed in Alox 12 [-/-] mice, which revealed that ALOX12 was a critical mediator of HQD protection against colorectal inflammatory cancer transformation. In summary, multiple omics analyses were applied to produce valuable data and theoretical support for the application of HQD as a promising intervention for the transformation of inflammatory CRC.},
}
@article {pmid40502530,
year = {2025},
author = {Smith, KB and Murack, M and Butcher, J and Hinterberger, A and Stintzi, A and Liang, J and Tata, DA and Ismail, N},
title = {Modulating effects of environmental enrichment on stress-induced changes in the gut microbiome.},
journal = {Brain, behavior, &amp; immunity - health},
volume = {46},
number = {},
pages = {101023},
pmid = {40502530},
issn = {2666-3546},
abstract = {Environmental enrichment (EE) involves adding non-standard stimuli, such as running wheels, mazes, and cage mates, to standard animal living conditions to facilitate physical activity, cognitive stimulation, and socialization. Interestingly, exposure to EE can modulate stress and immune responses. However, it is unclear whether housing environments can modulate the effects of stress on the gut microbiome. This study aimed to explore the effects of three different housing conditions-deprived (DH), social (SH), and enriched (EE)-on the central and peripheral immune responses, the HPA axis, and the gut microbiome in 180 male and female mice. Mice were housed in either the DH, SH, or EE condition for 3 weeks starting from post-natal day 21. At 6 weeks of age, during the pubertal stress-sensitive period, mice were treated with either saline or lipopolysaccharide (LPS), a bacterial endotoxin. Eight hours post-treatment, mice were euthanized, and brain, fecal samples, and trunk blood were collected to examine peripheral and central cytokine levels, glucocorticoid receptor (GR) and mineralocorticoid receptor (MR) expressions, along with diversity in the gut microbiome. Contrary to expectations, EE and SH mice showed higher plasma concentrations of TNFα, IL6, and IL12 cytokines than DH mice following LPS treatment, with male mice exhibiting significantly higher levels of these cytokines than their female counterparts. Moreover, EE mice exhibited significantly greater hypothalamic and hippocampal expressions of GR and MR compared to DH mice. The gut microbiome analysis revealed sex-specific beta diversity patterns post-LPS treatment, with male EE and SH mice displaying a more diverse microbiome compared to female counterparts. These findings enhance our understanding of how housing conditions influence the acute immune and stress responses and modulate their effects on the gut microbiome during puberty.},
}
@article {pmid40502457,
year = {2025},
author = {Otsuka, T and Ishizaki, Y and Yoshimoto, J and Takamori, K and Watanabe, S},
title = {Searching for bacteria within acute cholecystitis using next-generation sequencers.},
journal = {Surgery open science},
volume = {26},
number = {},
pages = {113-118},
pmid = {40502457},
issn = {2589-8450},
abstract = {INTRODUCTION: A biliary microbiome comprising flora within normal gallbladders was recently uncovered through analyses targeting the bacterial 16S ribosomal RNA (16S rRNA) gene, despite the gallbladder previously being regarded as a sterile environment. In the present study, we subjected bile samples from patients with acute cholecystitis to gene analysis targeting bacterial flora.<br><br>METHODS: We targeted patients diagnosed as having Grade I or Grade II acute cholecystitis (in accordance with the Tokyo Guidelines 2018 established by the Japanese Society of Hepato-Biliary-Pancreatic Surgery) who underwent laparoscopic cholecystectomy within 24&#xa0;h of diagnosis at Juntendo University Urayasu Hospital between July 2021 and January 2024 for evaluation. We drew bile sample from the gallbladder of each patient to confirm the presence of biliary bacterial flora, using both standard bacteriology (culture test) and 16S rRNA gene sequence.<br><br>RESULTS: Of the 29 samples, 15 yielded cultures positive for bacterial flora, and gene analysis revealed the presence of bacterial biliary flora in all 14 samples that had tested negative in standard bacteriology. Considering the bacterial flora of a normal gallbladder without lesions as "normal flora," bacteria other than normal flora-Propionibacterium spp., Coprococcus spp., Prevotella spp., Sediminibacterium spp., and Collinesella spp.-were detected in 25 of the 29 cases (86&#xa0;%).<br><br>CONCLUSIONS: Bacteria not detected in non-inflammatory gallbladders such as Propiobacterium spp., Coprococcus spp., Prevotella spp., Sediminibacterium spp., and Collinesella spp. may play a role in the mechanism underlying development of acute cholecystitis.},
}
@article {pmid40502320,
year = {2024},
author = {Kim, N},
title = {[The Relationship of Dysbiosis of Duodenal Microbiome and Functional Dyspepsia].},
journal = {The Korean journal of helicobacter and upper gastrointestinal research},
volume = {24},
number = {4},
pages = {327-338},
pmid = {40502320},
issn = {2671-826X},
abstract = {Functional dyspepsia (FD) is a common gastrointestinal disorder characterized by chronic or recurrent epigastric pain or discomfort and postprandial fullness, without a definite organic cause. Despite the importance of FD in terms of decreased quality of life and recurrence, treatment modalities have been unsatisfactory, mainly because of their complex and heterogeneous nature. A link between microbiome dysbiosis and low-grade inflammation, along with mucosal barrier disruption of the duodenal mucosa, has been suggested and may be a potential target for FD treatment. This link supports the gut-brain (overactive visceral signaling and pain modulation) and the brain-gut (abnormal central processing) axes in FD. A definite increase in Streptococcus and a reduced abundance of Prevotella, Veillonella, and Actinomyces have also been observed. In addition, bacterial overgrowth is frequently observed in the small intestine, and rifaximin treatment improves the symptoms of FD, especially in women. This evidence highlights the importance of bacterial ecology in the development of FD symptoms. However, further research is necessary to prove the causal relationship between duodenal mucosal microbiota dysbiosis and FD.},
}
@article {pmid40502184,
year = {2025},
author = {Verna, G and De Santis, S and Islam, B and Sommella, EM and Licastro, D and Zhang, L and De Almeida Celio, F and Merciai, F and Caponigro, V and Campiglia, P and Pizarro, TT and Chieppa, M and Cominelli, F},
title = {A missense mutation in Muc2 promotes gut microbiome- and metabolome-dependent colitis-associated tumorigenesis.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.05.31.657160},
pmid = {40502184},
issn = {2692-8205},
abstract = {UNLABELLED: Colitis-associated cancer (CAC) arises from a complex interplay between host and environmental factors, including the gut microbiome. Since ulcerative colitis (UC), a significant risk factor for CAC, is rising in prevalence worldwide, an integrative approach is essential to identify potential triggers linking inflammation to cancer. In the present study, we investigated the role of the gut microbiome using Winnie mice, a UC-like model with a relevant missense mutation in the Muc2 gene. Upon transfer from a conventional (CONV) to a specific-pathogen-free (SPF) facility, Winnie mice exhibited a more severe colitis phenotype, and notably, spontaneous CAC as early as four weeks of age, which progressively worsened over time. In contrast, CONV Winnie developed only mild colitis but with no overt signs of tumorigenesis. Notably, when rederived into germ-free (GF) conditions, SPF Winnie mice were protected from colitis or colon tumor development, indicating an essential role for the gut microbiome in the initiation and progression of CAC in these mice. Using shotgun metagenomics, metabolomics, and lipidomics, we identified a distinct pro-inflammatory microbial and metabolic signature that potentially drives the transition from colitis to CAC. Fecal microbiota transplantation (FMT), using either SPF Winnie or WT (Bl/6) donors into GF Winnie recipients, demonstrated that while colitis developed regardless of donor, only FMT from SPF Winnie donors resulted in CAC, revealing a microbiota-driven, host-specific susceptibility to tumorigenesis in Winnie mice. Our studies present a novel and relevant model of CAC, providing further evidence that the microbiome plays a key role in the pathogenesis of CAC, thereby challenging the concept of colon cancer as a strictly non-transmissible disease.<br><br>LAY SUMMARY: This study reveals a distinct metagenomic, metabolomic, and lipidomic profile associated with tumorigenesis in a murine model of ulcerative colitis, highlighting the risks of specific intestinal dysbiosis in genetically predisposed subjects.<br><br>WHAT YOU NEED TO KNOW: Background and context: Colitis-associated colorectal cancer arises from complex host-environment interactions, including gut microbiome influences, driving chronic inflammation, with the intestinal lumen environment remaining a largely unexplored potential risk factor in cancer development.New findings: Winnie mice in specific pathogen-free conditions developed severe colitis, and a novel juvenile colon dysplasia and cancer, with gut microbiome changes driving colitis-associated cancer initiation and progression.Limitations: We identified a pro-inflammatory microbial/metabolic signature promoting colitis-to-CAC transition in Winnie mice, with FMT confirming microbiota-driven tumor susceptibility. However, further research is needed to pinpoint the key bacteria-metabolite-lipid combination driving CAC.Clinical research relevance: This newly characterized microbiota-metabolome-based model of CAC, challenges the dogma of cancer as a non-transmittable disease, providing a foundation for developing microbiota-based strategies for CAC prevention and treatment.Basic research relevance: Unlike genetic or chemically induced models, the Winnie mouse model uniquely serves as a dual model for spontaneous colitis and juvenile CAC, offering a fast, 100% penetrant phenotype that enhances reliability, accelerates research, and provides valuable insights into IBD and CAC.},
}
@article {pmid40502178,
year = {2025},
author = {Tristao Santini, A and Cerqueira, AES and Moran, NA and Resende, HC and Santana, WC and de Paula, SO and da Silva, CC},
title = {Gut microbiota of Brazilian Melipona stingless bees: dominant members and their localization in different gut regions.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.06.03.657762},
pmid = {40502178},
issn = {2692-8205},
abstract = {The gut microbiome of eusocial corbiculate bees, which include honeybees, bumblebees, and stingless bees, consists of anciently associated, host-specific bacteria that are vital for bee health. Two symbionts, Snodgrassella and Gilliamella , are ubiquitous in honeybees and bumblebees. However, their presence varies in the stingless bee clade (Meliponini), a group with pantropical distribution. They are absent or rare in the diverse genus Melipona , indicating a shift in microbiota composition in this lineage. To identify the main members of the Melipona microbiota, we combined newly collected and published data from field-collected individuals of several species. Additionally, we identified the localization of the dominant microbiota members within the gut regions of Melipona quadrifasciata anthidioides . The dominant microbiota of Melipona species includes members of the genera Bifidobacterium, Lactobacillus, Apilactobacillus, Floricoccus , and Bombella . Among these, Apilactobacillus and Bombella dominate in the crop, whereas Apilactobacillus and other members of the Lactobacillaceae dominate the ventriculus. The ileum lacks Snodgrassella or Gilliamella but contains a putative new symbiont close to Floricoccus , as well as strains of Bifidobacterium , Lactobacillaceae (including Apilactobacillus), and Bombella . The rectum is dominated by Bifidobacterium and Lactobacillus . In summary, the Melipona microbiota is compositionally distinct but shows spatial organization paralleling that of other eusocial corbiculate bees.},
}
@article {pmid40502161,
year = {2025},
author = {Tao, J and Antoine, D and Jalodia, R and Valdes, E and Boyles, SM and Hulme, W and Roy, S},
title = {Single-cell transcriptomics reveals probiotic reversal of neonatal morphine-induced gene disruptions underlying adolescent pain hypersensitivity.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.05.30.657034},
pmid = {40502161},
issn = {2692-8205},
abstract = {Neonatal morphine is commonly administered in the Neonatal Intensive Care Unit (NICU) to manage pain. However, its long-term effects on neurodevelopment of pain pathways, remain a significant concern. The midbrain is a core region that plays a central role in pain processing and opioid-mediated analgesia. Here, we performed single-cell RNA sequencing to study gene expression in 107,427 midbrain single cells from adolescent mice neonatally exposed to either saline, morphine, or morphine with the probiotic Bifidobacterium infantis (B. infantis). We found broad alterations in transcriptomics within neurons, astrocytes, oligodendrocytes, and microglial cells. Analysis of differentially regulated genes revealed down regulation of HOX genes and upregulation of pathways related to neurotransmitter signaling and pain in adolescence that were neonatally treated with morphine. Interestingly, neonatal probiotic supplementation mitigated these morphine-induced alterations on the transcriptome. This study presents the first single-cell RNA sequencing dataset of the adolescent midbrain following neonatal morphine exposure and probiotic intervention. These findings offer new insights into the neurodevelopmental impact of early opioid exposure and highlight the therapeutic potential of microbiome-targeted interventions.},
}
@article {pmid40502158,
year = {2025},
author = {Millington, JW and Lopez, JA and Sajjadian, AM and Scheffler, RJ and DeFelice, BC and Ludington, WB and Good, BH and O'Brien, LE and Huang, KC},
title = {Gut microbe-derived lactic acid optimizes host energy metabolism during starvation.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.05.27.656452},
pmid = {40502158},
issn = {2692-8205},
abstract = {Gut microbes convert dietary compounds into an array of metabolites that can directly provide energy to their host and indirectly impact host metabolism as systemic endocrine signals. Here, we show that gut microbe-derived metabolites can extend Drosophila melanogaster survival during starvation, despite minimal alteration of dietary energy intake. Combining survival assays with mathematical modeling and untargeted metabolomics, we identify a single, dominant mediator of starvation resilience: lactic acid produced by the commensal bacterium Lactiplantibacillus plantarum . We discover that the basis of starvation resilience is not catabolism of lactic acid using lactate dehydrogenase, but rather increased dietary energy yield through lactic acid-driven promotion of oxidative phosphorylation. Our findings emphasize the role of the microbiome as a source of endocrine cues coordinating host metabolism and underscore the potential of microbiome-derived metabolites as therapeutic molecules for manipulating metabolic health and preventing disease.},
}
@article {pmid40502111,
year = {2025},
author = {Villarreal, ES and Marinho, Y and Loya, O and Aboagye, SY and Williams, DL and Sun, J and Erzurum, S and de Jesus Perez, V and Oliveira, SD},
title = {Endothelial c-IAP2 Loss Amplifies P2X7 Receptor-Driven Inflammation and Worsens Infection-Associated Pulmonary Hypertension.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.05.22.655387},
pmid = {40502111},
issn = {2692-8205},
abstract = {Schistosomiasis-associated Pulmonary Hypertension (Sch-PH) is the most common form of group I PH worldwide. Recently, data revealed that the preclinical animal model of Sch-PH exhibited gut and lung microbiome dysbiosis linked to significant endothelial dysfunction and microvascular apoptosis, but the role of pro/anti-apoptosis sensors, such as the inhibitor of apoptosis protein 2 (c-IAP2) and purinergic receptor P2X7 (P2X7R), remained unclear. Using a novel Cdh5cre-ER [T2] ;cIAP1 [-/-] ;cIAP2 [fl/fl] animal model, this study investigated the contribution of endothelial c-IAP2 in this process, revealing P2X7R overexpression as a putative target in the onset of Sch-PH. Pharmacologically, inhibition of P2X7R function confirmed its role in promoting lung endothelial death and disease progression. Moreover, data suggest that microbiome-associated metabolic alterations in Sch-PH seem linked to microvascular endothelial apoptosis driven by ATP/P2X7R overactivation and suppressed c-IAP2 expression. Indeed, genetic ablation of endothelial c-IAP2 expression was sufficient to induce PH-like features in mice, with echocardiography indicating a higher pulmonary acceleration time (PAT), PAT/pulmonary ejection time (PET), and right ventricular free wall thickness after IP/IV-Egg challenge compared to controls. These findings suggest a significant contribution of lung endothelial P2X7R activation and c-IAP2 suppression to Sch-PH pathology, highlighting them as promising novel therapeutic targets for this life-threatening illness.},
}
@article {pmid40502000,
year = {2025},
author = {Mohssen, M and Zayed, AA and Kigerl, KA and Du, J and Smith, GJ and Schwab, JM and Sullivan, MB and Popovich, PG},
title = {The Spinal Cord-Gut Axis Regulates Gut Microbial Homeostasis: Insights from a New Murine Metagenomic Catalog.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.05.27.656368},
pmid = {40502000},
issn = {2692-8205},
abstract = {The spinal cord, a nexus for brain-body crosstalk, controls gut physiology and microbial homeostasis. Here, >6,500 microbial metagenome-assembled genomes were recovered de novo , from male and female C57BL/6 mice gut metagenomes before and up to 6 months after disrupting the "spinal cord-gut axis". This "Mouse B6 Gut Catalog" improved or doubled species- and strain-level representation in other published catalogs. Analyses showed that breaking the spinal cord-gut axis caused persistent microbial changes that varied by sex, spinal lesion level, and time. A key bacterium, Lactobacillus johnsonii , was consistently reduced, and feeding this to mice with a clinically relevant spinal cord injury improved host health. Genome-resolved, community-contextualized metabolic profiling showed that spinal-dependent effects on microbe-encoded carbohydrate metabolism explain the reduction of L. johnsonii . These data improve murine microbiome catalogs and emphasize that mammalian health and gut ecosystem function depend on a functional spinal cord-gut axis.},
}
@article {pmid40501963,
year = {2025},
author = {Chouhan, D and Grossman, AS and Kerns, KA and Stocke, KS and Kim, M and Dong, PT and Kumar, A and Lei, L and Lamont, RJ and McLean, JS and He, X and Bor, B},
title = {Episymbiotic Saccharibacteria suppresses epithelial immunoactivation through Type IV pili and TLR2 dependent endocytosis.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.05.30.656655},
pmid = {40501963},
issn = {2692-8205},
abstract = {Saccharibacteria are episymbionts that require host-bacteria to grow. They are positively associated with inflammatory diseases within the human microbiome, yet their mechanisms for interacting with the human host and contributing to diseases remain unknown. This study investigated interactions between a Saccharibacterium (Nanosynbacter lyticus), its host-bacteria (Schaalia odontolytica), and oral epithelial cells. The host-bacteria induced proinflammatory cytokines in epithelial cells, while Saccharibacteria were immune silent. Remarkably, Saccharibacteria dampened cytokine responses to host-bacteria during coinfection. This effect was driven by Saccharibacteria-induced clustering of TLR2 receptors, a process likely facilitated by type IV, ultimately leading to reduced TLR2-mediated cytokine signalling. High resolution imaging showed that Saccharibacteria were endocytosed by oral epithelial cells, and colocalized with endosome markers, eventually trafficking to lysosomes. Moreover, a subset of the Saccharibacteria survive endocytosis long-term, and retains their capability to reinfect host-bacteria, highlighting a mechanism for persistence in the oral microbiome and a vital role in mammalian immune system modulation.},
}
@article {pmid40501924,
year = {2025},
author = {Huang, K and Zhang, S and Wang, H and Qu, Y and Lu, Y and Roohani, Y and Li, R and Qiu, L and Li, G and Zhang, J and Yin, D and Marwaha, S and Carter, JN and Zhou, X and Wheeler, M and Bernstein, JA and Wang, M and He, P and Zhou, J and Snyder, M and Cong, L and Regev, A and Leskovec, J},
title = {Biomni: A General-Purpose Biomedical AI Agent.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.05.30.656746},
pmid = {40501924},
issn = {2692-8205},
abstract = {Biomedical research underpins progress in our understanding of human health and disease, drug discovery, and clinical care. However, with the growth of complex lab experiments, large datasets, many analytical tools, and expansive literature, biomedical research is increasingly constrained by repetitive and fragmented workflows that slow discovery and limit innovation, underscoring the need for a fundamentally new way to scale scientific expertise. Here, we introduce Biomni, a general-purpose biomedical AI agent designed to autonomously execute a wide spectrum of research tasks across diverse biomedical subfields. To systematically map the biomedical action space, Biomni first employs an action discovery agent to create the first unified agentic environment - mining essential tools, databases, and protocols from tens of thousands of publications across 25 biomedical domains. Built on this foundation, Biomni features a generalist agentic architecture that integrates large language model (LLM) reasoning with retrieval-augmented planning and code-based execution, enabling it to dynamically compose and carry out complex biomedical workflows - entirely without relying on predefined templates or rigid task flows. Systematic benchmarking demonstrates that Biomni achieves strong generalization across heterogeneous biomedical tasks - including causal gene prioritization, drug repurposing, rare disease diagnosis, micro-biome analysis, and molecular cloning - without any task-specific prompt tuning. Real-world case studies further showcase Biomni's ability to interpret complex, multi-modal biomedical datasets and autonomously generate experimentally testable protocols. Biomni envisions a future where virtual AI biologists operate alongside and augment human scientists to dramatically enhance research productivity, clinical insight, and healthcare. Biomni is ready to use at https://biomni.stanford.edu , and we invite scientists to explore its capabilities, stress-test its limits, and co-create the next era of biomedical discoveries.},
}
@article {pmid40501842,
year = {2025},
author = {Shamorkina, TM and Pañeda, LP and Kadavá, T and Schulte, D and Pribil, P and Heidelberger, S and Narlock-Brand, AM and Yannone, SM and Snijder, J and Heck, AJR},
title = {Deep Coverage and Extended Sequence Reads Obtained with a Single Archaeal Protease Expedite de novo Protein Sequencing by Mass Spectrometry.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.05.26.656138},
pmid = {40501842},
issn = {2692-8205},
abstract = {The ability to sequence proteins without reliance on a genomic template defines a critical frontier in modern proteomics. This approach, known as de novo protein sequencing, is essential for applications such as antibody sequencing, microbiome proteomics, and antigen discovery, which require accurate reconstruction of peptide and protein sequences. While trypsin remains the gold-standard protease in proteomics, its restricted cleavage specificity limits peptide diversity. This constraint is especially problematic in antibody sequencing, where the functionally critical regions often lack canonical tryptic sites. As a result, exclusively trypsin-based approaches yield sparse reads, leading to sequence gaps. Multi-protease and hybrid-fragmentation strategies can improve the sequence coverage, but they add complexity, compromise scalability and reproducibility. Here, we explore two HyperThermoacidic Archaeal (HTA)-proteases as single-enzyme solutions for de novo antibody sequencing. Each HTA-protease generated about five times more unique peptide reads than trypsin or chymotrypsin, providing high redundancy across all CDRs. Combined with EAciD fragmentation on a ZenoTOF 7600 system, this approach enabled complete, unambiguous antibody sequencing. De novo analysis using PEAKS/DeepNovo and Stitch showed up to fourfold higher alignment scores and reduced the sequence errors within the HTA-generated data. Additionally, the HTA-EAciD approach offers short digestion times, eliminates extensive cleanup, and enables analysis in a single LC-MS/MS run. This streamlined, single-protease approach delivers therefore performance comparable to multi-enzyme workflows, offering a scalable and efficient strategy for de novo protein sequencing across diverse applications.},
}
@article {pmid40501780,
year = {2025},
author = {Dubinkina, V and Smith, B and Zhao, C and Pino, C and Pollard, KS},
title = {Linkage of nucleotide and functional diversity varies across gut bacteria.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.06.06.658399},
pmid = {40501780},
issn = {2692-8205},
abstract = {Understanding the forces shaping genomic diversity within bacterial species is essential for interpreting microbiome evolution, ecology, and host associations. Here, we analyze over one hundred prevalent gut bacterial species using the Unified Human Gut Genome (UHGG) collection to characterize patterns of intra-specific genomic variability. Gene content divergence scales predictably with divergence in core genome single nucleotide polymorphisms (SNPs), though there is substantial variability in evolutionary dynamics across species. Overall, accessory genes exhibit consistently faster linkage decay compared to core SNPs, highlighting the fluidity of functional repertoires within species boundaries. This signal is strongest for mobile genetic elements, which show minimal linkage to core genome SNPs. Together, our findings reveal species-specific recombination regimes in the gut microbiome, underscoring the importance of accounting for horizontal gene transfer and genome plasticity in microbiome-wide association studies and evolutionary models.},
}
@article {pmid40501688,
year = {2025},
author = {Zhao, Y and Lee, TF and Zhou, B and Wang, C and Schmidt, AM and Liu, M and Li, H and Hu, J},
title = {Joint Modeling of Longitudinal Biomarker and Survival Outcomes with the Presence of Competing Risk in Nested Case-Control Studies with Application to the TEDDY Microbiome Dataset.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.05.23.655653},
pmid = {40501688},
issn = {2692-8205},
abstract = {MOTIVATION: Large-scale prospective cohort studies collect longitudinal biospecimens alongside time-to-event outcomes to investigate biomarker dynamics in relation to disease risk. The nested case-control (NCC) design provides a cost-effective alternative to full cohort biomarker studies while preserving statistical efficiency. Despite advances in joint modeling for longitudinal and time-to-event outcomes, few approaches address the unique challenges posed by NCC sampling, non-normally distributed biomarkers, and competing survival outcomes.<br><br>RESULTS: Motivated by the TEDDY study, we propose "JM-NCC", a joint modeling framework designed for NCC studies with competing events. It integrates a generalized linear mixed-effects model for potentially non-normally distributed biomarkers with a cause-specific hazard model for competing risks. Two estimation methods are developed. fJM-NCC leverages NCC sub-cohort longitudinal biomarker data and full cohort survival and clinical metadata, while wJM-NCC uses only NCC sub-cohort data. Both simulation studies and an application to TEDDY microbiome dataset demonstrate the robustness and efficiency of the proposed methods.},
}
@article {pmid40501659,
year = {2025},
author = {Vemuganti, V and Kang, JW and Zhang, Q and Aquino-Martinez, R and Harding, S and Harpt, JL and Deming, Y and Johnson, S and Asthana, S and Zetterberg, H and Blennow, K and Engelman, CD and Ulland, TK and Bäckhed, F and Bendlin, BB and Rey, FE},
title = {Gut bacterial metabolite imidazole propionate potentiates Alzheimer's disease pathology.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.06.08.657719},
pmid = {40501659},
issn = {2692-8205},
abstract = {UNLABELLED: The gut microbiome modulates metabolic, immune, and neurological functions and has been implicated in Alzheimer's disease (AD), though the specific mechanisms remain poorly defined. The bacterial metabolite imidazole propionate (ImP) has been previously associated with several AD comorbidities, such as type 2 diabetes and cardiovascular disease. Here, we show that elevated plasma ImP levels are associated with lower cognitive scores and AD biomarkers in a cohort of >1,100 cognitively unimpaired individuals. Metagenomic profiling identified gut bacteria encoding putative orthologs of the ImP-synthesizing enzyme, urocanate reductase (UrdA), whose abundance correlated with both cognitive measures and multiple AD biomarkers. Chronic ImP administration to mice activated neurodegenerative pathways, worsened AD-like neuropathology, and increased blood-brain barrier (BBB) permeability. Complementary in vitro studies showed that ImP compromised the integrity of human brain endothelial cells. Collectively, these findings implicate ImP in AD progression via both neurodegenerative and cerebrovascular mechanisms, identifying it as a potential target for early intervention.<br><br>ONE SENTENCE SUMMARY: Gut bacterial metabolite increases dementia risk.},
}
@article {pmid40501599,
year = {2025},
author = {Price, DK and West, K and Cevallos-Zea, M and Cahan, SH and Nunez, JCB and Longman, EK and Yew, JY and Mederios, MJ},
title = {Microbiome composition shapes temperature tolerance in a Hawaiian picture-winged Drosophila.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.06.03.657679},
pmid = {40501599},
issn = {2692-8205},
abstract = {UNLABELLED: Hawaiian picture-winged Drosophila are undergoing rapid biodiversity loss, with twelve species listed as endangered and others in decline. Gut microbiota are increasingly recognized as contributors to host adaptation that are capable of influencing stress tolerance, reproduction, and other fitness-related traits. We investigated the role of microbial communities in local adaptation using two populations of Drosophila basisetae from Hawaiian rainforests at 900 m and 1200 m elevation. Microbiome profiling of wild flies by high throughput amplicon sequencing revealed distinct bacterial and fungal communities between sites. Whole-genome resequencing of the two Drosophila populations identified weak but significant population genetic structure, with evidence of admixture and gene flow. Despite this connectivity, 16 outlier SNPs across 18 genes showed patterns consistent with divergent selection, suggesting localized adaptation. To test microbiome effects on host physiology experimentally, we conducted a fully factorial research design with microbiome inoculations in laboratory-reared flies acclimated to 18 °C (control) or 24 °C (stressful). Flies treated with low-elevation microbiota had higher survival across temperatures, whereas those treated with high-elevation microbiota produced more eggs, indicating microbiome-mediated differences in reproductive investment. Activity levels at 18 °C were higher when flies received microbiota from their native population. Measures of critical thermal maximum (CTmax) and male accessory gland size showed complex interactions among microbiome source, temperature, and fly population. These results indicate that microbes may modulate host thermal tolerance and reproduction in environmentally-dependent and population-specific ways. Our findings suggest that microbiome-host-environment interactions may contribute to both phenotypic plasticity and evolutionary adaptation to enhance resilience to environmental stress, with important implications for conservation in rapidly changing Hawaiian ecosystems.<br><br>SUMMARY STATEMENT: This study demonstrates that microbiome composition influences thermal tolerance through alterations in survival and reproduction in the Hawaiian picture wing, Drosophila basisetae , potentially contributing to adaptive phenotypic changes between populations.},
}
@article {pmid40501527,
year = {2025},
author = {Roberson, JL and Pettke, EN},
title = {Dietary Risk Factors: Fiber and Beyond.},
journal = {Clinics in colon and rectal surgery},
volume = {38},
number = {4},
pages = {253-256},
pmid = {40501527},
issn = {1531-0043},
abstract = {The incidence of diverticulosis continues to rise throughout western nations with collateral increases in the frequency of diverticulitis. However, the mechanism behind the transition from asymptomatic diverticulosis to complicated diverticulitis is incompletely understood. Dietary intake has long been investigated as one of, if not the main, links in the continuum of disease. As the world's diet continues to evolve with increasingly prevalent processed and high-fat food, longitudinal studies have emerged with a goal of finally explaining how diet influences the development of diverticulitis. While low-fiber, high-fat diets are believed to play a role in the development of an index episode of diverticulitis, the role in recurrent disease remains uncertain. More recent avenues of interest include the role of the microbiome, probiotics, and adjunct treatments such as 5-ASA and rifaximin. While robust longitudinal studies have identified an association between low-fiber, high-fat diets and the development of index diverticulitis, the impact of dietary composition and modification on disease recurrence remains unclear and fails to meet the threshold for societal recommendations.},
}
@article {pmid40501526,
year = {2025},
author = {Troester, A and Weaver, L and Jahansouz, C},
title = {The Emerging Role of the Microbiota and Antibiotics in Diverticulitis Treatment.},
journal = {Clinics in colon and rectal surgery},
volume = {38},
number = {4},
pages = {269-276},
pmid = {40501526},
issn = {1531-0043},
abstract = {Diverticular disease is the leading cause of elective colon surgery. With a rising incidence in younger populations, it continues to pose a significant burden on the health care system. Traditional etiopathogenesis implicated an infectious mechanism, while recent challenges to this theory have demonstrated the microbiome playing a significant role, along with genetic predispositions and associations with obesity and diet. Therefore, the role of antibiotics in uncomplicated disease merits reconsideration. In this review, we aim to outline the current knowledge regarding antibiotics for diverticulitis treatment, broadly define the microbiome components, functions, and modifiability, and discuss newly proposed pathogenetic mechanisms for diverticular disease that incorporate information regarding the microbiome. Analytic techniques for microbiota characterization and function continue to advance at a rapid pace. As emerging technology advances, we will continue to elucidate the role of the microbiome in diverticular disease development.},
}
@article {pmid40501476,
year = {2025},
author = {Ma, C and Yang, J and Fu, XN and Luo, JY and Liu, P and Zeng, XL and Li, XY and Zhang, SL and Zheng, S},
title = {Microbial characteristics of gut microbiome dysbiosis in patients with chronic liver disease.},
journal = {World journal of hepatology},
volume = {17},
number = {5},
pages = {106124},
pmid = {40501476},
issn = {1948-5182},
abstract = {BACKGROUND: In this study, we are committed to exploring the characteristics of the gut microbiome in three different stages of chronic liver disease (CLD): Chronic hepatitis B, liver cirrhosis, and hepatocellular carcinoma (HCC).<br><br>AIM: To delineate the gut microbiota traits in individuals with chronic liver ailments (chronic hepatitis B, cirrhosis, HCC), scrutinizes microbiome alterations during the progression of these diseases, and assesses microbiome disparities among various Child-Pugh categories in cirrhosis sufferers.<br><br>METHODS: A cohort of 60 CLD patients from the Third People's Hospital of Yunnan Province were recruited from February to August 2023, together with 37 healthy counterparts. Employing 16SrDNA high-throughput sequencing, we evaluated the diversity and composition of the gut microbiota.<br><br>RESULTS: Compared to healthy subjects, patients exhibited a reduced presence of Firmicutes and a corresponding decline in butyrate-producing genera. In contrast, an upsurge in Proteobacteria was observed in the diseased cohorts, particularly an increase in Enterobacteriaceae that intensified with the disease's progression. At the genus level, the occurrence of Escherichia_Shigella, Parabacteroides, Streptococcus, Klebsiella, and Enterococcus was higher, with Escherichia_Shigella numbers augmenting as the disease advanced. Furthermore, in cirrhosis patients, an increase in Proteobacteria was noted as liver reserve diminished, alongside a decrease in Ruminococcaceae and Bacteroidaceae.<br><br>CONCLUSION: The reduced abundance of short-chain fatty acid-producing bacteria in the intestine, alongside the increased abundance of gram-negative bacteria such as Escherichia_Shigella and Parabacteroides, may promote the progression of CLD.},
}
@article {pmid40501467,
year = {2025},
author = {Goyal, MK and Goyal, P and Goyal, O and Sood, A},
title = {Gut feeling gone wrong: Tangled relationship between disorders of gut-brain interaction and liver disease.},
journal = {World journal of hepatology},
volume = {17},
number = {5},
pages = {105582},
pmid = {40501467},
issn = {1948-5182},
abstract = {Functional gastrointestinal disorders, now termed "disorders of gut-brain interaction" (DGBI), are characterized by a spectrum of chronic gastrointestinal symptoms driven by dysregulated gut-brain interaction. DGBIs frequently coexist with liver diseases, including cirrhosis, thereby exacerbating clinical manifestations and complicating management; this overlap is underpinned by shared mechanisms, including gut dysbiosis, increased intestinal permeability, systemic inflammation, and altered neuroimmune signaling. Portal hypertension in cirrhosis promotes small intestinal bacterial overgrowth and microbial translocation, thereby triggering inflammatory pathways that worsen gut and liver function. This minireview explores the gut-liver axis as a central mediator in the interplay between DGBIs and liver disease/cirrhosis. Clinically, these interactions manifest as refractory gastrointestinal symptoms, nutritional deficiencies, and impaired quality of life. Emerging research emphasizes the need for integrative diagnostic approaches, such as combining advanced imaging, microbiome analysis, and biomarker profiling, to unravel the complex interplay between DGBIs and liver disease/cirrhosis. Therapeutic interventions targeting the gut microbiome, neuroimmune pathways, and lifestyle modification can mitigate disease burden. This review underscores the importance of a multidisciplinary framework for enhancing patient outcomes and guiding future research in this intersectional field.},
}
@article {pmid40501442,
year = {2025},
author = {Maor, M and Levy Barazany, H and Kolodkin-Gal, I},
title = {The ladder of regulatory stringency and balance: an application to the US FDA's regulation of bacterial live therapeutics.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2517377},
doi = {10.1080/19490976.2025.2517377},
pmid = {40501442},
issn = {1949-0984},
mesh = {Humans ; United States ; United States Food and Drug Administration/legislation &amp; jurisprudence ; *Probiotics/therapeutic use ; *Fecal Microbiota Transplantation ; Bacteria/genetics ; Gastrointestinal Microbiome ; },
abstract = {The three main types of live bacterial therapies - probiotics, fecal/microbiome transplants, and engineered bacterial therapies - hold immense potential to revolutionize medicine. While offering targeted and personalized treatments for various diseases, these therapies also carry risks such as adverse immune reactions, antibiotic resistance, and the potential for unintended consequences. Therefore, developing and deploying these therapies necessitates a robust regulatory framework to protect public health while fostering innovation. In this paper, we propose a novel conceptual tool - the Ladder of Regulatory Stringency and Balance-which can assist in the design of robust regulatory regimes which encompass medicine practices based not only on definitive Randomized Controlled Trials (RCTs), but also on meta-analyses, observational studies, and clinicians experience. Regulatory stringency refers to the strictness of regulations, while regulatory balance concerns the degree of alignment between the regulatory framework governing a technology and the actual risks posed by specific products within that technology. Focusing on the US regulatory environment, we subsequently position the three types of live bacterial therapies on the Ladder. The insight gained from this exercise demonstrates that probiotics are generally positioned at the bottom of the Ladder, corresponding to low-stringency regulation, with a proportionate regulatory balance. However, probiotics intended for high-risk populations are currently subject to low-stringency regulations, resulting in under-regulation. Our analysis also supports the conclusion that fecal microbiota transplants (FMT) for recurrent Clostridium difficile infection should be positioned close to but below the threshold for under regulation by the U.S. Food and Drug Administration (FDA), and we recommend improved donor screening procedures, preservation and processing, storage, and distribution. Our framework can serve as a scale to assess regulatory gaps for live bacterial therapies and to identify potential solutions where such gaps exist.},
}
@article {pmid40501301,
year = {2025},
author = {Du, Y and Li, B and Yang, J and Zhang, Y and Qi, F and Meng, H},
title = {Analysis of Skin Microbiome in Facial and Back Acne Patients Based on High-Throughput Sequencing.},
journal = {Journal of cosmetic dermatology},
volume = {24},
number = {6},
pages = {e70259},
doi = {10.1111/jocd.70259},
pmid = {40501301},
issn = {1473-2165},
mesh = {Humans ; *Acne Vulgaris/microbiology ; *Microbiota/genetics ; *Skin/microbiology ; High-Throughput Nucleotide Sequencing ; Female ; Male ; Adult ; Young Adult ; Back ; Case-Control Studies ; Face/microbiology ; Adolescent ; Glucose/metabolism ; Sebum/metabolism ; Bacteria/isolation &amp; purification/genetics ; Skin Microbiome ; },
abstract = {OBJECTIVE: To study the composition and diversity of microorganisms in skin lesions of patients with facial acne and back acne, analyze the relationship between microorganisms and different parts of acne.<br><br>METHODS: A total of 30 facial acne patients, 30 back acne patients, and 30 healthy controls were included. Comprehensive data on demographics, skin conditions, and state of life were collected. Skin microbiota samples were obtained using standardized protocols, through high-throughput microbial sequencing and bioinformatics analysis, to assess microbiota diversity, composition, and function, as well as their correlations with skin characteristics.<br><br>RESULTS: The diversity of skin microbiota of back acne patients decreased significantly, and the abundance of p_actinomycetes and o_propionate bacteria increased significantly. They are closely related to glucose metabolism, which may lead to increased trans epidermal water loss, decreased skin moisture content, and increased skin oil content.<br><br>CONCLUSION: The skin microbiota diversity of patients with back acne is low, and high-abundance bacteria are closely related to glucose metabolism, which may lead to the breakdown of the skin barrier and increased sebum secretion.},
}
@article {pmid40500804,
year = {2025},
author = {Rocha, FI and Rodriguez-Ramos, JC and Fernando, M and Hale, L},
title = {Interrow cover crops in a semi-arid vineyard increase plant beneficial functional potential of the soil microbiome, both in vine rows and interrows, a benefit that increases with cover crop duration.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {66},
pmid = {40500804},
issn = {2524-6372},
support = {19-0689-000-SO//California Department of Food and Agriculture Healthy Soils Program/ ; 19-0689-000-SO//California Department of Food and Agriculture Healthy Soils Program/ ; 19-0689-000-SO//California Department of Food and Agriculture Healthy Soils Program/ ; 2034-13000-013//USDA ARS CRIS/ ; 2034-13000-013//USDA ARS CRIS/ ; },
abstract = {BACKGROUND: Cover crops are recognized for enhancing soil health and providing agroecosystem services, but are not widely adopted, particularly in water-limited regions. In Mediterranean vineyards, where water scarcity and soil degradation challenge productivity, interrow, cool-season cover cropping offers a promising strategy to improve microbial-mediated soil functions. However, the temporal and spatial effects of cover crops on vineyard soil microbiomes and soil health metrics remain poorly understood. This study evaluated the impacts of a California native (phacelia, Phacelia tanacetifolia) and introduced (rye, Secale cereale L.) plant species as interrow cover crops on soil properties in interrow and vine row soils across three years.<br><br>RESULTS: The study revealed distinct temporal and spatial dynamics in soil microbiomes elicited by the cover crop treatments. By the third year, phacelia exhibited the highest microbial biomass, fungal-to-bacterial ratios, and microbial network complexity. Interrow soils showed stronger responses to cover cropping, including enhanced microbial biomass and differentiation between treatments, while vine row soils demonstrated subtler but significant shifts in microbial metrics. Functional predictions indicated that cover crops reduced fungal pathogen prevalence and supported nutrient cycling processes. Deterministic processes driven by environmental selection became dominant under both treatments, promoting microbial resilience. Random Forest analysis identified NO3[-] as a key driver of microbial differentiation, with phacelia fostering communities reliant on labile organic inputs.<br><br>CONCLUSIONS: This study highlights a crucial benefit of interrow cover crops in improving soil health and enhancing microbial-mediated ecosystem functions in adjacent vine row soils, even after cover crop termination. Long-term application of cover crops offers a sustainable approach to building resilient agroecosystems in water-scarce environments, with implications for sustainable viticulture practices.},
}
@article {pmid40500778,
year = {2025},
author = {Lobato, C and Abdelfattah, A and Berg, G and Cernava, T},
title = {Defining the cultured and uncultured bacterial fractions in Cannabis seeds.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {68},
pmid = {40500778},
issn = {2524-6372},
abstract = {BACKGROUND: Seeds provide a unique environment shaped by co-evolutionary processes, hosting diverse microbial communities. While microbiome studies have uncovered an extensive diversity of microorganisms, culture-based approaches remain crucial for understanding microbial potential and functional interactions. However, the factors influencing microbial culturability within seeds are not well understood.<br><br>RESULTS: In this study, we investigated the culturing patterns of bacteria inside Cannabis seeds, assessing their phylogenetic diversity, abundance, and putative interactions. Bacteria were cultured from 54 different Cannabis accessions using germinated seeds and a range of nutrient media including those supplemented with Cannabis extracts. The cultured fraction consisted of taxa from five prominent classes-Gammaproteobacteria, Bacilli, Actinobacteria, Alphaproteobacteria, and Bacteroidia-encompassing 36 genera. Despite representing only 6.3% of the total microbiota, these cultured bacteria accounted for 89.2% of the microbial population. Almost 60% of the amplicon sequence variants (ASVs) were phylogenetically distant from cultured taxa. Rare bacterial groups such as Acidobacteriae and Verrucomicrobiae, known for their plant growth-promoting traits, were exclusively found in the uncultured fraction. Network analyses revealed that uncultured taxa are centralized and more connected to hubs, suggesting that interspecies interactions strongly influence culturability.<br><br>CONCLUSION: Our findings highlight the limitations of culture-based methods in capturing the full microbial diversity of Cannabis seeds and emphasize the importance of microbial interactions in determining culturability. The strong network connectivity of uncultured taxa suggests that interdependencies and competition within the seed microbiome may hinder the isolation of key bacterial groups. These insights provide a framework for refining cultivation strategies to recover ecologically significant microbes with potential agricultural applications.},
}
@article {pmid40500757,
year = {2025},
author = {Sussfeld, D and Lannes, R and Corel, E and Bernard, G and Martin, P and Bapteste, E and Pelletier, E and Lopez, P},
title = {New groups of highly divergent proteins in families as old as cellular life with important biological functions in the ocean.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {65},
pmid = {40500757},
issn = {2524-6372},
support = {615274/ERC_/European Research Council/International ; 615274/ERC_/European Research Council/International ; 615274/ERC_/European Research Council/International ; 615274/ERC_/European Research Council/International ; },
abstract = {BACKGROUND: Metagenomics has considerably broadened our knowledge of microbial diversity, unravelling fascinating adaptations and characterising multiple novel major taxonomic groups, e.g. CPR bacteria, DPANN and Asgard archaea, and novel viruses. Such findings profoundly reshaped the structure of the known Tree of Life and emphasised the central role of investigating uncultured organisms. However, despite significant progresses, a large portion of proteins predicted from metagenomes remain today unannotated, both taxonomically and functionally, across many biomes and in particular in oceanic waters.<br><br>RESULTS: Here, we used an iterative, network-based approach for remote homology detection, to probe a dataset of 40&#xa0;million ORFs predicted in marine environments. We assessed the environmental diversity of 53 core gene families broadly distributed across the Tree of Life, with essential functions including translational, replication and trafficking processes. For nearly half of them, we identified clusters of remote environmental homologues that showed divergence from the known genetic diversity comparable to the divergence between Archaea and Bacteria, with representatives distributed across all the oceans. In particular, we report the detection of environmental clades with new structural variants of essential SMC (Structural Maintenance of Chromosomes) genes, divergent polymerase subunits forming deep-branching clades in the polymerase tree, and variant DNA recombinases in Bacteria as well as viruses.<br><br>CONCLUSIONS: These results indicate that significant environmental diversity may yet be unravelled even in strongly conserved gene families. Protein sequence similarity network approaches, in particular, appear well-suited to highlight potential sources of biological novelty and make better sense of microbial dark matter across taxonomical scales.},
}
@article {pmid40500750,
year = {2025},
author = {Yang, B and Li, X and Wang, J and Xu, Y and Wang, L and Wu, Z and Zhao, D and Huang, L and Li, N and Chen, Q and Liu, Z},
title = {The efficacy and safety of fecal microbiota transplantation in the treatment of sarcopenia: a retrospective study.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {645},
pmid = {40500750},
issn = {1479-5876},
support = {2022YFA1304100//National Key R&amp;D Program of China/ ; 2022YFC2010101//National Key R&amp;D Program of China/ ; 82470701//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Sarcopenia/therapy/physiopathology/microbiology ; *Fecal Microbiota Transplantation/adverse effects ; Male ; Female ; Aged ; Retrospective Studies ; Treatment Outcome ; Middle Aged ; Resistance Training ; Inflammation ; },
abstract = {BACKGROUND: Sarcopenia, a prevalent geriatric syndrome, is influenced by factors such as inflammation, immune deficiency, and oxidative stress. In elderly individuals, alterations in the microbiome, including reduced biodiversity and functional changes, significantly contribute to the progression of the disease. Targeting the gut-muscle axis has emerged as a promising therapeutic strategy to mitigate age-related muscle atrophy and dysfunction.<br><br>METHODS: This study employed fecal microbiota transplantation (FMT) to restore intestinal homeostasis in patients with sarcopenia. Muscle mass was measured using bioelectrical impedance analysis, while muscle function was assessed through grip strength and the five-time sit-to-stand test. Inflammatory markers, including tumor necrosis factor-&#x3b1; (TNF-&#x3b1;) and C-reactive protein (CRP), were also analyzed. Eighty-seven patients received resistance training (RT) treatment, while eighty-five patients received FMT combined with RT treatment, with a follow-up period of 24 weeks.<br><br>RESULTS: After 24 weeks, the resistance training (RT) group showed a partial remission (PR) rate of 54.7% and a complete remission (CR) rate of 32.4%. The FMT plus RT group demonstrated a PR rate of 66.5% and a CR rate of 46.7%. Significant improvements induced by FMT treatment were observed in clinical markers of muscle mass, function, and inflammation.<br><br>CONCLUSIONS: These results underscore the promise of microbial-based therapies, including fecal microbiota transplantation (FMT), as groundbreaking strategies for addressing sarcopenia. The research indicates that integrating FMT with resistance training could improve muscle mass and function while alleviating inflammation in sarcopenia patients, presenting a hopeful avenue for effective management of the condition.},
}
@article {pmid40500582,
year = {2025},
author = {Lin, YS and Chen, JH and Zhuang, WH and Huang, JN and Chen, YH and Zhang, J and Li, J and Huang, M and Hou, JL and Qian, SJ and Chen, ZB and Zhang, YL and Xu, RT},
title = {Gut Microbiota Improve the Prediction of Stroke-Associated Pneumonia Risk and Outcomes in Acute Ischemic Stroke.},
journal = {Translational stroke research},
volume = {},
number = {},
pages = {},
pmid = {40500582},
issn = {1868-601X},
support = {2025KY1002//the Medical and Health Science and Technology Project of Zhejiang Province/ ; Y20220817//Wenzhou Municipal Science and Technology Bureau/ ; Y20210170//Wenzhou Municipal Science and Technology Bureau/ ; LQ23H090005//the Projects of Natural Science Foundation of Zhejiang Province/ ; },
abstract = {Stroke-associated pneumonia (SAP) is the most significant acute ischemic stroke (AIS) comorbidity. This investigation aimed to explore the relationship between gut microbiome composition and SAP risk in patients with moderate-to-severe AIS and to develop a robust and accessible SAP risk-prediction model for this population. This prospective study included AIS patients with an NIHSS score ≥ 9 within 48 h of onset who were admitted to the First Affiliated Hospital of Wenzhou Medical University. Rectal swabs and sputum samples were collected for 16S rRNA gene sequencing and analyzed via QIIME to evaluate microbial composition. Blood samples were subjected to untargeted metabolomics analysis via liquid chromatography‒mass spectrometry (LC‒MS). Logistic and Cox regression analyses were conducted (α = 0.05). Fifty of 104 AIS patients (48.1%) developed SAP. Microbiota abundances significantly differed between groups. Logistic regression analysis revealed that Finegoldia protected against SAP (OR 0.710, 95% CI: 0.533 - 0.946, p = 0.019), whereas Lactobacillus (OR 1.347, 95% CI: 1.015 - 1.789, p = 0.039) increased SAP risk. An improved SAP prediction model combining the A[2]DS[2] score with seven taxa yielded an AUC of 0.746 (95% CI: 0.650 - 0.841, p < 0.001). Cox regression analysis revealed that genus Clostridium (HR 1.618, 95% CI: 1.241 - 2.110, p < 0.001) was an independent risk factor for mortality, whereas genus Streptococcus (HR 0.751, 95% CI: 0.589 - 0.958, p = 0.021) was a protective factor. Our findings suggest that combining clinical indicators, gut microbiota, and blood metabolites enhances SAP prediction. Furthermore, microorganisms can potentially serve as prognostic markers and therapeutic targets for SAP in the future.},
}
@article {pmid40500467,
year = {2025},
author = {Hindson, J},
title = {Post-antibiotics microbiome restoration driven by diet.},
journal = {Nature reviews. Gastroenterology &amp; hepatology},
volume = {},
number = {},
pages = {},
pmid = {40500467},
issn = {1759-5053},
}
@article {pmid40500278,
year = {2025},
author = {Rodríguez Mazariegos, JR and Nam, NN and Bo, T and Wang, D and Hsu, JW and Chen, YC},
title = {Precocious puberty and gut microbiome: a systematic review and meta-analysis.},
journal = {Pediatric research},
volume = {},
number = {},
pages = {},
pmid = {40500278},
issn = {1530-0447},
abstract = {Central precocious puberty (CPP) is a condition that affects prepubertal children, particularly girls. Recent evidence suggests an association between the gut microbiome (GM) and CPP. This study aims to explore this association. We analyzed data from studies investigating the association between GM and CPP. Various databases were searched for relevant articles published from database inception to December 31, 2023. Standardized mean difference values were calculated and depicted in forest plots. Furthermore, subgroup analyses by type of study subject (animals vs. humans) were performed. The final analysis included 9 studies. Five were human studies, whereas the remaining four were animal (rats or mice) studies. In the precocious puberty group, the abundances (at the genus level) of Holdemania, Roseburia, Alistipes, Dialister, Enterococcus, Ruminococcus, Bilophila, and Lachnoclostridium increased significantly, whereas those of Bacteroides, Anaerostipes, Megamonas, and Gemella decreased significantly. Furthermore, for this group, the Shannon index for alpha diversity was increased in human studies and decreased in animal studies compared to the control group. Notably, the levels of major short-chain fatty acids, butyric and propionic acids, were significantly reduced in the precocious puberty group. There was an association between CPP and GM. Both subgroups revealed that microbiome profiles vary across individuals with precocious puberty. IMPACT: To our knowledge, this is the first systematic review and meta-analysis to explore the association between the gut microbiome and precocious puberty in both human and animal models. Our findings reveal distinct microbial patterns in individuals with CPP, including consistent alterations in 12 bacterial genera and significant changes in short-chain fatty acid levels. By identifying reproducible microbial signatures and metabolites associated with CPP, this study lays the groundwork for microbiome-targeted interventions alongside traditional hormonal therapies. The study addresses key methodological inconsistencies in existing literature, highlighting the need for standardized protocols in future research on the gut-puberty axis.},
}
@article {pmid40500261,
year = {2025},
author = {Dong, P and Yang, M and Hu, J and Cen, L and Zhou, P and Xu, D and Xiong, P and Li, J and He, X},
title = {Identification of a Fusobacterial RNA-binding protein involved in host small RNA-mediated growth inhibition.},
journal = {International journal of oral science},
volume = {17},
number = {1},
pages = {48},
pmid = {40500261},
issn = {2049-3169},
support = {DE030943//U.S. Department of Health &amp; Human Services | NIH | National Institute of Dental and Craniofacial Research (NIDCR)/ ; DE023810//U.S. Department of Health &amp; Human Services | NIH | National Institute of Dental and Craniofacial Research (NIDCR)/ ; DE029479//U.S. Department of Health &amp; Human Services | NIH | National Institute of Dental and Craniofacial Research (NIDCR)/ ; DE033794//U.S. Department of Health &amp; Human Services | NIH | National Institute of Dental and Craniofacial Research (NIDCR)/ ; DE031329//U.S. Department of Health &amp; Human Services | NIH | National Institute of Dental and Craniofacial Research (NIDCR)/ ; },
mesh = {*Fusobacterium nucleatum/genetics/metabolism/growth &amp; development ; *RNA-Binding Proteins/metabolism/genetics ; *Bacterial Proteins/metabolism/genetics ; RNA, Bacterial/metabolism ; Humans ; RNA, Transfer/metabolism ; },
abstract = {Host-derived small RNAs are emerging as critical regulators in the dynamic interactions between host tissues and the microbiome, with implications for microbial pathogenesis and host defense. Among these, transfer RNA-derived small RNAs (tsRNAs) have garnered attention for their roles in modulating microbial behavior. However, the bacterial factors mediating tsRNA interaction and functionality remain poorly understood. In this study, using RNA affinity pull-down assay in combination with mass spectrometry, we identified a putative membrane-bound protein, annotated as P-type ATPase transporter (PtaT) in Fusobacterium nucleatum (Fn), which binds Fn-targeting tsRNAs in a sequence-specific manner. Through targeted mutagenesis and phenotypic characterization, we showed that in both the Fn type strain and a clinical tumor isolate, deletion of ptaT led to reduced tsRNA intake and enhanced resistance to tsRNA-induced growth inhibition. Global RNA sequencing and label-free Raman spectroscopy revealed the phenotypic differences between Fn wild type and PtaT-deficient mutant, highlighting the functional significance of PtaT in purine and pyrimidine metabolism. Furthermore, AlphaFold 3 prediction provides evidence supporting the specific binding between PtaT and Fn-targeting tsRNA. By uncovering the first RNA-binding protein in Fn implicated in growth modulation through interactions with host-derived small RNAs (sRNAs), our study offers new insights into sRNA-mediated host-pathogen interplay within the context of microbiome-host interactions.},
}
@article {pmid40500078,
year = {2025},
author = {Liu, Z and Zhao, D and Wei, Y},
title = {Combination of L-methionine and chlorantraniliprole enhances the abundance of opportunistic pathogenic bacteria in the intestine of greater wax moth leading to increased mortality risk.},
journal = {Pesticide biochemistry and physiology},
volume = {212},
number = {},
pages = {106429},
doi = {10.1016/j.pestbp.2025.106429},
pmid = {40500078},
issn = {1095-9939},
mesh = {Animals ; *Moths/microbiology/drug effects ; *ortho-Aminobenzoates/toxicity/pharmacology ; *Insecticides/toxicity/pharmacology ; *Methionine/pharmacology/toxicity ; *Gastrointestinal Microbiome/drug effects ; Bees ; Intestines/microbiology/drug effects ; Bacteria/drug effects ; },
abstract = {Honey bees play an essential role in global crop production and agro-economic development due to their pollination properties. However, empirical evidence indicates a worldwide decline in bee colonies. The greater wax moth (GWM), a lepidopteran insect and natural enemy of honey bees, significantly contributes to this decline. Chlorantraniliprole (CH) is commonly used to control GWM in apiaries due to its efficacy and low toxicity to bees. However, long-term use of CH may lead to environmental pollution and GWM resistance. To enhance beekeeping safety and mitigate the risk of GWM resistance from prolonged CH use, we investigated the toxic effects of combining methionine (MET), which has demonstrated insecticidal activity against some lepidopteran pests, with CH on GWM. We conducted both individual and mixed exposure tests of MET and CH on GWM to finally evaluate the toxic effects of the combined treatment (MIX). The results indicated that the combination of MET and CH produced a synergistic lethal effect on GWM. Subsequent microbiome and immune-related gene expression assays, along with correlation analysis, revealed that the MIX treatment significantly reducing the abundance of Enterococcus spp., the primary genus in GWM, and induced immune stress in GWM. This phenomenon led to the proliferation of opportunistic pathogens such as Pseudomonas spp., ultimately leading to synergistic lethal effects on GWM mortality. This study provides new insights and data supporting the development of MET as a potential insecticide.},
}
@article {pmid40499711,
year = {2025},
author = {Zhang, RR and Zhang, JS and Huang, S and Lam, WY and Chu, CH and Yu, OY},
title = {The oral microbiome of root caries: A scoping review.},
journal = {Journal of dentistry},
volume = {},
number = {},
pages = {105899},
doi = {10.1016/j.jdent.2025.105899},
pmid = {40499711},
issn = {1879-176X},
abstract = {OBJECTIVE: This review characterizes shifts of the oral microbial community on carious root surfaces compared to sound root surfaces.<br><br>DATA AND SOURCES: A systematic search of English-language publications on clinical studies evaluating oral microbiomes in patients with root caries using high-throughput sequencing technologies published before April 1, 2025, was included. The search was conducted on PubMed, Cochrane Central Register of Controlled Trials, Web of Science, Embase, and Scopus. Gray literature was searched in ClinicalTrials.gov and Google Scholar.<br><br>STUDY SELECTION/RESULTS: Based on the eligibility criteria, 1,133 publications were screened, and 465 duplicates were removed. Of the remaining 16 studies assessed for full-text review, eight investigating the oral microbiome of saliva, carious roots, or dental plaque in patients with root caries were included. These studies reported the intra-community species diversity (alpha-diversity, 4/8 studies), inter-community compositional diversity (beta-diversity, 4/8 studies), dominant microbial genera/species (8/8 studies), and functional pathways (1/8 studies) of the microbial community in root caries patients. Alpha-diversity showed no significant difference between root caries and sound root surfaces in three studies, but root caries exhibited a significantly lower alpha diversity in one study. Beta-diversity differed significantly between root caries and sound root surfaces in three studies, with one study reporting no difference. The dominant microbial species in root caries varied among the included studies. However, Lactobacillus spp., Prevotella denticola, Propionibacterium acidifaciens, Streptococcus mutans, and Veillonella parvula/dispar were frequently identified in the root caries-associated microbiota. Furthermore, root caries-associated bacteria altered the predicted functional pathways, promoting organic acid production and accelerating collagen degradation.<br><br>CONCLUSION: Root caries microbiomes exhibit distinct compositional profiles, dysbiotic species predominance, and a shift in predicted functional pathways compared to healthy root surfaces.<br><br>CLINICAL SIGNIFICANCE: This review provides valuable insights into root caries' microbial landscape, potentially guiding future preventative and therapeutic strategies.},
}
@article {pmid40499683,
year = {2025},
author = {Yokomizo, S and Kaneko, N and Chen, H and Yan, L and Tsuji, S and Akagawa, S and Sameshima, J and Sueyoshi, T and Nagano, H and Miyahara, Y and Kamikaseda, Y and Kido, H and Hayashi, Y and Yamauchi, M and Kiyoshima, T and Goto, Y and Ohyama, Y and Kaneko, K and Moriyama, M and Kawano, S},
title = {Dysbiosis of the gut microbiome may contribute to the pathogenesis of oral lichen planus through Treg dysregulation.},
journal = {Mucosal immunology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.mucimm.2025.05.009},
pmid = {40499683},
issn = {1935-3456},
abstract = {Oral lichen planus (OLP) is a chronic inflammatory disorder with autoimmune features and malignant transformation risk, lacking a definitive treatment, with CD4[+] T cells being pivotal in its pathogenesis. Dysbiosis, an imbalance in the microbiome, is linked to various autoimmune and inflammatory diseases, where CD4[+] T cells play a significant role. Given these insights, the development of OLP might be influenced by dysbiosis. This study investigates the association between dysbiosis and CD4[+] T cells in OLP. We collected stool and saliva samples from OLP patients, conducting 16S rRNA gene analysis and mass spectrometry, and assessed CD4[+] T cell characteristics in lesions through multiplex immunofluorescence and single-cell RNA sequencing. Peripheral blood samples were subjected to flow cytometry and cell culture assays. Results showed extensive gut dysbiosis in OLP patients, notably a reduction in short-chain fatty acid (SCFA)-producing bacteria essential for regulatory T cell (Treg) differentiation. While various CD4[+] T cell subsets, including Tregs, were present in tissues, these Tregs as unresponsive to specific antigens, showing reduced immunosuppressive molecule expression. The decline in SCFA-producing bacteria correlated with fewer activated Tregs in tissues and blood. These findings suggest that gut dysbiosis may contribute to OLP by impairing Treg regulation, influencing disease pathogenesis.},
}
@article {pmid40499635,
year = {2025},
author = {Wen, C and Guan, J and Uea-Anuwong, T and Shang, J and Peng, C and Tang, X and Magouras, I and Sun, Y and Li, F},
title = {Dissecting the gut microbial communities and resistomes of wild rats from different ecological areas in Hong Kong.},
journal = {Environmental research},
volume = {},
number = {},
pages = {122108},
doi = {10.1016/j.envres.2025.122108},
pmid = {40499635},
issn = {1096-0953},
abstract = {Antimicrobial resistance (AMR) is one of the top global public health issues shared across all One Health domains. Wild rats, as one of key intersections of the animal and environmental domains, are understudied reservoirs and spreaders for AMR. Our study employed the whole-metagenome shotgun sequencing to characterize the caecal microbiome of wild rats and examine the presence of antimicrobial resistance genes (ARGs) from different ecological areas in Hong Kong. We trapped 88 live rats, belonging to the species of Rattus norvegicus (n=57), R. tanezumi (n=24), and R. andamanensis (n=7), from city regions, livestock farms, and stables of horse-riding schools (referred to as "suburbs"). We identified 9,672 ARGs belonging to 29 ARG types and 554 ARG subtypes. Among them, aminoglycosides, macrolide-lincosamide-streptogramin and chloramphenicol, known to be predominant in livestock gut resistome or manure compost were significantly more abundant in rats from livestock farms. Moreover, some ARGs with high-risk levels, including tetM, tetL, floR, mecR1 and lnuA , as well as plasmid-borne ARGs were significantly more abundant in rats from livestock farms than from city regions or suburbs. Furthermore, zoonotic antimicrobial-resistant bacteria (ARB) were detected, including but not limited to, prioritized antimicrobial-resistant Klebsiella pneumoniae, Proteus mirabilis, Escherichia coli, Enterococcus faecium, Acinetobacter baumannii, Campylobacter jejuni, and Staphylococcus aureus. Notably, resistant zoonotic bacteria of Streptococcus suis, Campylobacter coli, and Campylobacter jejuni were more abundant in wild rats from livestock farms. Our findings provides insights into the gut resistomes and zoonotic bacteria in wild rats in Hong Kong, highlighting the potential role of wild rats in the dissemination of ARGs and zoonotic pathogens, especially for those from agricultural settings.},
}
@article {pmid40499541,
year = {2025},
author = {Mannochio-Russo, H and Charron-Lamoureux, V and van Faassen, M and Lamichhane, S and Gonçalves Nunes, WD and Deleray, V and Ayala, AV and Tanaka, Y and Patan, A and Vittali, K and Rajkumar, P and El Abiead, Y and Zhao, HN and Gomes, PWP and Mohanty, I and Lee, C and Sund, A and Sharma, M and Liu, Y and Pattynama, D and Walker, GT and Norton, GJ and Khatib, L and Andalibi, MS and Wang, CX and Ellis, RJ and Moore, DJ and Iudicello, JE and Franklin, D and Letendre, S and Chin, L and Walker, C and Renwick, S and Zemlin, J and Meehan, MJ and Song, X and Kasper, D and Burcham, Z and Kim, JJ and Kadakia, S and Raffatellu, M and Bode, L and Chu, H and Zengler, K and Wang, M and Siegel, D and Knight, R and Dorrestein, PC},
title = {The microbiome diversifies long- to short-chain fatty acid-derived N-acyl lipids.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2025.05.015},
pmid = {40499541},
issn = {1097-4172},
abstract = {N-Acyl lipids are important mediators of several biological processes including immune function and stress response. To enhance the detection of N-acyl lipids with untargeted mass spectrometry-based metabolomics, we created a reference spectral library retrieving N-acyl lipid patterns from 2,700 public datasets, identifying 851 N-acyl lipids that were detected 356,542 times. 777 are not documented in lipid structural databases, with 18% of these derived from short-chain fatty acids and found in the digestive tract and other organs. Their levels varied with diet and microbial colonization and in people living with diabetes. We used the library to link microbial N-acyl lipids, including histamine and polyamine conjugates, to HIV status and cognitive impairment. This resource will enhance the annotation of these compounds in future studies to further the understanding of their roles in health and disease and to highlight the value of large-scale untargeted metabolomics data for metabolite discovery.},
}
@article {pmid40499421,
year = {2025},
author = {Fang, Z and Hodson, ME and Hu, CJ and Li, WJ and Li, J and Monroy, AB and Tong, L and Xiao, X},
title = {Combined toxicity of polyethylene microplastics and soil salinization to earthworms is generally antagonistic or additive.},
journal = {Journal of hazardous materials},
volume = {495},
number = {},
pages = {138843},
doi = {10.1016/j.jhazmat.2025.138843},
pmid = {40499421},
issn = {1873-3336},
abstract = {Microplastic (MP) accumulation and salinization frequently co-occur in terrestrial ecosystems, posing potential risks to soil health. However, their combined toxicity to soil invertebrates remains unclear. This study investigated combined effects of NaCl and polyethylene MPs (< 35, < 125, < 500 μm) on earthworms. The non-saline avoidance EC50 for < 35 μm MPs was 18 wt%, while avoidance only occurred at 50 wt% for < 125 μm MPs and not at all for < 500 μm MPs. Synergistic effects between NaCl and small MPs increased avoidance. High (10 wt%) MP concentrations by themselves did not increase earthworm mortality; mortality was lower with both MPs and 4000 mg/kg NaCl than with NaCl alone. Co-exposure to MPs and 1000 mg/kg NaCl further reduced growth rates by 16 % but increased cocoon production by 259 % compared to NaCl exposure alone. NaCl exposure induced earthworm oxidative and osmotic stress; overall stress levels were unchanged by MP co-exposure. 16S rRNA gene sequencing revealed that both NaCl and MPs significantly altered earthworm gut microbiome, suggesting potential impaired gut health. MPs more strongly impacted gut microbial community and functions when no salt was added. Overall, combined effects of NaCl and MPs on earthworms are mainly additive or antagonistic.},
}
@article {pmid40499249,
year = {2025},
author = {McDonagh, F and Murray, EK and Hallahan, B and Miliotis, G},
title = {Systematic examination of off-target effects of antipsychotic medications associated with microbiome disruption and heightened bacterial infection risks.},
journal = {Journal of psychiatric research},
volume = {189},
number = {},
pages = {171-183},
doi = {10.1016/j.jpsychires.2025.05.046},
pmid = {40499249},
issn = {1879-1379},
abstract = {OBJECTIVE: This systematic review aims to critically evaluate the link between antipsychotic drugs and bacterial infection risk, emphasising antimicrobial properties of antipsychotics, and microbiome changes that might heighten susceptibility to bacterial infections.<br><br>METHODS: A systematic literature search was conducted across PubMed, Scopus, and Google Scholar, up to March 2024. Peer-reviewed articles that investigated the relationship between antipsychotics, their antimicrobial effects, microbiome alterations, and bacterial infection risk were included. Data extracted included antipsychotic type, infection risks, patient demographics, and study methodologies. Risk-of-bias assessments were performed using tools such as the Newcastle-Ottawa Scale and the SYRCLE risk-of-bias tool.<br><br>RESULTS: The review analysed twenty-six studies detailing antimicrobial properties of antipsychotics, four studies on antipsychotic-induced microbiome alterations, and thirty-one studies assessing bacterial infection risk associated with antipsychotics. First-generation antipsychotics were observed to have broad antimicrobial properties, whereas second-generation antipsychotics primarily affected commensal bacteria. At least four antipsychotics were observed to disrupt the gut microbiota. A heightened risk of infection was observed among psychiatric cohorts as well as off-label antipsychotics use, with clozapine linked to a substantial increase in respiratory infection risk.<br><br>DISCUSSION: Although antipsychotics remain indispensable in psychiatric care, their association with an increased risk of bacterial infections underscores the need for judicious prescribing and vigilant monitoring. The review identifies significant knowledge gaps attributable to inconsistent research methodologies, small study cohorts, lack of controls, and focus on a limited range of antipsychotics. Further standardised research is essential to deepen our understanding of these associations and to inform improved prescribing practices and risk mitigation strategies.},
}
@article {pmid40499217,
year = {2025},
author = {Li, M and Zhang, Q and Zhao, W and Chen, J and Liu, Y and Zhou, L and Liu, Y and Wang, L and Guan, Y and He, J and Jiang, Q and Zeng, Z and Guo, X and Liu, C and Zhang, L and Zhang, Y and Luo, J and Hung, WL and He, J and Wang, R},
title = {Effects and Persistence of Bifidobacterium animalis subsp. lactis BL-99 and Fructooligosaccharides on Older Adults with Functional Constipation: A Randomized, Double-Blind, Placebo-Controlled Trial.},
journal = {The journal of nutrition, health &amp; aging},
volume = {29},
number = {8},
pages = {100598},
doi = {10.1016/j.jnha.2025.100598},
pmid = {40499217},
issn = {1760-4788},
abstract = {Research on effects of synbiotics in older adults with functional constipation (FC) is limited. This randomized, double-blind, placebo-controlled trial evaluated a 4-week synbiotic (Bifidobacterium animalis subsp. lactis BL-99 and fructooligosaccharides [FOS]) intervention in 67 participants ≥60 years old meeting Rome IV FC criteria. Compared to placebo, the synbiotic group showed significant improvements in weekly spontaneous bowel movements (Least squares mean ± standard error: 4.94 ± 0.25 vs. 3.00 ± 0.26, P < 0.001) and whole gut transit time (37.13 ± 3.78 vs. 50.64 ± 4.22 h, P = 0.019), with benefits sustained 2 weeks post-intervention. It also reduced time per toilet attempt and alleviated rectal discomfort symptoms more effectively than placebo. Fecal microbiome analysis revealed increased abundance of beneficial Bifidobacterium species, correlating with symptom improvement (P < 0.05). These findings demonstrate that BL-99/FOS supplementation ameliorates FC symptoms in older adults, with effects sustained post-discontinuation, potentially mediated through gut microbiota modulation. Further mechanistic investigation is warranted.},
}
@article {pmid40499189,
year = {2025},
author = {Fernandes, PMB and Fernandes, AAR and Maurastoni, M and Rodrigues, SP},
title = {Lab Legends and Field Phantoms: The Tale of Virus-Resistant Plants.},
journal = {Annual review of virology},
volume = {},
number = {},
pages = {},
doi = {10.1146/annurev-virology-092623-101850},
pmid = {40499189},
issn = {2327-0578},
abstract = {Plant viruses present significant challenges to global agriculture, causing crop losses, threatening food security, and imposing economic burdens. Advances in biotechnology have revolutionized strategies to attack these threats, with genetically modified and genome-edited virus-resistant plants, developed using precision tools such as RNA interference and CRISPR/Cas technology, playing pivotal roles. Despite these breakthroughs, fragmented regulatory frameworks and divergent policies across regions including the European Union and the Global South hinder the global adoption of such innovations. Multifaceted approaches, including gene pyramiding, microbiome-based strategies, and pathogen-targeted defenses, show promise for enhancing plant resilience. This review explores the biological, regulatory, and ethical dimensions of deploying virus-resistant crops, emphasizing the need for harmonization of international regulation to maximize biotechnological benefits. By addressing these challenges, biotechnology can advance sustainable agriculture, secure food systems, and mitigate the effect of plant viral diseases.},
}
@article {pmid40499078,
year = {2025},
author = {Xue, K and Wang, P and Lin, Q and Xie, J and Cong, L and Yan, Z},
title = {Uncovering the Single Amino-Acid Polymorphisms of the Human Gut Ecosystem.},
journal = {Journal of proteome research},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jproteome.5c00108},
pmid = {40499078},
issn = {1535-3907},
abstract = {Single nucleotide polymorphisms (SNPs) are the most common type of genetic variation in the gut microbial metagenome and the host genome, but they could not adequately represent the protein-level variants. Single amino-acid polymorphisms (SAP) derived from nonsynonymous SNPs can cause functional changes of proteins and are important forces of adaption. However, SAP remains quite unexplored for the human gut microbiome. Here, we present a comprehensive large-scale analysis of SAP in the gut ecosystem, introducing a rigorous computational pipeline for detecting such protein variation from 992 published human metaproteomes. We find varied yet elaborate SAP patterns, capturing both known and novel functions and adaptive strategies of gut microbes. Microbial SAP is enriched in the outermost shell, motility devices, and ribosomes. Generally, gut microbial SAP is more convergent in metabolic subpathway regions and is enriched in the initial steps of carbohydrate metabolism pathways that catalyze the formation and isomerization of phosphorylated sugars. Furthermore, microbial and host mutant peptide patterns were altered and exhibited significant correlations in both inflammatory bowel disease and type 1 diabetes. Our results highlight the functional and clinically relevant implications and potential host-microbial interactions of gut ecosystem SAP.},
}
@article {pmid40498998,
year = {2025},
author = {Marcos-Kovandzic, L and Avagliano, M and Ben Khelil, M and Srikanthan, J and Abdallah, R and Petrocelli, V and Rengassamy, J and Alfaro, A and Bied, M and Fidelle, M and Ferrere, G and Daillere, R and Arbab, A and Amine-Hneineh, R and Pages, A and Dartigues, P and Ly, P and Simon, S and Durand, S and Gottschlich, A and Ginhoux, F and Bleriot, C and Liu, P and Zhao, L and Creusot, L and Rolhion, N and Kroemer, G and Menger, L and Kobold, S and Castilla-Llorente, C and Sokol, H and Casola, S and Pasolli, E and Zitvogel, L and Bigenwald, C},
title = {Gut microbiota modulation through Akkermansia spp. supplementation increases CAR-T cell potency.},
journal = {Cancer discovery},
volume = {},
number = {},
pages = {},
doi = {10.1158/2159-8290.CD-24-1230},
pmid = {40498998},
issn = {2159-8290},
abstract = {This study investigates the clinical relevance of the gut microbiome at taxonomic and metabolic levels in anti-CD19 CAR-T cell therapy, both in patients and in a preclinical syngeneic tumor model. B cell lymphoma patients treated with CD19-CAR-T cells exhibited profound intestinal dysbiosis, exacerbated after CAR-T infusion. This dysbiosis was characterized by low bacterial richness, low sMAdCAM-1 and loss of Akkermansia species, associated with resistance to therapy. Mechanistically, oral Akkermansia massiliensis supplementation increased CAR-T cell infiltration into bone marrow, inverted the CD4/CD8 CAR-T ratio, favored Tc1 CD8+ T cell polarization and promoted release of tryptophan-derived indole metabolites, leading to better tumor control. The clinical benefit of Akkermansia spp. supplementation was abolished when CAR-T cells were genetically deficient for the indole receptor, aryl hydrocarbon receptor (Ahr). Ahr-agonistic indoles alone failed to replicate the bacterium's anticancer effects. These findings suggest Akkermansia supplementation could improve CAR-T cell potency in patients with intestinal Akkermansia deficiency.},
}
@article {pmid40498698,
year = {2025},
author = {Bußmann, A and Speckemeier, C and Ehm, A and Kollar, B and Neumann, A and Neusser, S},
title = {Approaches to predict future type 2 diabetes mellitus and chronic kidney disease: A scoping review.},
journal = {PloS one},
volume = {20},
number = {6},
pages = {e0325182},
doi = {10.1371/journal.pone.0325182},
pmid = {40498698},
issn = {1932-6203},
mesh = {Humans ; *Diabetes Mellitus, Type 2/epidemiology/diagnosis ; *Renal Insufficiency, Chronic/epidemiology/diagnosis ; Risk Factors ; },
abstract = {BACKGROUND: Demographic change and changing lifestyles are leading to a steady increase in so-called population diseases such as type 2 diabetes mellitus and chronic kidney disease. Both conditions are often preceded by a latency period during which lifestyle changes and/or medications have the potential to delay or even prevent disease onset. Thus, detection of those at an increased risk of these diseases is of great importance. A scoping review was conducted to collate different prediction approaches for type 2 diabetes mellitus and chronic kidney disease.<br><br>METHODS: Literature searches were performed in PubMed, Embase, Web of Science, and Google Scholar. A stepwise approach was used, consisting of searches for systematic reviews and primary literature, and additional Google searches for novel approaches. Included was literature that (1) presented an approach for risk prediction of incident type 2 diabetes mellitus or chronic kidney disease, (2) contained information on the risk factors considered and application, (3) targeted the general population, (4) was written in English or German language, and (5) for which an abstract and full-text was available. Literature screening was carried out by two persons independently.<br><br>RESULTS: Studies extracted literature from 1940 to 2023. Prediction approaches were included from 25 literature reviews, eight primary studies and nine studies found in additional searches. Several different approaches were identified, including methods based on clinical parameters, biological parameters (blood, urine, microbiome, genetics), the combinations of those, sequential approaches, and exposure and lifestyle factors. Most of the identified approaches were risk surveys that usually ask for simple and readily available parameters. Novel approaches cover transdermal optical imaging, prediction based on facial blood flow and using deoxyribonucleic acid methylation data.<br><br>CONCLUSION: This scoping review provides an overview of different tools for the risk prediction of type 2 diabetes mellitus and chronic kidney disease. In addition to established tools, which are primarily risk surveys, innovative approaches have been developed and evaluated in recent years in which the potential of machine learning is utilized. As cardio-renal-metabolic diseases share predicting factors and given the social and economic importance of these diseases, approaches that address multiple relevant diseases such as type 2 diabetes mellitus, chronic kidney disease and cardiovascular disease can be of great interest, especially in time- and resource-constrained healthcare settings.},
}
@article {pmid40498592,
year = {2025},
author = {Wagner, AD and Ahmed, MMA and Starks, VA and Boudreau, PD},
title = {Using Repeated Lysis Steps Fractionates Between Heterotrophic and Cyanobacterial DNA Extracted from Xenic Cyanobacterial Cultures.},
journal = {G3 (Bethesda, Md.)},
volume = {},
number = {},
pages = {},
doi = {10.1093/g3journal/jkaf135},
pmid = {40498592},
issn = {2160-1836},
abstract = {Extracting DNA from cyanobacteria can be a challenge because of their diverse morphologies, challenging cellular structure, and the heterotrophic microbiome often present within cyanobacterial cultures. As such, even with high DNA yields, the percentage of reads coming from the cyanobacterial host can be low, leading to an incomplete cyanobacterial genome assembly. In this research, we optimized a DNA isolation protocol using three iterative cell lysis steps to enrich the portion of DNA isolated coming from the cyanobacterial host rather than the heterotrophic microbiome. In order to utilize in-house nanopore sequencing, we faced a challenge using our lysis protocol: the iterative lysis approach led to more DNA shearing than is ideal for this sequencing technology. To solve this, we used two bead-based size selection steps to remove shorter molecules of DNA before nanopore sequencing. Analysis of the sequenced reads showed that, in the first lysis, the cyanobacterial sequences were only 35% of all reads. In the repeated lysis steps, however, the proportion of reads coming from the cyanobacterium increased to 75% or higher. Using our iterative lysis protocol, we were able to sequence the genomes of two fresh water cyanobacteria isolated from northern Mississippi, namely Leptolyngbya sp. BL-A-14 and Limnothrix sp. BL-A-16. The genomes of these isolates were assembled as closed chromosomes of 7.2 and 4.5 Mb for BL-A-14 and BL-A-16, respectively. As it is not always possible to prepare axenic cultures of cyanobacteria, we hope our approach will be useful for sequencing other xenic cultures of cyanobacteria.},
}
@article {pmid40498389,
year = {2025},
author = {Maître, M and Baradat, S and Froliger, M and Turlier, V and Simcic-Mori, A and Gravier, E and Géniès, C and Lauze, C and Huyghe, C and Noustens, A and Alvarez-Georges, S and Marinescu, R and Reygagne, P and Bessou-Touya, S and Mengeaud, V and Duplan, H},
title = {Scalp Microbiome Dynamics Can Contribute to the Clinical Effect of a Novel Antiseborrheic Dermatitis Shampoo Containing Patented Antifungal Actives: A Randomized Controlled Study.},
journal = {Dermatology and therapy},
volume = {},
number = {},
pages = {},
pmid = {40498389},
issn = {2193-8210},
abstract = {INTRODUCTION: Scalp seborrheic dermatitis (SD) can cause physical discomfort and social embarrassment in affected individuals. Mild-to-moderate scalp SD can be managed using topical products with antifungal, antiinflammatory, and keratolytic properties.<br><br>METHODS: A two-phase, randomized, controlled study was conducted to evaluate the clinical efficacy of a newly formulated anti-SD shampoo containing two patented antifungal actives and to investigate the associated changes in the scalp microbiota. The intervention involved a 2-week intensive phase for the 42 subjects included in the study, consisting of the application of the anti-SD shampoo three times a week; a randomized [1:1], controlled, parallel-group 8-week maintenance phase consisting of the test group applying the study shampoo once a week alternately with a neutral shampoo twice a week; and the control group applying the neutral shampoo alone three times a week.<br><br>RESULTS: Following the intensive phase, the scalp condition improved substantially, as evidenced by a significant decrease in the severity of dandruff, erythema, and pruritus, associated with an improvement of SD dysbiosis. These improvements were more sustained in the test group than in the control group during the maintenance phase. The rediversification of the scalp microbiota involved a significant increase in fungal and bacterial richness along with a decrease in the level of SD-predominant Malassezia fungi and Staphylococcus bacteria and an increase in the level of low-abundant fungi genera belonging to the Ascomycota phylum.<br><br>CONCLUSIONS: The synergistic effects of antimycotic and antiinflammatory agents in the study shampoo likely contributed to rebalancing the fungal and bacterial ecosystem, thus improving scalp symptoms.<br><br>GOV IDENTIFIER: NCT06578962 (retrospectively registered on 28 August 2024).},
}
@article {pmid40498370,
year = {2025},
author = {Cullen, JT and Lawlor, PG and Cormican, P and Gardiner, GE},
title = {Investigating the impact of sanitisation of a liquid feeding system for pigs on the bacteriome and mycobiome of the liquid feeding system surfaces and liquid feed.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxaf143},
pmid = {40498370},
issn = {1365-2672},
abstract = {AIMS: To investigate the effect of liquid feeding system sanitisation on the bacteriome and mycobiome of feeding system surfaces and liquid feed.<br><br>METHODS AND RESULTS: High-throughput 16S and ITS2 rRNA amplicon sequencing was performed on surface swabs and feed samples collected during a previous sanitisation experiment. Results confirmed that feed pipeline surface biofilms were disrupted post-cleaning (PC). Pre-cleaning, the pipeline was dominated by Lactobacillus, Leuconostoc and Apiotrichum. Microbial diversity increased PC, with Jeotgalicoccus and Brachybacterium predominating, although Lactobacillus became predominant again between wk8-wk10 PC. Sanitisation also impacted the feed microbial profile, with decreases in Lactobacillus, Leuconostoc and Chryseobacterium in the mixing tank feed. Weissella and Kazachstania became predominant in the trough-sampled liquid feed PC. Despite sanitisation, spontaneous fermentation was still observed in the feed, evidenced by decreased abundance of spoilage-associated Pantoea and Pseudomonas between the mixing tank and troughs and a concomitant increase in Lactobacillus. Nonetheless, previously reported improvements in feed quality PC suggest the changes in the liquid feed microbiota were beneficial.<br><br>CONCLUSIONS: Intensive cleaning and subsequent daily acid-rinsing of the feeding system disrupted feed pipeline biofilms, reduced spontaneous fermentation and improved liquid feed quality. Therefore, we recommend liquid feeding system sanitisation between batches of grow-finisher pigs followed by maintenance acid-rinsing.},
}
@article {pmid40498317,
year = {2025},
author = {Viets, C and Stevens, CA},
title = {Measuring and Analyzing Bacterial Movement in Mucus.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2942},
number = {},
pages = {187-197},
pmid = {40498317},
issn = {1940-6029},
mesh = {Humans ; *Mucus/microbiology/metabolism ; Mucins/metabolism ; *Time-Lapse Imaging/methods ; *Bacteria ; Microbiota ; },
abstract = {Humans are colonized by trillions of microbes that compose the human microbiome. Much of the microbiome inhabits the mucus layers. Mucus layers, covering digestive, reproductive, ocular, and respiratory tracts, are viscous networks consisting mainly of water and mucin glycoproteins. Mucins assemble into a dense, cross-linked network that can affect bacterial swimming patterns, and studying this behavior provides valuable insights into how the body regulates interactions with both harmful and beneficial microbes. Here we present the use of time-lapse imaging to track individual bacterial cells within mucin and discuss techniques for accurately extracting cell trajectory data from these images. By integrating theoretical and experimental approaches, we also describe how to quantify bacterial movement in terms of speed, persistence, and randomness.},
}
@article {pmid40498312,
year = {2025},
author = {Lisacek, F and Schnider, B and Ohayon, D and Imberty, A},
title = {Microbial Lectin-Targeting Mucus: A Glycobioinformatic Approach.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2942},
number = {},
pages = {131-143},
pmid = {40498312},
issn = {1940-6029},
mesh = {*Lectins/metabolism/chemistry ; Humans ; *Mucins/metabolism/chemistry ; *Mucus/metabolism ; Polysaccharides/metabolism/chemistry ; Protein Binding ; Microbiota ; },
abstract = {The motifs exposed on surface glycans of mucins serve as receptors to a range of proteins expressed by microorganisms. The specificity of microbial glycan-binding proteins, i.e., lectins, towards human mucin epitopes is the result of co-evolution. The binding of microbes to mucins is described in several databases hosted on the UniLectin portal. In particular, UniLectin3D provides structural details on the recognition process and LectomeXplore allows for the identification of putative lectins in the genomes of mucin-associated microbiome species. The usage of these resources is illustrated in this chapter.},
}
@article {pmid40498297,
year = {2025},
author = {Beraja, GE and Gruzmark, F and Pastar, I and Lev-Tov, H},
title = {What's New in Wound Healing: Treatment Advances and Microbial Insights.},
journal = {American journal of clinical dermatology},
volume = {},
number = {},
pages = {},
pmid = {40498297},
issn = {1179-1888},
abstract = {Recent advancements in wound healing are reshaping clinical practice by integrating dermatology, cutaneous microbiome research, and technology. This article discusses new diagnostic tools, such as imaging devices and microbial composition analysis, that enhance our understanding of wound environments. It highlights the importance of wound bed preparation and explores innovative treatment methods for optimal wound healing, including debridement techniques like ultrasound-assisted methods, hydrosurgery, and larval therapy. The evolution of wound management is further illustrated through the use of cellular and acellular matrix products and cellular therapies involving whole blood products. We also present the latest insights on the wound microbiome and antimicrobial treatments, including advanced dressings and antibiofilm surfactants. Finally, the potential of gene therapy for complex conditions like epidermolysis bullosa is discussed as a promising model for advancing wound healing. This review synthesizes current research to improve dermatological practices and patient outcomes in wound care.},
}
@article {pmid38796837,
year = {2024},
author = {Tomasics, G and Schandl, L and Polyák, A and Winkler, G},
title = {[The effect of pre-, pro- and synbiotics on the carbohydrate and lipid metabolism].},
journal = {Orvosi hetilap},
volume = {165},
number = {21},
pages = {803-812},
doi = {10.1556/650.2024.33064},
pmid = {38796837},
issn = {1788-6120},
mesh = {Humans ; *Synbiotics/administration &amp; dosage ; *Lipid Metabolism/drug effects ; *Gastrointestinal Microbiome/physiology ; *Prebiotics ; *Carbohydrate Metabolism ; *Diabetes Mellitus, Type 2/metabolism/prevention &amp; control ; Hypoglycemic Agents/therapeutic use/pharmacology ; Diabetes Mellitus, Type 1/metabolism ; Probiotics/therapeutic use/pharmacology ; },
abstract = {The prevalence of diabetes and its precursor state – the prediabetes – is exponentially spreading worldwide. More and more data suggest the role of gut microbiome in the pathogenesis of the aforementioned conditions. It is well known that pre-, probiotics, and their combination called synbiotics may influence the composition of the gut microflora. Thus they may play a key role in the progression or retardation of the pathogenetic process of diabetes. It is also supported by more and more observations that different drugs – in particular the antidiabetic drugs − can modify the composition of the microbiome. Based on literary data, the authors review the influencing effects of pre-, pro-, and synbiotics on the carbohydrate and lipid metabolism, as well as their potential role in the pathogenesis of type 1 and type 2 diabetes, and summarize briefly the role of antidiabetic drugs on the gut microbiome composition. Orv Hetil. 2024; 165(21): 803–812.},
}
@article {pmid38555569,
year = {2024},
author = {Rurik, I and Péter, S and Bánáti, D},
title = {[Actual challenges of nutritional science].},
journal = {Orvosi hetilap},
volume = {165},
number = {13},
pages = {483-488},
doi = {10.1556/650.2024.33013},
pmid = {38555569},
issn = {1788-6120},
mesh = {Humans ; *Nutritional Sciences ; },
abstract = {A balanced, healthy diet can ensure a longer lifespan and a better quality of life, so the huge challenge facing humanity is to provide the world’s growing population with healthy food from sustainable food systems, in sufficient quantity and quality. Malnutrition and the multiple burden of nutrition are also public health issues, as is the epidemic progression of obesity and its complications, and the increasing rates of food allergy or food intolerance to certain food substances. Our paper deals with different diets, the development of novel foods, the prospects for research on the microbiome and the nutritional aspects of healthy ageing. Sustainability and environmental aspects, animal welfare requirements, shorter food chains, reducing emissions from production and transport, controlling chemical residues of harmful substances, limiting advertising of unhealthy products, and socially responsible pricing are important. It is equally important to educate the public, develop and disseminate dietary and nutritional recommendations, develop and produce nutritious food items, and provide accurate, evidence-based consumer information. At the same time, there is a need to reduce food waste. Coordinated interventions are needed at all levels, with a strong governmental commitment. In addition to deeper study of the physiological aspects of nutrition, the main directions of research in nutrition science are the development of new technologies, new food ingredients, processing and preservation methods, and monitoring and possible optimization of the nutritional environment. Orv Hetil. 2024; 165(13): 483–488.},
}
@article {pmid38142414,
year = {2023},
author = {Pállinger, &#xc9; and Nagy, B and Király, A and Fülöp, V},
title = {[Immune cell functionality during pregnancy].},
journal = {Orvosi hetilap},
volume = {164},
number = {51},
pages = {2006-2015},
doi = {10.1556/650.2023.32935},
pmid = {38142414},
issn = {1788-6120},
mesh = {Pregnancy ; Female ; Humans ; *Heart Transplantation ; Trophoblasts ; },
abstract = {Immunological recognition of the fetus is the prerequisite of successful pregnancy. Decidualization enables the formation of embryo-competent tissue environment. The decidua is an independent organ performing endocrine and immunological function. On the other hand, the embryo itself is also an active participant of fertilization through the strictly regulated bidirectional communication between embryonic and maternal tissues. Immunological properties of fetomaternal interface dynamically change and pregnancy can be characterized by immunological stages. Chronology of pregnancy may be represented by the three phases “immune clock”: the implantation period is associated with the previously unimaginable inflammatory milieu, which is replaced by the anti-inflammatory environment essential to fetal growth, and followed by a second inflammatory state, which helps in labor. Adaptation to pregnancy requires great flexibility of the immune system in order to simultaneously achieve tolerance to paternal alloantigens, optimal development of the placenta and fetus, and protection against infections/xenobiotics. All this can only be achieved if a special and closely cooperating immune milieu develops at the fetal–maternal interface, where the cellular and soluble components of natural and adaptive immunity are attuned to the hormonal environment, cooperate with the microbiome and respond appropriately to the immunomodulatory effects of the trophoblasts. Characterization of the maternal immune system during pregnancy is important to understand how we can diagnose or treat immune dysregulation associated pregnancy complications, including infertility, implantation failure or pregnancy complications. Orv Hetil. 2023; 164(51): 2006–2015.},
}
@article {pmid40498283,
year = {2025},
author = {de Miranda, NFCC and Smit, VTHBM and van der Ploeg, M and Wesseling, J and Neefjes, J},
title = {Absence of lipopolysccharide (LPS) expression in breast cancer cells.},
journal = {Cellular oncology (Dordrecht, Netherlands)},
volume = {},
number = {},
pages = {},
pmid = {40498283},
issn = {2211-3436},
support = {852832/ERC_/European Research Council/International ; },
abstract = {The relationship between bacterial activity and tumorigenesis has gained attention in recent years, complementing the well-established association between viruses and cancer. A recent study employed immunodetection of lipopolysaccharide (LPS) to demonstrate the presence of intracellular bacteria within cancer cells across various cancer types, including breast cancer. The authors proposed that these bacteria might play a role in tumor development. We sought to replicate these findings using the same experimental methods on an independent cohort of breast cancer cases. Our analysis of 129 samples revealed no evidence of LPS expression within cancer cells. Instead, LPS immunoreactivity was observed in ducts or immune cells, specifically macrophages, as expected. These discrepancies in LPS immunodetection warrant caution in interpreting the original findings, and further research is needed to clarify the potential role of intracellular bacteria in cancer development.},
}
@article {pmid40498144,
year = {2025},
author = {Frederico, G and Quirino, MW and Andretta, I and Schmitt, E and Peripolli, V and da Rosa Ulguim, R and Bianchi, I},
title = {Lactation performance and fecal microbiome of sows supplemented with antioxidant-rich polyherbal extract.},
journal = {Tropical animal health and production},
volume = {57},
number = {5},
pages = {258},
pmid = {40498144},
issn = {1573-7438},
mesh = {Animals ; Female ; *Feces/microbiology ; *Lactation/drug effects/physiology ; *Antioxidants/administration &amp; dosage/metabolism/pharmacology ; Animal Feed/analysis ; Dietary Supplements/analysis ; *Plant Extracts/administration &amp; dosage/pharmacology/metabolism ; Diet/veterinary ; *Sus scrofa/physiology/microbiology ; *Gastrointestinal Microbiome/drug effects ; Animal Nutritional Physiological Phenomena ; },
abstract = {This study evaluated the lactation performance and fecal microbiome of sows supplemented with an herbal extract rich in antioxidants from day 110 of gestation until weaning. Ninety-five sows (parity 1 to 8) were assigned to either the control group (n = 48; 225.3 ± 4.1 kg), fed a non-supplemented lactation diet, or the herbal group (n = 47; 224.6 ± 4.2 kg), fed the same diet supplemented with an herbal extract (Herbal C Power[®], Nuproxa, Vaud, Switzerland). Environmental conditions in the farrowing facilities were within the critical temperature and humidity range. No differences were observed in sow rectal temperature, respiratory frequency, or number of weaned piglets (P = 0.15). However, piglets from the supplemented group showed lower pre-weaning mortality (0.72% vs. 1.23%), higher weight gain (213.8 g vs. 201.1 g), and greater weaning weight (6.1 kg vs. 5.8 kg; P ≤ 0.01). Supplemented sows produced more milk (11.0 kg/day vs. 9.9 kg/day; P < 0.01), though feed and water consumption remained similar (P ≥ 0.39). Antioxidant supplementation had no significant effect on sows' body weight, backfat thickness, or weaning-to-estrus interval, but supplemented sows had lower caliper units (12.1 vs. 13.0; P = 0.03). Serum levels of AST, ALT, C-reactive protein, and TNF-α were unaffected (P ≥ 0.17). Fecal analysis revealed a higher abundance of Enterobacteriales and Enterobacteriaceae in supplemented sows (P = 0.03). Antioxidant supplementation improved litter performance, reduced piglet mortality, increased milk production, and altered sow gut microbiota; however, further studies performed under more extreme conditions are needed.},
}
@article {pmid40498140,
year = {2025},
author = {Meurs, J and Henderson, B and van Dun, C and Batitsta, GL and Sakkoula, E and van Diepen, JA and Gross, G and Aarts, E and Cristescu, SM},
title = {Exploring the use of exhaled breath profiling for non-invasive monitoring of cognitive functioning in children: a pilot study.},
journal = {Metabolomics : Official journal of the Metabolomic Society},
volume = {21},
number = {4},
pages = {75},
pmid = {40498140},
issn = {1573-3890},
support = {PROJ-00405//European Regional Development Fund/ ; 818110//Horizon 2020/ ; },
mesh = {Humans ; Breath Tests/methods ; Child ; Pilot Projects ; Male ; Female ; *Cognition/physiology ; Gastrointestinal Microbiome/physiology ; Executive Function/physiology ; Exhalation ; Metabolomics/methods ; },
abstract = {INTRODUCTION: Childhood is a critical period for the development of executive functioning skills, including selective attention and inhibitory control, which are essential for cognitive development. Optimal brain development during this time requires appropriate levels of macronutrient intake. Metabolomics can offer valuable insights into which metabolites cognitive functioning and the underlying gut-brain interactions.<br><br>OBJECTIVES: This study aimed to explore to use of breathomics to investigate associations between exhaled metabolites and executive functioning in children.<br><br>METHODS: Children (8-10 years; N&#x2009;=&#x2009;31) were recruited via flyers at schools and after-school care. The assessment of executive functioning was done using Eriksen flanker task. Breath samples were collected in Tedlar[&#xae;] bags and analyzed with proton transfer reaction-mass spectrometry (PTR-MS). On-breath peaks were selected and subjected to partial least squares (PLS) regression. Significance multivariate correlation (sMC) was used afterwards to select metabolites bearing predictive power towards executive functioning.<br><br>RESULTS: Gut microbiome-related metabolites (methane, ethanol, and butyric acid) present in exhaled breath were associated with an improved executive functioning, whereas isoprene was linked to reduced executive functioning. Additionally, increased levels of inflammatory markers, ethylene and acetaldehyde, were associated with a higher compatibility effect in error rates, suggesting diminished cognitive control. These VOCs were putatively linked with specific gut microbial taxa; for instance, reduced Bacteroidetes abundance (associated with methane production) is associated with decreased inhibitory control, while Enterobacteriaceae were linked to lipopolysaccharide-induced inflammation which is also a process that causes increased ethylene production.<br><br>CONCLUSION: This proof-of-concept study demonstrates that VOCs in exhaled breath could serve as a promising non-invasive tool for assessing gut-brain interactions related to executive functioning in children.},
}
@article {pmid40497827,
year = {2025},
author = {Ning, W and Li, M and Jiang, L and Yang, M and Liu, M and Liu, Y},
title = {Endophytic Bacterial Community Structure and Function Response of BLB Rice Leaves After Foliar Application of Cu-Ag Nanoparticles.},
journal = {Nanomaterials (Basel, Switzerland)},
volume = {15},
number = {11},
pages = {},
doi = {10.3390/nano15110778},
pmid = {40497827},
issn = {2079-4991},
support = {RCZ202505//Xichang University Special project/ ; },
abstract = {Bacterial leaf blight (BLB) is a destructive disease caused by Xanthomonas oryzae pv. oryzae (Xoo). It has been proven that BLB adversely influences the growth and production of rice, resulting in substantial losses in yield. Nanoparticle-antimicrobial compounds possess excellent physicochemical properties, which have generated groundbreaking applications in protecting rice against BLB attacks. However, there is less research focused on the interaction between nanoparticles and the microbiome of BLB rice leaves, particularly the structure and function of endophytic bacteria, which are essential to plant health and pathogenesis. Therefore, the study explored how Cu-Ag nanoparticles influenced the endophytic bacteria's composition and functions in healthy and BLB rice leaves. The data demonstrated that the relative abundance of beneficial bacteria, Burkholderiales, Micrococcales, and Rhizobiales, increased after the introduction of Cu-Ag nanoparticles on the leaves of BLB rice. The examination of PAL activity demonstrated that nanoparticles limited the spread of Xoo in rice leaves. Furthermore, endophytic community functional prediction demonstrated that nanoparticles may regulate the physiological process associated with potential stress resistance and growth-promoting function in the endophytic communities. This investigation may enhance the understanding of interactions between nanoparticles and the composition of rice endophytic microbiome, which can contribute to the exploration and application of nanomaterials in crop pathogen management.},
}
@article {pmid40497754,
year = {2025},
author = {Cristofori, F and Castellaneta, S and Dargenio, C and Paulucci, L and La Grasta, G and Barone, M and Francavilla, R and Dargenio, VN},
title = {Unlocking the potential of the low FODMAP diet: comprehensive insights into clinical efficacy, microbiome modulation, and beyond.},
journal = {Expert review of gastroenterology &amp; hepatology},
volume = {},
number = {},
pages = {},
doi = {10.1080/17474124.2025.2519160},
pmid = {40497754},
issn = {1747-4132},
abstract = {INTRODUCTION: Functional gastrointestinal disorders (FGIDs) and inflammatory bowel diseases (IBD) present significant challenges for both pediatric and adult populations. The low FODMAP diet (LFD) has gained prominence as an evidence-based dietary intervention, offering symptom relief for abdominal pain, bloating, and altered bowel habits. However, concerns about adherence, nutritional adequacy, and long-term safety remain critical, particularly in pediatric populations.<br><br>AREAS COVERED: This narrative review examines the nature and physiological impact of FODMAPs, focusing on the practical application of the low-FODMAP diet (LFD) in adults and pediatric gastroenterology. Particular attention is given to emerging insights into its impact on gut microbiota and long-term safety.<br><br>EXPERT OPINION: While LFD effectively alleviates symptoms in FGIDs and functional symptoms in IBD, its restrictive nature demands professional supervision to mitigate nutritional risks. For pediatric patients, adherence and reintroduction protocols require optimization. Further research into personalized dietary approaches and microbiome-targeted strategies could enhance the clinical utility of the LFD, ensuring its long-term safety and efficacy for diverse patient groups.},
}
@article {pmid40497711,
year = {2025},
author = {Crosby, A and Krishnan, K and Baker, S},
title = {Andie Crosby, Calroy and Kiran Krishnan, Microbiome Labs Introducing Cartigenix HP for Pain Management.},
journal = {Alternative therapies in health and medicine},
volume = {31},
number = {4},
pages = {6-9},
pmid = {40497711},
issn = {1078-6791},
mesh = {Humans ; *Pain Management/methods ; *Microbiota ; },
abstract = {No Abstract Available.},
}
@article {pmid40497681,
year = {2025},
author = {Fan, Y and Li, Y and Wang, L and Zhao, D and Zhou, Y and Houpt, ER and Liu, J},
title = {Fecal microbiome profiling of children with Shigella diarrhea from low- and middle-income countries.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0057325},
doi = {10.1128/spectrum.00573-25},
pmid = {40497681},
issn = {2165-0497},
abstract = {Shigella is one of the leading pathogens causing diarrhea in children globally. Stool culture remains the standard for diagnosing Shigella infections; however, quantitative PCR (qPCR) offers greater sensitivity. In this study, we evaluated the fecal microbiomes of 27 diarrheal children with and without Shigella identified by culture and quantitative PCR, respectively, aiming to characterize the fecal microbiome profiles of children with Shigella diarrhea and to explore the differences in microbiome and the mechanisms associated with the culturability of Shigella. Our results showed that Shigella qPCR positive cases were characterized by a significantly higher abundance of Shigella and other Proteobacteria, alongside a lower abundance of the probiotic genus Bifidobacterium. This profile was associated with specific virulence factors (VFGs) and antimicrobial resistance genes (ARGs), indicating a unique pathogenic module related to Shigella infection. While no significant difference in Shigella abundance was found between the Shigella culture positive and culture negative groups, genera Bifidobacterium and Ligilactobacillus were enriched in the culture positive group. Interestingly, the culture positive group also possessed a higher abundance of virulence factors associated with pathogenicity, likely resulting from the higher copy number of pINV plasmid. The fecal metagenomic analyses from diarrheal children suggested a potentially distinct intestinal microbial profile associated with Shigella infection and a possible correlation between increased pathogenicity and the Shigella culturability. These findings might contribute to a more comprehensive understanding of Shigella pathogenicity and improving diagnostic methods for Shigella.IMPORTANCEDiarrhea represents the fifth leading cause of mortality among children under the age of five, with Shigella representing the second most common pathogen responsible for diarrhea-related mortality. In the current study, we employed metagenomics to comprehensively characterize the fecal microbiome profiles of children infected with Shigella and to investigate the factors affecting Shigella culturability. We identified a distinct intestinal microbial profile associated with Shigella-infected diarrheal children, observed a correlation between increased pathogenicity and the Shigella culturability, and also proposed some potential factors that might promote the in vitro growth of Shigella strains. These findings might provide evidence for improving diagnostic methods for Shigella.},
}
@article {pmid40497338,
year = {2025},
author = {Older, EA and Mitchell, MK and Campbell, A and Lian, X and Madden, M and Wang, Y and van de Wal, LE and Zaw, T and VanderVeen, BN and Tatum, R and Murphy, EA and Chen, YH and Fan, D and Ellermann, M and Li, J},
title = {Human gut commensal Alistipes timonensis modulates the host lipidome and delivers anti-inflammatory outer membrane vesicles to suppress colitis in an Il10-deficient mouse model.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2517380},
doi = {10.1080/19490976.2025.2517380},
pmid = {40497338},
issn = {1949-0984},
mesh = {Animals ; *Interleukin-10/deficiency/genetics ; Mice ; *Gastrointestinal Microbiome ; Disease Models, Animal ; *Colitis/microbiology/immunology ; Humans ; Mice, Inbred C57BL ; Macrophages/immunology/drug effects ; *Clostridiales/physiology ; Mice, Knockout ; Lipidomics ; *Anti-Inflammatory Agents/pharmacology ; Male ; },
abstract = {Correlative studies have linked human gut microbes to specific health conditions. Alistipes is one such microbial genus negatively linked to inflammatory bowel disease (IBD). However, the protective role of Alistipes in IBD is understudied, and the underlying molecular mechanisms remain unknown. In this study, colonization of Il10-deficient mice with Alistipes timonensis DSM 27924 delays colitis development. Colonization does not significantly alter the gut microbiome composition, but instead shifts the host plasma lipidome, increasing phosphatidic acids while decreasing triglycerides. Outer membrane vesicles (OMVs) derived from Alistipes are detected in the plasma of colonized mice, carrying potentially immunomodulatory metabolites into the host circulatory system. Fractions of A. timonensis OMVs suppress LPS-induced Il6, Il1b, and Tnfa expression in vitro in murine macrophages. We detect putative bioactive lipids in the OMVs, including immunomodulatory sulfonolipids (SoLs) in the active fraction, which are also increased in the blood of colonized mice. Treating Il10-deficient mice with purified SoL B, a representative SoL, suppresses colitis development, suggesting its contribution to the anti-inflammatory phenotype observed with A. timonensis colonization. Thus, A. timonensis OMVs represent a potential mechanism for Alistipes-mediated delay of colitis in Il10-deficient mice via delivery of immunomodulatory lipids and modulation of the host plasma lipidome.},
}
@article {pmid40497323,
year = {2025},
author = {Hui, Y and Sandris Nielsen, D and Krych, L},
title = {De novo clustering of long-read amplicons improves phylogenetic insight into microbiome data.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2516703},
doi = {10.1080/19490976.2025.2516703},
pmid = {40497323},
issn = {1949-0984},
mesh = {*Phylogeny ; Humans ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/isolation &amp; purification ; Vagina/microbiology ; Female ; Cluster Analysis ; High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; },
abstract = {Long-read amplicon profiling through read classification limits phylogenetic analysis of amplicons while community analysis of multicopy genes, relying on unique molecular identifier (UMI) corrections, often demands deep sequencing. To address this, we present a long amplicon consensus analysis (LACA) workflow employing multiple de novo clustering approaches based on sequence dissimilarity. LACA controls the average error rate of corrected sequences below 1% for the Oxford Nanopore Technologies (ONT) R9.4.1 and ONT R10.3 data, 0.2% for ONT R10.4.1, and 0.1% for high-accuracy ONT Duplex and Pacific Biosciences (PacBio) circular consensus sequencing (CCS) data in both simulated 16S rRNA and real 16-23S rRNA amplicon datasets. In high-accuracy PacBio CCS data, the clustering-based correction matched UMI correction, while outperforming 4× UMI correction in noisy ONT R10.3 and R9.4.1 data. Notably, LACA preserved phylogenetic fidelity in long operational taxonomic units and enhanced microbiome-wide phenotype characterization for synthetic mock communities and human vaginal samples.},
}
@article {pmid40497050,
year = {2025},
author = {Ma, X and Chen, Y and Li, L and Wang, T and Teng, K and Su, J and Li, L and Li, L and Li, H and Diao, W and Chen, G and Wang, J and Zhong, J},
title = {Efficient utilization of Shuanghuanglian medicine residues by microbial transformation with flavonoid glycosides-hydrolyzing strains.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1553399},
pmid = {40497050},
issn = {1664-302X},
abstract = {Shuanghuanglian, a traditional Chinese medicine, is well-known for its bioactive compounds, such as flavonoids, which offer significant health benefits. However, the production of Shuanghuanlian generates substantial pharmaceutical residues, which are often discarded as waste, posing significant environmental and economic challenges. To date, research on repurposing these medicine residues has been limited. This study utilized beneficial microbes to efficiently extract and utilize the residual bioactive compounds. Notably, a newly isolated Lactiplantibacillus plantarum strain LLB exhibited remarkable efficiency in converting flavonoid glycosides (e.g., phillyrin and luteoloside) into their corresponding aglycones. When combined synergistically with Bacillus subtilis and Saccharomyces cerevisiae, strain LLB maintained robust flavonoid glycoside conversion while enhancing lactobacilli viability in the fermented medicine residues. As a feed additive for broiler chickens, the fermented residue not only boosted antioxidant (superoxide dismutase) and anti-inflammatory (IL-10) markers, but also preserved growth performance and meat quality. Furthermore, the fermented residue modulated the gut microbiome, increasing Rikenella while reducing Elusimicrobiota and Parabacteroides abundances. Our findings demonstrate that microbial transformation of Shuanghuanglian residues offers a sustainable strategy for waste valorization and a novel feed additive for enhancing animal health.},
}
@article {pmid40497049,
year = {2025},
author = {Ren, X and Zheng, L and Huang, L and Zhao, J},
title = {The role of the gut microbiota in shaping the tumor microenvironment and immunotherapy of breast cancer.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1591745},
pmid = {40497049},
issn = {1664-302X},
abstract = {Breast cancer is the most prevalent malignancy among women worldwide and is a major contributor to cancer-related mortality. The tumor microenvironment (TME), composed of tumor cells, immune infiltrates, fibroblasts, and vascular components, is critically involved in tumor initiation, metastatic progression, and therapeutic response. In recent years, therapies targeting the TME have undergone rapid advancements, with the objective of enhancing antitumor immunity. Concurrently, mounting evidence underscores the pivotal role of the gut microbiota and its metabolites in modulating host immunity, influencing metabolic homeostasis, inflammation, and immune equilibrium. The composition and diversity of the gut microbiome influence breast cancer progression and patients' responses to immunotherapy. Therefore, modulating the gut microbiota is a promising strategy to enhance the clinical outcomes of TME-targeted immunotherapies. In this review, we discuss the influence of gut microbiota and its derived metabolites on breast cancer progression and immunotherapy prognosis and explore potential strategies to optimize immunotherapy through gut microbiota modulation.},
}
@article {pmid40496994,
year = {2025},
author = {Chen, J and Cao, J and Guo, B and Han, M and Feng, Z and Tang, J and Mo, X and Wang, J and Yang, Q and Pei, Y and Kuzyakov, Y and Ding, J and Makita, N and Yang, X and Zhang, H and Zhao, Y and Kong, D},
title = {Increased dependence on mycorrhizal fungi for nutrient acquisition under carbon limitation by tree girdling.},
journal = {Plant diversity},
volume = {47},
number = {3},
pages = {466-478},
pmid = {40496994},
issn = {2468-2659},
abstract = {Nutrient acquisition through symbiotic ectomycorrhizal fungi is carbon (C) costly but fundamental for plant growth, community, and ecosystem functioning. Here, we examined the functions of roots and mycorrhiza with respect to nutrient uptake after artificially inducing C limitation-seven months after girdling of an ectomycorrhizal tree, Pinus taeda. Root physiological activity (measured as root nitrogen content and root exudation) declined after girdling and was accompanied with 110% and 340% increases in mycorrhizal colonization and extramatrical hyphal length, respectively. Fungi colonizing roots switched to a community characterized by higher C efficiency (lower C cost) of nutrient acquisition (CENA, the amount of nutrient acquisition per unit C cost) and lower network complexity, indicating a tradeoff between CENA and stability of the fungal community. Root transcriptome analysis suggested a shift in metabolic pathways from a tricarboxylic acid cycle decomposition of carbohydrate to lipid biosynthesis to maintain closer associations with mycorrhiza for nutrient cycling after the girdling. By integrating multi-level evidence, including root transcriptome, fungal composition, and network complexity data, we demonstrate an increased dependence on mycorrhiza for nutrient acquisition under the C limitation condition, which is likely due to a shift to fungal community with higher CENA at the cost of lower stability.},
}
@article {pmid40496370,
year = {2025},
author = {Xia, Y and Liang, C and Luo, H and Zhang, Y},
title = {Therapeutic Potential of Flavonoids and Flavonoid-Rich Compounds in Irritable Bowel Syndrome.},
journal = {Drug design, development and therapy},
volume = {19},
number = {},
pages = {4895-4910},
pmid = {40496370},
issn = {1177-8881},
mesh = {*Flavonoids/pharmacology/therapeutic use/chemistry ; Humans ; *Irritable Bowel Syndrome/drug therapy/physiopathology ; Animals ; Gastrointestinal Microbiome/drug effects ; },
abstract = {Irritable bowel syndrome (IBS) is a group of functional gastrointestinal disorders, characterized by impaired brain-gut axis (BGA) interactions, leading to symptoms such as abdominal pain, bloating, and discomfort, which significantly affect patients' quality of life. Although individuals with IBS are commonly treated with medications and lifestyle modifications, the side effects of various treatments and their inconsistent efficacy often leads to a recurrence that poses a significant burden for patients. Flavonoids, flavonoid-rich compounds extensively found in plants and known for their low toxicity, have been identified as potentially beneficial for various digestive disorders in recent years; however, clinical trials have not been widely conducted. It was suggested that flavonoids and flavonoid-rich compounds may positively influence IBS symptoms through regulation of low-grade inflammation, oxidative stress in the gut, visceral hypersensitivity (VH), intestinal motility dysfunction, dysbiosis of gut microbiome, and BGA. This article reviews the potential role of flavonoids and their compounds in the therapy of IBS, along with the associated mechanisms. Additionally, we highlight key issues that warrant further investigation and discuss the prospects and challenges of using flavonoids for managing IBS.},
}
@article {pmid40496345,
year = {2025},
author = {Seneff, S and Nigh, G and Kyriakopoulos, AM},
title = {Is Deuterium Sequestering by Reactive Carbon Atoms an Important Mechanism to Reduce Deuterium Content in Biological Water?.},
journal = {FASEB bioAdvances},
volume = {7},
number = {6},
pages = {e70019},
pmid = {40496345},
issn = {2573-9832},
abstract = {Deuterium is a natural heavy isotope of hydrogen, having a neutron as well as a proton. Deuterium disrupts ATP synthesis in mitochondria, causing increased production of reactive oxygen species and reduced synthesis of ATP. Gut microbes likely play a significant role in providing deuterium depleted short chain fatty acids (SCFAs) to human colonocytes through hydrogen gas recycling. The production of deuterium depleted (deupleted) nutrients necessarily leaves behind deuterium enriched water, unless there is a process that can sequester deuterium in small molecules that are excreted through the feces. Here, we provide evidence that a small number of classes of uniquely structured carbon-nitrogen rings and bis-allylic carbon atoms in certain biologically active small molecules may play a crucial role in sequestering deuterium for export into feces or urine. Specifically, we have identified the imidazole ring present in histidine, histamine, and microbial derivatives of histidine, the tetraterpenoid lutein, bilirubin and the derivatives urobilinogen and stercobilinogen produced by gut microbes, and the bis-allylic carbons in polyunsaturated fatty acids as likely candidates for sequestering deuterium and thereby reducing the deuterium levels in the water-based medium. Normally, carbon atoms never exchange their bound protons with deuterons from the medium, but all the above classes of molecules are important exceptions to this rule, as has been shown experimentally.},
}
@article {pmid40496249,
year = {2025},
author = {Kit, A and Conway, K and Makarowski, S and O'Regan, G and Allen, J and Shultz, SR and Bodnar, TS and Christie, BR},
title = {Can the gut-brain axis provide insight into psilocybin's therapeutic value in reducing stress?.},
journal = {Neurobiology of stress},
volume = {36},
number = {},
pages = {100732},
pmid = {40496249},
issn = {2352-2895},
abstract = {There is growing interest in exploring the therapeutic potential and mechanisms of action of psilocybin on stress-related neuropsychiatric disorders, including depression, generalized anxiety disorder (GAD), post-traumatic stress disorder (PTSD), obsessive-compulsive disorder (OCD), addiction, and disordered eating. Despite promising progressions in preclinical and clinical research, the neurobiological and physiological mechanisms underlying the therapeutic effects of psilocybin remain complex, involving multiple systems with numerous homeostatic feedback signaling pathways throughout the body. This review paper explores how psilocybin mechanistically interacts with the gut microbiota, enteric nervous system, hypothalamic-pituitary axis, and how psilocybin influences the bidirectional communication between peripheral and neuronal systems. Shifting towards a more integrated paradigm to unravel the mechanisms through which psilocybin affects the bidirectional gut-brain axis holds the promise of significantly advancing our understanding of psilocybin-based therapies from preparation of treatment, administration, to proceeding long-term integration. Such an understanding can extend beyond the treatment of psychiatric disorders, further encompassing a broader spectrum of inflammatory-related disorders.},
}
@article {pmid40496070,
year = {2025},
author = {Ali, Z and Ayub, A and Lin, Y and Anis, S and Khan, I and Younas, S and Tahir, RA and Wang, S and Li, J},
title = {Lycium b arbarum's diabetes secrets: A comprehensive review of cellular, molecular, and epigenetic targets with immune modulation and microbiome influence.},
journal = {Journal of pharmaceutical analysis},
volume = {15},
number = {5},
pages = {101130},
pmid = {40496070},
issn = {2214-0883},
abstract = {Diabetes, a metabolic disease stemming from impaired or defective insulin secretion, ranks among the most severe chronic illnesses globally. While several approved drugs exist for its treatment, they often come with multiple side effects. Therefore, there is a pressing need for safe and effective anti-diabetic medications. Traditional Chinese medicine has recognized Lycium barbarum (LB; goji berry) plant, commonly known as "wolfberry fruit" in China, for over 2,000 years. Natural compounds derived from LB show promise in reducing diabetes levels. Although research on the impact of LB on diabetes is still limited, our review aims to explore the potential of LB in reducing the risk of diabetes and examine the underlying mechanisms involved. LB can modulate diabetes through various pathways, such as inhibiting α-amylase and α-glucosidase activities, promoting β-cell proliferation, stimulating insulin secretion, inhibiting glucagon secretion, improving insulin resistance and glucose tolerance, and enhancing antioxidant and anti-inflammatory activities. Additionally, LB improves gut flora and immunomodulation, further aiding diabetes management. These findings highlight the potential clinical utility of LB in managing diabetes and its complications within the framework of evidence-based modern medicine.},
}
@article {pmid40496020,
year = {2025},
author = {Ye, HL and Meng, XQ and Li, H and Sun, X and Lin, WZ and Zhou, LJ and Zhang, J and Hou, C and Xu, S and Chen, BY and Qiu, C and Li, YL and Wang, YL and Yan, LF and Duan, SZ},
title = {Periodontitis aggravates pulmonary fibrosis by Porphyromonas gingivalis-promoted infiltration of neutrophils and Th17 cells.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1595500},
pmid = {40496020},
issn = {2235-2988},
mesh = {Animals ; *Th17 Cells/immunology ; *Porphyromonas gingivalis/immunology/pathogenicity ; *Periodontitis/complications/microbiology/immunology ; Mice ; Disease Models, Animal ; *Neutrophils/immunology ; Humans ; Mice, Inbred C57BL ; Lung/microbiology/pathology ; *Bacteroidaceae Infections/microbiology/immunology/complications ; Interleukin-17/metabolism ; RNA, Ribosomal, 16S/genetics ; Male ; *Neutrophil Infiltration ; *Pulmonary Fibrosis/microbiology/immunology/pathology ; Mouth/microbiology ; Bleomycin ; Female ; Microbiota ; },
abstract = {INTRODUCTION: Idiopathic pulmonary fibrosis (IPF) is a fatal interstitial lung disease. However, the pathogeny of IPF is poorly understood, and therapeutic options are very limited. Periodontitis (PD) is a chronic inflammatory disease that leads to dysbiosis of both the oral microbiome and host immune responses. While previous studies have suggested a PD-IPF association, insights into the mechanisms remain limited.<br><br>METHODS: The PD mouse model was established by the ligation of molars and oral inoculation of subgingival plaques from PD patients and subsequently incorporated with a bleomycin-induced pulmonary fibrosis model. The effect of PD on pulmonary fibrosis was determined. Changes of immune cells were analysed using flow cytometry. Moreover, the microbiome changes of the lungs and oral cavity were assessed by 16S rRNA gene sequencing and fluorescence in situ hybridization. Finally, the effect and mechanism of the specific PD pathogen on pulmonary fibrosis were determined.<br><br>RESULTS: PD significantly aggravated pulmonary fibrosis in mice by increasing the infiltration of neutrophils and Th17 cells. Neutrophils and Th17 cells are critical in PD-induced aggravation of pulmonary fibrosis, and Th17 cells regulate neutrophils via IL-17A. The PD pathogen Porphyromonas gingivalis (Pg) was detected enriched in both the oral cavity and lungs. Pg was further determined to exacerbate pulmonary fibrosis by increasing the expansion of neutrophils and Th17 cells in mice.<br><br>CONCLUSION: PD aggravates pulmonary fibrosis in mice, which is likely induced by Pg-promoted infiltration of neutrophils and Th17 cells. Treatment targeting PD or Pg might be a promising strategy to clinically ameliorate IPF.},
}
@article {pmid40495681,
year = {2025},
author = {Xu, P and Uma Mageswary, M and Nisaa, AA and Balasubramaniam, SD and Samsudin, SB and Rusdi, NIBM and Jerip, ARA and Oon, CE and Bakar, MHA and Tan, JJ and Roslan, FF and Kadir, MN and Ismail, EHBE and Sany, SB and Tan, CS and Liong, MT},
title = {Impact of the Probiotic on the Modulation of Vaginal Bacterial and Fungal Microbiota in HPV-Positive Women.},
journal = {Molecular nutrition &amp; food research},
volume = {},
number = {},
pages = {e70142},
doi = {10.1002/mnfr.70142},
pmid = {40495681},
issn = {1613-4133},
support = {304/PTEKIND/6501096//USM-Probionic Grant/ ; 1001/PTEKIND/8070037//USM-Industry Research Matching Grant/ ; },
abstract = {This study examined the effects of administering the probiotic Lactiplantibacillus plantarum Probio87 on the vaginal microbiota of HPV-positive women, highlighting alterations in bacterial and fungal communities and their potential influence on vaginal and overall health. In a double-blind, randomized, placebo-controlled study, participants consumed daily doses of Probio87 (1 × 10[9] CFU/sachet) or a placebo for 12 weeks. Vaginal swabs were collected, and DNA was extracted for 16S rRNA and the internal transcribed spacer (ITS) region amplification via PCR, followed by sequencing of bacterial and fungal microbiota. The probiotic group showed improved alpha and beta diversity, with an increase in beneficial Lactobacillus (p = 0.014) and Phascolarctobacterium faecium (p = 0.041), while decreasing the abundance of pathogens like Streptococcus and Candida (p = 0.011). Additionally, vaginal health questionnaires linked probiotic use to improved vaginal and mental health in HPV-positive women. L. plantarum Probio87 demonstrated clinical and psychological benefits in HPV-positive women by balancing the vaginal microbiome, reducing pathogenic species, and promoting the growth of beneficial microorganisms.},
}
@article {pmid40495582,
year = {2025},
author = {Chalmers, JC and Hernandez-Kapila, YL},
title = {The role of the oral microbiome, host response, and periodontal disease treatment in Alzheimer's disease: A primer.},
journal = {Periodontology 2000},
volume = {},
number = {},
pages = {},
doi = {10.1111/prd.12631},
pmid = {40495582},
issn = {1600-0757},
support = {//OraPharma, Bridgewater, NJ/ ; },
abstract = {BACKGROUND: Alzheimer's disease (AD) is the leading cause of cognitive impairment and dementia in elderly patients worldwide. There is increasing evidence that periodontal disease may have an important role in the complex, multifactorial pathogenesis of AD.<br><br>AIM: This narrative review aims to (1) highlight the current understanding of the role of periodontal disease in AD, including molecular and immunological evidence, epidemiological studies, and biological mechanisms linking periodontal disease to AD; and (2) explore the potential impact of periodontal therapy as part of an individualized, multitherapeutic approach to AD.<br><br>MATERIALS AND METHODS: A literature search of the PubMed database was conducted using Boolean search strategies to identify publications related to the potential connections between periodontal disease and AD.<br><br>RESULTS: Most of the evidence for a link between periodontal disease and AD is limited to preclinical research and epidemiological investigations. A direct causal link has not yet been demonstrated in human clinical studies, but periodontal pathogenic bacteria have been detected in brain tissue and cerebrospinal fluid of patients with AD. Further, colocalization of gingipain proteases secreted by Porphyromonas gingivalis has been found in AD pathological lesions. Epidemiological studies support associations between periodontal disease and increased risk/prevalence of cognitive decline, AD, and AD mortality. Two mechanistic theories have been proposed to explain the connection between periodontitis and AD: the "microbial involvement" theory focuses on periodontal disease-associated pathogenic bacteria, whereas the "inflammatory cascade" theory focuses on proinflammatory mediators as drivers of neuroinflammation that may exacerbate pathologic lesions associated with AD. Preclinical studies of periodontal therapies targeting oral microbiota or their byproducts have investigated small-molecule gingipain inhibitors and novel therapeutics that restore oral microbial homeostasis (e.g., probiotic bacteriocin nisin). In animal models, gingipain inhibitors and nisin showed inhibitory effects on formation of pathological lesions of AD or neuroinflammation and microbiome changes, respectively; however, no impact on cognition was found with use of gingipain inhibitors in patients with mild-to-moderate AD.<br><br>CONCLUSIONS: Additional studies are needed to better understand the potential causal relationship between periodontal disease and AD, including further exploration of therapies targeting the oral-brain axis.},
}
@article {pmid40495530,
year = {2025},
author = {Rust, C and Tonge, D and van den Heuvel, LL and Asmal, L and Carr, J and Pretorius, E and Seedat, S and Hemmings, SMJ},
title = {Investigating the Blood Microbiome in Parkinson's Disease, Schizophrenia, and Posttraumatic Stress Disorder.},
journal = {Brain and behavior},
volume = {15},
number = {6},
pages = {e70629},
doi = {10.1002/brb3.70629},
pmid = {40495530},
issn = {2162-3279},
support = {//Stellenbosch University Postgraduate Scholarship Programme/ ; //South African Medical Research Council (SAMRC)/Stellenbosch University Genomics of Brain Disorders (GBD) Extramural Unit/ ; },
mesh = {Humans ; *Parkinson Disease/microbiology/blood ; *Schizophrenia/microbiology/blood ; Male ; *Stress Disorders, Post-Traumatic/microbiology/blood ; Female ; Middle Aged ; *Gastrointestinal Microbiome ; Aged ; Adult ; *Microbiota/physiology/genetics ; },
abstract = {INTRODUCTION: Recent studies have challenged the idea of sterile blood, suggesting the presence of a blood microbiome. The detection of microbial nucleic acids in blood is thought to reflect the status of distant microbial niches, including the gut. However, the origins and viability of these microbes remain debated. In this study, blood microbiome signatures in Parkinson's disease (PD), schizophrenia (SCZ), and posttraumatic stress disorder (PTSD) were evaluated by extracting RNA-sequencing (RNA-seq) reads that did not map to the human genome. Furthermore, we investigated the correlation between the gut and blood microbiome in PD, SCZ, and PTSD to gain insight into possible mechanisms behind disease etiology.<br><br>METHODS: We used whole-blood samples from PD (cases: n = 14; controls: n = 19), SCZ (cases: n = 17; controls: n = 22), and PTSD (cases: n = 45; trauma-exposed [TE] controls: n = 34) cohorts. The RNA paired-end sequence reads that did not map to the human reference genome (hg38/GRCH38) were isolated using the sequence alignment/map tools (SAMtools). These unmapped reads were classified against known archaeal, bacterial, and viral microbial genomes using Kraken2 (v2.1.3; k2_standard_08gb_20240112.taz.gz database), and further taxa abundances were estimated using Bracken (v2.9). The differential abundance of blood microbial signatures between case-control groups for each cohort was assessed using DESeq2 (v1.38.3). Each cohort was analyzed separately.<br><br>RESULTS: Statistically significant differences in the abundance of Pseudomonas aeruginosa and Acinetobacter wuhouensis in PD and Salmonella enterica, Staphylococcus aureus, Pseudomonas sp. CC6-YY-74, and Shinella sumterensis in SCZ were observed compared to cohort-specific controls. We observed no statistically significant differences in microbial signatures between PTSD cases and controls.<br><br>CONCLUSION: We found blood microbial signatures associated with PD and SCZ; however, no significant blood microbial signature was observed for PTSD. These results should be interpreted with caution as biases may have been introduced due to low concentrations of microbial signatures. Further research is required to understand the biological implications of these findings, in particular, taking into account the repurposed data source, and the potential for contamination (during phlebotomy, and background contamination from DNA extraction and reagents) known to impact the analysis of low-biomass samples.},
}
@article {pmid40495477,
year = {2025},
author = {Hurst, C and Zobel, G and Young, W and Olson, T and Parkar, N and Bracegirdle, J and Hannaford, R and Anderson, RC and Dalziel, JE},
title = {Social Isolation Induces Sex-Specific Differences in Behavior and Gut Microbiota Composition in Stress-Sensitive Rats.},
journal = {Brain and behavior},
volume = {15},
number = {6},
pages = {e70621},
doi = {10.1002/brb3.70621},
pmid = {40495477},
issn = {2162-3279},
support = {//Smarter Lives: New opportunities for dairy products across the lifespan/ ; C10X1706//Ministry of Business, Innovation and Employment/ ; },
mesh = {Animals ; Male ; Female ; *Gastrointestinal Microbiome/physiology ; Rats ; *Social Isolation/psychology ; *Stress, Psychological/microbiology/physiopathology ; *Behavior, Animal/physiology ; Rats, Inbred WKY ; Anxiety ; *Sex Characteristics ; Sex Factors ; Cecum/microbiology ; },
abstract = {BACKGROUND: Social isolation (SI) is an established rat model of chronic stress. We applied this to the stress-sensitive Wistar Kyoto (WKY) strain to explore brain-to-gut interactions associated with mood. Whether SI stress-induced behavioral changes are sex-specific or if they affect the microbiome in WKY is unknown. We hypothesized individually housed (IH) animals would be more anxious than pair-housed (PH), with sex differences. Male and female rats were either IH or PH from 70 to 112 days old and behavior was assessed in modified open field (OFTmod), elevated plus maze (EPM), and novel object recognition (NOR) tests. Cecal content DNA was analyzed by shotgun metagenome sequencing.<br><br>RESULTS: IH rats, particularly females, spent more time in the center of the OFTmod where the semi-novel feed was presented compared to PH group rats. There was a tendency for greater distance traveled, or potential hyperactivity, in IH female rats. Males stayed in the EPM closed arms more than females. No treatment difference occurred for recognition memory. SI altered cecal microbiome composition in females where housing was associated with seven differentially abundant taxa and 49 differentially abundant KEGG Level 3 ortholog/gene categories. Several relationships were noted between behavioral traits and relative abundance of microbiome taxa. There was a greater shift in female microbiome composition.<br><br>CONCLUSIONS: In summary, behavioral responses to the housing treatment were minimal. IH animals, particularly females, spent more time in the center of an OFT that contained food; this may have been an indication of depression, as opposed to anxiety. Housing status had a differential impact on the microbiome for females compared to males. The associations between cecal microbiota and activity in the modified OFT suggest that dietary interventions that influence the relative abundance of Bifidobacteria, Alistipes, and Muribaculaceae should be explored.},
}
@article {pmid40495475,
year = {2025},
author = {Wang, JY and Dunon, V and Ardevol, VN and Béguet, J and Jechalke, S and Pauwelyn, E and Lavigne, R and Smalla, K and Martin-Laurent, F and Springael, D},
title = {Dynamics of IS1071 and Its Accessory Gene Functions During Start-Up of an On-Farm Biopurification System.},
journal = {Environmental microbiology},
volume = {27},
number = {6},
pages = {e70120},
doi = {10.1111/1462-2920.70120},
pmid = {40495475},
issn = {1462-2920},
support = {222625//European Union's 7th Framework Programme (FP7) for Research and Technological Development/ ; RUN/19/001//KU Leuven/ ; C14/20/063//KU Leuven/ ; G0E8122N//the Research Foundation - Flanders (FWO) and the National Natural Science Foundation of China (NSFC)/ ; 202107650033//China Scholarship Council Fellowship/ ; },
mesh = {*DNA Transposable Elements/genetics ; *Microbiota/genetics ; *Pesticides/metabolism ; *Bacteria/genetics/metabolism/classification ; Wastewater/microbiology ; Farms ; Biodegradation, Environmental ; Betaproteobacteria/genetics/metabolism ; },
abstract = {Insertion sequences (IS) are drivers of bacterial diversification by facilitating recruitment and horizontal transfer of adaptive genes involving composite transposon structures, but their evolutionary role at the community level is rarely addressed. This study explores the dynamics of IS1071 and the cargo of IS1071-associated putative composite transposons in the establishment of a pesticide-degrading microbiome in an on-farm biopurification system (BPS)-which treats pesticide-contaminated wastewater and is considered a hotspot of microbial evolution-during the crucial start-up phase. Pesticide mineralisation assays and quantitative PCR targeting pesticide catabolic genes showed that the microbial community, upon feeding on the pesticide-contaminated wastewater, rapidly evolved into a pesticide-degrading microbiome. Concomitantly, an increase in the relative abundances of several mobile genetic elements, including IS1071, was observed, as well as a striking enrichment of xenobiotic catabolic genes in the cargo of putative IS1071-flanked composite transposons. The IS1071 cargo catabolic genes diversified over time and were mainly of Betaproteobacterial origin. Clear changes in community composition were observed both in the total bacterial community and the Betaproteobacterial community. We conclude that IS1071 supports the rapid establishment of pesticide catabolism in the BPS microbiome, highlighting the contribution of IS elements to microbial community adaptation to environmental changes.},
}
@article {pmid40495401,
year = {2025},
author = {Avendaño-Herrera, R and Tralma, L and Wicki, H and Barrios-Henríquez, F and Levipan, HA},
title = {Skin-Mucus Prokaryote Community of Atlantic Salmon (Salmo salar) in Response to Bath Challenge With Tenacibaculum dicentrarchi.},
journal = {Journal of fish diseases},
volume = {},
number = {},
pages = {e14157},
doi = {10.1111/jfd.14157},
pmid = {40495401},
issn = {1365-2761},
support = {FONDECYT 1230068//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; FONDECYT Iniciaci&#xf3;n 11200708//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; FONDAP 1523A0007//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; },
abstract = {Fish skin mucus is continuously replaced by epidermal cells, making it a highly dynamic microenvironment and an effective barrier against waterborne pathogens. The objective of this study was to understand the effects of tenacibaculosis, caused by the bacterium Tenacibaculum dicentrarchi, on the skin-associated microbiome of Atlantic salmon (Salmo salar). We used a vector-free and waterborne infection model of T. dicentrarchi strain TdCh05 in Atlantic salmon smolts for 21 days. Skin swab samples were collected at 2 h and 21 days post-infection (hpi and dpi, respectively) for 16S rRNA gene amplicon sequencing using DNA or complementary DNA (cDNA) as templates. Non-metric multidimensional scaling analysis grouped the samples into distinct clusters depending on the treatment and template. Similarity-Percentage (SIMPER) analysis indicated that between ~42% and 43% of the total amplicon sequence variants (ASVs) across all samples accounted for 90% of the compositional differences among all treatments and the two templates, highlighting the contribution of Tenacibaculum ASVs. Comparisons (by SIMPER) between non-infected and TdCh05-challenged fish at 2 hpi indicated that Tenacibaculum ASVs contributed to between ~52% and 58% of the differences in compositional clustering between samples. A significant drop in skin-mucus alpha diversity in TdCh05-challenged fish was also detected, followed by alpha diversity recovery at 21 dpi. In turn, at 21 dpi, microbiome changes were related to higher interaction complexity among taxa and community instability. Furthermore, 16S cDNA-based sequencing indicated that the potential activity of the Atlantic salmon skin-associated microbiome during disease progression was primarily driven by Tenacibaculum spp. Further research is needed to elucidate the role of other potentially active components (e.g., Pseudomonadales) of the skin-associated microbiome for the onset and/or progression of tenacibaculosis.},
}
@article {pmid40495357,
year = {2025},
author = {Brunetti, K and Zhou, Z and Shuchi, S and Berry, R and White, S and Zhang, Y and Allen, MS and Yang, S and Figueroa, JD and Colon-Perez, L},
title = {Longitudinal and Concurrent Changes in Brain and Gut due to Morphine Self-Administration.},
journal = {Addiction biology},
volume = {30},
number = {6},
pages = {e70059},
doi = {10.1111/adb.70059},
pmid = {40495357},
issn = {1369-1600},
support = {28334//Brain and Behavior Research Foundation/ ; K25DA047458/NH/NIH HHS/United States ; },
mesh = {Animals ; *Morphine/administration &amp; dosage/pharmacology ; Self Administration ; Magnetic Resonance Imaging ; Male ; *Brain/diagnostic imaging/drug effects ; Rats ; *Gastrointestinal Microbiome/drug effects ; *Analgesics, Opioid/administration &amp; dosage/pharmacology ; Feces/microbiology ; Rats, Sprague-Dawley ; *Brain-Gut Axis/drug effects ; },
abstract = {Opioid agonists are known for their effects on the opioid and dopaminergic systems; however, new research points to complementary changes in the gut underlying maladaptive changes associated with opioid use. The gut-brain axis (GBA) is a bidirectional signaling process that permits feedback between the brain and gut and is altered in subjects with opioid use disorders, but the spatiotemporal correspondence between quantitative translational measures of gut and brain health is not clear. In this work, we determined longitudinal and concurrent changes in the brain and gut of rodents trained to self-administer morphine for 14 days. Active lever presses delivered a single infusion of morphine (0.4 mg/kg/infusion). We used MRI and 16s rDNA analysis of faecal matter to identify changes from baseline (naïve, nondrug state) to an acute phase (early in the self-administration process, after 2 days of self-administration) and a chronic phase (late in the self-administration process, after 14 days of self-administration). Animals were scanned in a 7T MRI scanner three times (baseline, acute and chronic), and before scanning, faecal matter was collected from each rat. We found early changes in gut microbiota diversity and specific abundance as early as the acute phase that persisted into the chronic phase. In MRI, we identified alterations in diffusivity indices both within subjects and between groups, showing a main effect in the striatum and thalamus. We posit that gut changes precede the effects observed in MRI, with the striatum and thalamus emerging as crucial links mediating communication between the gut and the brain.},
}
@article {pmid40495179,
year = {2025},
author = {Liu, W and Zhou, X and Xiao, L and Huang, X and Chang, D and Zhong, X and Zeng, M and Xian, Y and Zheng, Y and Huang, W and Huang, R and Huang, M},
title = {The gut microbiota-mediated ferroptosis pathway: a key mechanism of ginsenoside Rd against metabolism-associated fatty liver disease.},
journal = {Chinese medicine},
volume = {20},
number = {1},
pages = {83},
pmid = {40495179},
issn = {1749-8546},
support = {2022YFC3501200//National Key Research and Development Program of China/ ; 82274080//National Natural Science Foundation of China Projects/ ; X2024019//School Management Project of Fujian University of Traditional Chinese Medicine/ ; X2024035//School Management Project of Fujian University of Traditional Chinese Medicine/ ; 2024Y9511//Fujian Provincial Science and Technology Innovation Joint Fund Project/ ; },
abstract = {BACKGROUND: Ginsenoside Rd (G-Rd), found in Panax species, has shown therapeutic potential against metabolism-associated fatty liver disease (MAFLD), but its mechanism has not been well elucidated. This study investigated the key mechanisms of G-Rd in modulating the gut microbiome and lipid peroxidation-mediated ferroptosis pathway in MAFLD.<br><br>METHODS: A high-fat diet-induced MAFLD model was established. Ultrastructural changes in liver tissue were observed using transmission electron microscopy. Metagenomics were employed to detect alterations in gut microbiota and their metabolites. Biochemical analysis and immunohistochemistry were used to examine liver injury, blood lipids, lipid peroxidation-related indicators, and tissue iron content.<br><br>RESULTS: G-Rd significantly reduced liver injury and steatosis in MAFLD mice and downregulated the elevated relative abundance of Firmicutes and the Firmicutes/Bacteroidetes ratio. It also significantly reduced the abundances of Faecalibaculum rodentium while increasing Muribaculum intestinale, with its functional role being relevant to lipid metabolism regulation. Moreover, G-Rd ameliorated mitochondrial damage and inhibited the ferroptosis pathway in the liver, which was associated with antioxidant-related factors mediated by Nrf2 signaling. The liver protective effect of G-Rd was driven by the regulation of gut microbiota, as demonstrated by antibiotic cocktail treatment and fecal microbiota transplantation.<br><br>CONCLUSIONS: G-Rd attenuated HFD-induced MAFLD by alleviating liver oxidative stress, lipid peroxidation, and ferroptosis through modulation of the gut microbiota. The antioxidant and anti-ferroptotic actions of G-Rd, mediated via the Nrf2 pathway, were found to contribute to the amelioration of liver injury and hepatic steatosis in MAFLD.},
}
@article {pmid40495162,
year = {2025},
author = {Wei, S and Shen, R and Lu, X and Li, X and He, L and Zhang, Y and Huang, X and Shu, Z},
title = {Integrative multi-omics investigation of sleep apnea: gut microbiome metabolomics, proteomics and phenome-wide association study.},
journal = {Nutrition &amp; metabolism},
volume = {22},
number = {1},
pages = {57},
pmid = {40495162},
issn = {1743-7075},
abstract = {BACKGROUND: Sleep apnea (SA) is linked to various diseases. This study examines the causal link between the gut microbiome and SA, exploring potential predictive factors and target proteins using a multi-omics approach with a Phenome-wide association study (PheWAS).<br><br>METHODS: Bidirectional Mendelian Randomization (MR) and Linkage Disequilibrium Score Regression (LDSC) were used to assess the genetic correlation and causal relationships between the gut microbiome and SA. Mediation analysis identified intermediate relationships involving "gut microbiome-inflammatory proteins-SA." Two-sample MR and colocalization analysis in the deCODE and UK Biobank Pharma Proteomics Project (UKB-PPP) databases identified protein quantitative trait loci (pQTL) associated with SA. Validation analysis used Fenland proteins, methylation quantitative trait loci (mQTL), and expression quantitative trait loci (eQTL). PheWAS screened 29 SA-associated SNPs and matched control SNPs (4:1 ratio) from UK Biobank data chosen through MR and LDSC analyses.<br><br>RESULTS: Inverse-variance weighted (IVW) bidirectional MR analysis did not establish a causal link between the gut microbiome and SA. C-C motif chemokine 28 showed causal relationships in both directions (forward IVW, P&#x2009;=&#x2009;0.0336; reverse IVW, P&#x2009;=&#x2009;0.0336). Intermediate connections were found between the Holdemanella genus and urinary plasminogen activator levels with SA. TIMP4 protein had a significant causal relationship with SA(IVW method: P&#x2009;>&#x2009;0.05, PH4&#x2009;=&#x2009;96.1%; P&#x2009;=&#x2009;7.85&#x2009;&#xd7;&#x2009;10[-6], PH4 in deCODE&#x2009;=&#x2009;97.4%). PRIM1 and BMP8 A were identified as potential influencers of SA through mQTL and eQTL analyses. PheWAS suggested body impedance and predicted mass as potential predictors of SA.<br><br>CONCLUSION: Bidirectional causal relationships exist between SA and inflammatory proteins, with TIMP4 identified as a pathogenic factor and potential therapeutic target. PRIM1 and BMP8 A may impact SA risk. Body impedance and predicted mass predict SA significantly.},
}
@article {pmid40494952,
year = {2025},
author = {Kerr, TD and Silver, NL and Duggal, R and Dai, J and Simmons, H and Singh, S and Shah, AA and Fredenburg, KM and Stacy, AR and McGrail, DJ},
title = {HPV status impacts oncobacteria abundance and prognostic relevance in head and neck squamous cell carcinoma.},
journal = {Oncogene},
volume = {},
number = {},
pages = {},
pmid = {40494952},
issn = {1476-5594},
support = {R00CA240689//U.S. Department of Health &amp; Human Services | NIH | National Cancer Institute (NCI)/ ; K08DE029503//U.S. Department of Health &amp; Human Services | NIH | National Institute of Dental and Craniofacial Research (NIDCR)/ ; },
abstract = {The intratumoral microbiome is emerging as an intrinsic microenvironment feature of some cancers, most notably those along the digestive tract. Opportunistic pathogenic bacteria, such as Fusobacterium nucleatum, can enrich within certain tumors, ultimately leading to alterations in the tumor microenvironment. However, why some tumors have a higher abundance of tumor-associated bacteria, or oncobacteria, than others remains unknown. To address this question, we quantified the presence of oncobacteria in head and neck squamous cell carcinomas (HNSCCs). We found that accumulation of oncobacteria was independent of tumor stage and size, as well as patient characteristics. In contrast, we discovered that human papillomavirus (HPV)-negative tumors exhibited significantly higher accumulation of oncobacteria than HPV+ tumors. Furthermore, the abundance of oncobacteria was associated with worse overall survival in HPV+ tumors. These findings were validated in an independent cohort. Subsequent analysis of Epstein-Barr virus (EBV)+ gastric cancer suggests this phenomenon generalizes to other virally mediated cancers. Co-culture studies of HNSCC cell lines with Fusobacterium nucleatum demonstrated that HPV-negative cells have enhanced proliferation in the presence of Fusobacterium nucleatum compared to HPV+ cells, suggestive of tumor cell intrinsic determinants of oncobacteria accumulation. Together, these results illuminate tumor features that contribute to the accumulation of oncobacteria.},
}
@article {pmid40494940,
year = {2025},
author = {Yajima, S and Kobayashi, S and Hashimoto, T and Nakamura, Y and Yamashita, R and Misumi, T and Sakamoto, Y and Horasawa, S and Fujisawa, T and Imai, M and Shibuki, T and Tsukada, Y and Bando, H and Masuda, H and Yoshino, T},
title = {Physical activity and cancer biology: a narrative review of molecular mechanisms and introduction of the SCRUM-MONSTAR LIFELOG study.},
journal = {International journal of clinical oncology},
volume = {},
number = {},
pages = {},
pmid = {40494940},
issn = {1437-7772},
support = {JP25ck0106950h0002//Japan Agency for Medical Research and Development/ ; 2024-A-05//National Cancer Center Research Development Fund/ ; },
abstract = {BACKGROUND: Physical activity (PA) has been consistently associated with improved cancer outcomes across multiple epidemiological studies. While the evidence for clinical benefits is strong, the underlying molecular mechanisms remain poorly understood. Recent technological advances now enable both continuous monitoring of PA through wearable devices and comprehensive molecular profiling through multi-omics approaches, including whole-genome sequencing (WGS)-based molecular residual disease (MRD) detection. This review examines current evidence regarding PA's effects on cancer biology and introduces the LIFELOG study, which aims to address critical knowledge gaps in this field.<br><br>METHODS: We review the current literature on PA and cancer with emphasis on molecular mechanisms, and present the design of the LIFELOG study, an ancillary study to MONSTAR-SCREEN-3. The LIFELOG study will enroll 170 post-surgical cancer patients who will wear the mSafety&#x2122; wrist device for continuous PA monitoring. We will investigate associations between PA metrics and multi-omics profiles including WGS-based MRD detection, transcriptome analyses, plasma proteomics, and gut microbiome analyses. The feasibility phase has already begun with encouraging preliminary results regarding device compliance and data quality.<br><br>DISCUSSION: Despite substantial evidence supporting PA's benefits in cancer prevention and survivorship, understanding which specific PA characteristics most effectively influence cancer outcomes remains unclear. The LIFELOG study represents the first comprehensive analysis integrating continuous PA monitoring with molecular profiling in cancer patients. By examining relationships between PA patterns and both MRD dynamics and multi-omics profiles, we aim to identify molecular mechanisms underlying exercise benefits and potentially guide development of evidence-based, precision PA interventions for cancer survivorship.<br><br>TRIAL REGISTRATION: This ancillary study (Institutional Review Board number: 2024-111, approved on November 18, 2024) is conducted under the MONSTAR-SCREEN-3 trial platform, which is registered in the UMIN Clinical Trials Registry (UMIN000053975, registered on March 27, 2024).},
}
@article {pmid40494904,
year = {2025},
author = {Mawarda, PC and van der Kaaij, R and Dini-Andreote, F and Duijker, D and Stech, M and Speksnijder, AG},
title = {Unveiling the ecological processes driving soil and lichen microbiome assembly along an urbanization gradient.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {99},
pmid = {40494904},
issn = {2055-5008},
support = {NWA.1389.20.111//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; NWA.1389.20.111//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; NWA.1389.20.111//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; NWA.1389.20.111//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; NWA.1389.20.111//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; PEN04908//The USDA National Institute of Food and Agriculture and Hatch Appropriations/ ; },
mesh = {*Soil Microbiology ; *Lichens/microbiology/classification ; *Microbiota ; *Urbanization ; Biodiversity ; *Bacteria/classification/genetics/isolation &amp; purification ; Ecosystem ; Soil/chemistry ; },
abstract = {Global biodiversity loss is accelerating due to the transformation of natural landscapes into agricultural and urban areas. Yet, research on the urbanization impact on environmental and host-associated microbiomes, particularly on the ecological processes that mediate their assembly and function, remains scarce. This study investigated the effects of an urbanization gradient on the diversity and assembly processes of the soil microbiome and the microbiomes of three epiphytic lichen species (Candelaria concolor, Physcia adscendens, and Xanthoria parietina). Our findings revealed that the urbanization gradient shaped the soil microbiome, while the lichen microbiomes exhibited strong host specificity and showed no significant changes in diversity along the urbanization gradient. Heterogeneous selection and dispersal limitation primarily governed the soil community assembly and higher community turnover in medium- and highly urbanized zones compared to low-urbanized zones, indicating an increased influence of environmental pressures, altered resources, and habitat fragmentation in more urbanized areas. The lichen microbiome assembly in each species was primarily governed by undominated processes regardless of urbanization level, indicating that both selection and stochasticity contributed to, but neither dominantly influenced, their assembly. The lichen microbiomes further revealed species-specific co-occurrence networks, with microbial compositional signatures and potential functions being essential for lichen fitness and urban ecosystem health. Taken together, our study contributes to understanding how microbial communities are assembled in urban environments, bridging the gap between conceptual theories and empirical findings in the urban ecology of soil and lichen-associated microbiomes.},
}
@article {pmid40494898,
year = {2025},
author = {Xu, F and Guo, Y and Thomas, SC and Saxena, A and Hwang, S and Vardhan, M and Li, X},
title = {Succinate modulates oral dysbiosis and inflammation through a succinate receptor 1 dependent mechanism in aged mice.},
journal = {International journal of oral science},
volume = {17},
number = {1},
pages = {47},
pmid = {40494898},
issn = {2049-3169},
support = {DE027074//U.S. Department of Health &amp; Human Services | NIH | National Institute of Dental and Craniofacial Research (NIDCR)/ ; DE028212//U.S. Department of Health &amp; Human Services | NIH | National Institute of Dental and Craniofacial Research (NIDCR)/ ; AG055787//U.S. Department of Health &amp; Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; },
mesh = {Animals ; *Dysbiosis/metabolism ; Mice ; *Succinic Acid/metabolism ; Mice, Knockout ; *Receptors, G-Protein-Coupled/metabolism ; *Inflammation/metabolism ; *Aging ; Alveolar Bone Loss/metabolism ; *Mouth/microbiology ; Mice, Inbred C57BL ; Male ; Microbiota ; },
abstract = {Aging involves the accumulation of various forms of molecular and cellular damage over time. Key features of aging, such as mitochondrial dysfunction, dysbiosis, and oxidative stress, are closely linked and largely driven by inflammation. This study examines the role of succinate, a key metabolite produced and utilized by cells of both host and microbes, and its receptor, succinate receptor 1 (SUCNR1), in age-related oral dysbiosis and inflammation. We examined young and aged wild-type (WT) and SUCNR1 knockout (KO) mice for this analysis. Our findings revealed significant aging-associated alveolar bone loss and succinate elevation in aged WT mice, along with notable changes in the oral microbiome. Conversely, aged KO mice showed reduced bone loss, lower succinate levels, less inflammation, and better-maintained microbial function. These results suggest that SUCNR1 is crucial in influencing aging-related succinate elevation, oral dysbiosis, and inflammation. Analysis of gene families and pathways in the oral microbiome demonstrated distinct aging-related changes between WT and KO mice, with the functional potential being preserved in the KO-aged group. This study underscores the importance of succinate elevation and signaling through SUCNR1 in regulating inflammation, alveolar bone loss, and shifts in the oral microbiome, offering potential targets for therapeutic interventions in age-related oral health issues.},
}
@article {pmid40494670,
year = {2025},
author = {McDowall, LS and McDermott, K},
title = {Review: Opportunities and challenges for the pork industry from circular livestock waste management systems.},
journal = {Animal : an international journal of animal bioscience},
volume = {},
number = {},
pages = {101547},
doi = {10.1016/j.animal.2025.101547},
pmid = {40494670},
issn = {1751-732X},
abstract = {Slurry management is becoming increasingly important as countries work to decarbonise towards Net Zero goals. After feed, slurry management and application is one of the main contributors to the greenhouse gas emissions and environmental pollution associated with pork production. Whilst traditionally considered a waste product, slurry is rich in nutrients and could be harnessed to reduce environmental impacts and improve on-farm resilience. Along with reducing the environmental impacts of pork production, farmers are increasingly looking to diversify their income streams and pig slurry offers tremendous potential to achieve this. This review identifies the opportunities and challenges to the pork sector from circular, sustainable waste management systems through insect bioconversion or on-farm biogas production, with a focus on the United Kingdom. Insect bioconversion of pig slurry, through the use of Black Soldier Fly larvae, presents opportunities not only to reduce the overall volume of slurry on a farm but also to reduce heavy metal contamination, alter the microbiome and provide a myriad of additional products. These products include fertiliser in the form of insect frass, protein, oils, and chitin from the insect exoskeleton, which has applications in industries such as wastewater treatment, pharmaceuticals and healthcare. Through on-farm biogas generation, farmers, particularly those in rural areas, could reduce their reliance upon volatile energy prices and generate electricity and heat to power on-farm activities. With additional infrastructure, biogas could be upgraded to produce biofuel and CO2 could be recovered, recycled, and sold into a variety of industries. Whilst there are still a number of outstanding questions that need to be answered and challenges that need to be addressed before the wide-scale rollout of these technologies, there is huge potential to harness the power of pig slurry. When designing the farm of the future, solutions will likely need to be tailored to an individual farm due to a range of variables including the stage of production, the number of pigs, the pig diet and the availability of co-products. However, despite these potential challenges, there is still considerable opportunity for the pork sector to harness this 'waste' product to decarbonise pig production and improve farm resilience.},
}
@article {pmid40493817,
year = {2025},
author = {Poole, R and Soffa, D and Hickman, K and Ognibene, O and Stuehr, M},
title = {Reproductive microbiota in humans: characterization and role in infertility.},
journal = {Systems biology in reproductive medicine},
volume = {71},
number = {1},
pages = {229-245},
doi = {10.1080/19396368.2025.2511323},
pmid = {40493817},
issn = {1939-6376},
mesh = {Humans ; Female ; *Microbiota ; Dysbiosis/microbiology ; *Infertility/microbiology ; Male ; *Infertility, Female/microbiology ; *Reproduction ; },
abstract = {Advancements in next generation sequencing technologies, including 16S rRNA amplicon sequencing, have vastly expanded our understanding of reproductive microbiota and its role in fertility. For example, in humans, the bacterial genus of Lactobacillus is the overwhelmingly dominant commensal bacterium within reproductive tissues and fluids, such as the vagina, and is an indicator of fertility in women. Shifts away from Lactobacillus allow for opportunistic pathogenic bacteria to inhabit the reproductive tract and result in dysbiosis and infertility. The goal of this review is to explore human reproductive microbiota including bacteria that commensally inhabit reproductive tissues and fluids as well as opportunistic pathogenic bacteria that can result in dysbiosis, infertility, and disease. Continued exploration of the microbiome and its association with reproductive health will aid in the development of targeted therapeutic strategies to positively modulate bacteria and improve fertility.},
}
@article {pmid40493448,
year = {2025},
author = {Ahoty, ESS and Fossou, RK and Magot, F and Ebou, ATE and Kouadjo-Zézé, CGZ and Marchesseau, B and Spina, R and Grosjean, J and Laurain-Mattar, D and Slezack, S and Zézé, A},
title = {Fusarium Antagonism Potential and Metabolomics Analysis of Endophytic bacteria isolated from Crotalaria retusa L., a traditional medicinal plant in Côte d'Ivoire.},
journal = {FEMS microbiology letters},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsle/fnaf056},
pmid = {40493448},
issn = {1574-6968},
abstract = {Sixty-four endophytic bacteria were isolated from roots, stems, and leaves of Crotalaria retusa L., a medicinal plant well-known for its antimicrobial properties in Côte d'Ivoire. Taxonomic characterisation revealed that these bacteria were mainly dominated by the genera Pseudomonas, Rhizobium, Bacillus and Inquilinus. The antagonistic activities of the endophytic bacteria against 2 phytopathogenic fungi affiliated with the genus Fusarium were tested using in vitro co-culture. Isolates belonging to the genus Inquilinus showed the highest inhibitory activities against Fusarium oxysporum f. sp. cubense, ranging from 40% to 57%, while the highest inhibitory activities against Fusarium graminearum were obtained with Bacillus isolates (∼66%). Finally, a metabolomic study of the leaves, stems, and seeds of the plant and of the endophytes presenting antifungal activity was carried out using LC-MS/MS analysis of the methanolic extracts of all active endophytic isolates. The identified metabolites of interest from the endophytes were mainly peptides, lipids, and steroids. Two pyrrolizidine alkaloids, monocrotaline and senecionine, were detected in the plant organs but not in the endophytic bacterial extracts. These results highlighted the potential of Crotalaria retusa L. plant and its endophytic microbiome as a source of bioactive molecules of interest and biocontrol agents against phytopathogenic Fusarium spp.},
}
@article {pmid40493444,
year = {2025},
author = {Bever, JD and Adelman, JS and Eppinga, MB and Archie, EA and Ezenwa, VO},
title = {Application of microbiome feedback theory to animals: Can parasites drive coexistence in ungulate communities?.},
journal = {Integrative and comparative biology},
volume = {},
number = {},
pages = {},
doi = {10.1093/icb/icaf087},
pmid = {40493444},
issn = {1557-7023},
abstract = {Parasites can have large impacts on host populations, but the extent to which parasite dynamics impact or respond to multi-species community structure remains uncertain. Empirical and theoretical studies within the host-microbiome feedback framework (often called plant-soil feedback) has provided strong evidence of the importance of soil pathogens to plant community structure and function. We adapt this framework to herd animals by extending the mathematics of host-microbiome feedback theory to accommodate increased likelihood of exposure to microbiomes from conspecific hosts rather than heterospecific hosts. We then integrate this framework with a model of interguild frequency dependence. Coupling this model with empirical observations, we estimate the host-specific fitness of gastro-intestinal nematodes living on ungulate species of Western United States. We find evidence that host-specific differences in nematode fitness could generate negative feedback on host fitness and contribute to coexistence of ungulates. Moreover, we find that this is more likely to be the case for pairs of ungulate species with high habitat overlap. If nematodes can indeed drive such negative feedbacks, then negative impacts of nematodes on their ungulate hosts should decline, i.e., be diluted, with increasing host diversity. While more work is necessary to confirm the underlying assumptions driving these conclusions, our work highlights the possibility that parasites play under appreciated roles in structuring animal communities.},
}
@article {pmid40493399,
year = {2025},
author = {Han, S and Zhang, Q and Zhang, H and Ma, J},
title = {Eucommia ulmoides and its inhibitory effects on prevotella in piglet gut microbiome through metagenomic and metabolomic analysis.},
journal = {Animal biotechnology},
volume = {36},
number = {1},
pages = {2503753},
doi = {10.1080/10495398.2025.2503753},
pmid = {40493399},
issn = {1532-2378},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Prevotella/drug effects ; Swine/microbiology/growth &amp; development ; *Eucommiaceae/chemistry ; Animal Feed/analysis ; Metagenomics ; Metabolomics ; Diet/veterinary ; Dietary Supplements ; Feces/microbiology ; },
abstract = {Eucommia ulmoides (EU) is a traditional medicinal plant widely cultivated across China. The combination of EU and feed significantly affects the growth performance, intestinal microbiota composition, and metabolic characteristics of weaned piglets. Forty Landrace x Yorkshire piglets were randomly assigned to four groups: a control group receiving a basal diet, three treatment groups receiving a basal diet supplemented with EU and EU with mix energy (EU+ME), and EU with high protein and energy (EU+HPE), respectively. Growth performance was monitored over a 25-day feeding period, and fecal samples were collected for subsequent metagenomic sequencing and metabolomic analysis. Piglets supplemented with EU, EU+ME, and EU+HPE exhibited significantly improved growth performance, compared to the control group. Metagenomic analysis revealed significant alterations in gut microbiota composition, with increased beneficial bacterial classes and suppression of Prevotella spp. Metabolomic profiling demonstrated distinct metabolic alterations among the treatment groups, with pathway impact analysis highlighting enhanced protein synthesis and energy metabolism. Furthermore, EU supplementation did not affect porcine epidemic diarrhea virus activity in vitro but reduced LPS-induced intestinal inflammation. These findings suggest that EU could be a promising natural additive for improving piglet health and growth, with potential implications for managing post-weaning challenges in swine production.},
}
@article {pmid40493213,
year = {2025},
author = {Vila Duplá, M},
title = {Advancements in Algal Microbiome Research: A Game-Changer for Climate Resilience and Invasion Success?.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {63},
pmid = {40493213},
issn = {1432-184X},
mesh = {*Microbiota ; *Climate Change ; *Seaweed/microbiology ; *Introduced Species ; },
abstract = {While marine microbiomes have been getting more attention in recent years, they remain understudied compared to those of terrestrial systems. With the refinement of molecular methods, microbiome research has extended to other key marine organisms such as macroalgae. The microbiome plays a key role in macroalgal health, adaptation to environmental conditions, and resilience to climate stressors. The main factors affecting the algal microbiome are host specificity (genetics, functional profile, phylum and species identity), life stage, morphology, thallus region, and tissue age. Other significant drivers of microbiome community structure include spatiotemporal distribution and environmental conditions, especially as global stressors intensify with climate change. The mechanisms through which the microbiome of invasive seaweeds might enhance their competitiveness over native species are still unclear. However, there is evidence that, like climate resilience, invasive potential is linked to the functional flexibility of associated microbiota, allowing the host to adapt to the new environmental conditions. The main objective of this review was to synthesize the current understanding of the macroalgal microbiome and propose future directions in microbiome research based on identified shortcomings. Based on the knowledge gaps detected, there is an urgent need for multi-factorial experimental studies that link host and microbiome gene expression through chemical signals under future climate change scenarios, standardization of analytical methods, and a focus on underrepresented geographical regions and species. While algal microbiome research holds great promise for predicting and mitigating the effects of climate change and invasive species, embracing new tools and tackling ecologically relevant mechanistic and applied questions will be essential to advancing this field.},
}
@article {pmid40492849,
year = {2025},
author = {Coccolini, F and Kirkpatrick, AW and Cremonini, C and Sartelli, M},
title = {Source control in intra-abdominal infections: What you need to know.},
journal = {The journal of trauma and acute care surgery},
volume = {},
number = {},
pages = {},
doi = {10.1097/TA.0000000000004654},
pmid = {40492849},
issn = {2163-0763},
abstract = {Providing optimal source control (SC) for intra-abdominal sepsis (IAS) is a critically important surgical principle, yet one that remains nebulous in terms of strict definitions and required conduct. The entire concept of SC has evolved in the last decades. Contemporary SC is not only surgical but also embraces minimally invasive percutaneous and medical therapies. We propose that adequate SC has evolved from the mere anatomical control of enteric leakage, cleansing of obvious contaminants and necrosis, to a more comprehensive anatomo-phyiological-biochemical model. While any breaches in the integrity of the gastrointestinal tract should be addressed urgently, SC should ultimately aim to control the generation and propagation of systemic biomediators, bacterial toxins, and toxic catabolites that perpetuate multisystem organ failure and death. Much urgently needs to be learned to understand and hopefully mitigate the dysbiotic influences of IAS on the human microbiome. Finally, the therapy offered should always be individualized, recognizing patient's unique pathophysiology, clinical condition, comorbidities, and predeclared preferences regarding invasive therapies and life-support.},
}
@article {pmid40492798,
year = {2025},
author = {Manjarres, Z and Plumb, AN and Sadler, KE},
title = {Bug in the Syndrome: Using the Gut Microbiome to Diagnose Complex Regional Pain Syndrome.},
journal = {Anesthesiology},
volume = {143},
number = {1},
pages = {20-21},
pmid = {40492798},
issn = {1528-1175},
}
@article {pmid40492779,
year = {2025},
author = {N S, S and Maske, VB and Punchappady Devasya, R and Rekadwad, BN},
title = {Draft genome sequence of an antibiotic-resistant Heyndrickxia oleronia strain UL23-01-03 isolated from the Arabian Sea coast, Dakshina Kannada, India.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0049425},
doi = {10.1128/mra.00494-25},
pmid = {40492779},
issn = {2576-098X},
abstract = {Here, we present the draft genome of antibiotic-resistant Heyndrickxia oleronia UL23-01-03 isolated from the Arabian Sea coast, Mangalore, India. The draft genome consists of 53 contigs totaling 5,003,978 bp, with a guanine-cytosine content of 34.8% and an OrthoANI of 97.37% compared to the reference strain.},
}
@article {pmid40492748,
year = {2025},
author = {LaGrutta, A and Arnold, D and Coetzee, O},
title = {Boosting Testosterone Naturally in Hashimoto's: A Case Report on Trans-Geranylgeraniol Supplementation.},
journal = {Alternative therapies in health and medicine},
volume = {},
number = {},
pages = {},
pmid = {40492748},
issn = {1078-6791},
abstract = {UNLABELLED: This case report details an integrative nutrition approach for a 27-year-old male diagnosed with Hashimoto's thyroiditis, suboptimal testosterone levels, and gut dysbiosis. Initially diagnosed in 2020, the patient presented with persistent thyroid autoimmunity and vitamin D insufficiency, but maintained stable androgen levels until 2023. Early interventions focused on foundational strategies, including anti-inflammatory dietary modifications, removal of gluten and dairy, and repletion of key nutrients such as vitamin D3/K2. Gut-directed therapies were added to support microbial diversity and intestinal barrier function, using digestive enzymes and increased intake of polyphenol-rich foods. Thyroid biomarkers showed steady improvement with these interventions. However, in 2023, the patient began to experience declining testosterone levels, accompanied by decreased muscle mass and athletic performance. To address this, a targeted supplementation protocol was introduced: 600 mg/day (two 300 mg capsules) of trans-geranylgeraniol (Annatto-GG™ 300) for nine weeks. Over the nine weeks, this intervention resulted in a clinically meaningful increase in total testosterone, accompanied by notable improvements in strength and physical performance. This case highlights the critical interplay between immune function, endocrine balance, and gastrointestinal health, illustrating the efficacy of a multifaceted, non-pharmacological approach in optimizing hormonal regulation and metabolic resilience. The findings emphasize the necessity of a systems-based, integrative framework in addressing complex, interrelated physiological imbalances.<br><br>KEYWORDS: case report, testosterone, low testosterone and thyroid function, autoimmune disease, Hashimoto's thyroiditis, TRT, mevalonate pathway, Leydig cell function, infammation, trans-geranylgeraniol, vitamin D, microbiome, gut-thyroid.},
}
@article {pmid40492742,
year = {2025},
author = {Edwin, NR and Duff, A and Deveautour, C and Brennan, F and Abram, F and O'Sullivan, O},
title = {Consistent microbial insights across sequencing methods in soil studies: the role of reference taxonomies.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0105924},
doi = {10.1128/msystems.01059-24},
pmid = {40492742},
issn = {2379-5077},
abstract = {Microbes play an important role in soil functioning, underpinning food production systems and delivering an array of essential ecosystem services. To elucidate how these microbes relate to ecosystem functions, accurate identification and classification of soil microorganisms are important. We evaluated the comparability of shotgun and amplicon sequencing approaches by profiling soil microbiota from 131 diverse temperate grassland soils across Ireland. We assessed method comparability in terms of (i) detection and classification of the most abundant phyla, (ii) their capacity to differentiate samples based on their microbial community, and (iii) their capacity to link microbial communities to measured nitrogen cycle functions. Our findings reveal that both methods offer moderately similar outcomes, providing consistent detection of major phyla, similar microbial community differentiation patterns, and largely identifying the same relationships between the phyla and nitrogen functions. The variations observed between the two methods were mostly associated with differences in the choice of reference taxonomy. Amplicon sequencing represents a cost-effective, less computationally demanding option, while shotgun sequencing provides deeper taxonomic resolution and access to the latest databases, making it suitable for detailed microbial profiling. Our study underscores the need for careful method selection based on project requirements, database availability, and financial resources.IMPORTANCEStudying the microorganisms in soil remains a challenge as soils are one of the most complex and diverse environments. Compounding these challenges is the lack of culturable representatives in soil, with over 99% of soil microorganisms yet to be cultivated in a laboratory setting. Leveraging next-generation sequencing technologies, which bypass traditional culture-dependent methods, scientists are now able to attain low-cost, high-throughput DNA sequencing that can detect even the rarest microorganisms within samples. The present study rigorously compares amplicon and shotgun sequencing techniques in profiling microbial communities across diverse temperate grassland soil samples, focusing on how different databases, classifiers, and sequencing methods influence the results. Our study underscores the crucial need for a harmonized taxonomic database that could greatly enhance comparability and accuracy in the understanding of soil microbiomes.},
}
@article {pmid40492703,
year = {2025},
author = {Alam, I and Marasco, R and Momin, AA and Aalismail, N and Laiolo, E and Martin, C and Sanz-Sáez, I and Foix, BB and Sá, EL and Kamau, A and Guzmán-Vega, FJ and Jamil, T and Acinas, SG and Gasol, JM and Gojobori, T and Agusti, S and Daffonchio, D and Arold, ST and Duarte, CM},
title = {Widespread distribution of bacteria containing PETases with a functional motif across global oceans.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf121},
pmid = {40492703},
issn = {1751-7370},
abstract = {Accumulating evidence indicates that microorganisms respond to the ubiquitous plastic pollution by evolving plastic-degrading enzymes. However, the functional diversity of these enzymes and their distribution across the ocean, including the deep sea, remain poorly understood. By integrating bioinformatics and artificial intelligence-based structure prediction, we developed a structure- and function-informed algorithm to computationally distinguish functional polyethylene terephthalate-degrading enzymes (PETases) from variants lacking PETase activity (pseudo-PETase), either due to alternative substrate specificity or pseudogene origin. Through in vitro functional screening and in vivo microcosm experiments, we verified that this algorithm identified a high-confidence, searchable sequence motif for functional PETases capable of degrading PET. Metagenomic analysis of 415 ocean samples revealed 23 PETase variants, detected in nearly 80% of the samples. These PETases mainly occur between 1000 and 2000 m deep and at the surface in regions with high plastic pollution. Metatranscriptomic analysis further identified PETase variants that were actively transcribed by marine microorganisms. In contrast to their terrestrial counterparts-where PETases are taxonomically diverse-those in marine ecosystems were predominantly encoded and transcribed by members of the Pseudomonadales order. Our study underscores the widespread distribution of PETase-containing bacteria across carbon-limited marine ecosystems, identifying and distinguishing the PETase motif that underpins the functionality of these specialised cutinases.},
}
@article {pmid40492462,
year = {2025},
author = {Zheng, Z and Liu, X and Zhang, Y and Zhang, H and Chen, S and Zhu, J},
title = {Research trends and hotspots on gut microbiota in rheumatoid arthritis: a bibliometric analysis from 2004 to 2024.},
journal = {Clinical and experimental rheumatology},
volume = {},
number = {},
pages = {},
doi = {10.55563/clinexprheumatol/3899sf},
pmid = {40492462},
issn = {0392-856X},
abstract = {OBJECTIVES: Rheumatoid arthritis (RA) is an autoimmune condition linked to alterations in the gut microbiota. This study aims to conduct a comprehensive analysis of the literature on gut microbiota and RA over the past 21 years through bibliometric methods, thereby identifying emerging trends and hotspots, and providing insights for the precision treatment of RA.<br><br>METHODS: The authors analysed articles on gut microbiota in RA published from 2004 to 2024 based on the Web of Science Core Collection database. Bibliometric methods employed tools such as CiteSpace, VOSviewer, and COOC to conduct visual analyses of countries, institutions, references, and keywords.<br><br>RESULTS: 1,267 articles from 80 countries led by China and the United States were included. A notable increase in annual publications reflects the growing interest in this field. Simultaneously, contributions and cooperation of institutions in the field are discussed. Furthermore, co-citation and keyword analysis revealed four research hotspots: 1. specific gut microbiota like Prevotella copri modulating immune responses in RA; 2. dietary interventions regulating gut microbiota as therapeutic approaches for RA; 3. high-throughput sequencing technologies enabling microbiome analysis for diagnostic RA; and 4. probiotics and plant-derived bioactive compounds serving as promising adjunctive therapies for RA management.<br><br>CONCLUSIONS: The relationship between RA and gut microbiota has been extensively studied. The hotspot of future research may be to further study the pathological mechanism of gut microbiota in RA and how to improve the symptoms of RA patients through dietary therapy and adjustment of the homeostasis of gut microbiota.},
}
@article {pmid40492389,
year = {2025},
author = {Shen, H and Ma, X and Zhang, L and Li, H and Zheng, J and Wu, S and Zuo, K and Yin, Y and Wang, J and Tan, B},
title = {Targeted Intervention Strategies for Maternal-Offspring Transmission of Christensenellaceae in Pigs via a Deep Learning Model.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e03411},
doi = {10.1002/advs.202503411},
pmid = {40492389},
issn = {2198-3844},
support = {2021YFD1300401//National Key R&amp;D Program/ ; U24A20445//National Natural Science Foundation of China/ ; U20A2054//National Natural Science Foundation of China/ ; U22A20510//National Natural Science Foundation of China/ ; 2024JJ1004//Natural Science Foundation of Hunan Province/ ; 2024RC3188//Natural Science Foundation of Hunan Province/ ; },
abstract = {Understanding the mechanisms of maternal microbial transmission is crucial for early gut microbiota development and long-term health outcomes in offspring. However, early maternal microbial interventions remain a challenge due to the complexity of accurately identifying transmitted taxa. Here, the maternal-offspring microbial transmission model (MOMTM), a deep learning framework specifically designed to map maternal microbiota transmission dynamics across pig breeds and developmental stages, is introduced. Using MOMTM, key transmitted taxa, such as the Christensenellaceae R-7 are successfully predicted, which show high transmission centrality during early development periods. Additionally, it is demonstrated that galacto-oligosaccharide intervention in sows promotes a Christensenellaceae R-7-dominated enterotype and improves fiber digestibility in offspring. Further analysis reveals that Christensenellaceae, particularly Christensenella minuta, have enhanced adhesion and mucin utilization capabilities, facilitating its gut colonization. These findings highlight MOMTM's potential as a novel approach for microbiota-targeted health interventions in early life, offering insights into strategies that promote gut health and development from birth.},
}
@article {pmid40492293,
year = {2025},
author = {O'Hare, MA and Rust, C and Malan-Müller, S and Pirovano, W and Lowry, CA and Ramaboli, M and van den Heuvel, LL and Seedat, S and , and Hemmings, SMJ},
title = {Preliminary Insights Into the Relationship Between the Gut Microbiome and Host Genome in Posttraumatic Stress Disorder.},
journal = {Genes, brain, and behavior},
volume = {24},
number = {3},
pages = {e70025},
pmid = {40492293},
issn = {1601-183X},
support = {//South African Medical Research Council Genomics of Brain Disorders Unit/ ; //Stellenbosch University Postgraduate Scholarship Programme/ ; 847635//Una4Career/ ; PID2021-126468OA-I00//Knowledge Generation Grant from the Ministry of Science and Innovation (Spain)/ ; PNSD 2022I033//Ministry of Health (Spain) Research Grant/ ; 138430//National Research Foundation of South Africa/ ; //South African Medical Research Council: Self-Initiated Research Grant/ ; 024.004.012//NWO Gravitation: BRAINSCAPES - a roadmap from neurogenetics to neurobiology, grant no./ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Stress Disorders, Post-Traumatic/genetics/microbiology ; Male ; Female ; Adult ; Genome-Wide Association Study ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Polymorphism, Single Nucleotide ; },
abstract = {Posttraumatic stress disorder (PTSD) may develop following trauma exposure; however, not all trauma-exposed individuals develop PTSD, suggesting the presence of susceptibility and resilience factors. The gut microbiome and host genome, which are interconnected, have been implicated in the aetiology of PTSD. However, their interaction has yet to be investigated in a South African population. Using genome-wide genotype data and 16S rRNA (V4) gene amplicon sequencing data from 53 trauma-exposed controls and 74 PTSD cases, we observed no significant association between the host genome and summed abundance of Mitsuokella, Odoribacter, Catenibacterium and Olsenella, previously reported as associated with PTSD status in this cohort. However, PROM2 rs2278067 T-allele was significantly positively associated with the summed relative abundance of these genera, but only in individuals with PTSD and not trauma-exposed controls (p < 0.014). Polygenic risk scores generated using genome-wide association study summary statistics from the PGC-PTSD Overall Freeze 2 were not predictive of gut microbial composition in this cohort. These preliminary results suggest a potential role for the interaction between genetic variation and gut microbial composition in the context of PTSD, underscoring the need for further investigation.},
}
@article {pmid40492114,
year = {2025},
author = {Zhang, Y and Fan, J and Zhao, J and Zhu, H and Xia, Y and Xu, H},
title = {A telomere-associated molecular landscape reveals immunological, microbial, and therapeutic heterogeneity in colorectal cancer.},
journal = {Frontiers in molecular biosciences},
volume = {12},
number = {},
pages = {1615533},
pmid = {40492114},
issn = {2296-889X},
abstract = {BACKGROUND: Colorectal cancer (CRC) ranks among the most prevalent malignancies of the gastrointestinal tract and remains a leading cause of cancer-related mortality worldwide. Although telomere biology has been increasingly implicated in immune modulation and tumor progression, its clinical significance in CRC remains poorly understood.<br><br>METHODS: We developed a telomere score, termed TELscore, by integrating transcriptomic and intratumoral microbiome profiles from publicly available colorectal cancer (CRC) cohorts. To comprehensively characterize TELscore subgroups, we performed pathway enrichment analysis, tumor immune microenvironment (TIME) profiling, and microbiome niche assessment. Whole-slide histopathological images (WSIs) and immunohistochemical (IHC) staining were utilized to visualize immune features, including tertiary lymphoid structures (TLSs), across subgroups. Patients were stratified into high and low TELscore categories, and the predictive robustness was validated across multiple independent training and validation cohorts. Chemotherapeutic drug sensitivity was evaluated using pharmacogenomic data from the Genomics of Drug Sensitivity in Cancer (GDSC) database. Furthermore, the predictive capacity of TELscore for immunotherapy response was independently assessed in an external cohort. Finally, single-cell RNA sequencing (scRNA-seq) analysis was conducted to further dissect the cellular landscape and immunological heterogeneity within the TME.<br><br>RESULTS: TELscore stratified patients into two biologically and clinically distinct subgroups. The high TELscore group, which exhibited significantly shorter DFS, showed marked enrichment of tumorigenic pathways such as EMT, along with a distinctly immunosuppressive TME. This was reflected by elevated ESTIMATE/TIDE scores and corroborated by CIBERSORT, which revealed increased infiltration of M0 macrophages and upregulation of immunosuppressive signatures. In contrast, the low TELscore group was enriched for cell cycle related pathways, including E2F targets and the G2/M checkpoint, and demonstrated higher infiltration of pro-inflammatory M1 macrophages. 16S rRNA sequencing further revealed a divergent intratumoral microbiome between subgroups, the high TELscore group harbored significantly greater relative abundance of Selenomonas and Lachnoclostridium, two pathogenic genera previously associated with colorectal tumorigenesis. Complementary histopathological assessment via WSI demonstrated a marked absence of intraTLSs in high TELscore tumors. From a therapeutic standpoint, high TELscore tumors exhibited reduced sensitivity to standard chemotherapeutic agents-including Fluorouracil, Irinotecan, Oxaliplatin, and Docetaxel-as reflected by elevated IC50 values. Conversely, these tumors demonstrated increased susceptibility to MAPK pathway inhibitors, such as Selumetinib and Trametinib. Notably, TELscore also served as a robust predictor of immunotherapy response, which was validated in the IMvigor210 cohort. Finally, scRNA analysis highlighted profound cellular and functional divergence between TELscore subgroups. We identified intensified intercellular communication between inflammatory macrophages and fibroblasts, reinforcing the presence of an immunosuppressive niche.<br><br>CONCLUSION: TELscore is a robust stratification tool that captures the interplay between tumor biology, immune characteristics, and microbial ecology in colorectal cancer. By identifying clinically relevant subtypes with distinct therapeutic vulnerabilities, TELscore offers a powerful framework to advance personalized treatment and precision oncology.},
}
@article {pmid40492113,
year = {2025},
author = {Nuñez-Selles, AJ and Nuñez-Musa, RA and Guillen-Marmolejos, RA},
title = {Linking oxidative stress biomarkers to disease progression and antioxidant therapy in hypertension and diabetes mellitus.},
journal = {Frontiers in molecular biosciences},
volume = {12},
number = {},
pages = {1611842},
pmid = {40492113},
issn = {2296-889X},
abstract = {Oxidative stress (OS) is increasingly recognized as a key factor linking hypertension (HTN) and diabetes mellitus (DM). This review summarizes recent evidence regarding the dual role of OS as both an instigator and an amplifier of cardiometabolic dysfunction. In HTN, reactive oxygen species (ROS) produced by NADPH oxidases (NOXs) and mitochondrial dysfunction contribute to endothelial impairment and vascular remodeling. In DM, hyperglycemia-induced ROS production worsens beta-cell failure and insulin resistance through pathways such as the AGE-RAGE signaling, protein kinase C (PKC) activation, and the polyol pathway. Clinically validated biomarkers of OS, such as F2-isoprostanes (which indicate lipid peroxidation), 8-OHdG (which indicates DNA damage), and the activities of redox enzymes like superoxide dismutase (SOD) and glutathione peroxidase (GPx), show strong correlations with disease progression and end-organ complications. Despite promising preclinical results, the application of antioxidant therapies in clinical settings has faced challenges due to inconsistent outcomes, highlighting the need for targeted approaches. Emerging strategies include: 1. Mitochondria-targeted antioxidants to enhance vascular function in resistant HTN; 2. Nrf2 activators to restore redox balance in early diabetes; and 3. Specific inhibitors of NOX isoforms. We emphasize three transformative areas of research: (i) the interaction between the microbiome and ROS, where modifying gut microbiota can reduce systemic OS; (ii) the use of nanotechnology to deliver antioxidants directly to pancreatic islets or atherosclerotic plaques; and (iii) phenotype-specific diagnosis and therapy guided by redox biomarkers and genetic profiling (for example, KEAP1/NRF2 polymorphisms). Integrating these advances with lifestyle modifications, such as following a Mediterranean diet and exercising regularly, may provide additional benefits. This review outlines a mechanistic framework for targeting OS in the comorbidity of HTN and DM while identifying critical knowledge gaps, particularly regarding the timing of antioxidant signaling and the development of personalized redox medicine, which may serve as a reference for researchers and clinicians working in this area.},
}
@article {pmid40492077,
year = {2025},
author = {Ahrens, AP and Lynch, K and Hyöty, H and Lloyd, RE and Petrosino, J and Triplett, EW and Agardh, D},
title = {Temporal dynamics of the gut microbiome preceding celiac disease in genetically at-risk children.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.05.29.25328357},
pmid = {40492077},
abstract = {Longitudinal study of the microbial dysbiosis preceding celiac disease (CD) is needed, particularly in the first several years of life. Within the Environmental Determinants of Diabetes in the Young (TEDDY) multi-national prospective cohort study, a case-cohort study of 306 CD cases (i.e., seroconverting by 48 months of age), with controls matched 2:1 by site, gender, and time of birth, was assessed. Temporal microbiome case-control dynamics were modelled by 16S rRNA analysis of monthly sequential stool samples taken from age three months up to age four (or until the development of CD). Significant differences were identified across time, including key taxa that break down gluten and influence inflammation, all before the development of autoantibodies. Key bacterial associations with environmental factors such as diet were assessed using detailed longitudinal nutrient intake and diary data, along with genetic variants conferring high CD risk.},
}
@article {pmid40491929,
year = {2025},
author = {Hao, J and Jie, Y and Lu, Z and Ye, T and Meng, J and Liu, C and Yan, J and Zheng, Y and Dong, Z and Gu, Z},
title = {Integrated transcriptomic and microbiomic analyses reveal mechanisms of Decapod iridescent virus 1 resistance in Macrobrachium rosenbergii.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1611481},
pmid = {40491929},
issn = {1664-3224},
mesh = {Animals ; *Palaemonidae/virology/microbiology/genetics/immunology ; *Transcriptome ; *Disease Resistance/genetics ; Gene Expression Profiling ; *Gastrointestinal Microbiome ; Hepatopancreas/virology ; },
abstract = {Selective breeding for DIV1-resistant Macrobrachium rosenbergii is an effective strategy to mitigate aquaculture losses; however, the underlying resistance mechanisms remain poorly understood. In this study, approximately 2,300 prawns from 46 families were subjected to a DIV1 challenge test. Based on survival rate, viral load, histopathological observations, and viral gene detection in the transcriptome, one resistant family (R27-1) and one susceptible family (S2-2) were identified. Hepatopancreas transcriptomic (RNA-Seq) and gut microbiome analyses were conducted on samples at 0, 24, and 48 hours post-infection (hpi) from both families. A total of 144, 68, and 1,170 differentially expressed genes (DEGs) were identified at the respective timepoints. Three DEGs-including one corresponding to an uncharacterized lncRNA, an esterase E4-like protein, and a CUB-serine protease-were consistently differentially expressed at all timepoints. Transcriptomic data suggest that Melanogenesis, energy metabolism, and Steroid hormone biosynthesis pathways are associated with DIV1 resistance. Notable DEGs included hemocyanin, cytochrome P450, alkaline phosphatase-like, Friend leukemia integration 1 transcription factor-like, cytochrome P450 9e2-like, interferon regulatory factor 4-like, dual specificity protein phosphatase 10-like, trypsin II-P29-like, and cytochrome c oxidase subunit III. In addition, the potential probiotic Enterococcus casseliflavus (relative abundance: 0.51% vs 0.03%) was more abundant in the resistant family, whereas Lactococcus garvieae (RA: 20.18% vs 70%) was enriched in the susceptible one. These findings highlight the combined contribution of host transcriptomic responses and gut microbial communities to DIV1 resistance. To the best of our knowledge, this is the first study to integrate transcriptomic and microbiomic analyses for investigating DIV1 resistance in M. rosenbergii. These findings provide novel insights into the host-pathogen interaction and offer valuable targets for selective breeding of DIV1-resistant M. rosenbergii in aquaculture.},
}
@article {pmid40491838,
year = {2025},
author = {Tian, C and Zhang, Z},
title = {Sociobiome signals by high income for increased mobile genetic elements in the gut microbiome of Chinese individuals.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1596101},
pmid = {40491838},
issn = {1664-302X},
abstract = {INTRODUCTION: Mobile genetic elements (MGEs) play a crucial role in the dissemination of antibiotic resistance genes (ARGs), posing significant public health concerns. Despite their importance, the impact of socioeconomic factors on MGEs within the human gut microbiome remains poorly understood.<br><br>METHODS: We reanalyzed 1,382 publicly available human gut metagenomic datasets from Chinese populations, including 415 individuals from high-income eastern regions and 967 individuals from low- and middle-income western regions. MGEs were identified and categorized into functional groups, and statistical analyses were conducted to assess regional differences and correlations with economic indicators.<br><br>RESULTS: A total of 638,097 nonredundant MGEs were identified. Among these, MGEs related to integration/excision had the highest mean abundance, while those involved in stability/transfer/defense had the lowest. The abundance of MGEs was significantly higher in the eastern population compared to the western population. Moreover, MGE abundance was positively correlated with regional GDP per capita and with ARG abundance within individuals.<br><br>DISCUSSION: Our findings suggest that socioeconomic development and industrialization are associated with increased MGE abundance in the human gut microbiome, which may in turn facilitate the spread of ARGs. These results highlight a potential unintended consequence of economic advancement on public health through microbiome-mediated antibiotic resistance.},
}
@article {pmid40491716,
year = {2025},
author = {Zhang, Y and Wu, H and Jin, M and Feng, G and Wang, S},
title = {The gut-heart axis: unveiling the roles of gut microbiota in cardiovascular diseases.},
journal = {Frontiers in cardiovascular medicine},
volume = {12},
number = {},
pages = {1572948},
pmid = {40491716},
issn = {2297-055X},
abstract = {The gut microbiome refers to the collective genomes of the approximately 1,000-1,150 microbial species found in the human gut, called the gut microbiota. Changing the gut microbiota composition has been shown to affect cardiovascular health significantly. Numerous studies have demonstrated the part that gut microbiota and its metabolites play in the development and course of several illnesses, including colon cancer, heart failure, stroke, hypertension, and inflammatory bowel disease. With cardiovascular diseases responsible for more than 31% of all fatalities globally, conditions like hypertension, atherosclerosis, and heart failure are serious global health issues. Developing preventive measures to fight cardiovascular diseases requires understanding how the gut microbiota interacts with the cardiovascular system. Understanding the distinctive gut microbiota linked to cardiovascular diseases has been made possible by microbial sequencing analysis. The gut microbiota and cardiovascular diseases are closely related, and more profound knowledge of this association may result in treatment strategies and broad guidelines for enhancing cardiovascular health through gut microbiome modification. This review summarizes the role of gut microbiota in cardiovascular diseases, highlighting their influence on disease progression and potential therapeutic implications.},
}
@article {pmid40491555,
year = {2025},
author = {Cheng, H and Li, H and Li, Z and Wang, Y and Liu, L and Wang, J and Ma, X and Tan, B},
title = {The role of glycosylated mucins in maintaining intestinal homeostasis and gut health.},
journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)},
volume = {21},
number = {},
pages = {439-446},
pmid = {40491555},
issn = {2405-6383},
abstract = {The intestinal mucus barrier is a crucial component of the host's innate defense system, playing a vital role in regulating intestinal microecology and maintaining intestinal homeostasis. Glycosylated mucins, the core components of this barrier, are essential for preserving its integrity by preventing bacterial degradation. Additionally, mucins significantly contribute to establishing a balanced symbiotic relationship between the host and microbes. These mucins have the potential to mitigate intestinal epithelial damage by capturing and transporting cell debris and pathogenic bacteria. Meanwhile, certain bacteria help maintain the equilibrium and stability of the gut microbiome by degrading glycosylated mucins to utilize the carbohydrate chains, thus affecting the cytokine expression to regulate the synthesis and secretion of specific glycans. Investigating the complex connections between the mucus barrier and mucin glycosylation holds great promise for advancing our understanding of gastrointestinal disease mechanisms, paving the way for innovative prevention and treatment strategies.},
}
@article {pmid40491539,
year = {2025},
author = {Ronchetti, F and Schmitt, T and Keller, A and García-Reina, A and De la Rua, P and Steffan-Dewenter, I and Polidori, C},
title = {The Significance of Genetic Relatedness and Nest Sharing on the Worker-Worker Similarity of Gut Bacterial Microbiome and Cuticular Hydrocarbon Profile in a Sweat Bee.},
journal = {Ecology and evolution},
volume = {15},
number = {6},
pages = {e71519},
pmid = {40491539},
issn = {2045-7758},
abstract = {The cuticular hydrocarbon (CHC) profile and the gut microbiome (GM) are crucial traits which have a significant impact on the life of bees. In honey bees, the CHC profile and the GM interact finely through trophallaxis, such that the characteristics of the GM are partially defined by the chemical recognition among sisters. However, most of the known primitively eusocial bees show simpler social traits, including moderate genetic relatedness among colony members, often due to workers' nest drifting or dispersal, and lack of trophallaxis. Hence, primitively eusocial bees offer a great opportunity to evaluate the respective role of worker-worker genetic relatedness and of the environment in which the adult lives (residency nest) on the interaction between CHC profile and GM. Here, we investigated such relationships in the primitively eusocial digger bee Halictus scabiosae (Halictidae). We found a high rate of nest-drifting by workers, which leads to a consequent highly variable intra-colonial genetic relatedness. Genetically closely related workers, even occupying distant nests, did possess both a more similar microbiome profile and a more similar CHC profile. Additionally, sharing the same nest seemed to account for the similarity of both CHC profile and GM among workers. Interestingly, differences in microbiome profile and in CHC profile were highly and positively correlated across workers, even after controlling for genetic relatedness. The results of our study point towards an impact of genetic relatedness on the GM and the CHC profile, but also suggest that microbiome and CHC profile are partially acquired through adult nest environment, and that microbiome possibly has a role in shaping the cuticular chemistry.},
}
@article {pmid40491474,
year = {2025},
author = {Vuong, N and Alomia, M and Byne, A and Gade, P and Philipson, TR and Alhammad, RI and Skislak, CJ and Alruwaili, I and Alsaab, FM and Zhou, W and Howard, M and Brothers, A and Still, AH and Araujo, RP and Van Hoek, M and Birkaya, B and Espina, V and Hoefer, RA and Liotta, L and Luchini, A},
title = {Lactobacillus rhamnosus-derived extracellular vesicles influence calcium deposition in a model of breast cancer intraductal calcium stress.},
journal = {iScience},
volume = {28},
number = {6},
pages = {112538},
pmid = {40491474},
issn = {2589-0042},
abstract = {Extracellular calcium export by the breast ductal epithelium is crucial during lactation and plays a significant role in breast cancer progression. Intraductal calcium deposition is a hallmark of aggressive premalignant lesions. This study tested the hypothesis that microbiome-derived extracellular vesicles (EVs) influence calcium modulation in premalignant breast cancer lesions. Based on the analysis of plasma, serum, saliva, and tissue collected from breast cancer patients and controls (N = 150), Lactobacillus rhamnosus (Lr) was chosen as the model microbiota. In a BT-474 human breast cancer cell line monolayer culture under acute calcium stress, Lr EVs enhanced intracellular calcium intake. In a BT474 3D spheroid model under chronic calcium stress, Lr EVs increased extracellular calcium deposition and mRNA expression of calcium export channel plasma membrane calcium-transporting ATPase 2 (PMCA2) and stromal interaction molecule 1 (STIM1) in a dose-dependent manner. We propose that Lr EVs influence calcium regulation and mineral deposition, thereby affecting premalignant breast cancer progression.},
}
@article {pmid40491460,
year = {2025},
author = {Manning, SK and Taylor, SL and Leong, LEX and Papanicolas, LE and Canoy, I and Morgan, LC and Rogers, GB},
title = {Direct assessment of airway microbiota in primary ciliary dyskinesia end-stage lung disease.},
journal = {ERJ open research},
volume = {11},
number = {3},
pages = {},
pmid = {40491460},
issn = {2312-0541},
abstract = {Microbiome assessment of sputum and lung tissue in primary ciliary dyskinesia identified rapid replacement by a single P. aeruginosa clone during end-stage lung disease https://bit.ly/4eV5s0H.},
}
@article {pmid40491436,
year = {2025},
author = {Li, D and Zhang, DY and Chen, SJ and Lv, YT and Huang, SM and Chen, C and Zeng, F and Chen, RX and Zhang, XD and Xiong, JX and Chen, FD and Jiang, YH and Chen, Z and Mo, CY and Chen, JJ and Zhu, XL and Zhang, LJ and Bai, FH},
title = {Long-term alterations in gut microbiota following mild COVID-19 recovery: bacterial and fungal community shifts.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1565887},
pmid = {40491436},
issn = {2235-2988},
mesh = {Humans ; *COVID-19/microbiology ; *Gastrointestinal Microbiome ; *Fungi/classification/genetics/isolation &amp; purification ; Female ; *Bacteria/classification/genetics/isolation &amp; purification ; Male ; Adult ; Middle Aged ; Feces/microbiology ; SARS-CoV-2 ; *Mycobiome ; Probiotics ; Metagenomics ; China ; },
abstract = {OBJECTIVE: COVID-19 has had a profound impact on public health globally. However, most studies have focused on patients with long COVID or those in the acute phase of infection, with limited research on the health of individuals who have recovered from mild COVID-19. This study investigates the long-term changes in bacterial and fungal communities in individuals recovering from mild COVID-19 and their clinical relevance.<br><br>METHODS: Healthy individuals from Hainan Province were enrolled before the COVID-19 outbreak, along with individuals recovering from COVID-19 at 3 months and 6 months post-recovery. Stool, blood samples, and metadata were collected. Metagenomic sequencing and Internal Transcribed Spacer (ITS) analysis characterized bacterial and fungal communities, while bacterial-fungal co-occurrence networks were constructed. A random forest model evaluated the predictive capacity of key taxa.<br><br>RESULTS: The gut microbiota of COVID-19 recoverees differed significantly from that of healthy individuals. At 3 months post-recovery, probiotics (e.g., Blautia massiliensis and Kluyveromyces spp.) were enriched, linked to improved metabolism, while at 6&#xa0;months, partial recovery of probiotics (e.g., Acidaminococcus massiliensis and Asterotremella spp.) was observed alongside persistent pathogens (e.g., Streptococcus equinus and Gibberella spp.). Dynamic changes were observed, with Acidaminococcus massiliensis enriched at both baseline and 6 months but absent at 3 months. Co-occurrence network analysis revealed synergies between bacterial (Rothia spp.) and fungal (Coprinopsis spp.) taxa, suggesting their potential roles in gut restoration. The bacterial random forest model (10 taxa) outperformed the fungal model (8 taxa) in predicting recovery status (AUC = 0.99 vs. 0.80).<br><br>CONCLUSION: These findings highlight the significant long-term impacts of mild&#xa0;COVID-19 recovery on gut microbiota, with key taxa influencing metabolism and immune regulation, supporting microbiome-based strategies for recovery management.},
}
@article {pmid40491434,
year = {2025},
author = {Liu, L and Guo, L and Dai, J and Cai, X and Wu, B},
title = {Fecal 16S rRNA sequencing and metabolomics reveal abnormal metabolism activity in preterm infants with different gestational ages.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1530653},
pmid = {40491434},
issn = {2235-2988},
mesh = {Humans ; *Infant, Premature/metabolism ; *Feces/microbiology ; *Gestational Age ; *RNA, Ribosomal, 16S/genetics ; Infant, Newborn ; *Metabolomics/methods ; *Gastrointestinal Microbiome/genetics ; Female ; Male ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Chromatography, Liquid ; Tandem Mass Spectrometry ; Metabolome ; Metabolic Networks and Pathways ; Sequence Analysis, DNA ; DNA, Bacterial/genetics/chemistry ; },
abstract = {OBJECTIVE: This study aims to conduct a comprehensive analysis of the differences in gut microbiota and metabolomics in preterm infants stratified by gestational age.<br><br>METHODS: Fresh fecal samples were collected from neonates within the first 3 days after birth. The gut microbiota composition and the changes in specific taxa abundance were analyzed using 16S rRNA sequencing. Metabolomic profiling was performed using liquid chromatography-tandem mass spectrometry (LC-MS/MS). Participants were categorized into four groups based on gestational age at birth: PreA group (34-36 weeks), PreB group (32-33 weeks), PreC group (28-31 weeks), and control group (37-42 weeks). Metabolic pathways were identified through metabolomics analysis, referencing the Kyoto Encyclopedia of Genes and Genomes (KEGG) database.<br><br>RESULTS: Notably, Principal Coordinates Analysis (PCoA) showed clear separation among samples from all groups, with significant differences noted in the PreC group when compared with the other three. We found a strong association between Escherichia-Shigella and Ureaplasma genera with infants born before 32 weeks of gestation, suggesting a higher risk of opportunistic infections for preterm infants under this gestational threshold. As gestational age increases, Megamonas and Prevotella gradually emerged, while Escherichia-Shigella and Ureaplasma progressively diminished. KEGG enrichment analysis indicated that Pyrimidine metabolism was a differentially regulated pathway between the PreA group and the control group. Interestingly, the only major differential metabolic pathway between the PreB group and the control group was Arachidonic acid metabolism. The bubble diagram revealed significant enrichment of differential metabolites in Pyrimidine and beta-Alanine metabolism pathways when comparing the PreC group with the control group.<br><br>CONCLUSION: Significant differences were observed in the fecal microbiome and metabolome between preterm and full-term infants, particularly in those born before 32 weeks of gestation. These findings suggested that the gut microbial system in preterm infants undergone progressive maturation, approaching a "healthy" state characteristic of full-term infants as gestational age increases.},
}
@article {pmid40491237,
year = {2025},
author = {Rosas, HD and Morgan, XC and Tao, Y and Lai, F and Mercaldo, ND},
title = {Gut dysbiosis in Down syndrome: A potentially unexplored culprit for early Alzheimer's disease.},
journal = {Alzheimer's &amp; dementia : the journal of the Alzheimer's Association},
volume = {21},
number = {6},
pages = {e70330},
doi = {10.1002/alz.70330},
pmid = {40491237},
issn = {1552-5279},
support = {//Libbi Thomas Foundation/ ; /NH/NIH HHS/United States ; /AG/NIA NIH HHS/United States ; U01 AG051406/AG/NIA NIH HHS/United States ; U01 AG051412/AG/NIA NIH HHS/United States ; U19 AG068054/AG/NIA NIH HHS/United States ; },
mesh = {Humans ; *Down Syndrome/microbiology/complications ; *Dysbiosis/microbiology/complications ; *Gastrointestinal Microbiome/genetics ; *Alzheimer Disease/microbiology/etiology ; Male ; Female ; *Cognitive Dysfunction/microbiology ; Middle Aged ; Feces/microbiology ; RNA, Ribosomal, 16S/genetics ; Aged ; Adult ; },
abstract = {INTRODUCTION: Gut dysbiosis has been found to play a role in sporadic Alzheimer's disease (AD) but has not been explored in Down syndrome (DS), despite the strong relationship between DS and early AD. Here, we compared the gut microbiomes of 20 adults with DS, either cognitively stable or with mild cognitive impairment.<br><br>METHODS: DNA from stool samples was profiled using 16S rRNA sequencing.<br><br>RESULTS: Cognitive status was associated with a significant difference in overall microbiome composition (p&#xa0;<&#xa0;0.01) and with significant differences in the abundance of Bacteroidaceae, Enterobacteriaceae, and Christensenellaceae.<br><br>CONCLUSION: Just as in sporadic AD, AD in DS is associated with gut dysbiosis. Our work suggests that this is an important area for future investigation, one that may provide a novel and important target for therapeutic intervention.<br><br>HIGHLIGHTS: Alterations in the gut microbiome are present in adults with Down syndrome (DS) with mild cognitive impairment (MCI). Increased taxa in DS-MCI that contribute to inflammation and disrupt blood-brain barrier. Suggests a possible role of gut dysbiosis in Alzheimer's disease in adults with DS.},
}
@article {pmid40491066,
year = {2025},
author = {Elisia, I and Yeung, M and Kowalski, S and Wong, A and Dietrich, C and Chang, V and Wu, S and Hollman, S and Dyer, R and Nguyen, KN and Krystal, G},
title = {Low Carbohydrate Diet Containing Soy Protein and Fish Oil Reduces AOM/DSS-Induced Colon Cancer, in Part, by an Acetate-Mediated Reduction in TH17 Cell Differentiation.},
journal = {Molecular nutrition &amp; food research},
volume = {},
number = {},
pages = {e70113},
doi = {10.1002/mnfr.70113},
pmid = {40491066},
issn = {1613-4133},
abstract = {Since our previous studies found a low-carbohydrate (CHO) diet containing soy protein and fish oil (i.e., 15%Amylose/Soy/FO) significantly reduced tobacco carcinogen-induced lung nodules in A/J mice, breast tumors in C3(1)/Tag mice, and myelomalignancy in miR-146a knockout mice, we asked herein if this CHO diet could also reduce colorectal cancer. We tested the efficacy of the 15%Amylose/Soy/FO diet in preventing colitis-induced colorectal cancer using an azoxymethane/dextran sodium sulfate BALB/c mouse model. The 15%Amylose/Soy/FO diet significantly reduced colon tumor numbers compared to a Western diet and this was associated with a reduction in blood glucose, and a trend towards an increase in plasma β-hydroxybutyrate and an increase in liver fatty acid synthase, suggesting a systemic metabolic shift from glucose to fatty acids as an energy source. In addition, our CHO diet reduced proinflammatory cytokines, induced a marked change in the fecal microbiome, an increase in cecal and fecal acetate, and a reduction in interleukin-17A expressing cells in the colonic tumors of mice on the 15%Amylose/Soy/FO diet. Taken together, our results suggest the 15%Amylose/Soy/FO diet ameliorates colitis and prevents the subsequent development of colorectal cancer, in part by an acetate-mediated reduction in TH17 cell development.},
}
@article {pmid40490836,
year = {2025},
author = {Zhang, L and Fei, Z and Ding, Y and Zhang, Y and Ding, Z and Huang, Y and Wang, J and Liu, G and Bai, L and Wu, J},
title = {Inonotus obliquus fermentation product improves growth performance and meat quality probably through intestine and antioxidant capacity enhanced by gut microbes and metabolites regulation in rabbits.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {61},
pmid = {40490836},
issn = {2524-4671},
support = {SDAIT-21-12//Shandong Province Modern Agricultural Industry Technology System/ ; 2023YFD1800301//National Key R&amp;D Program of China/ ; ts201511069//Distinguished Talent Projects/ ; },
abstract = {BACKGROUND: Inonotus obliquus is a medicinal edible fungus that contains a variety of biologically active ingredients and has multiple physiological effects. When supplemented in avian diet, Inonotus obliquus has proved to be beneficial. However, information regarding these effects on mammals is scanty. The present study aims to investigate the effect of supplementation of Inonotus obliquus fermentation product (IOFP) on the growth performance, antioxidant capacity, meat quality, intestinal function and gut microbiota of rabbit exploratorily, which may act as an important feed additive and also as an antibiotic alternative with its medicinal properties.<br><br>RESULTS: Dietary supplementation of IOFP increased body weight (P&#x2009;<&#x2009;0.01) at the initial 21 d and improved feed efficiency throughout the 35 d experimental period when compared to control group. At the same time it was observed that meat quality and carcass parameters improved upon supplementation of IOFP. Additionally, IOFP supplementation resulted in significant increases (P&#x2009;<&#x2009;0.05) in total antioxidant capacity (T-AOC), superoxide dismutase (SOD), and nitric oxide (NO) activity or concentration in the serum and muscle. The crypt depth decreased significantly, whereas the villus height/crypt depth (V/C) value&#xa0;increased (P <&#xa0;0.05). The concentration of secrete IgA (sIgA) of the intestine also increased (P&#x2009;<&#x2009;0.05). IOFP supplementation significantly increased the fold change expression of Claudin 1, Occludin, ZO1, and ZO2 (P&#x2009;<&#x2009;0.05) when compared to the respective gene expression levels of the duodenum and jejunum tissues of control group. Further study on cecum microbiota revealed that IOFP supplementation increased the microbiota diversity by increasing the number of beneficial bacteria and reducing the numbers of pathological bacteria. It was observed that cecum metabolites produced in the treated group were related to antioxidants, antiinflammation and antidepressive effects. The harmful metabolites related to fat deposition, loss of appetite and cytotoxic conditions decreased. Pearson's correlation studies between different bacteria and metabolites revealed that the metabolites produced were regulated by the beneficial and harmful bacteria respectively.<br><br>CONCLUSIONS: IOFP enhanced intestinal morphology and function, and organismic antioxidant capacity, probably by increasing the concentration of beneficial microbiota and metabolites resulting in improvement of body weight, feed efficiency, and parameters related to meat quality and carcass traits of rabbits.},
}
@article {pmid40490712,
year = {2025},
author = {Wang, W and Liu, M and Wang, Z and Ma, L and Zhao, Y and Ye, W and Li, X},
title = {Causal associations between gut microbiota, metabolites, and idiopathic normal pressure hydrocephalus: a two‑sample Mendelian randomization study.},
journal = {BMC neurology},
volume = {25},
number = {1},
pages = {249},
pmid = {40490712},
issn = {1471-2377},
mesh = {*Gastrointestinal Microbiome/genetics ; Humans ; *Mendelian Randomization Analysis/methods ; *Hydrocephalus, Normal Pressure/genetics/microbiology/metabolism ; Genome-Wide Association Study ; Aged ; Male ; Female ; },
abstract = {BACKGROUND: Implying connections with gut microbiome and serum metabolites, idiopathic normal pressure hydrocephalus (INPH) emerges as a prevalent neuropsychiatric condition in the elderly. Our objective was to systematically evaluate the potential causality between gut microbiome, derived metabolites, and INPH through the implementation of Mendelian randomization (MR) methodology.<br><br>METHODS: We utilized summary data from extensive genome-wide association studies, encompassing 196 gut microbiomes from the MiBioGen consortium (n&#x2009;=&#x2009;18,340), 486 serum metabolites from the KORA and TwinsUK studies (n&#x2009;=&#x2009;7,824), and individuals with INPH (case&#x2009;=&#x2009;767, control&#x2009;=&#x2009;375,610), for MR causal estimates. The leading analysis utilized the inverse-variance weighted (IVW) method, supplemented by weighted mode, MR-Egger, weighted median and simple mode approaches. Sensitivity analyses included MR-Egger intercept, Cochran's Q test, leave-one-out analysis and MR-PRESSO.<br><br>RESULTS: Our study primarily relied on the IVW method, confirming a causality between 9 genetically predicted abundance of gut microbiomes and INPH. We found an adverse correlation with genetically predicted abundance of order Clostridiales, genus Eubacteriumeligensgroup, genus Gordonibacter, genus Ruminococcus1 concerning INPH. Conversely, class Melainabacteria, genus Eubacteriumruminantiumgroup, genus Adlercreutzia, genus Dialister, genus RikenellaceaeRC9gutgroup potentially correlated with increased INPH risk. As for derived metabolites, IVW estimates indicated a causal connection between 25 genetically predicted serum metabolites and INPH. Sensitivity analysis underscored the robustness of our findings.<br><br>CONCLUSION: Our MR analysis provides evidence supporting the causality of certain gut microbial taxa and their derived metabolites on INPH. This underscores the potential for interventions targeting specific gut microbiota and derived metabolites in the treatment and prevention of INPH.},
}
@article {pmid40490500,
year = {2025},
author = {Robinson, CM and Carreño, D and Weber, T and Chen, Y and Riglar, DT},
title = {A discovery platform for identification of host-induced bacterial biosensors from diverse sources.},
journal = {Molecular systems biology},
volume = {},
number = {},
pages = {},
pmid = {40490500},
issn = {1744-4292},
support = {211230/Z/18/Z//Wellcome Trust (WT)/ ; President's PhD Scholarship//Imperial College London (ICL)/ ; },
abstract = {Synthetic biology approaches such as whole-cell biosensing and 'sense-and-respond' therapeutics aim to enlist the vast sensing repertoire of gut microbes to drive cutting-edge clinical and research applications. However, well-characterised circuit components that sense health- and disease-relevant conditions within the gut remain limited. Here, we extend the flexibility and power of a biosensor screening platform using bacterial memory circuits. We construct libraries of sensory components sourced from diverse gut bacteria using a bespoke two-component system identification and cloning pipeline. Tagging unique strains using a hypervariable DNA barcode enables parallel tracking of thousands of unique clones, corresponding to ~150 putative biosensors, in a single experiment. Evaluating sensor activity and performance heterogeneity across various in vitro and in vivo conditions using mouse models, we identify several biosensors of interest. Validated hits include biosensors with relevance for autonomous control of synthetic functions within the mammalian gut and for non-invasive monitoring of inflammatory disease using faecal sampling. This approach will promote rapid biosensor engineering to advance the development of synthetic biology tools for deployment within complex environments.},
}
@article {pmid40490486,
year = {2025},
author = {Hendricks, H and Israel, S and Weitkamp, JH and Pakala, S and Rajagopala, S and Banerjee, R},
title = {Associations between antibiotic exposure intensity, intestinal microbiome perturbations, and outcomes in premature neonates with bacteremia.},
journal = {Journal of perinatology : official journal of the California Perinatal Association},
volume = {},
number = {},
pages = {},
pmid = {40490486},
issn = {1476-5543},
support = {5UL1TR002243-03//Vanderbilt Institute for Clinical and Translational Research (VICTR)/ ; },
abstract = {BACKGROUND: Neonatal microbiome dysbiosis is associated with infectious complications.<br><br>METHODS: Prospective weekly stools were collected over 1 year from hospitalized preterm infants with birthweight &#x2264;2000&#x2009;g and postnatal age (PNA)&#x2009;&#x2264;2 months. Neonates with bacteremia (cases) were matched to uninfected controls. Stools were analyzed using whole metagenome sequencing. Intensity of antibiotic exposure was compared using an Antibiotic Spectrum Index (ASI).<br><br>RESULTS: We analyzed 398 stools from 40 cases and 39 controls. Cases had lower &#x3b1; diversity beyond 4 weeks PNA. Cases with subsequent infections after index bacteremia had persistently lower &#x3b1; diversity, while cases without subsequent infections demonstrated recovery of microbiome diversity. Compared to controls, cases had greater ASI at multiple timepoints, higher Enterococcus spp. and lower anaerobe abundance.<br><br>CONCLUSIONS: Compared to controls, premature neonates with bacteremia had intestinal microbiomes with lower &#x3b1; diversity, higher Enterococcus spp. and lower anaerobe abundance. These changes were associated with recurrent infectious complications.},
}
@article {pmid40490465,
year = {2025},
author = {Yong, SB and Ha, M and Cho, S},
title = {Microbiome Metabolite-Incorporated Lipid Nanoparticles Augment CD8[+] T Cell Memory Potential and Immunity for mRNA Cancer Vaccines.},
journal = {ACS biomaterials science &amp; engineering},
volume = {},
number = {},
pages = {},
doi = {10.1021/acsbiomaterials.5c00738},
pmid = {40490465},
issn = {2373-9878},
abstract = {Recently, mRNA/lipid nanoparticle (LNP)-based vaccines have been successfully applied to prevent infectious diseases, and several types of neoantigen-encoding mRNA cancer vaccines are currently under clinical trials. While mRNA vaccines effectively induce adaptive immune responses to antigens, mRNA vaccine-induced immunity is shortly maintained, and the longevity of the immune memory, especially improving the CD8[+] T cell memory potential, could be even more important. Previously, microbiome metabolites have shown T cell memory potential-augmenting effects via regulating the immunometabolism. Herein, we develop microbiome metabolite-incorporated LNPs (mmi-LNPs) and evaluate their potential to enhance T cell memory responses following mRNA vaccination. In various ionizable LNP formulations, mmi-LNPs elicited more stem cell-like memory T cells (T-SCMs) and augmented central and effector memory T cell responses, which indicates the general applicability of mmi-LNPs. Notably, butyrate-incorporated mmi-LNP exhibited the strongest effects. In conclusion, we suggest microbiome metabolite-incorporated LNP as a next-generation delivery vehicle for mRNA vaccines.},
}
@article {pmid40490101,
year = {2025},
author = {Lev-Tov, H and Balukoff, NC and Gonzalez, T and Chopra, D and Yaghi, M and Amornpairoj, W and Strbo, N and Tomic-Canic, M and Pastar, I},
title = {Minimally Invasive Procedure for Hidradenitis Suppurativa Using Antimicrobial Wound Gel Resolves Tunnels, Reverses Microbial Dysbiosis, Decreases Inflammation, and Improves Quality of Life: Prospective, Single-Center, Single-Arm Trial.},
journal = {Journal of the American Academy of Dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jaad.2025.06.008},
pmid = {40490101},
issn = {1097-6787},
}
@article {pmid40490097,
year = {2025},
author = {Ortiz, AM and Casta, FC and Bodykevich, EG and Flynn, JK and Fennessey, CM and Brooks, K and Ruiz, D and Yee, DS and Simpson, J and Rahmberg, AR and Keele, BF and Brenchley, JM},
title = {Repeated enema administration in rhesus macaques is not sufficient to promote bacterial dysbiosis or gastrointestinal dysfunction.},
journal = {Mucosal immunology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.mucimm.2025.06.002},
pmid = {40490097},
issn = {1935-3456},
abstract = {Chronic gastrointestinal diseases are a significant global health burden that can require the use of gastrointestinal-cleansing regimens for diagnostics or therapeutic treatment. These regimens are beneficial for facilitating surgical preparation, drug delivery, colorectal cancer screenings, and personal use is common among proponents of natural health and among certain populations at high risk of HIV acquisition. It remains unclear, however, whether repeated clearance of the colonic microbiome induces persistent changes in the microbiome, intestinal immunity, and viral disease susceptibility. We addressed these parameters by repeatedly administering iso-osmolar enemas to rhesus macaques prior to low-dose intra-rectal challenge with simian immunodeficiency virus (SIV). Considering both longitudinal and cross-sectional analyses, we observed no consistent changes in the fecal microbiome or intestinal immune parameters of treated animals, nor were significant differences observed in susceptibility to SIV acquisition. Unexpectedly, enema-treated animals exhibited significantly lower setpoint viral loads after infection, although we were unable to clearly identify attributing causes. Our study demonstrates that repeated microbiome clearance using clinically administered iso-osmolar enemas is not sufficient to restructure the fecal microbiome, perturb intestinal immune parameters, or increase susceptibility to mucosal SIV challenge. This research framework serves as a model for the development of colonic-administered diagnostics and interventions.},
}
@article {pmid40489796,
year = {2025},
author = {Andersen, S and Kennedy, GA and Banks, M and Flanagan, BM and Henden, AS},
title = {Prebiotic fibre enteral supplementation post allogeneic transplantation; feasibility and impact on the microbiome.},
journal = {Blood advances},
volume = {},
number = {},
pages = {},
doi = {10.1182/bloodadvances.2024015703},
pmid = {40489796},
issn = {2473-9537},
abstract = {The decline in diversity of the gastrointestinal microbiome during haematopoietic stem cell transplantation (HSCT) is associated with poorer clinical outcomes. While provision of enteral nutrition (EN) is common during HSCT, provision of a prebiotic fibre containing formula has not been explored. This pilot study compared tolerance, clinical, microbiome and metabolomic outcomes between patients who received standard EN (n= 10) versus prebiotic fibre EN (n=20) post allogeneic HSCT. Stool samples were collected at baseline and at peri-engraftment and were analysed with shotgun metagenomic sequencing. Provision of prebiotic EN increased daily fibre intake post-transplant to an average 22g per day compared with 4g per day in the standard care group. High tolerance of both EN formulas was observed with only 20% (n=2) of the standard and 15% of the prebiotic group (n=3) requiring parenteral nutrition (p=1.0). There was no difference in the amount of EN provided, EN duration or clinical outcomes. Microbial diversity declined in both groups with no difference post EN provision (p=0.93), however, there was a significant difference in relative abundance of lactobacillus_C rhamnosus with an increase in the prebiotic group only (p=0.022). The relative abundance of faecalicatena gnavus increased in the standard group and declined in the prebiotic group (p=0.0027). Functional analysis of the microbial genome showed decreased expression of antibiotic resistance genes in the prebiotic group only post EN provision (p = 0.00035). A longer fibre intervention should be trialled to optimise clinical outcomes and a more diverse microbiome. The trial was registered at www.anzctr.org.au as ACTRN12621000832875.},
}
@article {pmid40489582,
year = {2025},
author = {Zhou, X and Zheng, W and Kong, W and Zhang, J and Liao, Y and Min, J and Zeng, T},
title = {Glucose Parameters, Inflammation Markers, and Gut Microbiota Changes of Gut Microbiome-Targeted Therapies in Type 2 Diabetes Mellitus: a Systematic Review and Meta-Analysis of Randomized Controlled Trials.},
journal = {The Journal of clinical endocrinology and metabolism},
volume = {},
number = {},
pages = {},
doi = {10.1210/clinem/dgaf340},
pmid = {40489582},
issn = {1945-7197},
abstract = {PURPOSE: This meta-analysis aims to summarize the effects of gut microbiome-targeted therapies (MTTs) on glucometabolic, inflammatory factors and gut microbiota in patients with type 2 diabetes mellitus (T2DM).<br><br>METHODS: 4 databases were searched for randomized controlled trials (RCTs) that included subjects with T2DM who received MTTs. All results were presented as standardized mean difference (SMD)/MD and 95% confidence intervals (95% CIs). In addition, subgroup analyses were performed according to region, type of MTTs, number of probiotic strains, probiotics dose, prebiotics dose, duration of MTTs, mean age, and baseline body mass index.<br><br>RESULTS: Fifty-four RCTs were included, encompassing 60 groups and 3,390 subjects. Overall, MTTs intervention decreased fasting plasma glucose (MD&#x2009;= -7.97&#x2009;mg/dL, 95%CI&#x2009;=-10.82, -5.12; p&#x2009;&#xff1c;0.00001), 2h-postprandial blood glucose (MD&#x2009;=&#x2009;-43.30&#x2009;mg/dL, 95%CI&#x2009;=&#x2009;-75.83, -10.77; p&#x2009;=&#x2009;0.009), fasting insulin (MD&#x2009;=&#x2009;-1.73uU/ml, 95%CI&#x2009;=&#x2009;-2.63, -0.84; p&#x2009;=&#x2009;0.0001), HbA1c (MD&#x2009;=&#x2009;-0.28%, 95%CI&#x2009;=&#x2009;-0.39, -0.17; p&#x2009;&#xff1c;0.00001), and Homeostatic Model Assessment of Insulin Resistance (MD&#x2009;=-0.53, 95%CI&#x2009;=&#x2009;-0.85, -0.20; P=0.0002). Furthermore, MTTs supplementation reduced high-sensitivity C-reactive protein, tumor necrosis factor alpha, and lipopolysaccharides. Meanwhile, the levels of Interleukin-10 were increased. Moreover, the abundance of Actinobacteria, Lactobacillus, and Lactobacillus casei subgroup increased.<br><br>CONCLUSION: MTTs modestly improved glucometabolic parameters, reduced pro-inflammatory cytokines, and enriched beneficial microbes (e.g., Actinobacteria, Lactobacillus) in T2DM. However, heterogeneity and limited long-term data highlight the need for large-scale RCTs.},
}
@article {pmid40489496,
year = {2025},
author = {Boddu, SS and Martini, KM and Nemenman, I and Vega, NM},
title = {Variance in C. elegans gut bacterial load suggests complex host-microbe dynamics.},
journal = {PLoS computational biology},
volume = {21},
number = {6},
pages = {e1013110},
doi = {10.1371/journal.pcbi.1013110},
pmid = {40489496},
issn = {1553-7358},
abstract = {Variation in bacterial composition inside a host is a result of complex dynamics of microbial community assembly, but little is known about these dynamics. To deconstruct the factors that contribute to this variation, we used a combination of experimental and modeling approaches. We found that demographic stochasticity and stationary heterogeneity in the host carrying capacity or bacterial growth rate are insufficient to explain quantitatively the variation observed in our empirical data. Instead, we found that the data can be understood if the host-bacteria system can be viewed as stochastically switching between high and low growth rates phenotypes. This suggests the dynamics significantly more complex than logistic growth used in canonical models of microbiome assembly. We develop mathematical models of this process that can explain various aspects of our data. We highlight the limitations of snapshot data in describing variation in host-associated communities and the importance of using time-series data along with mathematical models to understand microbial dynamics within a host.},
}
@article {pmid40489211,
year = {2025},
author = {Gautam, P and Yadav, R and Vishwakarma, RK and Shekhar, S and Pathak, A and Singh, C},
title = {An Integrative Analysis of Metagenomic and Metabolomic Profiling Reveals Gut Microbiome Dysbiosis and Metabolic Alterations in ALS: Potential Biomarkers and Therapeutic Insights.},
journal = {ACS chemical neuroscience},
volume = {},
number = {},
pages = {},
doi = {10.1021/acschemneuro.5c00254},
pmid = {40489211},
issn = {1948-7193},
abstract = {ALS is a severe neurodegenerative disorder characterized by motor neuron degeneration, gut dysbiosis, immune dysregulation, and metabolic disturbances. In this study, shotgun metagenomics and [1]H nuclear magnetic resonance (NMR)-based metabolomics were employed to investigate the altered gut microbiome and metabolite profiles in individuals with ALS, household controls (HCs), and nonhousehold controls (NHCs). The principal component analysis (PCA) explained 33% of the variance, and the partial least-squares discriminant analysis (PLS-DA) model demonstrate R[2] and Q[2] values of 0.97 and 0.84, respectively, indicating an adequate model fit. The relative bacterial abundance was 99.34% in the ALS group and 98.94% in the HC group. Among the ten identified genera, Bifidobacterium, Lactobacillus, and Enterococcus were more prevalent in ALS individuals, while Lactiplantibacillus and Klebsiella were more abundant in the HC group. We identified 70 metabolites, including short-chain fatty acids (SCFAs), branched-chain amino acids (BCAAs), carbohydrates, and aromatic compounds, using NMR. Orthogonal partial least-squares discriminant analysis (O-PLS-DA) explained 15.8% of the variance, with a clear separation between the ALS and HC groups. Univariate receiver operating characteristic (ROC) analysis identified three fecal metabolites with AUC values above 0.70, including butyrate (0.798), propionate (0.727), and citrate (0.719). These metabolites may serve as potential biomarkers for ALS. The statistical model for metabolic pathway analysis revealed interconnected pathways, highlighting the complexity of metabolic dysregulation, as well as potential microbial and metabolic biomarkers in ALS. These results highlight the role of gut microbiome alterations in ALS and suggest potential avenues for therapeutic intervention.},
}
@article {pmid40488951,
year = {2025},
author = {Liu, Y and Huang, G and Wei, F and Hu, Y},
title = {Non-negligible role of gut morphology in shaping mammalian gut microbiomes.},
journal = {Science China. Life sciences},
volume = {},
number = {},
pages = {},
pmid = {40488951},
issn = {1869-1889},
abstract = {Because of the overemphasis on the roles of diet and phylogeny in shaping the gut microbiome, the gut morphology is seldom independently considered and even often ignored. To address this research gap, we investigated a large-scale dataset of mammalian gut microbiomes, comprising 16S ribosomal RNA and metagenomic sequencing data from 292 species spanning 20 orders. We dissected the effects of various factors on the gut microbiome across four distinct gut morphology categories (foregut/hindgut/simple, foregut/hindgut, functional ruminant/ruminant-like, and colon fermenter/cecum fermenter) and uncovered the synergistic effect between phylogeny and gut morphology. Moreover, we identified the significant role of gut morphology in the gut microbiomes of hosts occupying specific niches, as well as those within the same taxonomic order but with different gut morphologies. We also identified three enterotype indices-Fusobacterium, UCG-005, and Prevotella-which could predict the three gut morphology types of mammals: simple, foregut, and hindgut. These findings enhance our understanding of mammalian gut microbial assembly and provide novel insights into host-microbe coevolution.},
}
@article {pmid40488937,
year = {2025},
author = {Paul, C and Roy, T and Roy, M and Rajeev, AC and Pan, A and Maitra, M and Das, N},
title = {Genome wide analysis of Priestia aryabhattai_OP, an endobacterium, modulating growth, development and biochemical compositions of sporophores in edible oyster mushroom Pleurotus ostreatus (MTCC 1802).},
journal = {World journal of microbiology &amp; biotechnology},
volume = {41},
number = {6},
pages = {194},
pmid = {40488937},
issn = {1573-0972},
support = {G.O. No. 52-Edn (B)/5B-15/2017//by Higher Education Department, Govt. of West Bengal, India as fellowship/ ; BT/INF/22/SP41296/2020//Department of Biotechnology (DBT), Govt. of India as DBT Builder Grant/ ; },
mesh = {*Pleurotus/growth &amp; development/metabolism ; *Genome, Bacterial ; Phylogeny ; Laccase/metabolism/biosynthesis ; RNA, Ribosomal, 16S/genetics ; Metagenomics ; Siderophores/metabolism ; Whole Genome Sequencing ; Fruiting Bodies, Fungal/growth &amp; development ; },
abstract = {The increasing global interest in the consuming and producing of edible oyster mushrooms (Pleurotus spp.) is driven by their well-documented nutritional and health benefits. The metagenomic analysis of fruiting body revealed a distinct microbial composition in P. ostreatus, predominantly comprising Pseudomonodota (~ 82%) and Bacillota (~ 10%). An endobacterium Priestia aryabhattai_OP, associated with internal tissue of P. ostreatus (MTCC 1802), was isolated and characterized through biochemical and microscopic analyses as well as 16 S rRNA and whole genome sequencing. Co-cultivation of P. ostreatus with this bacterium significantly enhanced the in vitro production of laccase, a key growth-promoting enzyme. Additionally, the endobacterium improved the biological efficiency (BE) of the mushroom, enriched its nutraceutical profile, and facilitated the biosynthesis of beneficial compounds, including IAA, siderophores, and antimicrobials like lassopeptides, phosphonates, non-ribosomal iron-binding siderophores (NI- siderophore), carotenoids, paeninodins, synechobactins, and surfactins. The present findings offer novel insights into microbe-microbe interactions and their pivotal roles in fungal biology, with significant implications for sustainable mushroom production as well as nutrient enrichment and biotechnological advancements.},
}
@article {pmid40488826,
year = {2025},
author = {Lee, CJ and Carpenter, PA},
title = {Modern-Era Challenges in the Clinical Management of Graft-Versus-Host Disease.},
journal = {Advances in experimental medicine and biology},
volume = {1475},
number = {},
pages = {103-128},
pmid = {40488826},
issn = {0065-2598},
mesh = {*Graft vs Host Disease/therapy/diagnosis/immunology/etiology ; Humans ; *Hematopoietic Stem Cell Transplantation/adverse effects ; Animals ; Disease Management ; },
abstract = {For several decades, graft-versus-host disease (GVHD) has been a long-standing barrier to successful allogenic hematopoietic cell transplantation and a significant cause of post-transplant morbidity and mortality. Initially described as secondary disease or wasting syndrome in transplanted mice, the pathobiology of GVHD is increasingly understood as a dynamic interplay between innate and adaptive immunity in response to initial tissue damage, leading to inflammation and end-organ damage. In parallel, more uniform symptom capture, diagnosis, and response criteria have facilitated rigorous clinical trial design and conduct; together, these advancements have facilitated the development of novel GVHD prevention and treatment strategies. While these advancements have improved the GVHD treatment paradigm, new questions arise within this complex patient population. This chapter discusses several of the most pertinent current clinical practice challenges in GVHD, including its earlier diagnosis, risk stratification, initial and more advanced stage management, as well as a renewed focus on supportive care, given our increased understanding of key roles played by the human microbiome.},
}
@article {pmid40488812,
year = {2025},
author = {Bajaj, P and Sharma, M},
title = {Chrononutrition and Gut Health: Exploring the Relationship Between Meal Timing and the Gut Microbiome.},
journal = {Current nutrition reports},
volume = {14},
number = {1},
pages = {79},
pmid = {40488812},
issn = {2161-3311},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Circadian Rhythm/physiology ; *Meals/physiology ; *Feeding Behavior/physiology ; Lipid Metabolism ; },
abstract = {PURPOSE OF REVIEW: This review explores the relationship between circadian rhythms and meal timing, or chrononutrition, and how it affects gut health. Since the gut microbiota plays a critical role in immunological response, metabolic control, and digestion, it is critical to comprehend how circadian misalignment impacts gut microbial equilibrium. This review examines research from the last ten years to assess the effects of circadian rhythm disturbances and meal time variations on the composition of the gut microbiota, the integrity of the gut barrier, and metabolic consequences.<br><br>RECENT FINDINGS: Using search terms like "Chrononutrition AND Gut health," "Circadian Rhythm AND Meal timing," and similar combinations, 31 peer-reviewed publications from PubMed, Google Scholar, and Scopus were included. There is evidence that circadian misalignment, which can be brought on by shift work, irregular eating habits, or social jet lag, affects lipid metabolism, short-chain fatty acid (SCFA) synthesis, and gut microbial rhythms. According to research, microbial diversity and function are enhanced by early-time-restricted feeding (eTRF), which synchronizes with circadian cycles. Changes in tight junction proteins have been linked to irregular meal timing, which increases intestinal permeability and inflammation. Additionally, new research indicates a bidirectional relationship in which the gut bacteria might affect the central and peripheral circadian clocks. Chrononutrition is a promising non-pharmacological approach to preventing metabolic dysregulation and promoting gut health. Consistently timing meals, especially early-time-restricted feeding, can help maintain microbial balance, improve gut barrier function, and lower the risk of chronic diseases by bringing food intake into alignment with circadian cycles. The need for integrated approaches to food and lifestyle changes in future research and clinical practice is highlighted by the bidirectional relationship between the gut microbiota and circadian systems.},
}
@article {pmid40488793,
year = {2025},
author = {Liu, S and Tai, Z and Li, M and Zhang, R and Shao, G and Guo, J and Lu, W},
title = {Improving intestinal barrier function and intestinal microbiome of weaned piglets fed a low-protein diet through tryptophan and N-Acetylglutamic acid supplementation.},
journal = {Tropical animal health and production},
volume = {57},
number = {5},
pages = {252},
pmid = {40488793},
issn = {1573-7438},
mesh = {Animals ; *Tryptophan/administration &amp; dosage/metabolism ; *Gastrointestinal Microbiome/drug effects ; Dietary Supplements/analysis ; Animal Feed/analysis ; *Diet, Protein-Restricted/veterinary ; Weaning ; *Glutamates/administration &amp; dosage/metabolism ; *Sus scrofa/microbiology/physiology/growth &amp; development ; Animal Nutritional Physiological Phenomena ; *Intestines/physiology/drug effects/microbiology ; Swine ; Male ; Diet/veterinary ; Intestinal Barrier Function ; },
abstract = {The research aimed to evaluate how incorporating NAG and Trp into a low-protein diet affects intestinal functions and alterations in the microbiota, ultimately focusing on enhancing the growth and stress resistance of weaned piglets aged 3-4 weeks.A total of 120 weaned piglets were categorized into five distinct groups: a control group (CON), a low-protein diet group (LP), a low-protein diet group with 0.2% N-acetylglutamic acid (LP + NAG), a low-protein diet group with 0.2% tryptophan (LP + Trp), and a low-protein diet group with 0.2% N-acetylglutamic acid and 0.2% tryptophan (LP + NAG + Trp). The results revealed that the LP + NAG + Trp group exhibited a higher feed-to-gain ratio and improved growth performance, with significantly greater average daily gain and feed intake than the control group. Antioxidant capacity was enhanced, as indicated by elevated levels of catalase and glutathione peroxidase. The expression of tight junction proteins ZO-1 and claudin-1 increased, strengthening the intestinal barrier. Additionally, immunoglobulin levels and the abundance of actinomycetes in the gut microbiota rose, indicating improved immune function and gut health.The increased digestive capacity of the intestine may be linked to the growth in the population of actinomycetes, which is attributed to the combined addition of the NAG + Trp group.},
}
@article {pmid40488777,
year = {2025},
author = {Chen, Y and Zhang, R and Zhang, Y and Guo, J and Guo, Z and Han, Y and Wang, F and Zhao, X and Ren, T},
title = {Integrated Microbiome, Transcriptome, and Physiology Analyses Reveal the Response Of Kuruma Shrimp (Penaeus japonicus) to Oxygen Nanobubble Exposure.},
journal = {Marine biotechnology (New York, N.Y.)},
volume = {27},
number = {3},
pages = {92},
pmid = {40488777},
issn = {1436-2236},
support = {No. 2022YFE0117900//the National Key Research and Development Program of China/ ; No. 2022YFE0117900//the National Key Research and Development Program of China/ ; No. 2022YFE0117900//the National Key Research and Development Program of China/ ; No. 2022YFE0117900//the National Key Research and Development Program of China/ ; No. 2022YFE0117900//the National Key Research and Development Program of China/ ; No. 2022YFE0117900//the National Key Research and Development Program of China/ ; No. 2022YFE0117900//the National Key Research and Development Program of China/ ; No. 2022YFE0117900//the National Key Research and Development Program of China/ ; No. 2022YFE0117900//the National Key Research and Development Program of China/ ; },
mesh = {Animals ; *Penaeidae/microbiology/physiology/genetics/drug effects/growth &amp; development ; *Oxygen/pharmacology ; *Transcriptome ; *Gastrointestinal Microbiome/drug effects ; Aquaculture ; Adaptation, Physiological ; },
abstract = {Penaeus japonicus is a high-value crustacean species, but its response to oxygen nanobubble (NB-O2) remains poorly understood. This study evaluated the effects of NB-O2 exposure on juvenile P. japonicus cultured in two recirculating aquaculture systems (RAS). The control group (LS) was maintained with low-saturation dissolved oxygen (DO) at 7.5 ± 0.5 mg/L, while the experimental group (HS) was exposed to high-saturation DO of 15.0 ± 0.5 mg/L using NB-O2 technology. The investigation focused on changes in intestinal microbiota, transcriptomic responses, and physiological adaptation. Results demonstrated that NB-O2 significantly improved growth performance metrics, including specific growth rate (SGR), feed conversion ratio (FCR), molting rate (MR), and survival rate (SR). The intestinal microbiota exhibited an increased abundance of beneficial microorganisms, such as Lactobacillales and Rhodopseudomonas palustris, while maintaining microbial stability. Transcriptome analysis identified key pathways associated with adaptation to hyperoxia, particularly those involved in amino acid metabolism, energy metabolism, and antioxidant capacity. These findings were supported by physiological analysis, which showed changes in the amino acid profile and total free amino acids (T-AA), as well as a balanced interaction between glycogen (Gn), adenosine triphosphatase (ATP), and lactate dehydrogenase (LDH) in energy regulation. Antioxidant enzyme activities were all elevated under hyperoxia, including peroxidase (POD), catalase (CAT), total antioxidant capacity (T-AOC), total superoxide dismutase (T-SOD), and glutathione peroxidase (GSH-Px). Additionally, the expression of stress-resistance genes (HSP70, CAP3, LYZ-C) indicated no adverse effects. Overall, P. japonicus exhibited strong physiological and molecular adaptations to NB-O2-induced hyperoxia, highlighting the potential of this technology to enhance aquaculture productivity.},
}
@article {pmid40488530,
year = {2025},
author = {Gao, H and Zhuang, D and Zhou, H and Su, Q and Hu, X and Wang, Y and Bao, W and Zhu, L},
title = {A comprehensive analysis of human gut microbial biosynthesis gene clusters unveiling the dominant role of Paenibacillus.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0061025},
doi = {10.1128/msystems.00610-25},
pmid = {40488530},
issn = {2379-5077},
abstract = {The secondary metabolites produced by the gut microbiota serve as crucial signaling molecules and substrates for gastrointestinal metabolic reactions, thereby playing a pivotal role in human physiological and pathological processes. In this study, we explore the complex symbiotic relationship between the gut microbiota and the human host by systematically annotating the biosynthetic gene clusters (BGCs) across 4,744 human gut microbiota genomes, sourced from the Unified Human Gastrointestinal Genome database. Our comprehensive analysis compares the differential biosynthetic potentials of microbiota from diverse continents and phyla while also elucidating the biosynthetic profiles of gut archaea. Notably, our findings identify Paenibacillus as a dominant genus within the human gut microbiota, characterized by its extensive biosynthetic capacity. This study presents the first global atlas of BGCs within the human gut microbiome, offering valuable insights into gut-derived secondary metabolic pathways and their intricate interactions with host physiology. These results lay the groundwork for future investigations into the microbiota's role in health and disease, underscoring the importance of understanding microbiota-derived metabolites in microbiology and gastroenterology.IMPORTANCEThis study provides a comprehensive analysis of biosynthetic gene clusters in the human gut microbiome, revealing a vast diversity of natural products with potential therapeutic applications. We identified Paenibacillus as a key genus with exceptional biosynthetic capabilities, including the production of leinamycin, a potent anticancer compound previously thought to be exclusive to Streptomyces. The findings highlight the gut microbiome as a rich, untapped resource for novel drug discovery, particularly in cancer therapy and immune modulation.},
}
@article {pmid40488505,
year = {2025},
author = {Hoque, MN and Rana, ML and Gilman, MAA and Pramanik, PK and Islam, MS and Punom, SA and Hassan, J and Islam, T and Ramasamy, S and Schreinemachers, P and Oliva, R and Rahman, MT},
title = {Mapping of urban garden soil microbiomes in Bangladesh.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0037525},
doi = {10.1128/mra.00375-25},
pmid = {40488505},
issn = {2576-098X},
abstract = {Shotgun metagenomics revealed distinct microbiome profiles in the garden soils of Dhaka and Gazipur district, Bangladesh, with Bacillus spp. demonstrating ecological dominance (>53% relative abundance) and location-specific distribution patterns. These findings highlight Bacillus species as prevalent microbes in urban garden soils.},
}
@article {pmid40488500,
year = {2025},
author = {Berríos-Farías, V and Guajardo-Leiva, S and Gallardo-Cerda, J and Galbán-Malagón, C and Ballesteros, G and Egas, C and Molina-Montenegro, M and Castro-Nallar, E},
title = {Rhizosphere and soil metagenomes and metagenome-assembled genomes from the Byers Peninsula, Livingston Island (62°S), Antarctica.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0017125},
doi = {10.1128/mra.00171-25},
pmid = {40488500},
issn = {2576-098X},
abstract = {Rhizosphere microbes establish functional interactions with their hosts, impacting plant fitness. To further understand plant effects on microbial composition and functional diversity, we present 52 metagenomes and 1,484 metagenome-assembled genomes (MAGs) from soil and the rhizosphere of Colobanthus quitensis and Deschampsia antarctica.},
}
@article {pmid40488467,
year = {2025},
author = {Liu, Y and Qiu, Q and Chen, Y and Deng, Y and Huang, W and Sun, C and Shang, X and Chen, X and Wang, C and Han, L and Chen, S and Yuan, J and Xu, F and Yang, Z and Fang, X and Huang, L},
title = {Integrated multi-omics analysis reveals the functional signature of microbes and metabolomics in pre-diabetes individuals.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0145924},
doi = {10.1128/spectrum.01459-24},
pmid = {40488467},
issn = {2165-0497},
abstract = {Pre-diabetes (PD) represents a critical stage in the progression toward type 2 diabetes, with significant alterations observed in the human microbial community among pre-diabetic individuals in observational studies. However, understanding the interaction between human microbiota and the host during pre-diabetes remains limited. Therefore, this study aims to understand the alterations in the human microbial community during pre-diabetes, a critical stage toward type 2 diabetes. Using an integrated analysis of human microbiota and metabolomics data, we seek to identify the functional signature associated with PD and gain insights into potential mechanisms driving its progression to type 2 diabetes. These findings could inform the development of early intervention strategies for those at high risk. Samples were collected from pre-diabetes, diabetes, and healthy control groups. Through metagenome and 16S rRNA sequencing, we analyzed the gut microbial and tongue coating compositions, respectively. Untargeted metabolomics techniques were also applied for comprehensive plasma data. Using integrated multi-omics analysis, we aim to understand the metabolic potentials of the human microbiome, its molecular links with host targets, and their effects on pre-diabetes, thereby deepening our understanding of microbiome-host interactions in this context. The pre-diabetes group exhibited distinct clinical characteristics, particularly in blood glucose levels and a higher average level of γ-glutamyl transferase. We identified 509 intestinal bacterial species, with Megamonas funiformis and Parabacteroides merdae showing higher abundance in the PD group. In tongue coating samples, we found 1,122 bacterial genera, with the PD group showing altered levels of Corynebacterium and Johnsonella. Furthermore, we detected 795 metabolites, primarily involved in carbohydrate and lipid metabolism. Importantly, our integrated multi-omics analysis suggested Flavonifractor plautii's role in modulating blood glucose through influencing carbohydrate metabolism. Our integrated multi-omics analysis revealed significant alterations in several regulatory pathways associated with pre-diabetes, particularly emphasizing the impact of gut bacterium Flavonifractor plautii on blood glucose levels through its influence on carbohydrate metabolism. These intricate relationships among gut microbiota, metabolites, and blood glucose levels underscore the significance of personalized treatment approaches and preventive strategies for pre-diabetes. The insights gained from this research hold considerable promise for advancing our understanding and management of pre-diabetes.IMPORTANCEThis study investigates alterations in the human microbial community during PD, a critical stage leading to type 2 diabetes. Through integrated analysis of metagenomic and metabolomics data from pre-diabetes, diabetes, and healthy control groups, we identified distinct clinical characteristics in the PD group, including elevated blood glucose levels and γ-glutamyl transferase. A total of 509 intestinal bacterial species were identified, with Flavonifractor plautii playing a key role in modulating blood glucose levels via its influence on carbohydrate metabolism. Our findings underscore the complex interactions among gut microbiota, metabolites, and blood glucose levels, highlighting the potential for personalized treatment approaches and early intervention strategies for individuals at high risk of developing type 2 diabetes.},
}
@article {pmid40488407,
year = {2025},
author = {Grossman, AS and Lei, L and Botting, JM and Liu, J and Nahar, N and Liu, J and McLean, JS and He, X and Bor, B},
title = {Saccharibacteria deploy two distinct type IV pili, driving episymbiosis, host competition, and twitching motility.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf119},
pmid = {40488407},
issn = {1751-7370},
abstract = {All cultivated Patescibacteria, also known as the candidate phyla radiation, are obligate episymbionts residing on other microbes. Despite being ubiquitous in many diverse environments, including mammalian microbiomes, molecular mechanisms of host identification and binding amongst ultrasmall bacterial episymbionts remain largely unknown. Type 4 pili are well conserved in this group and could potentially facilitate these symbiotic interactions. To test this hypothesis, we genetically targeted pili genes in Saccharibacteria Nanosynbacter lyticus strain TM7x to assess their essentiality and roles in symbiosis. Our results revealed that Nanosynbacter lyticus assembles two distinct type 4 pili: a non-essential thin pilus that has the smallest diameter of any type 4 pili and contributes to host-binding and episymbiont growth; and an essential thick pilus involved in twitching motility. To understand the role of these pili in vivo we developed Saccharibacteria competition assays and species specific Fluorescence in situ hybridization probes. Competition between different Saccharibacteria within mock communities demonstrated consistent competitive outcomes that were not driven by priority effects but were dependent on the thin pilus. Collectively our findings demonstrate that Saccharibacteria encode unique extracellular pili that enable their underexplored episymbiotic lifestyle and competitive fitness within a community.},
}
@article {pmid40488306,
year = {2025},
author = {Yoshimura, E and Hamada, Y and Hatamoto, Y and Nakagata, T and Nanri, H and Nakayama, Y and Iwasaka, C and Hayashi, T and Suzuki, I and Ando, T and Ishikawa-Takata, K and Tanaka, S and Ono, R and Araki, M and Kawashima, H and Chen, YA and Park, J and Hosomi, K and Mizuguchi, K and Kunisawa, J and Miyachi, M},
title = {Effect of short-term dietary intervention on fecal serotonin, gut microbiome-derived tryptophanase, and energy absorption in a randomized crossover trial: an exploratory analysis.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2514137},
doi = {10.1080/19490976.2025.2514137},
pmid = {40488306},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Feces/chemistry/microbiology ; Cross-Over Studies ; Male ; *Serotonin/analysis/metabolism ; Adult ; Female ; Young Adult ; *Tryptophanase/metabolism/analysis/genetics ; Energy Metabolism ; *Diet ; Bacteria/classification/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; },
abstract = {In this study, we investigated the effects of short-term energy loads on changes in gut microbiome-derived tryptophanase and fecal serotonin levels and their association with variations in energy absorption. This randomized crossover energy-load intervention study included 15 healthy participants subjected to three dietary conditions - overfeeding, control, and underfeeding - for eight days. The effects of the dietary conditions on energy absorption (digestible and metabolizable energy) were assessed using a bomb calorimeter. Fecal serotonin levels were assessed using LC-MS/MS, and the gut microbiota was analyzed using the 16S rRNA gene and metagenomic shotgun analysis. Significant differences were observed in digestible energy (p < 0.001), with higher values in the overfeeding than in the control (p = 0.032) conditions. Furthermore, significant differences were noted in metabolizable energy and gut transit time (p < 0.001), both of which were higher in the overfeeding than in the control (metabolizable energy: p = 0.001; gut transit time: p = 0.014) and underfeeding (metabolizable energy: p < 0.001; gut transit time: p = 0.004) conditions. Fecal serotonin levels differed significantly (p < 0.001), with significantly lower levels in the overfeeding than in the control (p = 0.005) and underfeeding (p < 0.001) conditions. Tryptophanase exhibited significant differences (p = 0.0019), with lower gene abundance in the overfeeding than in the underfeeding (p = 0.001) condition. Tryptophanase positively correlated with Bacteroides abundance under all conditions (correlation coefficient: 0.696-0.896). Intra-individual variability in fecal serotonin levels was significantly negatively associated with digestible energy (β = -0.077, p = 0.019). The findings suggest that short-term energy loads dynamically alter fecal serotonin, Bacteroides, and tryptophanase levels. Moreover, changes in fecal serotonin levels might be indirectly associated with energy absorption.},
}
@article {pmid40487791,
year = {2025},
author = {Stewart, AG and Harris, PNA and Graham, RMA and Jennison, AV and Schlebusch, S and Kakkanat, A and Harris-Brown, T and Paterson, DL and Forde, BM},
title = {Differences in antimicrobial resistance gene abundance and microbial diversity of the gut microbiome in patients on antibiotics enrolled in a clinical trial.},
journal = {Therapeutic advances in infectious disease},
volume = {12},
number = {},
pages = {20499361251337597},
pmid = {40487791},
issn = {2049-9361},
abstract = {BACKGROUND: Understanding how the gut microbiome adapts on exposure to individual antibiotics, with respect to antimicrobial resistance gene (ARG) enrichment, is important.<br><br>OBJECTIVES: To characterise the changes that occur in the gut microbiome of patients enrolled in an antibiotic clinical trial and to propose methods in which to embed gut microbiome analysis into clinical trials.<br><br>DESIGN: This was a prospective cohort study of hospitalised patients who were successfully enrolled and randomised into two clinical trials between January 2021 to December 2021.<br><br>METHODS: Adult patients admitted to the hospital with a bloodstream infection have been randomised to receive either benzylpenicillin, ampicillin, cefazolin, ceftriaxone, piperacillin-tazobactam or meropenem at a single institution. Faecal specimens were collected at enrolment and every second day until discharge. Each specimen underwent DNA sequencing to determine microbial diversity and ARG abundance.<br><br>RESULTS: Ten patients (including six females) were included. DNA concentration and sampling quality were markedly lower for rectal swabs compared to stool samples. Relative abundance of Enterococcus faecium was increased in individual patients where treatment included ampicillin, meropenem and piperacillin-tazobactam. Piperacillin-tazobactam also increased the abundance of key beta-lactamase genes (bla SHV-100, bla OXA-392, bla CMY-18). Ampicillin increased the abundance of bla TEM-1A. There were no extended-spectrum beta-lactamase (ESBL) or carbapenemase genes detected in our study. The presence of key anaerobes such as Clostridium and Bifidobacterium species appeared to play an important role in colonisation resistance of E. faecium and Clostridioides difficile.<br><br>CONCLUSION: Differential changes in anaerobic bacterial genera on exposure to antibiotics may be a key determinant of colonisation resistance. The pre-analytical phase of microbiome analysis is a critical factor in data quality and interpretation.},
}
@article {pmid40487754,
year = {2025},
author = {Wang, M and Zhu, Y},
title = {Gut microbiome versus thyroid cancer: Association and clinical implications (Review).},
journal = {Oncology letters},
volume = {30},
number = {1},
pages = {368},
pmid = {40487754},
issn = {1792-1082},
abstract = {Thyroid cancer (TC) is one of the most prevalent endocrine tumors, and its incidence rates are increasing. Recent studies have shown that TC disrupts the gut microbiomes (GM) by influencing the levels of thyroid hormones, estrogen levels, weight and insulin resistance. Traditional treatments, including thyroid surgery, radioactive iodine (RAI) therapy and checkpoint inhibitors, also alter the GM. Additionally, GM affects the proliferation of TC by influencing chronic inflammation and metabolism (e.g., effects on short-chain fatty acids and amino acid metabolism). Notable changes in the GM of patients with TC include increased numbers of Clostridium, Streptococcus, Proteus and Lachnospiraceae, and decreased numbers of Lactobacillus, Prevotella and Ruminococcaceae bacteria. In addition, the GM may serve as a biomarker for diagnosis, prognosis and predicting metastasis in patients with TC, potentially enhancing diagnostic efficiency. Furthermore, the GM presents an opportunity to improve the efficacy of RAI therapy and immunotherapy in patients with TC. Probiotic combination approaches may also enhance clinical outcomes and the quality of life for individuals with TC. In conclusion, the present review discussed how there are bidirectional causal relationships between the GM and TC, emphasizing the role of the 'gut-thyroid' axis. Clostridium, Streptococcus, Proteus and Lachnospiraceae may be potential risk factors, whereas Lactobacillus, Prevotella and Ruminococcaceae may have protective roles for TC. Further investigations into macrobiotics-associated mechanisms should prove to be helpful in terms of optimizing strategies for the early prevention and treatment of TC.},
}
@article {pmid40487637,
year = {2025},
author = {Chen, M and Peng, Y and Hu, Y and Kang, Z and Chen, T and Zhang, Y and Chen, X and Li, Q and Yuan, Z and Wu, Y and Xu, H and Zhou, G and Liu, T and Zhou, H and Yuan, C and Huang, W and Zhang, W},
title = {A critical role for Phocaeicola vulgatus in negatively impacting metformin response in diabetes.},
journal = {Acta pharmaceutica Sinica. B},
volume = {15},
number = {5},
pages = {2511-2528},
pmid = {40487637},
issn = {2211-3835},
abstract = {Metformin has been demonstrated to attenuate hyperglycaemia by modulating the gut microbiota. However, the mechanisms through which the microbiome mediates metformin monotherapy failure (MMF) are unclear. Herein, in a prospective clinical cohort study of newly diagnosed type 2 diabetes mellitus (T2DM) patients treated with metformin monotherapy, metagenomic sequencing of faecal samples revealed that Phocaeicola vulgatus abundance was approximately 12 times higher in nonresponders than in responders. P. vulgatus rapidly hydrolysed taurine-conjugated bile acids, leading to ceramide accumulation and reversing the improvements in glucose intolerance conferred by metformin in high-fat diet-fed mice. Interestingly, C22:0 ceramide bound to mitochondrial fission factor to induce mitochondrial fragmentation and impair hepatic oxidative phosphorylation in P. vulgatus-colonized hyperglycaemic mice, which could be exacerbated by metformin. This work suggests that metformin may be unsuitable for P. vulgatus-rich T2DM patients and that clinicians should be aware of metformin toxicity to mitochondria. Suppressing P. vulgatus growth with cefaclor or improving mitochondrial function using adenosylcobalamin may represent simple, safe, effective therapeutic strategies for addressing MMF.},
}
@article {pmid40487442,
year = {2025},
author = {Hisamatsu, D and Masuoka, H and Takeshige-Amano, H and Kurokawa, R and Ogata, Y and Suda, W and Hatano, T and Asaoka, D and Mabuchi, Y and Naraoka, Y and Sato, N and Asada, T and Hattori, N and Hattori, M and Akazawa, C},
title = {Acetylcholinesterase inhibitors considerably affect the salivary microbiome in patients with Alzheimer's disease.},
journal = {iScience},
volume = {28},
number = {6},
pages = {112593},
pmid = {40487442},
issn = {2589-0042},
abstract = {Microbiome alterations are reportedly linked to systemic disease progression and medication. However, the effects of central nervous system drugs on the microbiome of patients with neurodegenerative diseases, such as Alzheimer's or Parkinson's disease, are poorly understood. Here, we comprehensively analyzed the effects of medication on the salivary and gut microbiomes of patients with Alzheimer's or Parkinson's disease. Comparative analyses of the effects of disease severity and drug use revealed that anti-dementia (DE) drugs, particularly acetylcholinesterase inhibitors, had a greater effect on compositional changes in the salivary microbiome than on those in the gut microbiome. Multivariate analyses incorporating anti-DE drug use showed that microbial signatures may serve as promising disease biomarkers, enabling the development of more precise predictors of cognitive function. Our findings will facilitate the advancement of diagnostic tools leveraging the salivary microbiome.},
}
@article {pmid40487326,
year = {2025},
author = {Bornbusch, SL and Dami, KA},
title = {Connecting microbial ecology to human fertility and reproduction: perspectives from the reproductive microbiomes of animals.},
journal = {F&amp;S reports},
volume = {6},
number = {Suppl 1},
pages = {45-49},
pmid = {40487326},
issn = {2666-3341},
abstract = {In all vertebrates, reproduction occurs in the context of host-associated microbiomes, which are increasingly recognized for their contributions to reproductive success. Although host-associated microbiomes are species specific, synthesizing patterns in microbial ecology across human and animal taxa provides perspectives for understanding the factors that shape microbial communities and their contributions to reproduction. Additionally, the fertility and reproductive physiology of animals under human care-particularly endangered species-is often meticulously monitored to maximize reproductive opportunities. In this mini-review, we examine current knowledge on reproductive microbiomes in animals, focusing, when available, on the sparse literature for wildlife species. We suggest ways in which studying animal microbial ecology may advance human fertility and reproduction by focusing on 3 microbial communities-vaginal, milk, and seminal microbiomes-which represent a large portion of literature and have clear implications for reproductive health. We identify avenues of future research that will further strengthen the linkages between reproductive research in wildlife species and humans and provide potential guidelines for practical applications of microbiome science to human reproductive health.},
}
@article {pmid40487272,
year = {2025},
author = {Phipps, AI and Hill, CM and Lin, G and Malen, RC and Reedy, AM and Kahsai, O and Ammar, H and Curtis, K and Ma, N and Randolph, TW and Ma, J and Ogino, S and Newcomb, PA and Hullar, MA},
title = {Fusobacterium nucleatum Enrichment in Colorectal Tumor Tissue: Associations With Tumor Characteristics and Survival Outcomes.},
journal = {Gastro hep advances},
volume = {4},
number = {6},
pages = {100644},
pmid = {40487272},
issn = {2772-5723},
abstract = {BACKGROUND AND AIMS: Fusobacterium nucleatum (Fn) is linked to colorectal cancer (CRC) etiology and survival. We hypothesized that CRC tumor attributes and survival are associated with the amount and presence of Fn in tumors.<br><br>METHODS: Fn abundance was measured via droplet digital polymerase chain reaction in patient-matched CRC tumor and normal tissue samples from 859 Puget Sound CRC Cohort participants. Fn enrichment was defined as the continuous difference in normalized abundance between patient-matched tumor and normal tissue samples. Fn presence in tumor was classified categorically as not present, low, or high, regardless of Fn status in matched normal tissue. Associations of Fn enrichment and presence with tumor site, stage, DNA mismatch repair (MMR) status, CpG island methylator phenotype (CIMP) status, BRAF and KRAS mutation status, and molecular subtypes based on combinations of tumor markers were assessed using logistic regression. Associations of Fn enrichment and presence with CRC survival was estimate with Cox regression.<br><br>RESULTS: Fn was present in 20% of tumor tissues and 10% of normal tissues, with higher average abundance in tumors. High Fn presence was independently associated with deficient MMR (dMMR) status and in the context of molecular subtypes for type 1 tumors (dMMR, CIMP-high, BRAF-mutated) and type 5 tumors (dMMR, CIMP-low or negative, BRAF-wildtype). Fn enrichment was associated with type 5 and type 2 tumors (proficient MMR, CIMP-high, BRAF-mutated). Fn enrichment and presence were associated with poorer CRC survival, with some suggestion that associations differed by MMR status.<br><br>CONCLUSION: Detectable Fn in CRC tissue is associated with certain CRC tumor attributes and survival; however, associations may vary based on Fn definition.},
}
@article {pmid40487213,
year = {2025},
author = {Wu, S and Tian, B and Shan, C and Wang, X and Xie, X and Xie, H and Jia, X and Zhang, F and Han, J},
title = {Integrated physiological, microbial, and metabolomics analyses revealed the differences in different varieties of Paeonia lactiflora Pall.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1577695},
pmid = {40487213},
issn = {1664-462X},
abstract = {Paeonia lactiflora Pall (P. lactiflora) is a perennial herb with high medicinal and economic value. In the growth process of P. lactiflora, the plant's root secondary metabolism is intricately linked to the microbial communities that surround it. However, few systematic studies have reported the changes in the microbiome and metabolites during P. lactiflora cultivation thus far. In this study, amplicon sequencing technology was used to determine the difference in rhizosphere microorganisms of P. lactiflora. The non-targeted metabolomics method was used to determine the changes in root metabolites, and the relationship between microorganisms and metabolites was demonstrated by co-expression network analysis. The paeoniflorin content (PC) was determined by HPLC. The total phenol content (TPC) was determined by the Folin-Ciocalteu method, and the total flavonoid content (TFC) was determined by the NaNO2-Al (NO3)3 method. The antioxidants were evaluated with the DPPH, ABTS, and FRAP methods. Results showed that Proteobacteria had the highest relative abundance among all phyla, Halomonas had the highest relative abundance among all genera. The results of metabolomics showed that 693 metabolites and 207 differential metabolites were detected in the four groups, which were mainly enriched in the biosynthesis of phenylpropanoids, phenylpropanoid biosynthesis, taste transduction, central carbon metabolism in cancer, and biosynthesis of plant secondary metabolites. The results also showed that the PC, TPC, TFC, and antioxidant capacity of the white P. lactiflora group were higher than those of the other groups. This study revealed the differences between different varieties of P. lactiflora and provided theoretical support for breeding and data reference for improving the quality of P. lactiflora by regulating microbial species.},
}
@article {pmid40487195,
year = {2025},
author = {Geese, T and Dempfle, A},
title = {From variability to stability: Sensitivity of network properties in IBD human gut microbiome studies.},
journal = {Computational and structural biotechnology journal},
volume = {27},
number = {},
pages = {1945-1961},
pmid = {40487195},
issn = {2001-0370},
abstract = {BACKGROUND: The gut microbiome's role in inflammatory bowel disease (IBD) is well-established, but capturing its complexity is challenging. Network analysis offers a valuable approach, but selecting suitable measures is crucial. This study examines the sensitivity of network properties to abundance variations. It evaluates whether these properties reflect the microbiome in IBD or are too sensitive to variability from e.g. laboratory conditions or intra-individual changes.<br><br>METHODS: Using genetically unrelated individuals from the KINDRED cohort (IBD n&#x202f;=&#x202f;522, healthy controls n&#x202f;=&#x202f;365) and the PRISM cohort (IBD n&#x202f;=&#x202f;42, healthy controls n&#x202f;=&#x202f;42), microbial networks were constructed with genera as nodes and significant pairwise correlations as edges, separately for IBD patients and controls. Important IBD-related nodes, identified through centrality measures, and non-disease-related nodes were varied in abundance (&#x202f;&#xb1;&#x202f;30&#x202f;%), and networks were re-constructed and compared with initial networks regarding local and global properties.<br><br>RESULTS: Network properties in IBD were sensitive to abundance variations, with small and large changes producing similar effects. Sensitivity to increasing read counts of disease-related and non-disease-related genera was similar. Local properties showed magnitude-dependent changes of up to 50&#x202f;% in response to the depletion of disease-related genera, relative to no modification applied, and an almost binary sensitivity pattern when modifying non-disease-related genera. Global case network properties changed less than 10&#x202f;% in most settings, potentially indicating a certain stability of dysbiosis.<br><br>CONCLUSION: Caution is needed with network-based approaches, as even small variations, stemming from sources of microbiome variability, can affect results and reproducibility. The relatively stable dysbiosis in IBD could pose challenges for microbiome-directed therapies.},
}
@article {pmid40487108,
year = {2025},
author = {Ortiz-Chura, A and Corral-Jara, KF and Tournayre, J and Cantalapiedra-Hijar, G and Popova, M and Morgavi, DP},
title = {Rumen microbiota associated with feed efficiency in beef cattle are highly influenced by diet composition.},
journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)},
volume = {21},
number = {},
pages = {378-389},
pmid = {40487108},
issn = {2405-6383},
abstract = {Given the role of the rumen microbiome in providing nutrients to the host ruminant, it is expected that rumen microbes contribute to inter-animal variations in feed efficiency. However, the link between microbial structure and an "efficient" host phenotype is unclear. We hypothesized that extreme residual feed intake (RFI) phenotypes would display distinctive microbiome features regardless of the diet. In this study, we selected the 32 most extreme RFI Charolais bulls from a cohort of 100 animals fed corn-silage (CS; n = 50) or grass-silage (GS; n = 50) based diets. Rumen samples were obtained 3 h after feeding, at slaughter, for fermentation and metataxonomic and metatranscriptomic microbial analysis. Volatile fatty acid profiles showed no differences between diets and between extreme RFI phenotypes (P > 0.05). Total bacteria and methanogen populations did not differ between extreme RFI phenotypes (P > 0.05), although methanogens expressed per liquid rumen digesta weight tended to decrease in the most efficient bulls compared to the least efficient ones (P = 0.10). The rumen microbial community structure differed between diets (P < 0.001), and between extreme RFI phenotypes in the GS diet. In the whole dataset, we identified Succiniclasticum, Saccharofermentans, Clostridia_258483 and CAG-238 as bacteria discriminant between extreme RFI phenotypes (q < 0.10). Within diets, these four genera were also discriminant in the GS diet and were all associated with the least efficient bulls. In contrast, in bulls fed the CS diet, only Saccharofermentans and Succiniclasticum were discriminant but they were positively associated with the most efficient bulls. Rumen microbial functional features did not differ between extreme RFI phenotypes but did differ between diets. In conclusion, the rumen microbiome was mainly influenced by diet, with the RFI phenotype being a marginal effector. Succiniclasticum, Saccharofermentans, Clostridia_258483, and CAG-238 were discriminant between extreme RFI phenotypes regardless of diet. However, the direction of the association with RFI was diet dependent, indicating a diet-RFI interaction and suggesting that these discriminating microbes may be suitable microbial indicator species for RFI only when considered in conjunction with the diet information.},
}
@article {pmid40487096,
year = {2025},
author = {Han, H and Liu, K and Wang, Y and Song, M and Lian, H and Gao, T and Zhang, L and Fu, T},
title = {Supplementation of the probiotic Lactobacillus rhamnosus GG to pre-weaning calves decreases diarrhea incidence by modulating gut bacteria and associated metabolites.},
journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)},
volume = {21},
number = {},
pages = {234-244},
pmid = {40487096},
issn = {2405-6383},
abstract = {The aim of the present study was to investigate whether Lactobacillus rhamnosus GG (LGG) could be utilized as an effective strategy to promote growth performance of calves and to further study its impact on decreasing diarrhea. A total of 18 healthy Holstein calves (age 8 ± 3 days, weight 42.48 ± 1.04 kg) were raised in a centralized manner to minimize differences and then divided into two groups: one group received LGG supplementation (1 × 10[10] CFU per calf per day), while the other served as the control (CON). Each group consisted of 9 replicates, with 1 calf per replicate. The experimental period spanned 6 weeks. The experimental results demonstrated an increase of the average daily growth (P = 0.094) and a highly significant reduction in diarrhea (P = 0.001) for the LGG group compared with the CON group. The supplementation of LGG resulted in an increased abundance of endogenous beneficial bacteria in the gut including Lysinbacillus (P = 0.012) and Rikenellaceae_RC9_gut_group (P = 0.041) while reducing levels of pathogenic bacteria in the Escherichia-Shigella (P = 0.066). These particular groups could serve as biomarker bacteria for calf diarrhea and gut health. The alteration of metabolite production and metabolic pathways were also closely associated with the variation of bacterial composition in the gut microbiome of calves, of which included enrichment of biosynthesis of unsaturated fatty acids, α-linolenic acid and steroid biosynthesis. Overall, LGG administration had a positive impact on improving the intestinal homeostasis, alleviating diarrhea, and enhancing growth performance by modulating gut bacteria and metabolites in pre-weaning calves. Thus, LGG could be a potential alternative to prophylactic antibiotic treatment that would lower associated costs and provide new insights into preventing and treating calf diarrhea.},
}
@article {pmid40486854,
year = {2025},
author = {Qian, D and Xu, P and Wang, X and Du, C and Zhao, X and Xu, J},
title = {Bacterial extracellular vesicles for gut microbiome-host communication and drug development.},
journal = {Acta pharmaceutica Sinica. B},
volume = {15},
number = {4},
pages = {1816-1840},
pmid = {40486854},
issn = {2211-3835},
abstract = {As the intricate interplay between microbiota and the host garners increasing research attention, a significant parallel surge has emerged in the investigation of intestinal bacterial extracellular vesicles (BEVs). Most intestinal bacteria secrete BEVs, which harbor specific cargo molecules and exhibit diverse functions, encompassing interactions among bacteria themselves and between bacteria and the host. These interactions can either bolster host health or contribute to various pathologies. By integrating the characteristics of BEVs, we summarized the current research landscape, delving into the intricate interplay between BEVs and different diseases. Furthermore, we offer a succinct overview of the challenges faced in BEVs-based research, encompassing separation, detection, engineering for drug purposes, clinical diagnostics, safety, and future study. In essence, these summaries may serve as invaluable guides for BEVs as communication tools between the gut microbiome and host, ultimately propelling the discovery of novel studies and drug discovery.},
}
@article {pmid40486513,
year = {2025},
author = {Chen, LZ and Cai, Q and Zheng, PF},
title = {Mitochondrial metabolic rescue in post-COVID-19 syndrome: MR spectroscopy insights and precision nutritional therapeutics.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1597370},
pmid = {40486513},
issn = {1664-3224},
mesh = {Humans ; *COVID-19/metabolism/complications/diet therapy ; *Mitochondria/metabolism ; *SARS-CoV-2 ; Magnetic Resonance Spectroscopy/methods ; Precision Medicine ; *Nutrition Therapy/methods ; Energy Metabolism ; Oxidative Stress ; Ubiquinone/analogs &amp; derivatives ; },
abstract = {Post-COVID-19 Condition (PCC), impacting 30-90% of survivors, is characterized by persistent fatigue and metabolic dysfunction, often linked to underlying mitochondrial impairment. This review examines current evidence on mitochondrial-targeted nutrition therapies, with a focus on magnetic resonance spectroscopy (MRS) as a tool for assessing metabolic recovery. Key findings highlight reduced adenosine triphosphate (ATP) production, heightened oxidative stress, and disrupted mitochondrial biogenesis- metabolic abnormalities that closely mirror those seen in chronic fatigue syndromes. While mitochondrial dysfunction is recognized as central, debate continues on whether systemic inflammation or direct viral damage primarily drives these abnormalities. Current evidence supports nutrients, such as, CoQ10, NAC, and creatine for restoring energy metabolism and reducing oxidative stress. MRS biomarkers (τPCr, Qmax), offer valuable tools for monitoring personalized intervention. However, several limitations persist, including variability in nutritional protocols, inconsistencies in MRS methodologies, and limited consideration of microbiome-psychosocial interactions. Most clinical trials focus on short-term outcomes, lacking data on long-term efficacy or stratification based on mitochondrial dysfunction severity. Future research priorities include multi-omics investigations into mitochondrial-epigenetic interactions, the development of targeted antioxidants, and exploration of engineered microbial metabolites. Standardizing MRS protocols, validating composite endpoints, and optimizing nutrient delivery systems require interdisciplinary collaboration. This review advocates for a precision medicine approach, combining MRS-based metabolic profiling with personalized nutritional strategies, to address the multifactorial nature of PCC and advance clinical translation.},
}
@article {pmid40486510,
year = {2025},
author = {Yang, P and Song, Y and Li, M},
title = {Biological mechanisms of pulmonary inflammation and its association with seropositive rheumatoid arthritis.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1530753},
pmid = {40486510},
issn = {1664-3224},
mesh = {Humans ; *Arthritis, Rheumatoid/immunology/complications ; Extracellular Traps/immunology ; *Pneumonia/immunology ; *COVID-19/immunology ; SARS-CoV-2/immunology ; Animals ; Lung/immunology/pathology ; Gastrointestinal Microbiome/immunology ; },
abstract = {Although the pathogenesis of seropositive rheumatoid arthritis (RA) remains unclear, studies suggest that pulmonary inflammation-related biological mechanisms play a significant role in its development. This review thoroughly explores the mechanisms underlying early pulmonary lesions in seropositive RA, focusing on the mucosal barrier hypothesis, neutrophil extracellular traps, pathogenic microbial infections like COVID-19, Vitamin D, the microbiome and gut-lung axis, inhalation exposures and chronic pulmonary diseases. This study seeks to provide novel insights and theoretical foundations for the prevention and treatment of seropositive rheumatoid arthritis.},
}
@article {pmid40486234,
year = {2025},
author = {Shilov, S and Korotetskiy, I and Kuznetsova, T and Zubenko, N and Ivanova, L and Solodova, E and Tugeyeva, A and Kaziyev, A and Korotetskaya, N and Izmailov, T},
title = {The chicken gut resistome data from different regions of Kazakhstan.},
journal = {Data in brief},
volume = {60},
number = {},
pages = {111608},
pmid = {40486234},
issn = {2352-3409},
abstract = {Antibiotic resistance (AR) is a serious global health problem affecting both human medicine and animal agriculture. The poultry farming, especially industrial poultry, antibiotics are widely used for disease prevention and growth promotion, leading to the accumulation and dissemination of antibiotic resistance genes (ARGs) within the intestinal microbiomes of birds. Poultry, which often have close contact with humans, can serve as reservoirs for resistant microorganisms, posing potential public health risks. Determination of avian intestinal resistomes through metagenomic sequencing and bioinformatics analysis enables the identification of diversity and transmission dynamics of ARGs, and to evaluate the influence of environmental factors and conditions of poultry on resistance gene distribution. The article presents data of resistome analysis of gut microbiota in populations of chickens from different regions of Kazakhstan. The data obtained will allow to develop a strategy to reduce the spread of antibiotic-resistant pathogens and improve safety in poultry farming, as well as to predict the risk of transmission of resistant microorganisms between animals and humans.},
}
@article {pmid40485985,
year = {2025},
author = {Cerioni, NL and Uhl, HL and Welty, MA and Adler, JJ},
title = {Soil microbiome analysis of cultivated tomato (Solanum lycopersicum) plants.},
journal = {microPublication biology},
volume = {2025},
number = {},
pages = {},
pmid = {40485985},
issn = {2578-9430},
abstract = {Microbial biodiversity is critical to tomato plant health. The symbiotic relationship between tomato plants and their soil microbiome influences the plants' ability to absorb nutrients and adapt to environmental stresses. This study compared the soil microbiome between tomato plants appearing healthy versus those appearing unhealthy. There were no significant differences in overall bacterial biodiversity between the conditions. However, a specific beneficial genus (Sphingomonas) and its phylum Proteobacteria (Pseudomonadota) were found at significantly higher amounts in healthy plants' soil compared to unhealthy plants' soil. Our findings show the need for further examination of the benefits of Sphingomonas for tomato plants.},
}
@article {pmid40485830,
year = {2025},
author = {Magagula, P and Swart, V and Fourie, A and Vermeulen, A and Nelson, JH and van Rooyen, Z and van den Berg, N},
title = {Avocado rhizosphere community profiling: white root rot and its impact on microbial composition.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1583797},
pmid = {40485830},
issn = {1664-302X},
abstract = {INTRODUCTION: The avocado rhizosphere supports diverse microbial communities essential for plant health and defence against pathogens. This study aimed to investigate the impact of Dematophora necatrix, the causal agent of white root rot (WRR), on the microbial composition and soil physicochemical properties of infected and non-infected avocado trees in two South African orchards.<br><br>METHODS: ITS and 16S metabarcoding was used to compare the composition and diversity of the rhizosphere microbiome. Soil physicochemical properties were also assessed, and culturable bacterial and fungal isolates from the rhizosphere were screened for antagonistic activity against D. necatrix.<br><br>RESULTS: We found that D. necatrix did not significantly alter overall microbial diversity but influenced relative abundance of specific taxa. In Orchard A, dominant bacterial genera included Sphingomonas, Rokubacteriales and Lysobacter, while Orchard B featured Sphingomonas and Acidothermus while beneficial microbes such as Streptomyces and Bacillus were enriched in WRR non-infected (WRR-N) soils. The fungal profiles revealed Trichoderma and Penicillium as potential biocontrol agents enriched in WRR-N soils. Furthermore, dual-culture assays demonstrated that Bacillus, Pseudomonas, Penicillium and Trichoderma isolates inhibited D. necatrix, highlighting their biocontrol potential. Key parameters, such as soil pH and iron (Fe), correlated strongly with microbial composition, suggesting they play an important role in pathogen resilience.<br><br>DISCUSSION: These findings underscore the complexity of the avocado rhizosphere and its role in managing WRR, offering a foundation for developing integrated disease management strategies to enhance avocado productivity.},
}
@article {pmid40485679,
year = {2025},
author = {Fargue, S and Suryavanshi, M and Wood, KD and Crivelli, JJ and Oster, RA and Assimos, DG and Miller, A and Knight, J},
title = {Inducing Oxalobacter formigenes Colonization Reduces Urinary Oxalate in Healthy Adults.},
journal = {Kidney international reports},
volume = {10},
number = {5},
pages = {1518-1528},
pmid = {40485679},
issn = {2468-0249},
abstract = {INTRODUCTION: Oxalate-degrading intestinal bacteria, including the oxalate-degrading specialist, Oxalobacter formigenes (O formigenes), have the potential to reduce urinary oxalate excretion in humans, and thus limit the risk of calcium oxalate kidney stone formation. The aim of this proof-of-concept study, which was performed in healthy adults, was to demonstrate that ingestion of live O formigenes is safe, can establish sustainable gut colonization, and reduce urinary oxalate excretion.<br><br>METHODS: Twenty-two healthy adults without a history of kidney stones and not colonized with O formigenes ingested diets controlled in oxalate and calcium. In these participants, 24-hour urine and stool oxalate levels were quantified using ion chromatography coupled with mass spectrometry before and after ingestion of O formigenes.<br><br>RESULTS: All 22 participants were successfully colonized after a single dose of O formigenes (&#x223c;10[10] cells); 10 remained colonized for at least 1 year. Colonization was lost in 11 participants, of whom 9 reported antibiotic use. Six participants who lost colonization were redosed, and 5 were successfully recolonized. Stool oxalate concentration and urine oxalate excretion significantly decreased by 54% and 14%, respectively, with varied responses after colonization. Microbiome molecular analyses of precolonized stool samples highlighted the abundance and diversity of other potential oxalate-degrading bacteria, which may have influenced the effect of O formigenes colonization on urinary oxalate excretion.<br><br>CONCLUSION: These findings support future investigations to examine the effectiveness of O formigenes colonization in reducing urinary oxalate excretion in disease cohorts, including calcium oxalate kidney stone formers with enteric hyperoxaluria.},
}
@article {pmid40485603,
year = {2025},
author = {Ma, J and Fu, S and Tan, J and Han, Y and Chen, Y and Deng, X and Shen, H and Zeng, S and Peng, Y and Cai, C},
title = {Mechanistic Foundations of KRAS-Driven Tumor Ecosystems: Integrating Crosstalk among Immune, Metabolic, Microbial, and Stromal Microenvironment.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e02714},
doi = {10.1002/advs.202502714},
pmid = {40485603},
issn = {2198-3844},
support = {82173342//National Natural Science Foundation of China/ ; 82203015//National Natural Science Foundation of China/ ; 82373275//National Natural Science Foundation of China/ ; 82403920//National Natural Science Foundation of China/ ; 2024JJ6662//Natural Science Foundation of Hunan Province/ ; 2025JJ20077//Natural Science Foundation of Hunan Province/ ; 2024RC3042//Science and Technology Innovation Program of Hunan Province/ ; 2023Q01//Youth Science Foundation of Xiangya Hospital/ ; GZC20242044//Postdoctoral Fellowship Program of the CPSF/ ; 2024M753679//China Postdoctoral Science Foundation/ ; kq2403008//Nature Science Foundation of Changsha/ ; },
abstract = {Kirsten rat sarcoma viral oncogene homolog (KRAS) is the most frequently mutated member of the RAS family of small GTPases (RAS). It affects about one-fifth of cancer cases. The tumor microenvironment (TME) is a multifaceted network of immune cells, metabolites, microbiota, stromal components, and extracellular matrix. It creates a dynamic ecosystem that supports malignant initiation, progression, and therapy resistance through bidirectional crosstalk with tumor cells. Emerging evidence reveals distinct TME landscapes shaped by wild-type versus oncogenic KRAS variants. Additionally, TME rewiring occurs during KRAS-targeted therapies. Deciphering these KRAS-dependent TME architectures and their therapeutic vulnerabilities represents a critical frontier for precision oncology. This review synthesizes key milestones and persistent challenges in KRAS inhibitor development. And it systematically evaluates how KRAS mutations orchestrated immunosuppressive niches, metabolic symbiosis, stromal remodeling, and microbiome dysbiosis, supported by mechanistic insights from preclinical and clinical studies. It further explores therapeutic opportunities arising from targeting TME interactions, including rational combinations of KRAS inhibitors with immune checkpoint blockade, metabolic agents, or microbiota-modulating strategies.},
}
@article {pmid40485371,
year = {2025},
author = {Wang, SJ and Glass, R and Jiang, B and Kirkwood, C and Parashar, U and Duan, ZJ and Wang, XY},
title = {A report for the fifth International Workshop on Rotavirus and Norovirus in China.},
journal = {Human vaccines &amp; immunotherapeutics},
volume = {21},
number = {1},
pages = {2512647},
doi = {10.1080/21645515.2025.2512647},
pmid = {40485371},
issn = {2164-554X},
mesh = {Humans ; China/epidemiology ; *Rotavirus Infections/prevention &amp; control/epidemiology/immunology ; *Norovirus/immunology ; *Rotavirus/immunology ; *Gastroenteritis/prevention &amp; control/virology/epidemiology ; *Rotavirus Vaccines/immunology/administration &amp; dosage ; *Caliciviridae Infections/prevention &amp; control/epidemiology/immunology ; },
abstract = {The fifth International Workshop on Rotavirus and Norovirus in China was convened in Shanghai May 8-9, 2024. The workshop was organized by Fudan University and China Center for Disease Control and Prevention (China CDC), with strong support from Bill &amp; Melinda Gates Foundation and the Centers for Disease Control and Prevention in the United States (US CDC). Over 230 participants from 10 countries, including experts and representatives from government and non-government organizations, academia and vaccine manufacturers, attended the meeting. Progress on reduced rotavirus disease burden, the impact of currently licensed oral vaccines, new vaccines and technologies under development to control and prevent acute gastroenteritis caused by rotavirus and norovirus, mucosal immunity and its measurement, as well as the association between the effectiveness of rotavirus vaccine and intestinal microbiome were discussed extensively. This report summarized the latest information shared at the convening.},
}
@article {pmid40485285,
year = {2025},
author = {Sze, SH},
title = {An Exact Matching Method for 16S rRNA Taxonomy Classification.},
journal = {Journal of computational biology : a journal of computational molecular cell biology},
volume = {},
number = {},
pages = {},
doi = {10.1089/cmb.2024.0615},
pmid = {40485285},
issn = {1557-8666},
abstract = {One popular approach to taxonomy classification in the microbiome utilizes 16S ribosomal RNA sequences. The main challenge is that 16S rRNA sequences could be almost identical in closely related species, and it is difficult to distinguish them at the species level. Recent approaches are able to achieve almost single nucleotide resolution by constructing an error model of the reads. We develop an exact matching algorithm to utilize the single nucleotide resolution directly. We show that our algorithm is able to obtain improved accuracy in recent samples of mock communities and in samples of high compositional complexity when compared to existing algorithms. A software program implementing this algorithm is available at http://faculty.cse.tamu.edu/shsze/kmpmatch.},
}
@article {pmid40484980,
year = {2025},
author = {Tang, G and Millar, EKA and Graham, PH and Beretov, J},
title = {Interaction between the breast tumor microenvironment and gut microbiome.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2514136},
doi = {10.1080/19490976.2025.2514136},
pmid = {40484980},
issn = {1949-0984},
mesh = {Humans ; *Breast Neoplasms/microbiology/immunology/pathology/metabolism ; *Tumor Microenvironment ; *Gastrointestinal Microbiome ; Female ; Dysbiosis/microbiology ; Probiotics ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; },
abstract = {Previously believed to be sterile, the breast microenvironment has been revealed by modern DNA sequencing technologies to harbor a diverse community of microorganisms. The breast tumor microenvironment (TME) has a microbial signature unique to that of other breast pathologies as well as between breast cancer subtypes and stage. Among the plethora of microorganisms identified, Methylobacterium radiotolerans and Sphingomonas yanoikuyae stand out, both elevated in breast cancer tissue and associated with cancer stage. Breast cancer is the most common malignancy affecting women and the second most common cause of cancer-specific death in women worldwide. Gut dysbiosis has recently emerged as a key player, although the exact mechanisms are still unclear. Hypothesized mechanisms include bacterial metabolites inducing genomic instability, imbalances in the local and systemic immune system, the role of gut microbiota in the regulation of estrogen metabolism. Probiotic commensals Akkermansia muciniphila and Bifidobacterium appear to have a protective effect, with evidence of gut wall protection, correlation with less advanced disease and better treatment efficacy and tolerability. This review outlines the relationship between the breast microbiome, the gut microbiome, the 'estrabolome', and the immune system in breast cancer. This characterization could make a significant clinical contribution, potentially leading to new methods of primary prevention, better prognostication and prediction, as well as new avenues of treatment.},
}
@article {pmid40484974,
year = {2025},
author = {Smith, ME and Kavamura, VN and Hughes, D and Mendes, R and Lund, G and Clark, I and Mauchline, TH},
title = {Uncovering functional deterioration in the rhizosphere microbiome associated with post-green revolution wheat cultivars.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {64},
pmid = {40484974},
issn = {2524-6372},
support = {FR2021-02017//Svenska Forskningsr&#xe5;det Formas/ ; BB/N016246/1//Bilateral BBSRC-Embrapa gran/ ; BBS/E/C/00005196//Bilateral BBSRC-Embrapa grant/ ; BB/X010953/1//Growing Health Institute Strategic Programme/ ; },
abstract = {BACKGROUND: During the Green Revolution, one of the biggest developments of wheat domestication was the development of new cultivars that respond well to fertilisers and produce higher yields on shorter stems to prevent lodging. Consequently, this change has also impacted the wheat microbiome, often resulting in reduced selection of taxa and a loss of network complexity in the rhizospheres of modern cultivars. Given the importance of rhizosphere microbiomes for plant health and performance, it is imperative that we understand if and how these changes have affected their function. Here, we use shotgun metagenomics to classify the functional potential of prokaryote communities from the rhizospheres of pre-green revolution (heritage) cultivars to compare the impact of modern wheat breeding on rhizosphere microbiome functions.<br><br>RESULTS: We found distinct taxonomic and functional differences between heritage and modern wheat rhizosphere communities and identified that modern wheat microbiomes were less distinct from the communities in the surrounding soil. Of the 113 functional genes that were differentially abundant between heritage and modern cultivars, 95% were depleted in modern cultivars and 65% of differentially abundant reads best mapped to genes involved in staurosporine biosynthesis (antibiotic product), plant cell wall degradation (microbial mediation of plant root architecture, overwintering energy source for microbes) and sphingolipid metabolism (signal bioactive molecules).<br><br>CONCLUSIONS: Overall, our findings indicate that green revolution breeding has developed wheat cultivars with a reduced rhizosphere effect. The consequences of this are likely detrimental to the development of microbiome-assisted agriculture which will require a strong rhizosphere selective environment for the establishment of a beneficial plant root microbiome. We believe our results are of striking importance and highlight that implementation of microbiome facilitated agriculture will benefit from deliberately incorporating the development of beneficial plant-microbiome interactions, alongside traditional yield traits, to advance sustainable wheat production.},
}
@article {pmid40484955,
year = {2025},
author = {Lin, A and Huang, L and Jiang, A and Zhu, L and Mou, W and Li, Y and Zhang, C and Liu, Z and Zhang, J and Cheng, Q and Wei, T and Luo, P},
title = {Microbiota boost immunotherapy? A meta-analysis dives into fecal microbiota transplantation and immune checkpoint inhibitors.},
journal = {BMC medicine},
volume = {23},
number = {1},
pages = {341},
pmid = {40484955},
issn = {1741-7015},
support = {2021A1515012593//Natural Science Foundation of Guangdong Province/ ; 82373129//National Natural Science Foundation of China/ ; 82172750//National Natural Science Foundation of China/ ; 2022A1515111212//Basic and Applied Basic Research Foundation of Guangdong Province/ ; 2023A04J1257//Science and Technology Program of Guangzhou/ ; NO.2023RC3074//Hunan Youth Science and Technology Talent Project/ ; },
mesh = {Humans ; *Fecal Microbiota Transplantation/methods ; *Immune Checkpoint Inhibitors/therapeutic use ; *Neoplasms/therapy ; *Gastrointestinal Microbiome ; *Immunotherapy/methods ; Treatment Outcome ; },
abstract = {BACKGROUND: Immune checkpoint inhibitors (ICIs) are a cornerstone of modern cancer treatment, but their effectiveness is limited. Fecal microbiota transplantation (FMT), which alters the gut microbiome, has shown promise in enhancing ICIs' therapeutic effects.<br><br>METHODS: We conducted a comprehensive search of relevant studies available up to September 30, 2024, to analyze the clinical efficacy and safety of combining FMT with ICIs in cancer treatment. The primary endpoint was the objective response rate (ORR), with secondary evaluations of survival outcomes and safety.<br><br>RESULTS: A total of 10 studies involving 164 patients with solid tumors were included. The pooled ORR was 43% (95% CI: 0.35-0.51). Subgroup analysis revealed that the combination of anti-PD-1 and anti-CTLA-4 therapies was associated with a significantly higher ORR (60%) compared to anti-PD-1 monotherapy (37%; P&#x2009;=&#x2009;0.01). The incidence of grade 1-2 adverse events (AEs) was 42% (95% CI: 0.32-0.52), while grade 3-4 AEs occurred in 37% of patients (95% CI: 0.28-0.46).<br><br>CONCLUSIONS: This meta-analysis provides preliminary evidence supporting the use of FMT as a strategy to enhance the efficacy of ICIs in patients with advanced or refractory solid tumors. However, larger-scale randomized controlled trials with long-term follow-up are required to confirm and optimize treatment protocols.},
}
@article {pmid40484738,
year = {2025},
author = {Nohesara, S and Mostafavi Abdolmaleky, H and Dickerson, F and Pinto-Tomas, AA and Jeste, DV and Thiagalingam, S},
title = {Corrigendum to "Associations of microbiome pathophysiology with social activity and behavior are mediated by epigenetic modulations: Avenues for designing innovative therapeutic strategies" [Neurosci. Biobehav. Rev. 174 (2025) 106208].},
journal = {Neuroscience and biobehavioral reviews},
volume = {},
number = {},
pages = {106240},
doi = {10.1016/j.neubiorev.2025.106240},
pmid = {40484738},
issn = {1873-7528},
}
@article {pmid40484562,
year = {2025},
author = {Feng, Y and Xiao, Y and Li, X and Guo, M and Huang, L and Lu, W and Zhao, J and Chen, W},
title = {Prebiotic roles and anti-aging effects of xylo-oligosaccharide: Keystone responsive bacteria and their metabolic interactions.},
journal = {Food research international (Ottawa, Ont.)},
volume = {215},
number = {},
pages = {116673},
doi = {10.1016/j.foodres.2025.116673},
pmid = {40484562},
issn = {1873-7145},
mesh = {*Prebiotics/administration &amp; dosage ; *Gastrointestinal Microbiome/drug effects ; *Oligosaccharides/pharmacology ; Humans ; Feces/microbiology ; Animals ; *Aging/drug effects ; Mice ; Male ; Metabolomics ; *Glucuronates/pharmacology ; *Bacteria/metabolism/drug effects/genetics/classification ; Mice, Inbred C57BL ; Female ; Fermentation ; Adult ; },
abstract = {Xylo-oligosaccharide (XOS), a prebiotic oligosaccharide, has been reported to exert the beneficial effects on the host, primarily by modulating the gut microbiota and associated metabolism. However, the specific microbes, their metabolic interactions and mechanistic insights remain understudied. In this study, we aim to investigate the response of gut microbiota to XOS at the fine-grained level using combined approaches of microbiome sequencing, genomic analyses, and metabolomic analyses based on in vitro fecal fermentation using healthy human fecal samples. The results showed that XOS significantly altered the composition of the gut microbiota and enriched numerous bacterial taxa, such as Blautia, Bifidobacterium longum subsp. longum, and Faecalibacterium prausnitzii. Functional genomic analyses further confirmed that specifically identified XOS-responsive bacteria harbored varied XOS-utilizing capacities, consistent with the levels of their abundance elevation. The fecal metabolomics analysis revealed that XOS intervention significantly altered the metabolic profile (γ-aminobutyric acid, serotonin, and inosine). The microbe-microbe and microbe-metabolite interaction networks consistently identified three independent groups, potentially representing different levels of XOS degradation and/or other response mechanisms. Finally, the beneficial effects of XOS on the gut microbiota and metabolism were confirmed by the alleviation D-galactose-induced aging in mouse model. This study supports the role of XOS as prebiotics and highlights the potential of XOS in alleviating host aging-associated phenotypes in a D-galactose-induced aging mouse model in terms of improvements on cognitive function, inflammatory markers, and oxidative stress levels.},
}
@article {pmid40484540,
year = {2025},
author = {Grant-St James, A and Lee, AC and Lee, AJ and Wist, J and Sohel, F and Wong, KW and Yeap, BB and Loo, RL and Henry, A and Susic, D and El-Omar, E and Nicholson, JK and Holmes, E and Whiley, L and Gray, N},
title = {Analytical quality control in targeted lipidomics: Evaluating the performance of commercial plasma as a surrogate for pooled study samples.},
journal = {Analytica chimica acta},
volume = {1365},
number = {},
pages = {344225},
doi = {10.1016/j.aca.2025.344225},
pmid = {40484540},
issn = {1873-4324},
mesh = {*Lipidomics/standards ; Quality Control ; *Lipids/blood ; Humans ; },
abstract = {BACKGROUND: Pooled quality control (PQC) samples are the gold standard for data quality monitoring in metabolic phenotyping studies. Typically composed of equal parts from all study samples, PQCs can be challenging to generate in large cohorts or when sample volumes are low. As an alternative, externally sourced matrix-matched surrogate QCs (sQC) have been proposed. This study evaluates the performance of sQCs against PQCs for assessing analytical variation, data pre-processing, and downstream data analysis in a targeted lipidomics workflow.<br><br>RESULTS: Plasma samples (n&#xa0;=&#xa0;701) from the Microbiome Understanding in Maternity Study, along with PQC (n&#xa0;=&#xa0;80) and sQC (n&#xa0;=&#xa0;80) samples, were analyzed using a lipidomics assay targeting 1162 lipids. QC samples were injected throughout acquisition, and data pre-processing was performed using each strategy. For simplicity, a subset (n&#xa0;=&#xa0;381) of the study samples was used to assess differences in downstream statistical analyses. Both QC approaches demonstrated high analytical repeatability. While PQC and sQC compositions differed, use of PQCs retained less than 4&#xa0;% more lipid species during pre-processing. Univariate analysis identified more statistically significant lipids with PQC-based pre-processing, but multivariate model performance was similar between datasets.<br><br>SIGNIFICANCE: This study provides a comprehensive comparison of QC strategies and emphasizes the importance of careful QC workflow selection. While PQCs offer advantages, sQCs serve as a suitable alternative for quality assessment and pre-processing. Their commercial availability also supports use as intra- and inter-laboratory long-term references, aiding data harmonization across studies and laboratories.},
}
@article {pmid40484397,
year = {2025},
author = {Adachi, A and Dominguez, JJ and Utami, YD and Fuji, M and Kirita, S and Imai, S and Murakami, T and Hongoh, Y and Shinjo, R and Kamiya, T and Fujiwara, T and Minamisawa, K and Ono, N and Kanaya, S and Saijo, Y},
title = {Field Dynamics of the Root Endosphere Microbiome Assembly in Paddy Rice Cultivated under No Fertilizer Input.},
journal = {Plant &amp; cell physiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/pcp/pcaf045},
pmid = {40484397},
issn = {1471-9053},
abstract = {Plants accommodate diverse microbial communities, termed the microbiome, which can change dynamically during plant adaptation to varying environmental conditions. However, the direction of these changes and the underlying mechanisms driving them, particularly in crops adapting to the field conditions, are not well understood. Here, we investigate the root endosphere microbiome of rice (Oryza sativa ssp. japonica) across four consecutive cultivation seasons in a high-yield, non-fertilized, and pesticide-free paddy field, compared to a neighboring fertilized and pesticide-treated field. Using 16S rRNA amplicon and metagenome sequencing, we analyzed three Japonica cultivars-Nipponbare, Hinohikari, and Kinmaze. Our findings reveal that the root endosphere microbiomes diverge based on fertilization regime and plant developmental stages, while the effects of cultivar variation are less significant. Machine learning model and metagenomic analysis of nitrogenase (nif) genes suggest enhanced nitrogen fixation activity in the non-fertilized field-grown roots, highlighting a potential role of diazotrophic, iron-reducing bacteria Telmatospirillum. These results provide valuable insights into the assembly of the rice root microbiome in nutrient-poor soil, which can aid in managing microbial homeostasis for sustainable agriculture.},
}
@article {pmid40484360,
year = {2025},
author = {Wu, H and He, K and Wang, H and Li, W and Huo, R and Jiang, SH and Xue, J},
title = {The Gut-Brain Axis in the Context of Colorectal Cancer.},
journal = {Pharmacological research},
volume = {},
number = {},
pages = {107816},
doi = {10.1016/j.phrs.2025.107816},
pmid = {40484360},
issn = {1096-1186},
abstract = {The gut-brain axis (GBA) plays a pivotal role in the pathophysiology of colorectal cancer (CRC), influencing tumor progression, immune responses, and therapeutic outcomes. Bidirectional communication between the gut and the brain, mediated through microbial metabolites, neurotransmitters, and neural signaling pathways, shapes the tumor microenvironment and systemic inflammation. CRC cells not only modify the gut microbiota but also release neuroactive molecules that influence neural circuits, further impacting tumor growth. The autonomic nervous system regulates gut motility, immune responses, and inflammation, contributing to CRC progression. The gut microbiome's production of bioactive molecules, such as short-chain fatty acids and neurotransmitters, further modulates brain activity, promoting tumor metastasis and immune evasion. This review summarizes the complex interactions within the GBA and their implications for CRC, with a focus on immune modulation, microbial dysbiosis, and neuroimmune interactions. We highlight the therapeutic potential of targeting the GBA, including microbiome modulation, neurotransmitter-specific therapies, and psychological interventions, which could complement existing CRC treatments. Future research is essential to further elucidate the precise molecular mediators of the GBA and their impact on CRC biology, laying the groundwork for novel, targeted therapeutic strategies that could improve patient outcomes.},
}
@article {pmid40484186,
year = {2025},
author = {Ayres, KR and Liuzzi, JP and Lewis, FC and Mobarki, HM},
title = {Investigating Zinc's role in Mitigating Blood Lead Levels' Toxicity on Gut Microbiota Diversity: NHANES 2007-2010.},
journal = {Toxicology letters},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.toxlet.2025.06.001},
pmid = {40484186},
issn = {1879-3169},
abstract = {INTRODUCTION: Zinc serves as a cofactor for numerous vital processes across species. Microorganisms that make up the gut microbiome rely on these zinc-dependent mechanisms to perform essential functions, contributing to a diverse and stable microbial environment. Environmental contaminants, such as lead, has been shown to disrupt diversity and stability. The purpose of this study was to determine whether zinc serves as an effect modifier against elevated blood lead levels (BLL) on gut microbiota diversity.<br><br>METHODS: The 2007-2008 and 2009-2010 NHANES datasets were utilized to conduct a cross-sectional complex survey analysis aimed at determining whether zinc intake acts as a protective factor against changes in microbiome diversity associated with BLL, using enterolactone (ENL) as a biomarker. A multiple linear regression was conducted to evaluate whether an interaction between BLL and zinc intake could predict ENL. The model included fiber intake and BMI as covariates.<br><br>RESULTS: BMI and fiber intake were identified as covariates. Fiber intake was a confounding variable in the relationship between zinc and ENL levels. Lead was found to decrease ENL levels (p= 0.002). The interaction between zinc and BLL was marginally significant (p=0.089).<br><br>CONCLUSION: This study suggests that lead's impact on gut microbial diversity may depend on zinc status. These findings emphasize the importance of accounting for dietary confounders, such as fiber intake, to improve model accuracy and interpretation. While additional research is needed to confirm zinc's potential protective role, public health strategies encouraging adequate zinc and fiber intake may in part help support microbial resilience and reduce lead's effects on the gut microbiota.},
}
@article {pmid40484124,
year = {2025},
author = {Liu, Y and Li, Z and Shen, L and Shuai, K and Zhang, C and Ning, Z},
title = {Trends in Food Protein-Induced Allergic Proctocolitis (FPIAP): Mechanisms and Treatment Targeting Gut Microbiome.},
journal = {Clinics and research in hepatology and gastroenterology},
volume = {},
number = {},
pages = {102634},
doi = {10.1016/j.clinre.2025.102634},
pmid = {40484124},
issn = {2210-741X},
abstract = {BACKGROUND: Food protein-induced allergic proctocolitis (FPIAP) is a non-IgE-mediated food allergy characterized by subacute or chronic inflammatory processes in the gut. Unlike IgE-mediated food allergies that may cause multi-organ syndromes, non-IgE-mediated food allergies mainly affect the gastrointestinal tract. The incidence of FPIAP is rising globally, becoming a significant health concern.<br><br>OBJECTIVES: This article aims to systematically review the epidemiological characteristics, pathogenesis, cell death programs involved in FPIAP, and its relationship with the gut microbiota. It also explores therapeutic developments targeting the intestinal microbiota.<br><br>METHODS: We conducted a comprehensive literature search across multiple databases, including PubMed, Web of Science, and Scopus, up to December 2024. Studies were selected based on predefined inclusion and exclusion criteria. Data extraction and quality assessment were performed by two independent reviewers.<br><br>RESULTS: The review identified key epidemiological trends, highlighting the increasing incidence of FPIAP. The pathogenesis section elucidates the mechanisms underlying non-IgE-mediated allergies, emphasizing the role of the gut microbiome in mediating dietary factors and immune responses. Specific cell death programs, such as apoptosis and pyroptosis, were found to be involved in the progression of FPIAP. Therapeutic strategies targeting the gut microbiota show promise in managing FPIAP, with probiotics and prebiotics emerging as potential interventions.<br><br>CONCLUSIONS: This review provides valuable insights into the mechanisms of FPIAP and highlights the potential of microbiota-targeted therapies. Future research should focus on large-scale clinical trials to validate the efficacy of these interventions and further explore the complex interplay between diet, gut microbiota, and immune responses in FPIAP.},
}
@article {pmid40484118,
year = {2025},
author = {Jin, MJ and Barron, AB and He, SY and He, XJ and Huang, Q and Zhang, LZ and Wang, ZL and Wu, XB and Yan, WY and Zeng, ZJ},
title = {Bombella intestini: A probiotic honeybee(Apis mellifera) gut bacterium.},
journal = {Journal of insect physiology},
volume = {},
number = {},
pages = {104836},
doi = {10.1016/j.jinsphys.2025.104836},
pmid = {40484118},
issn = {1879-1611},
abstract = {Honey bee colonies are facing increasing environmental stressors that threaten their health and lifespan. While the gut microbiota may play a role in honey bee physiology, the specific functions of certain bacterial species remain unclear. This study investigates whether Bombella intestini, a bacterium highly enriched in the queen gut but nearly absent in worker bees, can act as a probiotic to promote honey bee growth, metabolism, and lifespan. Our results show that B. intestini can survive in larval food and the larval gut. When larval food is inoculated with B. intestini there is increased tryptophan in both the larval diet and larval hemolymph. Bees fed this diet had a longer lifespan. This study identifies B. intestini as a potential probiotic for honey bees, providing a microbiome-based strategy to enhance their growth and longevity. These findings open new avenues for improving honey bee health management through microbial supplementation.},
}
@article {pmid40483843,
year = {2025},
author = {Azevedo, MJ and Ferreira, AF and Loginov, D and Novák, P and Falcão-Pires, I and Ramalho, C and Buijs, MJ and Brandt, BW and Zaura, E and Trindade, F and Sampaio-Maia, B},
title = {Salivary proteome and microbiome in pregnancy and postpartum: An exploratory study on the relation with arterial hypertension.},
journal = {Archives of oral biology},
volume = {177},
number = {},
pages = {106319},
doi = {10.1016/j.archoralbio.2025.106319},
pmid = {40483843},
issn = {1879-1506},
abstract = {OBJECTIVES: Arterial hypertension (AH) influences salivary gland physiology and oral health, being associated with a higher incidence of periodontal disease in pregnant women. Evidence points to a bidirectional relationship between the oral microbiota and blood pressure regulation. Therefore, this study aimed to characterize the oral health of pregnant women and AH-associated changes in the salivary proteome and microbiome during pregnancy and postpartum.<br><br>DESIGN: Ten healthy women and ten women with AH were enrolled. Saliva was collected during pregnancy and six months postpartum. The salivary proteome was characterized by shotgun label-free mass spectrometry analysis. Specific proteins were validated through parallel reaction monitoring (PRM). The oral microbiota was characterized via 16S rRNA gene amplicon sequencing (V4 region). The periodontal health and the caries history was assessed during pregnancy.<br><br>RESULTS: Pregnant women with AH had lower junction plakoglobin (JUP)- and desmoplakin (DSP)-specific peptide levels than healthy women, confirmed by the PRM approach. The levels of these proteins correlated negatively with periodontal health indexes, which were higher in pregnant women with AH. In AH, nitrate-reducing microorganisms had lower abundance, correlating positively with JUP and DSP-specific peptides.<br><br>CONCLUSIONS: The salivary proteome and microbiota are shaped by AH during and after pregnancy. Further research is required to understand the underlying mechanisms impairing oral health in AH.},
}
@article {pmid40483796,
year = {2025},
author = {Liu, MY and He, SF and Li, YY and Shen, JJ and Li, JJ and Li, YS and Liu, YY and Wu, T and Li, JB and Hu, LF},
title = {Alterations in the intestinal fungal microbiome of patients with severe fever with thrombocytopenia syndrome.},
journal = {Journal of infection and public health},
volume = {18},
number = {9},
pages = {102837},
doi = {10.1016/j.jiph.2025.102837},
pmid = {40483796},
issn = {1876-035X},
abstract = {BACKGROUND: Aspergillus coinfection in patients with severe fever with thrombocytopenia syndrome (SFTS), is a serious clinical challenge associated with increased mortality. Understanding the factors contributing to this co-infection is crucial for improving patient outcomes. This study aimed to reveal the role of the intestinal mycobiome in SFTS severity and the risk of Aspergillus coinfection, with the goal of identifying potential therapeutic targets.<br><br>METHODS: Fecal samples were collected from 80 patients both during their hospitalization and post-discharge. Internal transcribed spacer (ITS) amplicon sequencing and fungal profiling of intestine were performed. R statistical software (version 3.5.1) was used for data processing and analysis.<br><br>RESULTS: The intestinal mycobiomes of SFTS patients showed strong alterations characterized by increased Aspergillus species, and a highly heterogeneous mycobiome con&#xfb01;guration compared to healthy controls. The Aspergillus had a positive correlation with coinfection of invasive pulmonary aspergillosis (IPA) and disease severity of SFTS (p&#x202f;<&#x202f;0.001), whereas Saccharomycetales and Candida were more abundant in SFTS patients without IPA (p&#x202f;<&#x202f;0.001). In SFTS patients with IPA, A. subversicolor, A. flavus and A. penicillioides were the three most common fungal species. Longitudinal dynamic detection revealed that patients who experienced significant fluctuations in their intestinal mycobiome tended to have more severe illness. After recovering, the gut mycobiome of patients can recover and stabilize within a month.<br><br>CONCLUSION: The research highlighted enrichment of intestinal Aspergillus was conducive to IPA and disease severity in SFTS patients. Monitoring the gut mycobiome could potentially be used as a biomarker to assess disease severity of SFTS.},
}
@article {pmid40483759,
year = {2025},
author = {Zhang, F and Peng, R and Xie, Y and Ji, X and Liu, S and Jiang, H},
title = {Cultivar-specific response of a root-associated microbiome assembly of rice to cadmium pollution.},
journal = {Plant physiology and biochemistry : PPB},
volume = {227},
number = {},
pages = {110128},
doi = {10.1016/j.plaphy.2025.110128},
pmid = {40483759},
issn = {1873-2690},
abstract = {Rice (Oryza sativa L.) cadmium (Cd) contamination is a serious threat to global food security and human health. However, the response of rice root-associated microbiomes to Cd pollution remains unclear. This study investigate the interactions between the root-associated microbiome and plant metals using environmental and microbial analysis methods, to reveal the potential mechanisms of the root microbiomes regulating the Cd accumulation in rice. The results showed that the grain Cd concentrations of the two low-Cd accumulation (LA) cultivars were 34-46 % lower than that of the high-Cd accumulation (HA) cultivars, whereas the iron (Fe) content in the LA roots was significantly higher than that in the HA roots. The root Fe content was significantly negatively correlated with the Cd concentration of grain (R = -0.681, p < 0.05). 16S rRNA amplicon sequencing showed that rice planting significantly changed the diversity of the root-associated bacterial community and formed a unique core endophytic microbiome (such as Xanthobacteraceae and Sphingomonas) under Cd stress. LA cultivars assembled more root core microbial taxa, which promoted siderophore secretion and root Fe uptake, thereby inhibiting Cd uptake by rice. Chrome azurol S plate detection confirmed that the LA rhizosphere was enriched with 1-9-fold more siderophore-secreting microorganisms than the HA rhizosphere. This study provides new insights into the effects of root-associated microbiomes on Cd accumulation in plant and will help develop new strategies for the safe production of rice.},
}
@article {pmid40483691,
year = {2025},
author = {Burgmer, S and Meyer Zu Altenschildesche, FL and Gyenis, A and Lee, HJ and Vilchez, D and Giavalisco, P and Fichant, A and Uhlirova, M and Storelli, G},
title = {Endosymbiont control through non-canonical immune signaling and gut metabolic remodeling.},
journal = {Cell reports},
volume = {44},
number = {6},
pages = {115811},
doi = {10.1016/j.celrep.2025.115811},
pmid = {40483691},
issn = {2211-1247},
abstract = {Animals coexist with bacteria and need to keep these microorganisms under tight control. To achieve such control, pattern recognition receptors (PRRs) sense bacterial cues and induce the production of antimicrobials. Here, we uncover a metabolic arm in the control of symbionts by PRRs. We show that, in Drosophila, the PRRs PGRP-LC and PGRP-LE act independently of canonical NF-κB signaling to repress essential metabolic functions in the gut, such as digestion and central carbon metabolism. This metabolic switch affects commensal populations and drastically reduces intestinal and systemic populations of the intracellular parasite Wolbachia. We propose that intestinal metabolic remodeling complements immune responses by imposing nutrient restriction on intracellular bacteria, whose lifestyle protects them from antimicrobials. Our findings reveal a role for PRRs in bacterial control beyond canonical immune pathways and provide insights into how microbial signals modulate symbiotic populations but also nutrition and metabolism in animals.},
}
@article {pmid40483623,
year = {2025},
author = {Chi, Y and Luo, M and Ding, C},
title = {The role of microbiota in fish spoilage: biochemical mechanisms and innovative preservation strategies.},
journal = {Antonie van Leeuwenhoek},
volume = {118},
number = {7},
pages = {89},
pmid = {40483623},
issn = {1572-9699},
support = {202411049301XJ//National College Student Innovation and Entrepreneurship Training Program Funding Project/ ; },
mesh = {*Fishes/microbiology ; *Microbiota ; Animals ; *Food Preservation/methods ; *Food Microbiology ; *Seafood/microbiology ; *Bacteria/metabolism/classification/genetics ; },
abstract = {Fish spoilage is a microbially-mediated biochemical process resulting in quality deterioration, economic losses, and food safety risks. Studies have indicated that spoilage microbiota are phylogenetically diverse, with Gram-negative bacteria (Pseudomonas, Shewanella, Photobacterium) representing primary spoilage organisms, and Gram-positive bacteria (Lactobacillus, Brochothrix) causing spoilage only under specific conditions. Microorganisms cause spoilage through the utilization of three main metabolic processes: (i) proteolytic degradation of muscle proteins, (ii) lipolytic breakdown of triglycerides, and (iii) production of volatile bioactive organic compounds and biogenic amines. By combining high-throughput sequencing with metabolomics, researchers have been uncovering strain-specific metabolic networks and how they are influenced by environmental factors such as temperature, pH, and packaging. This review systematically examines: (1) patterns of taxonomic succession in spoilage microbiota, (2) enzymatic and biochemical pathways involved in spoilage, and (3) innovative preservation strategies targeting spoilage consortia. Emerging technologies, such as bacteriocin-mediated biopreservation, phage therapy, and modified atmosphere packaging, show considerable promise in inhibiting spoilage organisms while maintaining the sensory qualities of the fish. Microbiome-directed interventions combined with predictive modeling and precision storage systems also represent a novel approach to fish preservation. There is a critical need to integrate traditional microbiology with the use of multi-omic technologies for the development of sustainable, microbiota-based preservation strategies that address global seafood security challenges.},
}
@article {pmid40483501,
year = {2025},
author = {Cuthbertson, L and Hatfield, L and Gavillet, H and Hardman, M and Marsh, R and Rivett, DW and van der Gast, C},
title = {Species turnover within cystic fibrosis lung microbiota is indicative of acute pulmonary exacerbation onset.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {140},
pmid = {40483501},
issn = {2049-2618},
support = {NE/H019456/1//Natural Environment Research Council/ ; NE/H019456/1//Natural Environment Research Council/ ; VIA 045//Cystic Fibrosis Trust/ ; VIA 045//Cystic Fibrosis Trust/ ; VIA 045//Cystic Fibrosis Trust/ ; VIA 045//Cystic Fibrosis Trust/ ; VIA 045//Cystic Fibrosis Trust/ ; VIA 045//Cystic Fibrosis Trust/ ; },
mesh = {*Cystic Fibrosis/microbiology ; Humans ; *Lung/microbiology ; *Microbiota ; Male ; Female ; *Bacteria/classification/genetics/isolation &amp; purification ; Adult ; Disease Progression ; Young Adult ; },
abstract = {BACKGROUND: Acute pulmonary exacerbations (PEx) are associated with increased morbidity and earlier mortality for people living with cystic fibrosis (pwCF). The most common causes of PEx in CF are by bacterial infection and concomitant inflammation leading to progressive airway damage. To draw attention to the seriousness of PEx they have been labelled as 'lung attacks', much like a 'heart attack' for acute myocardial infarction. Treatment typically starts when a pwCF presents with worsening respiratory symptoms. Hence, there is a pressing need to identify indicative biomarkers of PEx onset to allow more timely intervention. Set within an ecological framework, we investigated temporal microbiota dynamics to connect changes in the lung microbiota of pwCF to changes in disease states across a PEx event.<br><br>RESULTS: Species-time relationships (STR) describe how the richness of a community changes with time, here STRs were used to assess temporal turnover (w) within the lung microbiota of each pwCF (n&#x2009;=&#x2009;12, mean sample duration 315.9&#x2009;&#xb1;&#x2009;42.7&#xa0;days). STRs were characterised by high interpatient variability, indicating that turnover and hence temporal organization are a personalized feature of the CF lung microbiota. Greater turnover was found to be significantly associated with greater change in lung function with time. When microbiota turnover was examined at a finer scale across each pwCF time series, w-values could clearly be observed to increase in the exacerbation period, then peaking within the treatment period, demonstrating that increases in turnover were not solely a result of perturbations caused by PEx antibiotic interventions. STR w-values have been found to have a remarkable degree of similarity for different organisms, in a variety of habitats and ecosystems, and time lengths (typically not exceeding w&#x2009;=&#x2009;0.5). Here, we found w-values soon increased beyond that. It was therefore possible to use the departure from that expected norm up to start of treatment to approximate onset of PEx in days (21.2&#x2009;&#xb1;&#x2009;8.9&#xa0;days across the study participants).<br><br>CONCLUSIONS: Here, we illustrate that changes in turnover of the lung microbiota of pwCF can be indicative of PEx onset in considerable advance of when treatment would normally be initiated. This offers translational potential to enable early detection of PEx and consequent timely intervention. Video Abstract.},
}
@article {pmid40483308,
year = {2025},
author = {Behel, V and Hait, S and Noronha, V and Chowdhury, A and Chandrani, P and Patil, V and Menon, N and Mishra, R and Bawaskar, B and Dahimbekar, G and Shah, M and Kaushal, R and Veldore, V and Goswami, H and Bharde, A and Khandare, J and Shafi, G and Choughule, A and Tyagi, N and Desai, S and Prabhash, K and Dutt, A},
title = {Assessment of plasma derived microbiome profiles in lung cancer using targeted and whole exome sequencing.},
journal = {NPJ systems biology and applications},
volume = {11},
number = {1},
pages = {62},
pmid = {40483308},
issn = {2056-7189},
support = {01/ICMRCAREP-2023-0000278/AD/DevDiv//Indian Council of Medical Research/ ; },
mesh = {Humans ; *Lung Neoplasms/microbiology/blood/genetics ; *Exome Sequencing/methods ; *Microbiota/genetics ; Female ; Computational Biology/methods ; Male ; Adenocarcinoma of Lung/microbiology ; Middle Aged ; Aged ; },
abstract = {Microbial infections contribute to ~20% of malignancy. Plasma-derived cell-free DNA presents a promising avenue for non-invasive cancer diagnostics, capturing microbial signatures. We analyzed 261 plasma from 50 patients with lung adenocarcinoma by targeted and whole exome sequencing at 10,000 × and 340 × depth, respectively. Comparative analyses of Kraken 2 and IPD2 reveal substantial discrepancies, highlighting challenges in microbial DNA quantification and the need for stringent bioinformatics approaches to ensure accurate cancer microbiome profiling.},
}
@article {pmid40483298,
year = {2025},
author = {Leeflang, J and Wright, JA and Worthley, DL and Din, MO and Woods, SL},
title = {Evolutionary adaptation of probiotics in the gut: selection pressures, optimization strategies, and regulatory challenges.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {96},
pmid = {40483298},
issn = {2055-5008},
support = {2020305//Department of Health | National Health and Medical Research Council (NHMRC)/ ; Bushell fellowship//Gastroenterological Society of Australia (GESA)/ ; 1R01 EB030134-01A1//U.S. Department of Health &amp; Human Services | NIH | National Cancer Institute (NCI)/ ; },
mesh = {*Probiotics ; Humans ; *Gastrointestinal Microbiome ; *Bacteria/genetics/classification/growth &amp; development ; *Gastrointestinal Tract/microbiology ; Selection, Genetic ; *Adaptation, Physiological ; Biological Evolution ; },
abstract = {Probiotics and live bacterial therapeutics are garnering increased attention for use in human health and have the potential to revolutionise the treatment of gastrointestinal diseases. However, a pervasive feature of bacteria that must be considered in the design of safe and effective probiotics and live bacterial therapeutics is their capacity for rapid evolution, both at the individual (epi)genetic level and in terms of population dynamics. Here we summarise gastrointestinal-specific evolution of bacteria, focussing on genetic and population levels of adaptation to factors such as carbon source availability, environmental stressors, and interactions with the native microbiome. We also address regulatory and safety considerations for the development of probiotics and live biotherapeutics from an evolutionary perspective, with a discussion of methods that utilise evolution to improve probiotic safety and efficacy via directed evolution, in comparison to another popular approach, genetic engineering.},
}
@article {pmid40483244,
year = {2025},
author = {Duong, JT and Hayden, HS and Verster, AJ and Pope, CE and Miller, C and Kelsi Penewit, and Salipante, SJ and Rowe, SM and Solomon, GM and Nichols, D and Kelly, A and Schwarzenberg, SJ and Freedman, SD and Hoffman, LR},
title = {Fecal microbiota changes in people with cystic fibrosis after 6 months of elexacaftor/tezacaftor/ivacaftor: Findings from the promise study.},
journal = {Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jcf.2025.05.006},
pmid = {40483244},
issn = {1873-5010},
abstract = {BACKGROUND: People with cystic fibrosis (PwCF) often have fecal dysbioses relative to those without CF, characterized by increased pro-inflammatory microbiota and gastrointestinal (GI) inflammation as measured by fecal calprotectin, suggesting that inflammation contributes to CF GI disease. The multicenter observational PROMISE study (NCT04038047) found that calprotectin decreased in PwCF treated with elexacaftor/tezacaftor/ivacaftor (ETI). To better understand the dynamics between fecal dysbiosis and GI inflammation, we characterized the microbiomes of fecal samples from PROMISE and the relationships with calprotectin before, 1-month post, and 6-months post ETI.<br><br>METHODS: Fecal microbiota from participants &#x2265;12 y/o were determined by shotgun metagenomic sequencing with random forest modeling and multivariate linear regression analysis to define relationships between microbiota, calprotectin, and deltaF508 genotype before and after ETI.<br><br>RESULTS: We analyzed 345 samples from 124 participants. At baseline, we observed community-level differences in the fecal microbiota among participants with abnormal compared to normal calprotectin. With ETI, the relative abundances of 7 bacterial species - Escherichia coli, Staphylococcus aureus, Clostridium scindens, Enterocloster clostridioformis, Clostridium butyricum, Anaeroglobus geminatus, and Ruminococcus gnavus - decreased significantly, correlating with calprotectin decrease. We detected community-level differences in the fecal microbiota based on CFTR genotype and a distinct pattern of microbiota change in F508del homozygous compared to heterozygous participants after ETI.<br><br>CONCLUSIONS: We identified 7 species for which fecal abundances decreased with ETI and correlated with calprotectin decrease, supporting a close relationship between fecal microbiota and inflammation in PwCF. Future work will define these relationships with metabolites and GI symptoms during long-term ETI therapy.},
}
@article {pmid40483188,
year = {2025},
author = {Arif, SJ and Graham, SP and Abdill, RJ and Blekhman, R},
title = {Analyzing human gut microbiome data from global populations: challenges and resources.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2025.05.008},
pmid = {40483188},
issn = {1878-4380},
abstract = {Research on the human gut microbiome is expanding rapidly; yet, most published studies focus on populations from high-income regions such as North America and Europe. Underrepresentation of populations from low- and middle-income countries in the microbiome literature limits the generalizability of microbiome-health associations. These challenges are compounded by computational barriers, including biases in reference databases, nonrepresentative metadata, and infrastructure limitations in low- and middle-income countries. However, recent efforts in large-scale global sampling have begun to address these problems. This review provides recommendations for future research efforts applying computational analysis to global microbiome data, including guidelines to initiate and maintain equitable partnerships, identify representative datasets, overcome technical limitations, and contextualize results at the global scale.},
}
@article {pmid40482930,
year = {2025},
author = {Adiningrat, A and Maulana, I and Fadhlurrahman, AG and Yumoto, H},
title = {Probiotic bacteria from asymptomatic necrotic tooth can regulate the microbiome homeostasis.},
journal = {Microbial pathogenesis},
volume = {206},
number = {},
pages = {107791},
doi = {10.1016/j.micpath.2025.107791},
pmid = {40482930},
issn = {1096-1208},
abstract = {OBJECTIVE: This study was performed to identify and isolate the dominant bacteria from a chronic asymptomatic necrotic root canal and investigate in vitro its potential postbiotics effect at the biofilm maturation maintaining root canal microbiome homeostasis.<br><br>METHODS: For bacterial identification of an in vivo root canal sample, metagenomic analysis was applied, followed by single colony isolation and PCR analysis. Cell free supernatant (CFS) was then cultivated through serial L paracasei culture procedures prior antibiofilm analysis. Antibiofilm effects of the CFS product were evaluated using in vitro biofilm analysis against S. mutans and E. faecalis. Biofilm mass analysis was measured by using colorimetric approach with cresyl-vast violet staining, morphological appearance was observed using both phase-contrast and scanning electron microscope (SEM). Shapiro-Wilk analysis was applied for normality test, followed by the ANOVA to compare multiple groups or a student t-test for independent two groups mean comparisons.<br><br>RESULTS: The isolated root canal bacteria produced biofilm mass that was similar to the Enterococcus faecalis control pathogenic biofilm. From the morphological analysis suggested that population of the isolated bacteria were predominantly occupied by rod-shaped rather than cocci-shaped inhabitants. Further metagenomic analysis indicated that the isolated dominant bacteria in the mixed culture were mainly identified as probiotic bacteria, Lacticaseibacillus paracasei. Moreover, the functional analysis revealed that the L. paracasei cell free supernatant product (CFS) exhibited a promising positive effect in biofilm structure integrity disturbances of S. mutans and E. faecalis.<br><br>CONCLUSIONS: The isolated Lacticaseibacillus paracasei from the root canal of a chronic asymptomatic necrotic tooth, produces potential postbiotic products that demonstrated a disruptive ability against Streptococcus mutans and Enterococcus faecalis biofilm integrity.},
}
@article {pmid40482893,
year = {2025},
author = {Ning, Z and Dou, D and Liu, J and Qin, X and Ang, YH and Yang, T and Zhang, J},
title = {Sulfur modification enhances promotion of carbon-iron composites on carbon chain elongation.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {132776},
doi = {10.1016/j.biortech.2025.132776},
pmid = {40482893},
issn = {1873-2976},
abstract = {Efficient synthesis of caproate is crucial for efficient recovery of organic wastes. However, the yield and selectivity of caproate are limited by the efficiency of carbon chain elongation (CCE). This study presents sulfur-modified carbon-iron composites (BC[S-Fe]) as an innovative approach to enhance CCE for efficient caproate biosynthesis. Unlike conventional carbon-iron materials (BC[Fe]), sulfur modification stabilized nano-zero-valent iron (Fe[0]) against oxidation and amplified redox activity, achieving an 83 % higher caproate yield (6914 mg·L[-1]) and 58 % carbon conversion efficiency. BC[S-Fe [1/5]] (S:Fe = 1:5) outperformed BC, Fe[0] and BC[Fe] by enriching electroactive bacteria (e.g., Rummeliibacillus suwonensis, Seramator thermalis, and Rubeoparvulum massiliense) that upregulated electron transfer genes and CCE metabolic genes. Additionally, BC[S-Fe [1/5]] enhanced biofilm formation and quorum sensing, fostering microbial synergy to optimize electron flux. This work pioneers the integration of sulfur-modified composites into microbial CCE systems, offering a novel strategy to optimize caproate synthesis through enhanced electron transfer and functional microbiome engineering.},
}
@article {pmid40482791,
year = {2025},
author = {Gazi, U and Bahceciler, NN},
title = {Oral microbiota in allergic diseases, and sublingual allergen immunotherapy.},
journal = {Clinical immunology (Orlando, Fla.)},
volume = {},
number = {},
pages = {110538},
doi = {10.1016/j.clim.2025.110538},
pmid = {40482791},
issn = {1521-7035},
abstract = {Allergic diseases with their epidemic prevalence on the rise have been one of the major global health problems of the 21st century. The association of increased prevalence with lifestyle changes including increased urbanization, and hygiene practices highlighted the importance of host-microbiome interactions for maintaining immune homeostasis. In support, numerous studies demonstrated altered gut microbiome composition in allergic patients, and suggested dysbiosis as a possible cause of allergic diseases. Nevertheless, despite being the second largest microbiota in the human body, oral microbiota has not yet received the attention it deserves in the literature. With this review article, we aim to highlight its significance by summarizing the data obtained from studies evaluating oral microbiome composition in patients with allergic respiratory diseases. Additionally, their importance will be further elaborated by discussing the findings presented by animal and human studies investigating the possible effect of oral probiotic uptake to the clinical efficacy of sublingual allergen immunotherapy.},
}
@article {pmid40482721,
year = {2025},
author = {Araujo, ASF and Pereira, APA and de Medeiros, EV and Mendes, LW},
title = {Root architecture and the rhizosphere microbiome: shaping sustainable agriculture.},
journal = {Plant science : an international journal of experimental plant biology},
volume = {},
number = {},
pages = {112599},
doi = {10.1016/j.plantsci.2025.112599},
pmid = {40482721},
issn = {1873-2259},
abstract = {Understanding root architecture and exudation is fundamental for enhancing crop productivity and promoting sustainable agriculture. Historically, plant researchers have focused on above-ground traits to increase yield and reduce input dependence. However, below-ground traits, especially those related to the root system, are equally critical yet often overlooked due to phenotyping challenges. Root architecture, including some root traits, i.e., lateral root density, root hair abundance, and root tip number, plays central roles in plant establishment, stress tolerance, and the recruitment of beneficial microbes in the rhizosphere. Root exudates, a complex array of chemical compounds released by roots, vary with plant species, developmental stage, and environmental conditions. These compounds act as signals and nutrients, shaping the composition and function of rhizosphere microbial communities. In turn, the microbiome of rhizosphere contributes to plant health by facilitating nutrient uptake, enhancing stress resilience, and providing defense against pathogens. Integrating root traits into breeding programs offers promising opportunities to select for genotypes that are more efficient in recruiting beneficial microbes. Heritable root traits, such as increased branching, finer roots, and higher exudation capacity, can enhance microbiome assembly and stability. The assessment of genes can also regulate of these traits and represent targets for genomics-assisted selection. Some strategies, such as microbiome engineering, particularly through the design of synthetic microbial communities (SynComs), can be used to modulate root architecture and optimize plant-microbe interactions. Despite these promising outcomes, challenges remain in translating SynCom applications to the field due to environmental variability, native microbial competition, and limited understanding of host genetic controls. This review discusses how root architecture shapes the rhizosphere microbiome and explores strategies, such as trait-based breeding and microbiome engineering, for advancing sustainable crop production.},
}
@article {pmid40481438,
year = {2025},
author = {Babalola, OO and Osuji, IE and Akanmu, AO},
title = {Amplicon-based metagenomic survey of microbes associated with the organic and inorganic rhizosphere soil of Glycine max L.},
journal = {BMC genomic data},
volume = {26},
number = {1},
pages = {40},
pmid = {40481438},
issn = {2730-6844},
abstract = {OBJECTIVES: The metagenomic dataset of 16S rRNA and ITS gene amplicons of DNA were obtained from the cultivated soybean rhizosphere of organic and inorganic treatments. The organic treatments consisted of poultry waste, and cow dung treatments while the inorganic consisted of samples from untreated soybean plots and the bulk. Amplicon sequencing was performed on the Illumina platform, and the raw sequence data were processed and analyzed using Quantitative Insights Into Microbial Ecology (QIIME 2 version 2019.1.).<br><br>DATA DESCRIPTION: The analysis revealed a metagenomic library from soybean rhizospheric soils, providing insights into diversity and distribution of the bacterial and fungal community diversities. The most predominant bacteria phylum taxa across the treatments were Proteobacteria, Firmicutes, Actinobacteriota and Bacteriodota, while those for fungi were Ascomycota, Basidiomycota and Glomeromycota. The dataset provides insights into how different organic fertilization sources affect the structure, composition, and diversity of the microbiome in the soybean rhizosphere. The sequences have been deposited in the Sequence Read Archive (SRA) of the National Center for Biotechnology Information (NCBI) with assigned bioproject accession numbers; 16S rRNA (SRP540791) and ITS (SRP541849).},
}
@article {pmid40462893,
year = {2025},
author = {Xiong, X and Ho, M and Jaber, K and Mishra, R and Charytan, A and Zaidan, N and Schlamp, F and Fishman, GI and Nazzal, L},
title = {Colonization with Oxalobacter formigenes slows the progression of CKD and reduces cardiac remodeling in CKD.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {40462893},
issn = {2692-8205},
support = {P30 CA016087/CA/NCI NIH HHS/United States ; R01 DK129675/DK/NIDDK NIH HHS/United States ; R01 DK137473/DK/NIDDK NIH HHS/United States ; },
abstract = {Accumulation of oxalate in patients with chronic kidney disease (CKD) is associated with CKD progression and increased risk of cardiac death. Whether reducing plasma or urine oxalate slows CKD progression and prevents cardiovascular complications remains unexplored. We colonized the intestines of control and CKD mice with Oxalobacter formigenes (Oxf), an oxalate-degrading microorganism. The mice were fed with the oxalate precursor hydroxyproline for 23 weeks at which time we assessed pathological changes in the kidney and heart. We demonstrate that Oxf reduces plasma oxalate (pOx) and creatinine levels, mitigates inflammation and fibrosis in the kidney, and reduces pathologic cardiac remodeling in the hearts of CKD mice. RNA-seq analysis of ventricular tissue of CKD mice reveals dysregulated expression of metabolic pathways while Oxf colonization reverses these changes. These findings demonstrate that oxalate accumulation plays a role not only in CKD progression but also in associated cardiovascular complications and suggest that strategies to reduce plasma oxalate levels may have therapeutic benefit.},
}
@article {pmid40482640,
year = {2025},
author = {DeLeon, O and Mocanu, M and Tan, A and Sidebottom, AM and Koval, J and Ceccato, HD and Kralicek, S and Colgan, JJ and St George, MM and Lake, JM and Cooper, M and Xu, J and Moore, J and Su, Q and Xu, Z and Ng, SC and Chan, FKL and Tun, HM and Cham, CM and Liu, CY and Rubin, DT and Martinez-Guryn, K and Chang, EB},
title = {Microbiome mismatches from microbiota transplants lead to persistent off-target metabolic and immunomodulatory effects.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2025.05.014},
pmid = {40482640},
issn = {1097-4172},
abstract = {Fecal microbiota transplant (FMT) is an increasingly used intervention, but its suitability to restore regional gut microbiota, particularly in the small bowel (SB), must be questioned because of its predominant anaerobic composition. In human subjects receiving FMT by upper endoscopy, duodenal engraftment of anaerobes was observed after 4 weeks. We hypothesized that peroral FMTs create host-microbe mismatches that impact SB homeostasis. To test this, antibiotic-treated specific-pathogen-free (SPF) mice were given jejunal, cecal, or fecal microbiota transplants (JMTs, CMTs, or FMTs, respectively) and studied 1 or 3 months later. JMT and FMT altered regional microbiota membership and function, energy balance, and intestinal and hepatic transcriptomes; JMT favored host metabolic pathways and FMT favored immune pathways. MTs drove regional intestinal identity (Gata4, Gata6, and Satb2) and downstream differentiation markers. RNA sequencing (RNA-seq) of metabolite-exposed human enteroids and duodenal biopsies post-FMT confirmed transcriptional changes in mice. Thus, regional microbial mismatches after FMTs can lead to unintended consequences and require rethinking of microbiome-based interventions.},
}
@article {pmid40482531,
year = {2025},
author = {Yan, R and Manjunatha, V and Thomas, A and Shankar, V and Lumpkins, B and Hoerr, FJ and Greene, A and Jiang, X},
title = {Comparative effects of vegetarian diet and rendered animal by-product on the chicken gut health.},
journal = {Poultry science},
volume = {104},
number = {9},
pages = {105360},
doi = {10.1016/j.psj.2025.105360},
pmid = {40482531},
issn = {1525-3171},
abstract = {Rendered animal proteins and fats can provide vital nutrients for poultry at affordable prices. With growing interest in reintroducing rendered animal by-products into poultry diets, this study investigated the effects of replacing a portion of soybean meal and vegetable fat with rendered animal proteins and fats in a standard vegetarian chicken diet. The study focused on the changes in gut and liver histopathology, and gut microbiome composition and functions. Five diet treatments were formulated to be isocaloric and isonitrogenous and balanced for amino acids, including a standard vegetarian control diet and four diets containing rendered animal by-products. A total of 15 pens with 50 chickens each were assigned one of the five diets from hatch to 42 days of age, with three replicate pens per treatment. On days 28 and 42, six birds were randomly selected from two pens per treatment and humanely euthanized by cervical dislocation. Cecal samples were collected for microbial enumeration and DNA extraction, while gut and liver histopathology analyses were conducted on day 42. Enumeration of Clostridium perfringens was performed under anaerobic conditions using selective media and metagenomic sequencing was used to assess taxonomic and functional profiles of the microbiome. Statistical analysis included data transformation, permutational multivariate analysis of variance, and differential abundance testing. No significant differences were observed between the vegetarian control and rendered animal by-product diets in gut or liver histopathology, C. perfringens levels, or microbiome composition, indicating that inclusion of animal by-products did not significantly affect broiler intestinal health or microbial functions over a 42-day period. These findings suggest that partially replacing soybean meal and vegetable fat with rendered animal by-products can be a safe and cost-effective alternative to plant-based ingredients in poultry diets.},
}
@article {pmid40482059,
year = {2025},
author = {Rendina, M and Turnbaugh, PJ and Bradley, PH},
title = {Human xenobiotic metabolism proteins have full-length and split homologs in the gut microbiome.},
journal = {G3 (Bethesda, Md.)},
volume = {},
number = {},
pages = {},
doi = {10.1093/g3journal/jkaf131},
pmid = {40482059},
issn = {2160-1836},
abstract = {Xenobiotics, including pharmaceutical drugs, can be metabolized by both host and microbiota, in some cases by homologous enzymes. We conducted a systematic search for all known human proteins with gut microbial homologs. Because gene fusion and fission can obscure homology detection, we built a pipeline to identify not only full-length homologs, but also cases where microbial homologs were split across multiple adjacent genes in the same neighborhood or operon ("split homologs"). We found that human proteins with full-length gut microbial homologs disproportionately participate in xenobiotic metabolism. While this included many different enzyme classes, short-chain and aldo-keto reductases were the most frequently detected, especially in prevalent gut microbes, while cytochrome P450 homologs were largely restricted to lower-prevalence facultative anaerobes. In contrast, human proteins with split homologs tended to play roles in central metabolism, especially of nucleobase-containing compounds. We identify twelve specific drugs that gut microbial split homologs may metabolize; two of these, 6-mercaptopurine by xanthine dehydrogenase (XDH) and 5-fluorouracil by dihydropyrimidine dehydrogenase (DPYD), have been recently confirmed in mouse models. This work provides a comprehensive map of homology between the human and gut microbial proteomes, indicates which human xenobiotic enzyme classes are most likely to be shared by gut microorganisms, and finally demonstrates that split homology may be an underappreciated explanation for microbial contributions to drug metabolism.},
}
@article {pmid40481968,
year = {2025},
author = {van Iersel, LEJ and Beijers, RJHCG and Simons, SO and Schuurman, LT and Shetty, SA and Roeselers, G and van Helvoort, A and Schols, AMWJ and Gosker, HR},
title = {Characterizing gut microbial dysbiosis and exploring the effect of prebiotic fiber supplementation in patients with COPD.},
journal = {European journal of nutrition},
volume = {64},
number = {5},
pages = {210},
pmid = {40481968},
issn = {1436-6215},
support = {10.2.16.119//Longfonds/ ; },
mesh = {Humans ; *Pulmonary Disease, Chronic Obstructive/microbiology ; *Prebiotics/administration &amp; dosage ; *Gastrointestinal Microbiome/drug effects ; Male ; *Dietary Fiber/administration &amp; dosage ; Female ; *Dysbiosis/microbiology ; *Dietary Supplements ; Middle Aged ; Double-Blind Method ; Aged ; Feces/microbiology ; Cross-Sectional Studies ; Vitamin D/administration &amp; dosage ; Tryptophan/administration &amp; dosage ; },
abstract = {PURPOSE: Chronic Obstructive Pulmonary Disease (COPD) is associated with poor dietary quality that may lead to gut microbiota imbalances. A healthy gut microbiome contributes to metabolic health and immune function through production of metabolites like short-chain fatty acids. Prebiotic fibers positively influence microbiota by promoting the production of beneficial metabolites. This study aimed to assess altered gut microbiota composition in patients with COPD and to explore the effects of targeted multi-nutrient supplementation including prebiotic fibers on these outcomes.<br><br>METHODS: An exploratory analysis was performed within the double-blinded placebo-controlled NUTRECOVER-trial to gain preliminary insights into the effects of the nutritional intervention. The cross-sectional baseline comparison included 32 patients with COPD and 32 age-matched healthy references. Subsequently, patients were randomly assigned to a multi-nutrient supplement including prebiotic fibers, vitamin D, tryptophan, and N-3 long-chain poly unsaturated fatty acids (n&#x2009;=&#x2009;16) or placebo (n&#x2009;=&#x2009;16) for three months. Stool samples, blood samples and food diaries were obtained before and after the intervention.<br><br>RESULTS: Higher relative abundance of Bacteroidota (0.50&#x2009;&#xb1;&#x2009;0.13 vs. 0.41&#x2009;&#xb1;&#x2009;0.14, p&#x2009;=&#x2009;0.010), and lower Firmicutes (0.40&#x2009;&#xb1;&#x2009;0.14 vs. 0.49&#x2009;&#xb1;&#x2009;0.12, p&#x2009;=&#x2009;0.007) were found in patients compared with healthy controls. Patients also showed lower alpha diversity (5.80&#x2009;&#xb1;&#x2009;0.32 vs. 5.99&#x2009;&#xb1;&#x2009;0.30, p&#x2009;=&#x2009;0.017) and higher inter-individual variability (0.51&#x2009;&#xb1;&#x2009;0.16 vs. 0.48&#x2009;&#xb1;&#x2009;0.10, p&#x2009;<&#x2009;0.001). No effects of the nutritional intervention on gut microbiome and systemic inflammation were shown at 3 months.<br><br>CONCLUSION: Patients with COPD exhibit differences in gut microbiota composition compared with healthy controls. Three months of multi-nutrient supplementation is insufficient to show changes in microbiome composition. The ongoing NUTRECOVER-trial will show the potential of long-term prebiotic fiber supplementation in this susceptible patient population.<br><br>TRIAL REGISTRATION NUMBER: clinicaltrials.gov: NCT03807310.},
}
@article {pmid40481696,
year = {2025},
author = {Martínez-Montoro, JI and Sancho-Marín, R and Ocaña-Wilhelmi, L and Arranz-Salas, I and Ruiz-Campos, N and García-López, MJ and Tinahones, FJ and Gutiérrez-Repiso, C},
title = {Gastric microbiota-specific signatures in adults with obesity and Helicobacter pylori-negative gastritis.},
journal = {European journal of clinical investigation},
volume = {},
number = {},
pages = {e70085},
doi = {10.1111/eci.70085},
pmid = {40481696},
issn = {1365-2362},
support = {//Centro de Investigaci&#xf3;n Biom&#xe9;dica en Red-Fisiopatolog&#xed;a de la Obesidad y Nutrici&#xf3;n/ ; CM22/00217//Instituto de Salud Carlos III/ ; CP20/00066//Instituto de Salud Carlos III/ ; JR24/00006//Instituto de Salud Carlos III/ ; //European Regional Development Fund/ ; PTA2022-021854-I//Ministerio de Ciencia e Innovaci&#xf3;n/ ; //Funding for open access charge: Universidad de M&#xe1;laga/CBUA/ ; },
abstract = {BACKGROUND: The role of the gastric microbiome in the pathophysiology of gastritis beyond Helicobacter pylori (HP) infection is poorly understood and has remained unexplored in patients with obesity. The aim of this study was to analyse gastric mucosa-associated microbiota in patients with obesity and nonatrophic chronic gastritis in the absence of HP infection or history of HP eradication.<br><br>METHODS: This was a case-control study conducted at Virgen de la Victoria University Hospital in Malaga, performed in patients with severe obesity (body mass index &#x2265;40&#x2009;kg/m[2]) undergoing sleeve gastrectomy, without HP infection and no history of HP eradication. Gastric biopsy specimens were collected at surgery and were analysed by 16S rRNA sequencing. Participants were divided into two groups according to the histological evaluation: nonatrophic chronic gastritis and nongastritis. An exploratory prospective analysis to determine the influence of gastritis on short-term outcomes after surgery was also performed.<br><br>RESULTS: Sixty-seven participants (38 in the gastritis and 29 in the nongastritis group) were included. A lower alpha diversity (evenness and Shannon diversity indexes) and beta diversity (weighted Unifrac distance) were shown in the gastritis group. Higher relative abundances in the families Micrococcaceae, Streptococcaceae and Leuconostocaceae and the genera Streptococcus, Weissella and Cryptobacterium were observed in the gastritis group, compared with the nongastritis group. An enrichment in pathways involved in toluene degradation, heterolactic fermentation and secondary metabolites biosynthesis, such as ergothioneine and terpenoids, was found in the gastritis group. Also, higher total cholesterol levels 1&#x2009;year after the surgery were observed in the gastritis group compared with the nongastritis group, although no within-group differences from baseline to 1&#x2009;year were detected in this parameter.<br><br>CONCLUSION: Our results suggest a relationship between the gastric microbiome and nonatrophic chronic gastritis in obesity, beyond HP infection.},
}
@article {pmid40481630,
year = {2025},
author = {Parthasarathy, S and Aly, SH and Tharumasivam, SV and Giridharan, B and Chandran, J and Thirumurthy, P and Abd El Hafeez, MS and El-Shazly, M},
title = {Unlocking nature's secrets: a review on the pharmacokinetics of plant-based medicines and herbal remedies.},
journal = {Natural product research},
volume = {},
number = {},
pages = {1-25},
doi = {10.1080/14786419.2025.2513583},
pmid = {40481630},
issn = {1478-6427},
abstract = {Herbal and plant-based medicines have been used for centuries for their therapeutic properties. However, understanding their pharmacokinetics is essential for optimising their efficacy, ensuring their safety and guiding appropriate dosing regimens. Herbal and plant-based medications can be ingested, inhaled, applied topically or injected. Factors such as solubility, formulation and interactions with gut enzymes and transporters influence their absorption characteristics. Distribution of these compounds involves their movement throughout the body, influenced by factors like blood flow, tissue permeability and plasma protein binding. Herbal and plant-based medications are metabolised in the liver by cytochrome P450 enzymes and conjugation routes. Metabolism can vary by genetics and gut microbiome. These compounds can be excreted by the kidneys, liver, faeces, lungs, sweat and saliva. This review aims to decode the pharmacokinetics of herbal and plant-based medicines by providing a comprehensive overview of their absorption, distribution, metabolism and elimination processes.},
}
@article {pmid40481550,
year = {2025},
author = {Zhu, F and Ying, H and Siadat, SD and Fateh, A},
title = {The gut-lung axis and microbiome dysbiosis in non-tuberculous mycobacterial infections: immune mechanisms, clinical implications, and therapeutic frontiers.},
journal = {Gut pathogens},
volume = {17},
number = {1},
pages = {40},
pmid = {40481550},
issn = {1757-4749},
abstract = {Non-tuberculous mycobacteria (NTM) are emerging pathogens of global concern, particularly in regions with declining tuberculosis rates. This review synthesizes current evidence on the epidemiology, immune pathogenesis, and microbiome interactions underlying NTM infections. The rising incidence of NTM is driven by environmental factors, immunocompromised populations, and advanced diagnostics. Clinically, NTM manifests as pulmonary, lymphatic, skin/soft tissue, or disseminated disease, with Mycobacterium avium complex (MAC) and M. abscessus being predominant pathogens. Host immunity, particularly Th1 responses mediated by IL-12/IFN-γ and TLR2 signaling, is critical for controlling NTM, while dysregulated immunity (e.g., elevated Th2 cytokines, PD-1/IL-10 pathways) exacerbates susceptibility. Emerging research highlights the gut-lung axis as a pivotal mediator of disease, where microbiome dysbiosis-marked by reduced Prevotella and Bifidobacterium-impairs systemic immunity and promotes NTM progression. Short-chain fatty acids (SCFAs) and microbial metabolites like inosine modulate macrophage and T-cell responses, offering therapeutic potential. Studies reveal distinct airway microbiome signatures in NTM patients, characterized by enriched Streptococcus and Prevotella, and reduced diversity linked to worse outcomes. Despite advances, treatment remains challenging due to biofilm formation, antibiotic resistance, and relapse rates. This review underscores the need for microbiome-targeted therapies, personalized medicine, and longitudinal studies to unravel causal relationships between microbial ecology and NTM pathogenesis.},
}
@article {pmid40481461,
year = {2025},
author = {Yang, S and Li, J and Wu, Y},
title = {The association of lead and cadmium exposure with periodontitis: a systematic review and meta-analysis.},
journal = {BMC oral health},
volume = {25},
number = {1},
pages = {935},
pmid = {40481461},
issn = {1472-6831},
mesh = {Humans ; *Cadmium/adverse effects/toxicity ; *Lead/adverse effects/toxicity ; *Periodontitis/chemically induced/epidemiology ; *Environmental Exposure/adverse effects ; },
abstract = {OBJECTIVE: Periodontitis, a microbiome-driven chronic inflammatory disease that destroys the supporting structures of the teeth, is influenced by various environmental factors, including exposure to heavy metals such as lead and cadmium. This systematic review and meta-analysis aimed to evaluate the association between exposure to lead and cadmium and periodontitis.<br><br>METHODS: A comprehensive literature search was conducted in PubMed, Web of Science, Scopus, and Embase up to February 1, 2025, following PRISMA guidelines. Observational studies examining the association between lead and/or cadmium exposure and periodontitis were included. Required clinical data were extracted, and study quality was assessed using the Newcastle-Ottawa Scale. Random-effects models were used to compute either standardized mean differences (SMD) of concentration or pooled adjusted odds ratios (aORs). Heterogeneity was assessed with I&#xb2;.<br><br>RESULTS: Fourteen studies (13 datasets for either lead or cadmium) comprising 72,467 participants were eligible for inclusion. The meta-analysis found that cadmium and lead exposure were significantly associated with higher odds of periodontitis, with pooled aORs of 1.22 (95% CI: 1.08-1.37) and 1.85 (95% CI: 1.42-2.41), respectively. Sensitivity analyses confirmed the robustness of the findings.<br><br>CONCLUSION: This study provides evidence that exposure to lead and cadmium is significantly associated with periodontitis. These findings highlight the importance of reducing environmental exposure to these heavy metals as part of preventive strategies for periodontal disease. Further research is needed to explore the underlying biological mechanisms and evaluate potential interventions to reduce exposure-associated periodontitis.},
}
@article {pmid40481153,
year = {2025},
author = {Banila, C and Ladoukakis, E and Scibior-Bentkowska, D and Santiago, LR and Reuter, C and Kleeman, M and Nedjai, B},
title = {A longitudinal pilot study in pre-menopausal women links cervicovaginal microbiome to CIN3 progression and recovery.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {883},
pmid = {40481153},
issn = {2399-3642},
support = {C27045/A27046//Cancer Research UK (CRUK)/ ; },
mesh = {Humans ; Female ; Pilot Projects ; Adult ; *Microbiota ; *Vagina/microbiology ; Longitudinal Studies ; Middle Aged ; *Uterine Cervical Dysplasia/microbiology/pathology/surgery ; *Premenopause ; *Uterine Cervical Neoplasms/microbiology/pathology/surgery ; Young Adult ; Disease Progression ; *Papillomavirus Infections/microbiology ; *Cervix Uteri/microbiology ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Increasing evidence suggests vaginal dysbiosis is associated with persistent high-risk human papillomavirus (hrHPV) infection and cervical intraepithelial neoplasia (CIN) development. In this pilot longitudinal study, we investigate the potential of vaginal microbiome biomarkers to predict CIN3 development in hrHPV-positive (hrHPV+) women of reproductive age and assess loop electrosurgical excision procedure (LEEP) outcomes.Fifty-nine non-menopausal women 20-53 years old, with normal cytology, were selected from the ARTISTIC trial and followed up twice over six years. Vaginal microbiome was analysed by 16S rRNA sequencing. HrHPV+ women with CIN3 showed a significant overrepresentation of Sneathia amnii, Megasphaera genomosp., Peptostreptococcus anaerobius and Achromobacter spanius (p < 0.05). Successfully LEEP-treated hrHPV-negative women exhibited increased Lactobacillus species, especially Lactobacillus gasseri. Additionally, Lactobacillus helveticus, suntoryeus and vaginalis showed a potential protective role against CIN3 development.These unique microbial biomarkers associated with CIN3 development and recovery following LEEP treatment bring new insights into the vaginal microbiome's role on disease progression.},
}
@article {pmid40481059,
year = {2025},
author = {Cheng, G and Hardy, M and Feix, JB and Kalyanaraman, B},
title = {Inhibition of levodopa metabolism to dopamine by honokiol short-chain fatty acid derivatives may enhance therapeutic efficacy in Parkinson's disease.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {20004},
pmid = {40481059},
issn = {2045-2322},
support = {International Research Project SuperO2//Centre National de la Recherche Scientifique/ ; International Research Project SuperO2//Centre National de la Recherche Scientifique/ ; R21NS137244/NS/NINDS NIH HHS/United States ; R01CA208648/CA/NCI NIH HHS/United States ; },
mesh = {*Biphenyl Compounds/pharmacology/chemistry ; *Levodopa/metabolism/pharmacology ; *Fatty Acids, Volatile/pharmacology/chemistry ; *Parkinson Disease/drug therapy/metabolism ; *Lignans/pharmacology/chemistry ; *Dopamine/metabolism ; Humans ; Allyl Compounds ; Phenols ; },
abstract = {This study investigates the antimicrobial properties of honokiol (HNK), a naturally occurring polyphenol, when conjugated with short-chain fatty acids (SCFAs) such as butyrate. We examined the effects of HNK-SCFA ester conjugates on Enterococcus faecalis, a gut bacterium that metabolizes levodopa, a drug used to manage Parkinson's disease symptoms. Our findings indicate that HNK-SCFA-esters (e.g., HNK-acetate, HNK-propionate, HNK-butyrate, and HNK-hexanoate) inhibit E. faecalis growth in a dose-dependent manner, followed by a temporary recovery period during which levodopa remains intact and unmetabolized. Notably, HNK-SCFAs exhibit enhanced cellular permeability and are hydrolyzed within bacterial cells, releasing HNK and SCFAs. These results suggest that HNK-SCFAs may reversibly modulate the gut metabolism of levodopa to dopamine, potentially enhancing its therapeutic efficacy in treating Parkinson's disease.},
}
@article {pmid40480642,
year = {2025},
author = {Lok, J and Chen, C and Iannone, V and Babu, AF and Lo, EKK and Vazquez-Uribe, R and Vaaben, TH and Kettunen, M and Savolainen, O and Schwab, U and Sommer, MOA and Hanhineva, K and Kolehmainen, M and El-Nezami, H and Gómez-Gallego, C},
title = {Advanced Microbiome Therapeutics Accelerate MASLD Recovery by Restoring Intestinal Microbiota Equilibrium and the Gut-Liver Axis in a Mouse Model.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c01674},
pmid = {40480642},
issn = {1520-5118},
abstract = {Gut microbiota dysbiosis and endocrine dysregulation are key players in metabolic dysfunction-associated steatotic liver disease (MASLD) development. This study evaluated whether advanced microbiome therapeutics can restore intestinal microbial equilibrium and gut-liver axis balance during MASLD recovery. MASLD was induced in mice using a high-fat, high-sugar diet, and then shifted to a standard diet, where intervention groups received engineered Escherichia coli Nissle 1917 expressing IGF1 (EcNI) or aldafermin (EcNA), and control groups received E. coli Nissle 1917 vehicle (EcN) or no microbial intervention (CTRL). EcNI and EcNA improved MASLD recovery compared to controls by lowering hepatic fat, plasma cholesterol, and body weight, while increasing bacterial diversity, plasma acetate, and propionate, and modulating particular microbial groups, potentially alleviating dysbiosis. Additionally, EcNI and EcNA downregulated acetyl-CoA, the steroid hormone biosynthesis pathway, and EcNA upregulated the pentose phosphate pathway and pyruvate, which are related to oxidative stress reduction. These results suggest that EcNI and EcNA are potential novel treatments for MASLD.},
}
@article {pmid40480607,
year = {2025},
author = {Ogilvie, AR and Onishi, JC and Schlussel, Y and Kumar, A and Häggblom, MM and Kerkhof, LJ and Shapses, SA},
title = {Short-Term High Fat Diet Induced Metabolic Endotoxemia in Older Individuals with Obesity: A Randomized Crossover Study.},
journal = {The American journal of clinical nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ajcnut.2025.06.001},
pmid = {40480607},
issn = {1938-3207},
abstract = {BACKGROUND: Lipopolysaccharide, also known as endotoxin, in Gram-negative bacteria is associated with obesity and a high fat (HF) diet.<br><br>OBJECTIVE: The objective of this study was to determine whether short-term high compared to low fat (LF) intake affects serum endotoxin and gut microbiota in a controlled trial of older individuals with obesity or normal weight.<br><br>DESIGN: In this randomized crossover study, adults (50-79 years old) with obesity or normal weight were assigned to 5 days of HF (40%) or LF (20%) diet followed by a washout period and then the other diet. A 5-hour mixed meal tolerance test (46% fat) was performed after the LF diet. Serum was analyzed for endotoxin, zonulin, and inflammatory biomarkers. Fecal bacterial community was analyzed by rRNA operon profiling.<br><br>RESULTS: Participants were 64 years (95% CI: 62, 66) and 66% were female. Body mass index (BMI) was 24.3 kg/m[2] (95% CI: 23.5, 25.0) and 36.6 kg/m[2] (95% CI: 33.4, 39.8) in the group with normal body weight (n=16) and obesity (n=16), respectively. The rise in postprandial endotoxin was 1.8-fold higher in individuals with obesity compared to normal weight (p=0.010). After the study diets, fasting serum endotoxin was higher after the HF than LF diet in the group with obesity [mean difference: 0.13 EU/mL (95% CI: 0.02, 0.24), p=0.022], but not the normal weight group [mean difference: 0.03 EU/mL (95% CI: -0.07, 0.14), p=0.613]. Serum zonulin was higher after the HF compared to LF diet (p<0.001) and in the group with obesity compared to normal weight (p<0.001). Fecal community analysis indicated minimal changes in Gram-negative bacteria due to diet or BMI groups.<br><br>CONCLUSION: Serum endotoxin concentrations in individuals with obesity increase following a HF diet or meal and these data suggest it is explained by intestinal permeability rather than a shift in the gut microbiome.<br><br>CLINICAL TRIAL REGISTRATION: NCT05327868, https://clinicaltrials.gov/study/NCT05327868.},
}
@article {pmid40480235,
year = {2025},
author = {Glynn, VM and de Barros Marangoni, LF and Guglielmetti, M and Tapia, ER and Ali, V and Quintero, H and Rodriguez Guerra, EC and Yuval, M and Kline, DI and Leray, M and Connolly, SR and Barrett, RDH},
title = {The role of holobiont composition and environmental history in thermotolerance of Tropical Eastern Pacific corals.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2025.05.035},
pmid = {40480235},
issn = {1879-0445},
abstract = {Coral reefs support approximately 25% of all marine life, making it essential to understand the factors impacting their ability to withstand climate change. Corals' response mechanisms encompass both the host's own potential and that of a diverse microbial community, collectively known as the holobiont. Research investigating how these co-evolved taxa affect each other during thermal stress has revealed both the vulnerability and resilience of coral reefs, but the precise mechanisms underlying different bleaching trajectories are still poorly understood. We implemented a standardized acute thermal stress assay to investigate how seasonal upwelling in Panama's Tropical Eastern Pacific (TEP) influences Pocillopora coral's host-microbiome configurations, and we tested holobionts' resistance to increasing temperatures. Despite little host genetic differentiation, algal community shifts were modulated by both region and genetic lineage. This pattern strongly contrasted with temperature-driven dysbiosis for the prokaryotic community. Host stress responses differed among regions during acute thermal stress. Regional variation in total antioxidant capacity suggested that corals from the region with seasonal upwelling experience more stressful baseline conditions, which may contribute to their higher predicted thermal thresholds as estimated via host protein concentrations. Furthermore, shifts in algal microbiomes were associated with changes in host thermotolerance, as captured by host physiology and oxidative metabolism, suggesting a possible link between microbiome composition and host physiological performance. By leveraging the natural laboratory created by Panama's TEP, we demonstrate that coral holobionts from nearby gulfs with different thermal dynamics differ in their ability to withstand thermal stress, providing new insights into the factors driving coral thermotolerance.},
}
@article {pmid40480043,
year = {2025},
author = {Keating, C and Trego, A and O'Flaherty, V and Ijaz, UZ},
title = {Microbiomes of high-rate anaerobic digestors reveal 'Study'-specific factors and limitations of synthetic wastewater.},
journal = {Water research},
volume = {282},
number = {},
pages = {123931},
doi = {10.1016/j.watres.2025.123931},
pmid = {40480043},
issn = {1879-2448},
abstract = {Anaerobic digestion (AD) is a key technology for the treatment of organic wastes and the production of renewable energy. The stability of the process hinges on the underlying microbial populations. Amplicon sequencing is increasingly used to characterise AD microbiomes, yet sequencing efforts have not translated to process engineering of the microbiome or prediction of failure using microbial tools. Using high-rate biofilm wastewater bioreactors as a study system, we aimed to i) discern trends in archaeal and bacterial diversity, ii) identify a core AD microbiome, iii) determine the functional stability of AD microbiomes, and iv) correlate taxa to experimental conditions. We analysed amplicon sequencing data from 32 high-rate anaerobic digestor studies (> 1258 samples) at various operational conditions and applied a suite of statistical microbiome tools. We found that taxonomic archaeal diversity was highly study dependent, while functional diversity was highly shared across studies. A core AD microbiome was identified with > 100 bacterial genera and 6 archaeal genera which were present at > 1 % relative abundance in at least 50 % of samples. Interestingly, we observed that microbiome stability was significantly impacted by the choice of real or synthetic wastewater, with synthetic wastewaters yielding a more stable and less complex microbiome. This was correlated to the abundances of 37 taxa in the synthetic wastewater, including 3 key methanogens (Methanothrix, Methanobacterium, and Methanosphaerula). This suggests that when synthetic wastewater is used in experimental studies, it may not result in an AD microbiome representative of real wastewater treatment systems.},
}
@article {pmid40479975,
year = {2025},
author = {Zhang, H and Zhang, B and Lu, J and Yan, W and Tang, Y and Jiang, B and Xing, Y},
title = {Unraveling the distinct response patterns of abundant and rare fungi to vanadium at nationwide smelting sites.},
journal = {Journal of hazardous materials},
volume = {495},
number = {},
pages = {138829},
doi = {10.1016/j.jhazmat.2025.138829},
pmid = {40479975},
issn = {1873-3336},
abstract = {Fungi are essential members of the soil microbiome, exhibiting diverse response patterns to vanadium (V). However, the understanding for community response of both abundant and rare fungi remains poorly understood. This study employed ITS1-targeted amplicon sequencing to investigate the fungi microbiome across nationwide V smelters in China. Abundant and rare fungi were identified based on occurrence frequency and relative abundance. V exhibited a significant effect (p < 0.05) on abundant fungi diversity. Spatially structured environmental factors explained a greater proportion of variation in the abundant fungi (33.6 %), indicating a deterministic assembly pattern. In contrast, rare fungi showed a weaker association with environmental variables (10.2 %), suggesting a more stochastic assembly process. Interspecific association pattern of abundant fungi responded markedly to V levels compared to rare fungi. Keystone taxa in abundant subcommunity contributed more to the network stability, and were closely associated with functional potential related to vanadium detoxification and nutrient cycling, suggesting potential roles in community resilience under V stress. However, their specific functional roles remain to be experimentally validated. This study advances our understanding of fungal responses to vanadium contamination and offers a hypothesis-generating basis for future research aimed at utilizing the functional traits of fungal taxa in bioremediation strategies.},
}
@article {pmid40479865,
year = {2025},
author = {Lee, R and Song, H and Kim, J and Sung, HW and Kwon, HM and Hunter, CA and Park, J},
title = {Genetic regulation of short chain fatty acid on Leghorn male hepatoma cells infected with Fowl Adenovirus serotype-4.},
journal = {Veterinary microbiology},
volume = {307},
number = {},
pages = {110571},
doi = {10.1016/j.vetmic.2025.110571},
pmid = {40479865},
issn = {1873-2542},
abstract = {Fowl Adenovirus serotype 4 (FAdV-4) infection causes hepatitis-hydropericardium syndrome (HHS), a disease with high mortality in poultry. Short chain fatty acids (SCFAs) are a major gut metabolite that strengthens barrier function, impacts microbiome dynamics, and enhances protective immunity. Among SCFAs, butyrate has been suggested to promote anti-inflammatory effect that reduces tissue damage during viral infections. In this study, we pre-treated Leghorn male hepatoma (LMH) cell line with butyrate, infected them with FAdV-4, and examined genetic regulation related to protective immunity. Differentially expressed genes (DEGs) were identified through RNA sequencing, revealing significant alterations in various cellular pathways during FAdV-4 infection. Butyrate restored the expression of several genes involved in metabolic pathways, including the PPAR pathway. Additionally, butyrate reduced the expression of the anti-viral molecule Oasl and while upregulating il8, which plays a role in immune cell recruitment. These findings suggest that butyrate supports a beneficial antiviral response in host cells during FAdV-4 infection. This study provides the role of SCFAs in modulating host defense mechanisms against avian viral infections.},
}
@article {pmid40479795,
year = {2025},
author = {Zhimo, VY and Sharma, VK and Feygenberg, O and Salim, S and Whitehead, SR and Spadaro, D and Freilich, S and Wisniewski, M and Droby, S},
title = {Changes in microbial assembly and ecological processes following application of Aureobasidium pullulans on apple fruit surface.},
journal = {International journal of food microbiology},
volume = {441},
number = {},
pages = {111299},
doi = {10.1016/j.ijfoodmicro.2025.111299},
pmid = {40479795},
issn = {1879-3460},
abstract = {The apple fruit surface hosts a diverse microbiome that plays a vital role in fruit health and resistance to postharvest decay. Aureobasidium pullulans, a core member of this microbiome, has been extensively studied for its biocontrol properties, yet its ecological role in shaping microbial community dynamics remains poorly understood. This study aimed to evaluate the effect of manipulating a native Aureobasidium, to act both as a biocontrol agent and as a modulator of the epiphytic microbiome when applied at different stages of fruit development and storage. Among 28 Aureobasidium isolates recovered from 'Golden Delicious' apple surfaces, A69 demonstrated the most potent antagonistic activity against Penicillium expansum through volatile and diffusible metabolite production and effective suppression of lesion development in fruit. While preharvest field applications had limited effects on microbial diversity, postharvest and combined treatments significantly reshaped both fungal and bacterial communities on the apple fruit surface. Notably, A69 treatments inhibited decay incidence in stored fruit, reduced fungal diversity and enriched beneficial bacterial and yeast genera including Vishniacozyma, Cystobasidium, Buckleyzyma, Bacillus, and Frigoribacterium, many of which exhibited antagonistic activity against key postharvest pathogens. Cross-kingdom network and ecological assembly analyses revealed that A69 promoted deterministic selection within fungal communities and fostered competitive microbial interactions, resulting in a more stable and resilient microbiome. In contrast, bacterial communities remained largely governed by stochastic processes. These findings highlight the role of A69 as an effective biocontrol agent reducing decay while fostering a disease-suppressive microbiome, providing an eco-friendly microbiome-based strategy for sustainable postharvest disease control.},
}
@article {pmid40479762,
year = {2025},
author = {Liu, K and Zhang, G and Li, Y and Jiao, M and Guo, J and Shi, H and Ji, X and Zhang, W and Quan, K and Xia, W},
title = {Effects of feeding unprocessed whole black soldier fly (Hermetia illucens) larvae on performance, biochemical profile, health status, egg quality, microbiome and metabolome patterns of quails.},
journal = {Poultry science},
volume = {104},
number = {9},
pages = {105374},
doi = {10.1016/j.psj.2025.105374},
pmid = {40479762},
issn = {1525-3171},
abstract = {To address the global shortage of feed protein, black soldier fly larvae (BSFL) have garnered significant attention as a sustainable alternative protein source. Feeding whole BSFL represents an innovative approach that effectively reduces the high processing costs of dried BSFL powder and prevents nutrient loss during thermal treatment. However, limited research has been conducted on the application of whole BSFL in quail diets. This study aimed to evaluate the effects of incorporating whole BSFL into quail diets on production performance, serum biochemical parameters, immune and antioxidant responses, egg quality, intestinal microbiome and metabolome patterns. In this experiment, 180 quails aged 30-35 days were randomly assigned to four groups, each with three replicates of 15 quails. The experimental diets included 0 %, 10 %, 20 %, and 30 % unprocessed whole BSFL (con, L10, L20, L30), with a 14-day pre-experimental period followed by a 90-day main trial. Results indicated that the inclusion of BSFL significantly reduced the feed-to-egg ratio and enhanced quail production performance. Notably, the L20 group demonstrated significant improvements in liver and kidney function, metabolic levels, antioxidant capacity, and immune performance. Additionally, BSFL positively influenced the amino acid and fatty acid profiles of quail eggs, thereby improving egg quality. While BSFL did not significantly alter the diversity of intestinal microbiota or metabolites, it had a significant impact on protein digestion and absorption as well as mineral uptake. Therefore, we conclude that whole BSFL can serve as a high-quality ingredient in quails feed, with optimal results observed at a 20 % inclusion rate.},
}
@article {pmid40479599,
year = {2025},
author = {Zhang, L and Wu, S and Chen, J and Zhang, X and Yuan, J and Chen, Y and Ding, T and Li, J},
title = {Effects of Biodegradable Microplastics on Soil and Lettuce Health: Rhizosphere Microbiome and Metabolome Responses.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c02160},
pmid = {40479599},
issn = {1520-5118},
abstract = {Biodegradable microplastics (BMPs) have been widely detected in soils due to their widespread production and utilization. However, their impacts on rhizosphere microbial consortia and plant metabolic adaptation mechanisms have been insufficiently characterized. Here, two typical BMPs, polybutylene adipate-co-terephthalate and polyhydroxybutyrate, were selected to assess the effects of individual and combined exposure on the rhizosphere and metabolomes of lettuce at different concentration levels (0.1 and 2%). Results revealed that both 2% BMPs inhibited lettuce growth. Similarly, 2 wt % BMPs also altered community structures. Several biomarkers, including Bacillus and Streptomyces, were identified for BMP exposure. The metabolomic analysis revealed that 2% BMPs significantly altered the root and leaf metabolomes of lettuce. Pathways and metabolites related to plant defense toward environmental stresses, like aucubin, bisnorbiotin, l-rhamnose, and niazimin, were also enriched after BMPs treatment. This study highlights the impact of BMPs on soil and plant health, improving our comprehension of their combined ecological impact on the soil environment.},
}
@article {pmid40478912,
year = {2025},
author = {Gu, Y and Song, Y and Liu, J},
title = {Identification and characterization of eccDNA-driven genes in humans.},
journal = {PloS one},
volume = {20},
number = {6},
pages = {e0324438},
pmid = {40478912},
issn = {1932-6203},
mesh = {Humans ; *Neoplasms/genetics ; DNA Methylation ; *DNA, Circular/genetics ; Gene Expression Regulation, Neoplastic ; Epigenesis, Genetic ; Gene Expression Profiling ; },
abstract = {Extrachromosomal circular DNA (eccDNA) amplification promotes oncogene expression and cancer development. However, the global transcriptional landscape mediated by eccDNA has not yet been extensively profiled. Here we report a comprehensive analysis spanning cancer, non-cancerous disease and health by developing a new approach to catalog eccDNA-driven genes (EDGs). EDG expression is significantly higher than the average level. Our study identifies 27 common EDGs (CEDGs) existing in most cancer types. Integrated analysis of the CEDGs on gene expression, pathway and network, genetic alteration, epigenetic state, single-cell state, immune infiltration, microbiome and clinically-related features reveals their crucial roles in tumorigenesis and clinical significance. A 17-gene CEDG signature and nomogram was constructed to predict pan-cancer patients' outcomes. By a novel eccDriver algorithm, 432 candidate eccDNA-driven drivers were identified. We show the candidate drivers regulate five major biological processes including immune system process, developmental process, metabolic process, cell cycle and division, and regulation of transport. 275 of the 432 candidate drivers are clinically actionable with approved drugs. We also demonstrate that eccDNA generation is associated with DNA methylation. Our study reveals general EDG function in humans and provides the most comprehensive discovery of eccDNA-driven driver genes in cancer and non-cancerous diseases to date for future research and application.},
}
@article {pmid40478887,
year = {2025},
author = {Gomes, JA and Del-Rey, YC and de Freitas, AR and Sartori, IAM and do Nascimento, C},
title = {Microbiota and clinical outcomes of implant-supported full-mandible dentures on patients with a history of periodontitis: A 5-year prospective cohort study.},
journal = {Journal of prosthodontics : official journal of the American College of Prosthodontists},
volume = {},
number = {},
pages = {},
doi = {10.1111/jopr.14081},
pmid = {40478887},
issn = {1532-849X},
abstract = {PURPOSE: To characterize the microbiota of implant-supported full-mandible dentures and its correlation to clinical outcomes for up to 5 years after implant loading in patients with a history of periodontal disease.<br><br>MATERIALS AND METHODS: Twelve individuals with a history of periodontitis (Stage IV and Grade B) received five immediate implants and a fixed complete-arch mandibular prosthesis. Microbiological (total counts, microbial profile, and diversity) and clinical outcomes (probing depth, bleeding on probing, and bone resorption) were assessed before tooth extraction and at 4 and 5 years postloading. Thirty-five microbial species were detected and quantified by DNA checkerboard analysis.<br><br>RESULTS: The microbiota significantly changed after 5 years of implant loading, with an increase in the abundance of periodontal pathogens and microbial diversity over time. The biofilm microbial profile and genome counts of implants were substantially different from the ones found in the remaining teeth at baseline, but no correlations between microbial taxa/counts and clinical outcomes were observed.<br><br>CONCLUSION: The microbiota of dental implants was found to be different from the remaining teeth in patients with a history of periodontitis. Significant microbial shifts occurred in the microbiota of implants after 5 years of function; nonetheless, the microbiological changes did not impact clinical outcomes, which were consistent with health throughout the follow-up period.},
}
@article {pmid40478781,
year = {2025},
author = {Huang, Y and Hu, B and Li, T and Liu, T and Zhang, Z and Dong, Y},
title = {Intercropping and Nano Zinc Oxide Application Enhance Plant Resistance and Alleviate Pesticide Stress by Altering the Soil Microenvironment.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c02607},
pmid = {40478781},
issn = {1520-5118},
abstract = {Pesticide stress significantly reduces crop productivity. This study investigated wheat-fava bean intercropping combined with nano zinc oxide (nZnO) application as a strategy to alleviate pyroxasulfone (PYR) stress on fava beans. We examined the effect on plant growth, the rhizosphere microenvironment, and PYR degradation. The combined treatment effectively reduced the PYR toxicity and promoted fava bean growth. It enhanced plant antioxidant enzyme activities and soil nutrient cycling enzymes, leading to increased PYR degradation and decreased number of soil PYR residues. Furthermore, these treatments stimulated the secretion of rhizosphere flavonoids and organic acids, enriching beneficial bacterial communities, specifically Sphingomonas, Gemmatimonas, and Streptomyces. Functional predictions using FAPROTAX indicated significant changes in carbon, nitrogen, and sulfur cycling, suggesting a crucial microbial role in accelerating PYR degradation and improving plant resilience. These findings present a promising and sustainable agricultural strategy to mitigate pesticide pressure.},
}
@article {pmid40478762,
year = {2025},
author = {Barta, J and Santruckova, H and Novak, M and Cejkova, B and Jackova, I and Buzek, F and Stepanova, M and Curik, J and Veselovsky, F and Prechova, E},
title = {Microbial Community Dynamics in Two Central European Peatlands Affected by Different Nitrogen Depositions.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiaf056},
pmid = {40478762},
issn = {1574-6941},
abstract = {Changes in organic matter accumulation in wetlands are critical for climate dynamics. Different nitrogen (N) inputs in Sphagnum-dominated peat bogs can lead to varying rates of carbon (C) and N accumulation, influencing greenhouse gas emissions. We investigated how contrasting N deposition shapes microbial communities in two Czech peat bogs, focusing on biological N2 fixation (BNF) as a key N input in pristine wetlands. Higher N deposition resulted in a more active microbial community with increased enzyme activity and C acquisition, potentially accelerating decomposition and reducing C storage. Enhanced denitrification, indicated by active nosZ Clade I genes, suggests that higher N inputs may increase N losses through denitrification. In contrast, the lower N site showed a less active microbial community with slower decomposition, beneficial for C sequestration, though potentially less adaptable to future N increases. Experimental BNF rates were 70 times higher at the high N site, consistent with elevated diazotroph activity indicated by active nifH gene. Phosphorus (P) availability and NH4+/NO3- ratios appeared to drive BNF differences, emphasizing the need for managed N inputs to maintain peatland ecological functions.},
}
@article {pmid40478755,
year = {2025},
author = {Gaire, TN and Young, J and Wehri, T and Schwartz, M and Singer, R and Pieters, M and Noyes, NR},
title = {The impact of pooling on the observed microbiome profile of pre-weaned piglet feces.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiaf058},
pmid = {40478755},
issn = {1574-6941},
abstract = {Pooling individual samples could be an efficient approach for large-scale population-based microbiome studies. However, it is unknown whether pooled samples accurately reflect the microbiome composition and diversity obtained from individual samples. This study investigated the impact of various pooling methods on the observed fecal microbiome of pre-weaned piglets. Individual fecal samples were collected from 10 litters of day-old piglets (N=137) and 10 litters of 20-day-old piglets (N=121), as well as pen-floor samples from the same litters. The individually collected samples were processed individually and also used to create pools of both raw feces and extracted DNA. Individual samples, raw feces pools, DNA pools, and pen-floor samples were subjected to 16S rRNA gene sequencing. The microbial profile in pen-floor samples from litters of pre-weaned piglets was very different from individual piglet samples within the pen; thus, they may not be suitable for litter-level piglet microbiome studies. However, overall microbial diversity and composition from DNA and feces pools were comparable to individual samples, despite potentially underestimating some low-abundance or low-prevalence taxa. These results suggest that pooling can be used as an efficient and cost-effective approach to characterize litter-level microbial profiles for current and future population-level microbiome research in pre-weaned piglet populations.},
}
@article {pmid40478753,
year = {2025},
author = {Ouwehand, J and Brinkmann, BW and Peijnenburg, WJGM and Vijver, MG},
title = {Microbial custody: key microbiome inhabitant Sphingomonas alleviates silver nanoparticle toxicity in Daphnia magna.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiaf061},
pmid = {40478753},
issn = {1574-6941},
abstract = {Increased usage of nanotechnological applications inevitably leads to exposure of hosts and their associated microbiomes to metallic nanoparticles. Various bacteria within the microbiome harbour mechanisms to protect themselves against metal-related toxicity. These mechanisms have broadly been described in the absence of a host. Here, we studied how silver ion-resistant bacteria isolated from the Daphnia magna microbiome shape the host's exposure to silver nanoparticles. With germfree and mono-associated neonates, the effects of these microbes on the sensitivity of D. magna to silver nanoparticles were studied. By using this approach, a core member of the D. magna microbiome Sphingomonas yanoikuyae was identified to be silver-resistant. Neonates mono-associated with S. yanoikuyae were as sensitive to silver nanoparticles as naturally colonized neonates, whereas mono-association with Microbacterium and germfree neonates had increased sensitivity. Silver ions are the major attribution to toxicity in germfree and Microbacterium-associated neonates, whereas particles contribute more to the toxicity for the naturally- and Sphingomonas-colonized neonates. Sphingomonas accumulated in vivo more silver ions from its local environment than the other D. magna bacterial isolates. The current study shows that bacteria can play a vital role in shaping the speciation of nanomaterials and thereby modifying the toxicity to hosts.},
}
@article {pmid40478395,
year = {2025},
author = {Zhang, T and Liu, Y and Li, J and Yuan, M and Qiao, C and Huang, X and Yang, X and Gao, B and Lou, C and Yang, Y and Cao, Y},
title = {Toad's survivability and soil microbiome alterations impacted via individual abundance.},
journal = {Biologia futura},
volume = {},
number = {},
pages = {},
pmid = {40478395},
issn = {2676-8607},
support = {CI2021A04012//CACMS Innovation Fund/ ; ZZ16-YQ-04//Fundamental Research Funds of CACMS/ ; H2023406026//Hebei Natural Science Foundation/ ; QN2024119//Science Research Project of Hebei Education Department/ ; },
abstract = {Artificial breeding is a valid strategy for the reverse of current extinction tendency in wild population of amphibian like toads. Considering public health, an alternative to antibiotics is demanded for ameliorating survival of toads during the culture period. Relying on the cognition of probiotics or antagonistic bacteria, the present work investigated viability and soil microorganism variations induced by distribution characteristic on toads using high-throughput sequencing technology. Comparison and analysis of soil metagenome from clustered and depopulated groups distinguished by toad behavior showed differences of bacterial community composition (e.g., Proteobacteria bacterium TMED72 and Nannocystis exedens) and antibiotic resistance genes involving antibiotic efflux and inactivation (e.g., mdtB and acrF). There were 18 and 10 distribution-typical genes independently enriched in Proteobacteria bacterium TMED72 and bacterium TMED88 of clustered group and Nannocystis exedens of depopulated group. In Nannocystis exedens, one of the distribution-typical genes was annotated as 6-phosphogluconate dehydrogenase acting role on bacterial growth restriction. It implied that, compared with the group emerging rare traces, the reduction of soil bacteria which possess genes retarding bacterial growth putatively impairs competitiveness to pathogenic bacteria and results in poor survivability of toads under clustering behavior. With the co-occurrence of virulence genes, more evidences are needed on the antagonistic bacteria Nannocystis exedens as antibiotic substitute.},
}
@article {pmid40478177,
year = {2025},
author = {Tajima, K and Hosonuma, M and Funayama, E and Isobe, J and Baba, Y and Murayama, M and Narikawa, Y and Toyoda, H and Tsurui, T and Maruyama, Y and Sasaki, A and Amari, Y and Yamazaki, Y and Nakashima, R and Shida, M and Sasaki, A and Sambe, T and Wada, S and Tsuji, M and Kiuchi, Y and Kobayashi, S and Kuramasu, A and Tsunoda, T and Mori, M and Koyanagi, K and Yoshimura, K},
title = {Combination therapy with levofloxacin and the probiotic Clostridium butyricum MIYAIRI 588 enhances immune checkpoint inhibitor efficacy.},
journal = {International journal of cancer},
volume = {},
number = {},
pages = {},
doi = {10.1002/ijc.35472},
pmid = {40478177},
issn = {1097-0215},
abstract = {The gut microbiome influences immune checkpoint inhibitor (ICI) efficacy. In this study, we explored the effects of combined levofloxacin (LVFX) and Clostridium butyricum MIYAIRI 588 (CBM588) on ICI outcomes using a CT26 tumor model in BALB/c mice. When compared with the control, the LVFX+CBM588 combination enhanced anti-programmed cell death (PD)-1 therapy, with CD8[+] T cells playing a key role. Gut microbiota analysis showed reduced Lactobacillus relative abundance and increased Oscillibacter and Muribaculaceae in the LVFX+CBM588 group. A broad-spectrum antibiotic cocktail (ampicillin, neomycin, vancomycin, and metronidazole) with CBM588 diminished antitumor effects and reduced survival in mice when compared with the control, demonstrating the importance of microbiota-targeted therapeutic combinations. However, while LVFX+CBM588 improved ICI efficacy, it worsened dextran sulfate sodium (DSS)-induced colitis, suggesting immune activation contributes to inflammation. These findings emphasize the potential of customized antibiotic-probiotic combinations in cancer immunotherapy, while also stressing the necessity to manage immune-related adverse effects.},
}
@article {pmid40476758,
year = {2025},
author = {Taboada, S and Díez-Vives, C and Turon, M and Arias, MB and Galià-Camps, C and Cárdenas, P and Koutsouveli, V and de Carvalho, FC and Kenchington, E and Davies, AJ and Wang, S and Martín-Huete, M and Roberts, EM and Xavier, JR and Combosch, D and Riesgo, A},
title = {Connectivity and adaptation patterns of the deep-sea ground-forming sponge Geodia hentscheli across its entire distribution.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msaf145},
pmid = {40476758},
issn = {1537-1719},
abstract = {Geodia hentscheli, a species forming sponge grounds in the North Atlantic and Arctic Oceans, is a common deep-sea organism, playing a fundamental role forming biogenic habitats. However, there is little information about gene flow and adaptation patterns of this species, which is crucial to develop effective management/conservation plans under current global change scenarios. Here, we generated ddRADseq data from 110 specimens of G. hentscheli, together with microbial profiling, transcriptomics and metatranscriptomics for a selection of specimens to investigate their genetic diversity, molecular connectivity and local adaptations. Sampling covered the species' entire distribution within a wide bathymetric range. We obtained 1,115 neutral SNPs and identified long distance genetic connectivity among regions separated 1,000s of km, but strong genetic structure segregating populations by depth at ca. 1,300 m, in line with our microbial analyses. Coalescent analyses inferred the split of these depth-related genetic entities ∼10 KYA, coincident with the last post-glacial maximum. Analyses of SNPs under selection, combined with transcriptomic and metatranscriptomic data highlight the presence of several sponge genes and microbial metabolic pathways involved in adaptation to depth, including heat shock proteins and fatty acids, amongst others. The physiological plasticity of the sponge and its microbiome as a function of depth suggest the existence of a host-microbiome metabolic compensation for G. hentscheli. This study provides a multiscale paradigmatic example of the Depth Differentiation Hypothesis, a phenomenon mainly caused by changes in environmental conditions at different depths, mainly related to the presence of water masses with different characteristics, that drive local adaptations.},
}
@article {pmid40476734,
year = {2025},
author = {Marcos-Zambrano, LJ and Lacruz-Pleguezuelos, B and Aguilar-Aguilar, E and Marcos-Pasero, H and Valdés, A and Loria-Kohen, V and Cifuentes, A and Ramirez de Molina, A and Diaz-Ruiz, A and Pancaldi, V and Carrillo de Santa Pau, E},
title = {Microbiome gut community structure and functionality are associated with symptom severity in non-responsive celiac disease patients undergoing a gluten-free diet.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0014325},
doi = {10.1128/msystems.00143-25},
pmid = {40476734},
issn = {2379-5077},
abstract = {UNLABELLED: Non-responsive celiac disease (NRCD) challenges clinicians due to persistent symptoms despite a gluten-free diet (GFD). We present a cross-sectional pilot study including 39 NRCD patients to describe the underlying mechanisms contributing to symptom persistence by integrating different levels of data (fecal shotgun metagenomics, mucosal integrity markers, and metabolomic profiles) and using microbial networks to unravel the community structure of the patient's microbiome. Two distinct clusters of patients were identified based on clinical and demographic variables not influenced by gluten consumption. Cluster 1, labeled "Low-grade symptoms," displayed milder symptoms and lower inflammatory markers and a fragmented microbial network characterized by high modularity and a reliance on localized hubs, suggesting a microbial community under stress but capable of maintaining limited functionality. Cluster 2, named "High-grade symptoms," exhibited more severe symptoms, elevated inflammatory markers, and a more connected but antagonistic microbial network with a greater number of keystone taxa, including taxa associated with Th17 activation and inflammation. In contrast, the control network, representing asymptomatic treated celiac disease (tCD) patients, was highly interconnected, resilient, and cooperative, with a robust structure maintained even under simulated disruptions. Metabolomic analysis revealed differential metabolites between clusters, particularly those involved in amino acid metabolism pathways and microbial-derived metabolites such as indolelactic acid and mannitol, which were associated with symptom severity. This study identifies NRCD subgroups based on the gut microbiome and metabolic signatures associated with clinical manifestations, highlighting variations in microbial network stability and metabolite profiles as contributors to symptom persistence and potential therapeutic targets.<br><br>IMPORTANCE: Celiac disease (CD) is a chronic immune-mediated systemic disorder caused by consuming gluten in genetically susceptible individuals. There is currently no cure for CD, and the most effective treatment is maintaining a strict, lifelong gluten-free diet (GFD). This nutritional therapy aims to prevent the immune reaction triggered by gluten and promote the healing of the intestinal lining, resolving the clinical, serological, and histological abnormalities within 6-12 months. However, up to 30% of patients may continue to experience symptoms or exhibit laboratory abnormalities or intestinal inflammation suggestive of active CD, despite following a GFD. This challenge, which encompasses various diagnoses, is known as nonresponsive celiac disease (NRCD). In this study, we explored the role of intestinal microbiota in causing NRCD, finding an association between the persistence of symptoms and changes in mucosal integrity biomarkers, with different gut microbiome structures among NRCD patients, indicating a significant role of the microbiome in NRCD.},
}
@article {pmid40477893,
year = {2023},
author = {Yu, Y and Zhang, Q and Zhang, Z and Xu, N and Li, Y and Jin, M and Feng, G and Qian, H and Lu, T},
title = {Assessment of residual chlorine in soil microbial community using metagenomics.},
journal = {Soil ecology letters},
volume = {5},
number = {1},
pages = {66-78},
pmid = {40477893},
issn = {2662-2297},
abstract = {Chlorine-containing disinfectants have been widely used around the world for the prevention and control of the COVID-19 pandemic. However, at present, little is known about the impact of residual chlorine on the soil micro-ecological environment. Herein, we treated an experimental soil-plant-microbiome microcosm system by continuous irrigation with a low concentration of chlorine-containing water, and then analyzed the influence on the soil microbial community using metagenomics. After 14-d continuous chlorine treatment, there were no significant lasting effect on soil microbial community diversity and composition either in the rhizosphere or in bulk soil. Although metabolic functions of the rhizosphere microbial community were affected slightly by continuous chlorine treatment, it recovered to the original status. The abundance of several resistance genes changed by 7 d and recovered by 14 d. According to our results, the chlorine residue resulting from daily disinfection may present a slight long-term effect on plant growth (shoot length and fresh weight) and soil micro-ecology. In general, our study assisted with environmental risk assessments relating to the application ofchlorine-containing disinfectants and minimization of risks to the environment during disease control, such as COVID-19.},
}
@article {pmid40476583,
year = {2025},
author = {Jang, JY and Seo, JH and Choi, JJ and Ryu, HJ and Yun, H and Ha, DM and Yang, J},
title = {Insight into microbial extracellular vesicles as key communication materials and their clinical implications for lung cancer (Review).},
journal = {International journal of molecular medicine},
volume = {56},
number = {2},
pages = {},
doi = {10.3892/ijmm.2025.5560},
pmid = {40476583},
issn = {1791-244X},
mesh = {Humans ; *Extracellular Vesicles/metabolism ; *Lung Neoplasms/microbiology/metabolism/pathology/etiology ; Microbiota ; Animals ; Cell Communication ; *Bacteria/metabolism ; Dysbiosis ; Lung/microbiology ; },
abstract = {The complexity of lung cancer, driven by multifactorial causes such as genetic, environmental and lifestyle factors, underscores the necessity for tailored treatment strategies informed by recent advancements. Studies highlight a significant association between the lung microbiome and lung cancer, with dysbiosis potentially contributing to disease development via inflammation, immune response alterations and bacterial metabolite production. Furthermore, exposure to airborne bacteria may influence lung health by introducing pathogenic species or altering the human microbiome, thereby implicating certain dominant airborne bacteria in lung diseases, including the exacerbation of lung cancer. Extracellular vesicles (EVs) facilitate cell‑to‑cell communication, penetrating mucosal barriers to impact various organs, notably the lung. Epidemiological evidence suggests a strong relationship between the presence of microbial EVs (MEVs) in the air and chronic pulmonary diseases, with indications of a potential risk for lung cancer. MEVs play a significant role in pulmonary disease development by inducing airway inflammation and affecting lung function. The microbiome and MEVs offer considerable potential as novel tools in precision medicine for lung cancer. Biological data analysis and artificial intelligence technology advancements are pivotal for fully realizing their diagnostic and therapeutic capabilities. These developments can potentially shape the future landscape of lung cancer diagnostics, therapeutics and prevention strategies.},
}
@article {pmid40476565,
year = {2025},
author = {Fu, J and Chen, J and Ni, J and Liu, X and Yao, Q and Shou, Q and Fu, H},
title = {Dietary supplementation with beetroot modulates gut microbiota-derived diacylglycerol biosynthesis to enhance anti-tumor immunity in MMTV-PyMT (FVB) mice.},
journal = {Food &amp; function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5fo01116g},
pmid = {40476565},
issn = {2042-650X},
abstract = {Recent studies have established a strong connection between gut microbiota and the tumor immune microenvironment. Beetroot (BRT) has emerged as a promising functional food for cancer prevention and treatment, although its specific effects on breast cancer remain unclear. This study investigates the impact of BRT on polyomavirus middle T antigen (PyMT)-induced breast cancer by examining the gut microbiome, metabolites, and immune responses. Dietary supplementation of 80 g BRT powder per 1000 g of standard diet (8% w/w, 80 g per kg) significantly inhibited tumor growth and metastasis in mouse mammary tumor virus (MMTV)-PyMT (FVB) mice, while simultaneously enhancing anti-tumor immunity. 16S rRNA sequencing revealed that BRT supplementation altered the gut microbiota, notably increasing the abundance of Lachnospiraceae and Ruminococcaceae. An antibiotic (ABX) experiment confirmed that BRT restores gut microbiota balance, thereby enhancing anti-tumor immunity. Metabolomics and ELISA assays demonstrated that BRT regulates diacylglycerol (DAG) biosynthesis through microbiota modulation. Notably, diacylglycerol kinase ζ (DGKζ) inhibitors enhance CD8+ T cell responses by increasing DAG levels, thereby activating Mitogen-Activated Protein Kinase (MAPK) and Protein Kinase C (PKC) signaling pathways. Collectively, our findings suggest that microbiota-derived DAG plays a key role in BRT-mediated enhancement of anti-tumor immunity.},
}
@article {pmid40476383,
year = {2025},
author = {Kim, N and Kim, J and Choi, J and Kim, R},
title = {A collagen hydrogel-based intestinal model enabling physiological epithelial-immune cell interactions in host-microbe studies.},
journal = {Biomaterials science},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5bm00612k},
pmid = {40476383},
issn = {2047-4849},
abstract = {The human intestine orchestrates complex immune responses to external stimuli, including trillions of gut microbes. Understanding host-microbiota interactions remains challenging due to the complex cellular composition of intestinal tissues. In this study, we present InTRIC (Intestinal model with Tissue-Resident Immune Components), a three-dimensional intestinal model incorporating tissue-resident immune cells within a biomimetic extracellular matrix. We developed a hydrogel system by combining UV-crosslinked methacrylated collagen with a native collagen blend that prevents matrix shrinkage while maintaining physiologically relevant mechanical properties, a fibrillar microstructure and minimal toxicity for cell embedding. Prior to establishing InTRIC, we validated THP-1 viability in the collagen hydrogel (>14 days), verified their differentiation into distinct macrophage phenotypes, and confirmed appropriate gene expression in Caco-2 cells on the collagen substrates. The integrated model comprises THP-1 macrophages embedded within the collagen matrix and Caco-2 cells forming a functional epithelium with intact junctions and physiologically relevant TEER values. The InTRIC platform enables both the assessment of cytokine profiles and the visualization of transepithelial macrophage infiltration in response to commensal (Lacticaseibacillus rhamnosus) and pathogenic (Pseudomonas aeruginosa) bacteria. Notably, P. aeruginosa exposure induced a four-fold increase in macrophage infiltration and elevated IL-8 secretion. Compared to conventional cocultures without collagen, InTRIC exhibited attenuated inflammatory cytokine secretion, suggesting microenvironmental modulation of epithelial-immune communication. Additionally, M2-polarized macrophages showed reduced basal IL-8 secretion but increased responsiveness to bacterial stimulation. This proof-of-concept model demonstrates the importance of incorporating both immune cells and appropriate extracellular matrices in recapitulating intestinal conditions and offers a physiologically relevant test platform for applications in drug discovery, toxicology, and microbiome research.},
}
@article {pmid40476348,
year = {2025},
author = {Ducatelle, R and Goossens, E and Eeckhaut, V and Van Immerseel, F},
title = {The Gordon Memorial Lecture: Steering the gut microbiome for improved health and welfare in broilers.},
journal = {British poultry science},
volume = {},
number = {},
pages = {1-10},
doi = {10.1080/00071668.2025.2488014},
pmid = {40476348},
issn = {1466-1799},
abstract = {1. In fast growing broilers, intestinal health is continuously under pressure due to extremely high feed intake and environmental/management conditions that cause (oxidative) stress to the intestinal epithelium.2. The following review focuses on the contributions of the Livestock Gut Health Team at Ghent University into understanding the mechanisms governing the interactions between the intestinal microbiota and the host intestinal mucosa. It covers the development of tools to support intestinal health of broilers through nutritional manipulation of the microbiota.3. In the duodenum and jejunum, microbiota are suppressed by the secretion of enzymes and antibacterial peptides in order to avoid competition for the nutrients. These defence mechanisms can be re-enforced and/or the epithelial cells can be protected from damage by different feed additives.4. Metabolism in the caecal microbial network is fuelled by the fibre fraction in feed. Whenever this network is incomplete or the feed is lacking fibre, this may lead to a distortion of the microbiota, followed by insufficient production of beneficial microbial metabolites, such as butyrate. This can contribute to inflammation and leakage of the gut barrier, with, in severe cases, wet litter, foot pad lesions and poor performance as common consequences. Reenforcing the caecal microbial network can be achieved using prebiotics, probiotics and postbiotics, which will improve the health and well-being of the birds.5. Steering towards optimal microbial fermentation will help to protect the birds from Clostridium perfringens-associated necrotic enteritis and Salmonella spp. colonisation since both interact with the intestinal microbiota.},
}
@article {pmid40476157,
year = {2025},
author = {Rashid, M and Pereira, HS and Alissa, A and Keraidi, S and Wipf, N and Sowa, AM and McDonnell, JM and Darwish, S and Butler, JS},
title = {Microbiome dysbiosis in spinal pathology: Mechanisms, evidence, and research limitations.},
journal = {Brain &amp; spine},
volume = {5},
number = {},
pages = {104272},
pmid = {40476157},
issn = {2772-5294},
abstract = {INTRODUCTION: The microbiome's relevance has become increasingly discussed amid the rising prevalence of chronic illnesses. Microbiome research to date focuses predominantly on its relationship with the GI tract while largely ignoring any impact on the rest of the body. This narrative review aims to lay a foundation of knowledge to fill this gap in the literature and discuss other microbiomes within the human body and their relation to spinal health.<br><br>RESEARCH QUESTION: What is the relationship between the human microbiome and spinal pathologies?<br><br>MATERIALS AND METHODS: A narrative review of all available literature (written or translated to English) was performed using PubMed, MEDLINE, and Google Scholar using relevant search terms including: "microbiome", "spine", "spinal pathology", "ankylosing spondylitis", and "seronegative arthropathies".<br><br>RESULTS: This review found that with dysbiosis, specific bacterial such as Bacteroidaceae and Rikenellaceae proliferate, altering the cytokine microenvironment and subsequently increasing gut wall permeability. This immune overactivation and improper cell function results in an increased susceptibility to autoimmunity; specifically ankylosing spondylitis and seronegative arthropathies. This review also highlights the significant gaps in the available literature.<br><br>DISCUSSION AND CONCLUSION: This review aims to equip clinicians with an understanding of how the collection of microbiomes in the human body have specific implications for spinal health. By building on the current literature and integrating this knowledge into practice, more patient-specific practices in the treatment of spinal pathologies can be implemented, ultimately improving and optimizing patient care in a field in which the microbiome is not currently at the forefront of pathology.},
}
@article {pmid40475999,
year = {2025},
author = {Hwang, D and Chong, E and Li, Y and Li, Y and Roh, K},
title = {Deciphering the gut microbiome's metabolic code: pathways to bone health and novel therapeutic avenues.},
journal = {Frontiers in endocrinology},
volume = {16},
number = {},
pages = {1553655},
pmid = {40475999},
issn = {1664-2392},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Bone and Bones/metabolism ; Animals ; Probiotics/therapeutic use ; *Bone Remodeling/physiology ; *Osteoporosis/metabolism/microbiology/therapy ; Prebiotics ; Fecal Microbiota Transplantation ; Bone Diseases/metabolism/microbiology/therapy ; },
abstract = {The gut microbiome plays an important role in the protection against various systemic diseases. Its metabolic products profoundly influence a wide range of pathophysiological events, including the regulation of bone health. This review discusses the recently established connections between the gut microbiome and bone metabolism, focusing on the impact of microbiome-derived metabolites such as SCFAs, Bile Acids, and tryptophan to the control of bone remodeling and immunoreactions. Recent advances in metagenomics and microbiome profiling have unveiled new exciting therapeutic opportunities, ranging from the use of probiotics, prebiotics, engineered microbes, and to fecal microbiota transplantation. Understanding of the interplay among diet, microbiota, and bone health provides new avenues for tailored interventions aimed at reducing disease risk in osteoporosis and other related disorders. By drawing knowledge from microbiology, metabolism, and bone biology, this review highlights the potential of microbiome-targeted therapies to transform skeletal health and the management of bone diseases.},
}
@article {pmid40475850,
year = {2025},
author = {Liu, Y and Li, R and Liu, J and Liang, X and Su, M and Wang, S and Mu, B},
title = {Exploring the role of the vaginal microbiome in HPV infection dynamics: A prospective cohort study.},
journal = {iScience},
volume = {28},
number = {5},
pages = {112476},
pmid = {40475850},
issn = {2589-0042},
abstract = {Persistent human papillomavirus (HPV) infection is a key risk factor for cervical cancer, often associated with changes in the vaginal microbiome (VMB). High-throughput 16S rRNA sequencing was used to study the VMB in a prospective cohort of 731 individuals. Participants were monitored through two follow-up screenings and then categorized into two groups: 22 female patients with persistent HPV infection (PHI), 31 female patients who cleared the infection (HC). After excluding those with HPV and other urogenital infections, 43 female patients were selected as controls, and their samples were analyzed using the same high-throughput sequencing method. Results indicate that high-risk HPV infections correlate with increased microbial diversity and reduced Lactobacillus levels. Even after HPV clearance, distinct microbial differences persist, suggesting that VMB could serve as a biomarker for monitoring infection and cervical health management, especially in populations at higher risk.},
}
@article {pmid40475770,
year = {2025},
author = {Varghese, A and Hess, SM and Chilakapati, S and Conejo-Garcia, JR and McGray, AJR and Zsiros, E},
title = {Tertiary lymphoid structures: exploring opportunities to improve immunotherapy in ovarian cancer.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1473969},
pmid = {40475770},
issn = {1664-3224},
mesh = {Humans ; *Tertiary Lymphoid Structures/immunology/pathology ; Female ; *Ovarian Neoplasms/immunology/therapy/pathology ; Tumor Microenvironment/immunology ; *Immunotherapy/methods ; Animals ; Immune Checkpoint Inhibitors/therapeutic use ; Lymphocytes, Tumor-Infiltrating/immunology ; },
abstract = {Tertiary lymphoid structures (TLS) are organized ectopic lymphoid clusters of immune cells that develop in non-lymphoid tissue to promote antigen presentation, drive cytotoxic immune responses, and enhance humoral immunity via B cell clonal expansion. Their presence within the tumor microenvironment (TME) correlates with increased patient survival and an improved response to immune checkpoint inhibitors (ICIs), positioning TLS as potential predictive and prognostic biomarkers. Despite the widespread use of ICIs across various cancers, their effectiveness remains limited in gynecological malignancies, including ovarian cancer (OC), a notably challenging disease characterized by poor responses to both single and combination ICI therapies. Interestingly, the infiltration of T cells into the OC TME is linked to enhanced progression-free survival (PFS) and overall survival (OS), yet an immunosuppressive TME frequently impedes therapeutic efficacy, suggesting cell activity within localized immune niches can impact antitumor immunity. This review explores the roles of TLS, their maturity, functionality, identification, and related gene signatures; specific immune cells and cytokines that play a role in TLS formation and antitumor response; and other modifiable elements, including gut microbiota, that may drive improving OC survival by leveraging a TLS-driven antitumor response to bolster immunotherapy outcomes.},
}
@article {pmid40475712,
year = {2025},
author = {Zhou, R and Wu, Q and Qian, H and Wang, L and Liu, G and Zhang, B and Wu, W and Zhang, S},
title = {Long-term Metformin Alters Gut Microbiota and Serum Metabolome in Coronary Artery Disease Patients After Percutaneous Coronary Intervention to Improve 5-year Prognoses: A Multi-omics Analysis.},
journal = {Reviews in cardiovascular medicine},
volume = {26},
number = {5},
pages = {26835},
pmid = {40475712},
issn = {2153-8174},
abstract = {BACKGROUND: About 20% of patients with coronary artery disease (CAD) experience adverse events within five years of undergoing percutaneous coronary intervention (PCI) for acute myocardial infarction. In these patients, the impact of metformin on long-term prognosis remains uncertain.<br><br>METHODS: This study enrolled 22 metformin (Met)-CAD patients with diabetes mellitus (DM) who had been administered metformin for at least six months before PCI, 14 non-Met CAD-DM patients with DM who had never taken metformin or had stopped taking metformin for a year before PCI, and 22 matched healthy controls. A 5-year follow-up was conducted to collect clinical prognosis data. Fecal 16S rRNA sequencing and serum untargeted metabolomics analyses were performed. BugBase was utilized to analyze the possible functional changes in the gut microbiome. Multi-omics analysis was conducted using Spearman's correlation to explore the interactions between metformin, gut microbiome, serum metabolites, and clinical prognosis.<br><br>RESULTS: Metformin significantly lowered the 5-year major adverse cardiac events (MACEs) in Met CAD-DM patients. We found a higher abundance of Bacteroides coprocola, Bacteroides massiliensis, Phascolarctobacterium succinatutens, and Eubacterium coprostanoligenes in the Met CAD-DM patients, as well as an increase in hydroxy-alpha-sanshool (HAS) and decenoylcarnitine and a decrease in tridec-10-enoic acid, Z-vad-fmk (benzyloxycarbonyl-Val-Ala-Asp (OMe)-fluoromethylketone), 3,9-dimethyluric acid in blood serum. Multi-omics analysis revealed that alterations in the gut microbiome and serum metabolites are significantly associated with the 5-year prognosis of CAD-DM.<br><br>CONCLUSIONS: Metformin significantly improved the 5-year prognosis of CAD patients following PCI. Metformin tended to have more positive effects on the commensal flora and metabolic profiles, which may explain its beneficial effects on cardiovascular health. This study revealed the potential associations between metformin and the gut microbiome, an associated alteration in serum metabolome, and the impact on the host immune system and metabolic pathways.},
}
@article {pmid40475637,
year = {2025},
author = {Nia, LH and Alqudah, S and Markley, RL and DeLucia, B and Bobba, V and Elmallah, J and Nemet, I and Sangwan, N and Claesen, J},
title = {The antimicrobial metabolite nisin Z reduces intestinal tumorigenesis and modulates the cecal microbiome in Apc [Min/+] mice.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.05.18.654755},
pmid = {40475637},
issn = {2692-8205},
abstract = {UNLABELLED: Nisin Z, an antimicrobial metabolite produced by Lactococcus lactis spp., has been safely used as a food preservative for many years. Nisin Z also showed promising activity against various cancer types in vitro , and significantly reduced tumor size in an ectopic head and neck cancer model. Here, we investigate the activity of nisin Z for colorectal cancer treatment and observed an in vitro reduction in cellular proliferation, and a moderate enhancement in cell death. We next analyzed the effect of oral nisin Z administration in the Apc [min/+] intestinal adenoma mouse model. We measured tumor burden along the gastrointestinal tract and observed a decrease in tumor burden in the middle region of the small intestine, but not in the lower region or colon. Since tumor progression in the Apc [min/+] model is exacerbated by an inflammatory environment, we next determined whether nisin Z impacts this in a direct or indirect manner. We show that nisin Z can directly reduce NF-κB activation in a dose-dependent manner. In addition, nisin Z impacted the cecal microbiome composition as well as microbiota-associated plasma metabolites, causing an overall shift towards a more health-associated profile. Interestingly, the Apc [min/+] genotype differentially impacted the nisin Z-mediated differences in cecal microbiome composition and plasma metabolites compared to wildtype animals. In summary, our data suggest that the reduction in small intestinal tumor burden could be due to nisin Z's contribution to a reduced pro-inflammatory environment. Future studies will reveal whether nisin's localized effect is due to degradation of the peptidic compound in more distal regions of the gastrointestinal tract and focus on development of delivery systems to increase efficacy.<br><br>IMPORTANCE: With the increased incidence of colorectal cancer, especially among younger individuals, it is critical to study approaches that help with the prevention and treatment of this debilitating disease. Our study indicates that nisin Z, a bacterially produced peptide antibiotic, decreases the growth of colorectal cancer cells and moderately increases cell death in vitro . Oral administration of nisin Z in an intestinal adenoma mouse model revealed a reduction of tumor burden in the middle region of the small intestine. This decreased tumor burden might in part be attributed to a direct anti-inflammatory effect, as well as an indirect effect on the gut microbiota and their metabolites due to nisin Z's antibacterial activity. Overall, we demonstrate a potential activity for nisin Z in the prevention or amelioration of inflammation-associated colorectal cancer, underscoring the significance of investigating the properties of bacterial natural products in human health.},
}
@article {pmid40475569,
year = {2025},
author = {Rajczewski, AT and Mehta, S and Wagner, R and Gabriel, W and Johnson, J and Do, K and Vintila, S and Wilhelm, M and Kleiner, M and Searle, BC and Griffin, TJ and Jagtap, PD},
title = {Benchmarking Spectral Library and Database Search Approaches for Metaproteomics Using a Ground-Truth Microbiome Dataset.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.05.15.654320},
pmid = {40475569},
issn = {2692-8205},
abstract = {Mass spectrometry-based metaproteomics, the identification and quantification of thousands of proteins expressed by complex microbial communities, has become pivotal for unraveling functional interactions within microbiomes. However, metaproteomics data analysis encounters many challenges, including the search of tandem mass spectra against a protein sequence database using proteomics database search algorithms. We used a ground-truth dataset to assess a spectral library searching method against established database searching approaches. Mass spectrometry data collected by data-dependent acquisition (DDA-MS) was analyzed using database searching approaches (MaxQuant and FragPipe), as well as using Scribe with Prosit predicted spectral libraries. We used FASTA databases that included protein sequences from microbial species present in the ground-truth dataset along with background protein sequences, to estimate error rates and assess the effects on detection, peptide-spectral match quality, and quantification. Using the Scribe search engine resulted in more proteins detected at a 1% false discovery rate (FDR) compared to MaxQuant or FragPipe, while FragPipe detected more peptides verified by PepQuery. Scribe was able to detect more low-abundance proteins in the microbiome dataset and was more accurate in quantifying the microbial community composition. This research provides insights and guidance for metaproteomics researchers aiming to optimize results in their analysis of DDA-MS data.},
}
@article {pmid40475515,
year = {2025},
author = {De Allende, CC and Salter, SJ and Brigg, SE and Claassen-Weitz, S and Mwaikono, KS and Workman, L and Zar, HJ and Nicol, MP and Parkhill, J and Dube, FS},
title = {Characterisation of Ornithobacterium hominis colonisation dynamics and interaction with the nasopharyngeal microbiome in a South African birth cohort.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.05.24.655922},
pmid = {40475515},
issn = {2692-8205},
abstract = {UNLABELLED: Ornithobacterium hominis is a recently described Gram-negative bacterium that colonises the human nasopharynx and may be associated with poor upper respiratory tract health. Here, we describe the isolation of O. hominis from samples collected from a South African birth cohort, creating the first archive of cultured strains of the species from Africa. Sequenced genomes from this archive reveal that South African O. hominis is more similar to Australian strains than those from Southeast Asia, and that it may share genes with other members of the microbiome that are relevant for virulence, colonisation, and antibiotic resistance. Leveraging existing microbiome data from the cohort, O. hominis was found to be closely associated with bacterial co-colonisers that are rare in non-carrier individuals, including Suttonella , Helcococcus , Moraxella spp., and Gracilibacteria. Their collective acquisition has a significant impact on the diversity of nasopharyngeal communities that contain O. hominis . Individuals who have not yet acquired O. hominis have a higher abundance of Moraxella (particularly M. lincolnii) than individuals who never acquire O. hominis , suggesting that this could be a precursor state for successful colonisation. Finally, a novel co-coloniser species, Helcococcus ekapensis , was successfully isolated and sequenced.<br><br>DATA SUMMARY: Ornithobacterium hominis data have been deposited under project accession ERP149886. This comprises genome sequences for isolates SA-OH-C1 (ERR13967269), SA-OH-C2 (ERR13967270), SA-OH-C3 (ERR13967271), SA-OH-C4 (ERR13967272, ERR13967275), SA-OH-C5 (ERR13967273), SA-OH-C6 (ERR13967274, ERR13967276). Previously published 16S rRNA gene data are deposited under project accessions PRJNA790843 and PRJNA548658. Helcococcus ekapensis genome data are deposited under project accession PRJEB85661.<br><br>SOFTWARE USED: AMRFinderPlus v3.12.8: https://github.com/ncbi/amr AssembleBAC-ONT v1.1.1: https://github.com/avantonder/assembleBAC-ONT BAKTA v1.8.1: https://bakta.computational.bio/ BLAST v2.16.0: https://blast.ncbi.nlm.nih.gov/Blast.cgi Comprehensive Antibiotic Resistance Database (CARD) Resistance Gene Identifier (RGI) tool v1.2.1: https://card.mcmaster.ca/analyze/rgi Decontam v1.12 (R package): https://github.com/benjjneb/decontam Eggnog-mapper v2.0.1: http://eggnog-mapper.embl.de/ FastANI v1.1.0: https://github.com/ParBLiSS/FastANI Flye v2.9.2: https://github.com/fenderglass/Flye Guppy v6.5.7: https://community.nanoporetech.com/downloads/guppy/release_notes ISEScan v1.7.2.3: https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/isescan/isescan/1.7.2.3+galaxy1 Medaka v1.9.1: https://github.com/nanoporetech/medaka MEGA11: https://www.megasoftware.net/ MMseqs2 v17: https://github.com/soedinglab/MMseqs2 Mothur v1.44.3: https://github.com/mothur/mothur NetCoMi v1.2.0 (R package): https://github.com/stefpeschel/NetCoMi Panaroo v1.4.3: https://github.com/gtonkinhill/panaroo PHASTEST: https://phastest.ca/submissions/new Prowler (commit ID c3041ba): https://github.com/ProwlerForNanopore/ProwlerTrimmer R v4.4.3: https://www.r-project.org/.<br><br>DATABASES USED: Comprehensive Antibiotic Resistance Database (CARD): https://card.mcmaster.ca/ European Nucleotide Archive: https://www.ebi.ac.uk/ena/ Genome Taxonomy Database (GTDB) release 09-RS220: https://gtdb.ecogenomic.org/ RefSeq release 228: https://www.ncbi.nlm.nih.gov/refseq/about/prokaryotes/ SILVA v132: https://www.arb-silva.de/.<br><br>IMPACT STATEMENT: First described in 2019, Ornithobacterium hominis is an understudied bacterium that may be associated with poor respiratory health in children. The study builds upon existing knowledge of O. hominis by describing the first African isolates of the species, its potential as a reservoir of virulence and antibiotic resistance genes in the upper respiratory tract, and the unique microbiome profile of O. hominis carriers.},
}
@article {pmid40475494,
year = {2025},
author = {Mirji, G and Bhat, SA and El Sayed, M and Reiser, SK and Gavara, SP and Ye, Y and Miyamoto, T and Liu, Q and Goldman, AR and Kossenkov, A and Zhang, N and Shinde, RS},
title = {Aromatic Microbial Metabolite Hippuric Acid Potentiates Pro-Inflammatory Responses in Macrophages through TLR-MyD88 Signaling and Lipid Remodeling.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.05.19.654724},
pmid = {40475494},
issn = {2692-8205},
abstract = {The gut microbiome generates a diverse array of metabolites that actively shape host immunity, yet the pro-inflammatory potential of microbial metabolites remains poorly understood. In this study, we identified hippuric acid, an aromatic gut microbe-derived metabolite, as a potent enhancer of pro-inflammatory responses using a murine bacterial infection model and a non-targeted liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based metabolomics. Administering hippuric acid intraperitoneally in murine models of Escherichia coli infection or LPS-induced inflammation significantly heightened pro-inflammatory responses and innate immune cell activation. In vitro , hippuric acid selectively potentiated M1-like macrophage polarization (LPS + IFNγ) but had no effect on M2-like polarization (IL-4). Hippuric acid further enhanced responses to diverse MyD88-dependent TLR ligands, but not TRIF-dependent TLR3, implicating a possible mechanism of action via activation of TLR-MyD88 signaling. Genetic deletion of MyD88 abrogated the pro-inflammatory effects of hippuric acid both in vitro and in vivo , confirming its dependence on the MyD88 pathway. Transcriptomic and lipidomic analyses revealed that hippuric acid promoted cholesterol biosynthesis and lipid accumulation, linking microbial metabolism to lipid-driven immune activation. Notably, hippuric acid similarly enhanced pro-inflammatory responses in human macrophages, and its elevated levels correlated with increased sepsis mortality, highlighting its potential clinical relevance. These findings establish hippuric acid as a previously unrecognized microbial-derived inflammatory modulator, bridging gut microbial metabolism, lipid remodeling, and innate immune signaling, and offer new insights into its role in infection and inflammation.},
}
@article {pmid40475488,
year = {2025},
author = {Price, A and Rasolofomanana-Rajery, S and Manpearl, K and Robertson, CE and Krebs, NF and Frank, DN and Krishnan, A and Hendricks, AE and Tang, M},
title = {Network-based representation learning reveals the impact of age and diet on the gut microbial and metabolomic environment of U.S. infants in a randomized controlled feeding trial.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.11.01.621627},
pmid = {40475488},
issn = {2692-8205},
abstract = {While studies have explored differences in gut microbiome development for infant liquid diets (breastmilk, formula), little is known about the impact of complementary foods on infant gut microbiome development. Here, we investigated how different protein-rich foods (i.e., meat vs. dairy) affect fecal metagenomics and metabolomics during early complementary feeding from 5-12 months in U.S. formula-fed infants from a randomized controlled feeding trial. We used a network representation learning approach to model the time-dependent, complex interactions between microbiome features, metabolite compounds, and diet. We then used the embedded space to detect features associated with age and diet type and found the meat diet group was enriched with microbial genes encoding amino acid, nucleic acid, and carbohydrate metabolism. Compared to a more traditional differential abundance analysis, which analyzes features independently and found no significant diet associations, network node embedding represents the infant samples, microbiome features, and metabolites in a single transformed space revealing otherwise undetected associations between infant diet and the gut microbiome.},
}
@article {pmid40475274,
year = {2025},
author = {Lv, Y and Peng, S and Liu, Y and Yang, H and Li, G and Peng, Y},
title = {Cross-omics analysis reveals microbe-metabolism interactions characteristic of gingival enlargement associated with fixed orthodontic in adolescents.},
journal = {Journal of oral microbiology},
volume = {17},
number = {1},
pages = {2513739},
pmid = {40475274},
issn = {2000-2297},
abstract = {OBJECTIVES: To investigate the oral microbiome and metabolome longitudinal changes associated with orthodontic treatment-induced gingival enlargement (OT-GE).<br><br>METHODS: Twenty-six subjects were divided into case and control groups based on the gingival overgrowth index (GOi). The OT-GE group was divided into the no gingival enlargement (OT-GE0, n&#x2009;=&#x2009;5) and persistent gingival enlargement (OT-GE1, n&#x2009;=&#x2009;11). The control group included orthodontic treatment periodontal health (OT-GH, n&#x2009;=&#x2009;5), and no orthodontic treatment periodontal health (NOT-GH, n&#x2009;=&#x2009;5). Microbial composition and metabolites in saliva were investigated using cross-omics.<br><br>RESULTS: Longitudinal analysis linked orthodontic treatment-induced gingival enlargement to distinct oral microbiome and metabolome shifts. The OT-GE group showed significantly higher bleeding on probing (BOP), plaque scores (p&#x2009;<&#x2009;0.001), probing depth, GOi, and ligature wire differences (p&#x2009;<&#x2009;0.05) versus controls. Microbial diversity and species richness were elevated in OT-GE (p&#x2009;<&#x2009;0.05), though no differences emerged between OT-GE0 and OT-GE1) subgroup (p&#x2009;>&#x2009;0.05). Cross-omics identified specific periodontal pathogens and metabolites linked to gingival enlargement. Disrupted amino acid biosynthesis pathways, particularly citrulline metabolism, correlated with functional gene dysregulation and microbial imbalance. Aberrant citrulline intake appeared to drive dysbiosis, potentially contributing to gingival overgrowth.<br><br>CONCLUSIONS: OT-GE pathogenesis involves functional gene-regulated metabolite metabolism influencing periodontal pathogens.},
}
@article {pmid40475154,
year = {2025},
author = {Cotto, I and Durán-Viseras, A and Jesser, KJ and Zhou, NA and Hemlock, C and Albán, V and Ballard, AM and Fagnant-Sperati, CS and Lee, GO and Hatt, JK and Royer, C and Eisenberg, JNS and Trueba, G and Konstantinidis, KT and Levy, K and Fuhrmeister, ER},
title = {Environmental Exposures and the Human Gut Resistome in Northwest Ecuador.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.05.23.25327954},
pmid = {40475154},
abstract = {Inadequate water, sanitation, and hygiene (WASH) infrastructure may increase exposure to antimicrobial resistance (AMR). In addition, close human-animal interactions and unregulated antibiotic use in livestock facilitate the spread of resistant bacteria. We used metagenomic sequence data and multivariate models to assess how animal exposure and WASH conditions affect the gut resistome and microbiome in 53 pregnant women and 84 children in Ecuador. Escherichia coli , Klebsiella pneumoniae, and clinically relevant antimicrobial resistance genes (ARGs) were detected across all age groups, but the highest abundance was found in children compared to mothers. In mothers, higher animal exposure trended towards a higher number of unique ARGs compared to low animal exposure (β= -5.58 [95% CI: -11.46, 0.29]) and was significantly associated with greater taxonomic diversity (β= -1.29 [-1.96, -0.63]). In addition, mothers with sewer systems or septic tanks and piped drinking water had fewer unique ARGs (β= -3.52 [-6.74, -0.30]) compared to those without, and mothers with longer duration of drinking water access had lower total ARG abundance (β= -0.05 [-0.1, -0.01]). In contrast, few associations were observed in children, likely due to the dynamic nature of the gut microbiome during early childhood. Improving WASH infrastructure and managing animal exposure may be important in reducing AMR but could also reduce taxonomic diversity in the gut.},
}
@article {pmid40475140,
year = {2025},
author = {Schott, EM and Charbonneau, M and Kiel, DP and Bukata, S and Zuscik, MJ and Rosen, C and Ballok, A and Toledo, GV and Steels, E and Huntress, H and Rao, A and Travison, TG and Soto-Giron, MJ and Wolff, I and Easson, DD and Engelke, K and Vitetta, L},
title = {A randomized, double-blind, placebo-controlled clinical study to evaluate the efficacy of the synbiotic medical food, SBD111, for the clinical dietary management of bone loss in menopausal women.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.05.20.25325893},
pmid = {40475140},
abstract = {SUMMARY: This 12-month study in 286 early postmenopausal women evaluated the efficacy and safety of SBD111, a synbiotic medical food, in reducing bone loss. SBD111 did not significantly reduce bone loss for the full cohort, but did produce evidence of reduced bone loss in women with osteopenia and BMI ≥ 30.<br><br>PURPOSE: To determine the efficacy of SBD111, a synbiotic medical food comprising probiotics and prebiotics, in reducing bone loss in women post-menopause, including prespecified subpopulations of women with osteopenia or elevated BMI.<br><br>METHODS: In this prospective, multicenter, double-blind, randomized, placebo-controlled clinical food trial (NCT05009875), 286 healthy, non-osteoporotic women between 1-6 years post-menopause were enrolled and consumed SBD111 (4.75&#xd7;10 [10] colony forming units) or placebo (maltodextrin) capsules twice daily for 12-months. The primary endpoint was change in areal BMD at the lumbar spine (LS). Secondary endpoints included change in areal BMD at the femoral neck (FN) and total hip (TH), trabecular volumetric BMD at the LS, markers of bone turnover and inflammation, and safety. Changes in gut microbiome composition were exploratory. The hypotheses being tested were formulated before data collection.<br><br>RESULTS: 286 Women [age 55 &#xb1; 3 years (mean &#xb1; standard deviation)] were enrolled, with 221 (77%) completing the study. For the primary outcome, SBD111 administration was not associated with significantly less bone loss in the LS after 12-months [0.15% (-0.52%, 0.82%), mean effect size (95% CI) by linear mixed effects regression]. However, SBD111 was associated with reduced BMD loss in the TH for women with BMI &#x2265; 30 [0.97% (0.015%, 1.925%)] and modestly reduced BMD loss in the FN for women with osteopenia [0.89% (-0.277%, 2.051%)].<br><br>CONCLUSIONS: These findings indicate SBD111 did not significantly reduce BMD loss for the full cohort. However, the trial produced evidence that SBD111 reduced bone loss in women with osteopenia and BMI &#x2265; 30.},
}
@article {pmid40475064,
year = {2025},
author = {Liu, YY},
title = {Deep learning for microbiome-informed precision nutrition.},
journal = {National science review},
volume = {12},
number = {6},
pages = {nwaf148},
pmid = {40475064},
issn = {2053-714X},
}
@article {pmid40474970,
year = {2025},
author = {Vari, F and Serra, I and Friuli, M and Cavallo, V and Gammaldi, N and Vergara, D and Salzet, M and Giudetti, AM},
title = {Pharmacological potential of endocannabinoid and endocannabinoid-like compounds in protecting intestinal structure and metabolism under high-fat conditions.},
journal = {Frontiers in pharmacology},
volume = {16},
number = {},
pages = {1567543},
pmid = {40474970},
issn = {1663-9812},
abstract = {The intestine plays a crucial role in nutrient absorption, digestion, and regulation of metabolic processes. Intestinal structure and functions are influenced by several factors, with dietary composition being one of the most significant. Diets rich in various types of fats, including saturated, monounsaturated, and polyunsaturated fats, have distinct effects on intestinal cell metabolism and overall intestinal health. High consumption of saturated fats, frequently found in animal products, has been associated with inflammation, altered gut microbiota composition, and impaired intestinal barrier function, with potential consequences such as metabolic disorders, obesity, and insulin resistance. In contrast, monounsaturated fats, found in foods such as olive oil and avocado, promote intestinal cell integrity, reducing inflammation and supporting a healthier microbiome. Polyunsaturated fatty acids, especially omega-3 fatty acids, have shown anti-inflammatory effects and may improve the function and adaptability of intestinal cells, promoting better nutrient absorption and immune regulation. Recent evidence suggests that endocannabinoids and endocannabinoid-like compounds, such as oleoylethanolamide have a protective effect on the function and structure of the intestine. These endocannabinoid pathways modulating compounds can act on receptors in the intestinal epithelium, improving the intestinal barrier and counteracting inflammation, facilitating a more favorable environment for intestinal health. Understanding how different fats influence intestinal metabolism and the protective role of endocannabinoids and endocannabinoid-like compounds is essential to developing dietary strategies to improve intestinal health and prevent diet-related diseases. This review explores the impact of high fats on intestinal metabolism and the main role of endocannabinoids and endocannabinoid-like compounds on these effects.},
}
@article {pmid40474491,
year = {2025},
author = {Myint, SMMP and Lasher, AT and Liu, K and Geurts, AM and Austad, SN and Sun, LY},
title = {A Novel GH Deficient Rat Model Reveals Cross-Species Insights Into Aging.},
journal = {Aging cell},
volume = {},
number = {},
pages = {e70126},
doi = {10.1111/acel.70126},
pmid = {40474491},
issn = {1474-9726},
support = {AG050225/AG/NIA NIH HHS/United States ; AG057734/AG/NIA NIH HHS/United States ; AG048264/AG/NIA NIH HHS/United States ; P30DK056336//the NIH Nutrition and Obesity Research Center/ ; P30DK079626//Diabetes Research Center/ ; P30AG050886A//the UAB Nathan Shock Center/ ; },
abstract = {Multiple studies in mice with genetically disrupted growth hormone (GH) signaling have demonstrated that such disruption results in reduced body size, robustly increased longevity (> 50% in some cases), and improvements across multiple health parameters. However, it remains unclear how generalizable these findings are across mammals. Evidence in rats is limited and inconsistent. These conflicting results highlight the need for further investigation into the role of GH signaling in longevity across species. To address this gap, we developed a novel GH-deficient rat model using CRISPR/Cas9 technology to introduce a 10 bp deletion in exon 3 of the gene encoding rat GH-releasing hormone (GHRH) yielding a non-functional GHRH product. Physiological characterization of GHRH knockout (KO) rats revealed that they were half the body weight of wild-type controls. Additionally, relative to controls, they displayed an increased percent body fat, enhanced insulin sensitivity, reduced circulating insulin-like growth factor I (IGF-I) concentration, and a decreased reliance on glucose oxidation for energy metabolism, as determined by indirect calorimetry. Analysis of the gut microbial community in adult GHRH-KO rats further revealed a less diverse male microbiome, but a more diverse female KO microbiome compared to controls. Collectively, these findings demonstrate that multiple aspects of the GH activity-deficient phenotype, well-documented in mice, are faithfully recapitulated in our rat model. Therefore, the GHRH-deficient rat model represents a valuable new tool for advancing our understanding of the role of GH signaling in aging processes.},
}
@article {pmid40474448,
year = {2025},
author = {Fan, H and Li, C and Zhang, Z and Hu, M and Liu, S and Wu, A and Wang, Y and Lei, Z and Guo, L and Hu, L},
title = {pH-Responsive Probiotic-Liposome Hybrid System Synergistically Treats Radiation-Induced Injury via Dual Mechanisms of Anti-Inflammatory and Microbiome Modulation.},
journal = {Advanced healthcare materials},
volume = {},
number = {},
pages = {e2501642},
doi = {10.1002/adhm.202501642},
pmid = {40474448},
issn = {2192-2659},
support = {12205215//National Natural Science Foundation of China/ ; //Key Laboratory of Radiation Damage and Treatment of Jiangsu Provincial Universities and Colleges/ ; SJC2023001//Suzhou Fundamental Research Project/ ; //Priority Academic Program Development of Jiangsu Higher Education Institutions/ ; },
abstract = {Radiation-induced intestinal injury poses significant clinical challenges in radiotherapy. This study develops an oral pH-responsive probiotic-liposome hybrid system (EcN[PIN]-L) by conjugating Escherichia coli Nissle 1917 (EcN) with pinocembrin (PIN)-loaded liposomes (B-Lip-PIN) via biotin-streptavidin binding and encapsulating them in Eudragit L100-55 (L100-55). The system resists gastric acid, releases bacteria in intestinal pH conditions, and combines PIN's anti-inflammatory properties with EcN's probiotic effects. In irradiated mice, EcN[PIN]-L demonstrates effective intestinal colonization and multiple therapeutic benefits: it reduces pro-inflammatory cytokines (TNF-α, IL-17A), enhances intestinal barrier function, and decreases epithelial apoptosis. 16S rRNA sequencing reveals improved microbiota homeostasis with increased beneficial bacteria and decreased harmful species. The system shows superior efficacy compared to individual components, addressing both inflammatory damage and microbial dysbiosis while maintaining biocompatibility. These results highlight EcN[PIN]-L as a promising dual-mechanism therapy for radiation-induced intestinal injury, offering targeted delivery and combined anti-inflammatory/microbiome-modulating action.},
}
@article {pmid40474319,
year = {2025},
author = {Hu, Z and Wu, L and Lv, Y and Ge, C and Luo, X and Zhan, S and Huang, W and Shen, X and Yu, D and Liu, B},
title = {Integrated analysis of microbiome and transcriptome reveals the mechanisms underlying the chlorogenic acid-mediated attenuation of oxidative stress and systemic inflammatory responses via gut-liver axis in post-peaking laying hens.},
journal = {Journal of animal science and biotechnology},
volume = {16},
number = {1},
pages = {82},
pmid = {40474319},
issn = {1674-9782},
support = {2024C02004//Key Research &amp; Development Program of Zhejiang Province/ ; 2023ZDXT15//Collaborative Extension Program for Advancements in Agricultural Technologies of Zhejiang Province/ ; },
abstract = {BACKGROUND: Systemic inflammatory responses and oxidative stress occur in laying hens during the aging process, particularly during the post-peaking laying period, which generally result in multi-organ damages, leading to significant declines in egg performance and quality. Chlorogenic acid (CGA)-enriched extract from Eucommia ulmoides leaves has anti-inflammatory and antioxidant activities. However, the mechanisms underlying whether and how CGA alleviates systemic inflammatory responses and oxidative stress to improve egg performance and quality in post-peaking laying hens remain unclear. In this study, the potential regulatory mechanisms of CGA in alleviating inflammatory responses and oxidative stress along the gut-liver axis were investigated. A total of 360 55-week-old Hy-line white-laying hens were randomly selected and divided into four groups. The hens in the four groups were fed a basal diet (CON) or basal diets supplemented with 200, 400, and 800 mg/kg of CGA (CGA200, CGA400, and CGA800, respectively) for 10 weeks.<br><br>RESULTS: The results demonstrated that CGA significantly alleviated intestinal and hepatic damages resulting from systemic inflammatory responses and oxidative stress, thereby improving the laying performance and egg quality of post-peaking laying hens. CGA reduced systemic inflammation by improving intestinal barrier function and modulating inflammation-associated microbiota (Blautia and Megamonas), thus inhibiting endotoxin translocation. CGA can also reduce oxidative stress by upregulating the NRF-2 pathway-related genes and increasing antioxidant enzyme activities in the liver. The results of transcriptome sequencing revealed that CGA promoted lipid metabolism by regulating hepatic adipocytokine pathway-related genes/protein and reduced the inflammatory responses and apoptosis in liver by regulating PI3K/AKT pathway-related genes/proteins, which was also verified by qPCR and western blotting.<br><br>CONCLUSION: CGA alleviated multi-organ damages and dysfunction by suppressing the systemic inflammatory responses and oxidative stress in post-peaking laying hens, thereby improving egg performance and quality. The optimal dose of CGA is 400 mg/kg in this experiment. These results provide a sound theoretical basis for the application of CGA as an exogenous animal feed additive for laying hens.},
}
@article {pmid40474258,
year = {2025},
author = {Wang, L and Jiang, W and Yang, M and Danzeng, Q and Liu, S and Cui, M},
title = {Combination strategies of gut microbiota in cancer therapy through metabolic reprogramming and immune remodeling.},
journal = {Cell communication and signaling : CCS},
volume = {23},
number = {1},
pages = {270},
pmid = {40474258},
issn = {1478-811X},
support = {No. 82303116//Natural Science Foundation of China/ ; YDZJ202301ZYTS047//Natural Science Foundation of Jilin Province/ ; 2022JC069//Health Science and Technology Capacity improvement Project of Jilin Province/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Neoplasms/therapy/immunology/microbiology/metabolism ; Animals ; Tumor Microenvironment ; Metabolic Reprogramming ; },
abstract = {Over the past decade, there has been a qualitative improvement in the understanding of gut microbiota in cancer development and treatment. Gut microbiota regulates metabolic reprogramming that occurs in the competition between tumor cells and immune cells for essential nutrients in the tumor microenvironment (TME). Besides, gut microbiota dysbiosis is one of the key factors leading to the formation of aging environment, which has many similarities with the TME. Accumulating research findings have demonstrated that gut microbiota enhances the efficacy of cancer therapies by activating the immune system and facilitating the biotransformation of drugs. Other studies also have shown that specific microbial composition is the effective biomarker of drug resistance and toxicity for cancer treatment. Microbiota-directed therapies are being explored intensively for their potential in cancer prevention and treatment. In this review, we summarize the role of gut microbiota in metabolic reprogramming and immune remodeling; provide an overview of the relationship between gut microbiota and the efficacy, resistance, and toxicity of cancer treatment; propose a series of strategies to integrate gut microbiota into cancer treatment, optimizing antitumor effectiveness and reducing side effects.},
}
@article {pmid40474246,
year = {2025},
author = {Denison, ER and Pound, HL and Gann, ER and Gilbert, NE and Weston, DJ and Pelletier, DA and Wilhelm, SW},
title = {Identification of shared viral sequences in peat moss metagenomes reveals elements of a possible Sphagnum core virome.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {62},
pmid = {40474246},
issn = {2524-6372},
support = {DE-SC0020362//US Department of Energy, Office of Science, Office of Biological and Environmental Research, Genomic Science Program/ ; DE-SC0020362//US Department of Energy, Office of Science, Office of Biological and Environmental Research, Genomic Science Program/ ; DE-SC0020362//US Department of Energy, Office of Science, Office of Biological and Environmental Research, Genomic Science Program/ ; DE-SC0020362//US Department of Energy, Office of Science, Office of Biological and Environmental Research, Genomic Science Program/ ; DE-AC05-00OR22725//U.S. Department of Energy/ ; DE-AC05-00OR22725//U.S. Department of Energy/ ; },
}
@article {pmid40474179,
year = {2025},
author = {Ho, TE and Yang, YM and Gu, WJ and Meng, W and Chen, XY and Wu, SC and Lo, ECM and Li, F and Lu, HX},
title = {Construction of an early childhood caries risk prediction model based on the oral microbiome: a nested case‒control study.},
journal = {BMC oral health},
volume = {25},
number = {1},
pages = {923},
pmid = {40474179},
issn = {1472-6831},
support = {202240355//General Project of the Shanghai Municipal Health Committee/ ; 202240355//General Project of the Shanghai Municipal Health Committee/ ; 2022ZZ01017//Shanghai's Top Priority Research Center/ ; 2022ZZ01017//Shanghai's Top Priority Research Center/ ; 22410760200//Hong Kong Macao Taiwan Science and Technology Cooperation Project of the Shanghai Municipal Science and Technology Commission/ ; },
mesh = {Humans ; Case-Control Studies ; *Dental Caries/microbiology/epidemiology ; Child, Preschool ; *Microbiota ; Female ; Male ; Prospective Studies ; Risk Assessment ; *Mouth/microbiology ; Risk Factors ; Dental Plaque/microbiology ; Oral Hygiene ; Health Behavior ; },
abstract = {BACKGROUND: Research on dental caries risk prediction models that integrate socio-demographics, oral health behaviors, and oral microbiota remains insufficient. The present study aimed to compare differences in socio-demographics, oral health behaviors, and oral microbial diversity among preschoolers with different levels of ECC progression and to construct a caries risk prediction model to prevent the occurrence and development of ECC in young children.<br><br>METHODS: A nested case-control study was conducted in a prospective cohort study to follow up preschoolers from 36 months to 48 months of age. Dental caries status and supragingival plaque data were collected at each follow-up visit, and questionnaire surveys of their mothers were conducted to collect information on the socio-demographic backgrounds and oral health-related behaviors of the preschoolers. High-throughput 16&#xa0;S rRNA gene sequencing technology was used to observe the oral microbial diversity in children, and an ECC risk prediction model was constructed using the random forest method.<br><br>RESULTS: There were 18 preschoolers each in the caries-free to caries-free group (H2H), caries-free to decayed group (H2C) and decayed to decayed group (C2C) according to ECC progression. The alpha diversity analysis showed statistically significant differences in the Simpson and Shannon indices between the H2H and H2C groups (P&#x2009;<&#x2009;0.05), and the beta diversity analysis revealed statistically significant differences between the H2H group and the H2C and C2C groups. Therefore, an ECC risk prediction model was constructed based on the H2H and H2C groups. The results of risk prediction model showed that place of residence, maternal completion of oral hygiene, toothbrushing frequency and use of dental floss, and three oral microorganisms, including Selenomonas sp. oral taxon 137, Porphyromonas sp. oral taxon 278 str. W7784, and the human oral bacterium C73, were risk factors for ECC progression after one year, and the area under the curve of the model was 95.00% (95% CI, 86.50-100.00%).<br><br>CONCLUSION: The oral microbial diversity of consistently caries-free children differed considerably from that of children who eventually developed decay, and oral health behaviors such as toothbrushing frequency and some oral microorganisms had good ECC predictive ability.},
}
@article {pmid40474156,
year = {2025},
author = {Qiu, X and Xu, T and Huang, Y and Wei, C and Wang, L and Wu, B},
title = {Relationship between depression and oral microbiome diversity: analysis of NHANES data (2009-2012).},
journal = {BMC oral health},
volume = {25},
number = {1},
pages = {914},
pmid = {40474156},
issn = {1472-6831},
support = {72404193//National Natural Science Foundation of China (NSFC) Youth Fund/ ; 892003120//Guangdong Science and Technology Programs Youth Fund/ ; 20240813143325033//Shenzhen Natural Science Foundation General Program for Basic Research/ ; },
mesh = {Humans ; Male ; Female ; Cross-Sectional Studies ; Adult ; *Depression/microbiology ; *Microbiota ; *Mouth/microbiology ; Nutrition Surveys ; Middle Aged ; RNA, Ribosomal, 16S ; United States ; },
abstract = {BACKGROUND: While the association between the gut microbiome and depression is well studied, the association between the oral microbiome and depression is less well characterized.<br><br>METHODS: This cross-sectional study analyzed the association between depression and diversity of oral microbiome using data from the 2009-2012 National Health and Nutrition Examination Survey (NHANES). The gene sequencing of 16S ribosomal RNA was adopted for the profiling of oral microbiome. Alpha diversity, quantified by the observed number of amplicon sequence variants (ASVs), and beta diversity, assessed using Bray-Curtis dissimilarity, were evaluated to represent oral microbiome diversity. Depressive symptoms were measured by the Patient Health Questionnaire-9 (PHQ-9) scale, with alpha diversity as the primary predictor. Weighted logistic regression was employed to examine the relationship between depression and microbial alpha diversity. Threshold effect analysis was performed to explore potential nonlinear relationships between the observed ASVs and depression. Subgroup analysis indicated that smoke, excessive alcohol consumption, and oral treatment influenced the association between oral microbiology and depression, with interaction effects observed across gender and racial groups. Beta diversity differences were evaluated using Bray-Curtis dissimilarity and visualized via non-metric multidimensional scaling (NMDS).<br><br>RESULTS: A total of 15,018 participants were included, with an average age of 42.25&#x2009;&#xb1;&#x2009;15.2&#xa0;years. In the fully adjusted model, the alpha diversity of oral microbiome was significantly negatively correlated with depression (OR&#x2009;=&#x2009;-0.51, 95% CI: -0.79--0.23, P&#x2009;=&#x2009;0.003). Threshold analysis also revealed a nonlinear association in this relationship, with a significant inflection point as Log10ASVs of 2.32. Furthermore, beta diversity of the oral microbiome differed significantly between the normal and depression groups (p&#x2009;=&#x2009;0.001). Sensitivity analyses showed that the relationship between depression and oral microbial diversity observed in this research was particularly pronounced among non-Hispanic Whites (OR&#x2009;=&#x2009;0.16, 95% CI: 0.07-0.35) and men (OR&#x2009;=&#x2009;0.14, 95% CI: 0.06-0.30). Additionally, significant differences in oral microbiome beta diversity were observed between the normal and depression groups (p&#x2009;=&#x2009;0.001).<br><br>CONCLUSIONS: The findings suggest that the diversity of oral microbiome is negatively correlated with depressive symptoms. Hence, oral dysbiosis may serve as a therapeutic target or biomarker of depression. However, the underlying mechanisms require further investigation.},
}
@article {pmid40474070,
year = {2025},
author = {Boodaghidizaji, M and Jungles, T and Chen, T and Zhang, B and Yao, T and Landay, A and Keshavarzian, A and Hamaker, B and Ardekani, A},
title = {Machine learning based gut microbiota pattern and response to fiber as a diagnostic tool for chronic inflammatory diseases.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {353},
pmid = {40474070},
issn = {1471-2180},
mesh = {Humans ; *Machine Learning ; *Dietary Fiber ; *Gastrointestinal Microbiome ; Crohn Disease/diagnosis/microbiology ; Feces/microbiology ; Parkinson Disease/diagnosis/microbiology ; Colitis, Ulcerative/diagnosis/microbiology ; HIV Infections/diagnosis/microbiology ; Dysbiosis/microbiology/diagnosis ; Bacteria/classification/genetics/isolation &amp; purification ; Algorithms ; Female ; Male ; *Inflammation/diagnosis/microbiology ; Chronic Disease ; },
abstract = {Gut microbiota has been implicated in the pathogenesis of multiple gastrointestinal (GI) and systemic metabolic and inflammatory disorders where disrupted gut microbiota composition and function (dysbiosis) has been found in multiple studies. Thus, human microbiome data holds significant potential as a source of information for diagnosing and characterizing diseases-such as phenotypes, disease course, and therapeutic response-associated with dysbiotic microbiota communities. However, multiple attempts to leverage gut microbiota taxonomic data for diagnostic and disease characterization have failed due to significant inter-individual variability of microbiota community and overlap of disrupted microbiota communities among multiple diseases. One potential approach is to look at the microbiota community pattern and response to microbiota modifiers like dietary fiber in different disease states. This approach has become feasible with the advent of machine learning, which can uncover hidden patterns in human microbiome data and enable disease prediction. Accordingly, the aim of our study was to test the hypothesis that machine learning algorithms can distinguish stool microbiota patterns-and their responses to fiber-across diseases with previously reported overlapping dysbiotic microbiota profiles. Here, we applied machine learning algorithms to distinguish between Parkinson's disease, Crohn's disease (CD), ulcerative colitis (UC), human immune deficiency virus (HIV), and healthy control (HC) subjects in the presence and absence of fiber treatments. We demonstrated that machine learning algorithms can classify diseases with accuracy as high as 95%. Furthermore, applying machine learning to microbiome data to distinguish UC from CD yielded a prediction accuracy of up to 90%.},
}
@article {pmid40474023,
year = {2025},
author = {Kavitha, SA and Zainab, S and Muthyalaiah, YS and John, CM and Arockiasamy, S},
title = {Mechanism and implications of advanced glycation end products (AGE) and its receptor RAGE axis as crucial mediators linking inflammation and obesity.},
journal = {Molecular biology reports},
volume = {52},
number = {1},
pages = {556},
pmid = {40474023},
issn = {1573-4978},
mesh = {Humans ; *Obesity/metabolism ; *Glycation End Products, Advanced/metabolism ; *Inflammation/metabolism ; *Receptor for Advanced Glycation End Products/metabolism ; Signal Transduction ; Oxidative Stress ; Animals ; Gastrointestinal Microbiome ; Insulin Resistance ; Metabolic Syndrome/metabolism ; Epigenesis, Genetic ; },
abstract = {Advanced glycation end products (AGEs) are heterogenous compounds that play a central role in various chronic diseases, such as diabetes, neurodegenerative disorders, cardiovascular diseases, and cancer. These are formed by non-enzymatic reaction between reducing sugar and amino group of proteins, lipids and nucleic acids. Elevated levels of AGEs are associated with obesity, which is linked to hyperglycemia, dyslipidemia and insulin resistance, contributing to metabolic syndrome and diabetes. Both dietary and endogenous AGEs contribute to persistent oxidative stress and inflammation directly through glycated biomolecules and indirectly through its receptor, receptor for advanced glycation end products, RAGE. In this context, inflammation is a sustained, systemic immune response with macrophage infiltration into adipose tissues, high pro- inflammatory cytokines leading to immune dysregulation, activation of key inflammatory pathways such as NF-kB and JNK signaling, increase oxidative stress, insulin resistance suggesting inflammation as both a cause and consequence of metabolic dysfunction. Persistent oxidative stress and inflammation accelerates AGEs formation, disrupt cellular signaling, alter extracellular matrix integrity, impair release of enzymes and hormones. Also, AGE-induced gut microbiome imbalance elicits conditions such as systemic inflammation, intestinal barrier dysfunction and metabolic imbalance, promoting obesity and its complications. This review explores the central role of AGEs in obesity-associated inflammation, emphasizing AGE-RAGE signaling, epigenetic regulation and gut microbiome dysfunction. Understanding this interplay mediated by AGEs is critical for identifying potential biomarkers of metabolic risk and strategize means to prevent AGEs formation, block AGE-RAGE interaction and signaling, thus mitigating the effects of obesity and its associated diseases.},
}
@article {pmid40474000,
year = {2025},
author = {Cottam, DE and Cosgrove, DW and Megía-Palma, R and Žagar, A and Blázquez-Castro, S and Faria, JF and Turner, AE and Silva, DO and Pie, MR},
title = {Does the Gut Microbiome of the Insular Lizard Gallotia galloti Reflect Variation in Sex, Environment, and Population Genetic Differentiation?.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {61},
pmid = {40474000},
issn = {1432-184X},
mesh = {Animals ; *Lizards/microbiology/genetics ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; Male ; Female ; Spain ; *Bacteria/classification/genetics/isolation &amp; purification ; Environment ; Genetic Variation ; Genetics, Population ; Sex Factors ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Despite their critical role in maintaining organismal health, the factors driving intraspecific variation in gut microbiotas in the wild are poorly understood. Gallotia galloti is a lizard endemic to the Canary Islands characterized by substantial phenotypic and genetic differentiation across populations, as well as by its ability to occur across considerably different environmental conditions. However, the extent to which such diversity is reflected in their gut microbiota is still unknown. Here, we use metabarcoding of fecal samples to explore how the gut microbiome of G. galloti reflects variation in sex, environment, human footprint, and subspecies identity. Fecal samples of 47 individuals were obtained across 13 locations to reflect the extent of intraspecific variation in the species. We found no evidence for consistent differences in microbiota richness across the studied groups, regardless of whether analyses were carried out at the genus, family, or phylum levels. Moreover, neither the richness nor composition of the microbiota was associated with variation in mean annual temperature, annual precipitation, and human footprint. Our results suggest that the generalist diet of G. galloti exposes them to a broad range of food items that provide a common template across the island, despite ecological and historical differences between populations.},
}
@article {pmid40473637,
year = {2025},
author = {Bar, O and Vagios, S and Barkai, O and Elshirbini, J and Souter, I and Xu, J and James, K and Bormann, C and Mitsunami, M and Chavarro, JE and Foessleitner, P and Kwon, DS and Yassour, M and Mitchell, C},
title = {Harnessing vaginal inflammation and microbiome: a machine learning model for predicting IVF success.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {95},
pmid = {40473637},
issn = {2055-5008},
mesh = {Humans ; Female ; *Vagina/microbiology/immunology ; Pregnancy ; *Microbiota ; *Fertilization in Vitro ; Adult ; *Machine Learning ; Pilot Projects ; *Inflammation/microbiology ; Male ; Pregnancy Outcome ; },
abstract = {Humans are the only species with a commensal Lactobacillus-dominant vaginal microbiota. Reproductive tract microbes have been linked to fertility outcomes, as has intrauterine inflammation, suggesting immune response may mediate adverse outcomes. In this pilot study, we compared vaginal microbiota composition and immune marker concentrations between patients with unexplained or male factor infertility (MFI), as a control. We applied a supervised machine learning algorithm that integrated microbiome and inflammation data to predict pregnancy outcomes.Twenty-eight participants provided vaginal swabs at three IVF cycle time points; 18 achieved pregnancy. Pregnant participants had lower microbial diversity and inflammation. Among them, MFI cases had higher diversity but lower inflammation than those with unexplained infertility. Our model showed the highest prediction accuracy at time point 2 of the IVF cycle. These findings suggest that vaginal microbiota and inflammation jointly impact fertility and can inform predictive tools in reproductive medicine.},
}
@article {pmid40473402,
year = {2025},
author = {Barnich, N and Arthur, JC and Buisson, A and Campbell, BJ and Carbonnel, F and Chassaing, B and Coombes, BK and Denizot, J and Dogan, B and Faith, J and Kamada, N and Longman, RS and Martinez-Medina, M and O'Brien, CL and Sartor, RB and Zhang, S and , and Colombel, JF and Simpson, KW and , },
title = {Adherent-invasive Escherichia coli in Crohn's disease: the 25th anniversary.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2025-335331},
pmid = {40473402},
issn = {1468-3288},
abstract = {In 1998, Arlette Darfeuille-Michaud, Christel Neut and Jean-Frederic Colombel discovered a novel pathovar of Escherichia coli, adherent and invasive Escherichia coli (AIEC), in the ileum of patients with Crohn's disease (CD), that was genetically distinct from diarrheagenic E. coli, could adhere to and invade intestinal epithelial cells and survive in macrophages. The consistent association between AIEC and CD (approximately 30% across the world), their ability to exploit CD-associated genetic traits, and virulence in preclinical colitis models but not healthy hosts spurred global research to elucidate their pathogenicity. Research focused on integrating AIEC with the microbiome, metabolome, metagenome, host response and the impact of diet and antimicrobials has linked the luminal microenvironment and AIEC metabolism to health and disease. This deeper understanding has led to therapeutic trials and precision medicine targeting AIEC-colonised patients. In November 2023, prominent members of the AIEC research community met to present and discuss the many facets of basic, translational and clinical AIEC fields at 'AIEC: past, present and future' in NYC. This review is a summary of this international meeting highlighting the history of AIEC, knowledge accumulated over the past 25 years about its pathogenic properties and proposes a standardised approach for screening patients for AIEC.},
}
@article {pmid40473400,
year = {2025},
author = {Szeto, CC and Ng, JKC},
title = {Toxic microbiome and progression of chronic kidney disease: insights from a longitudinal CKD-microbiome study.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2025-335600},
pmid = {40473400},
issn = {1468-3288},
}
@article {pmid40473134,
year = {2025},
author = {Sadeghi, S and Faramarzi, MA and Siroosi, M},
title = {Design of Novel Human Microbiome-Derived Peptides for Inhibition of OXA-48 Carbapenemase: An In-Silico and In-Vitro Approach.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {107779},
doi = {10.1016/j.micpath.2025.107779},
pmid = {40473134},
issn = {1096-1208},
abstract = {Drug-resistant bacteria have become a global healthcare challenge, especially due to their acquisition of resistance to last-resort antibiotics. OXA-48 carbapenemase is one of the notorious enzymes that inactivates carbapenems through hydrolysis. The emergence of OXA-48 and OXA-48-like carbapenemases is a significant concern as they are responsible for many outbreaks of hospital-acquired infections in various countries, with limited treatment options available. Thus, targeting this enzyme and inhibiting its activity can be an attractive therapeutic strategy. In this study, a rational computer-aided approach was applied to design effective inhibitory peptides against OXA-48 carbapenemase. The primary library was constructed based on peptides derived from the Human Antimicrobial Peptide (HAMP) database. The binding of peptides to the enzyme was investigated through molecular docking studies using ClusPro. After each screening step, numerous targeted amino acid substitutions were performed to enhance the affinity and physicochemical properties of the selected peptides. The final selected peptides, in complex with the enzyme, were subjected to 200 ns Molecular Dynamics (MD) simulations using the GROMACS package, and MM/PBSA analysis was conducted to evaluate the binding free energy of the enzyme-peptide complexes. Finally, the inhibitory effects of the designed peptides were also computationally assessed on OXA-48-like carbapenemases. Homology modeling was used to generate 3D structures of the enzymes whose structures were not solved experimentally. Results indicated that the two final selected peptides effectively interacted with the important residues of OXA-48 carbapenemase and spatially blocked its active site. These peptides also demonstrated high binding affinity to the most common OXA-48-like carbapenemases in silico. In vitro studies on the efficacy of one of the designed peptides, M104, demonstrated that this peptide enhanced the activity of meropenem against a meropenem-resistant, clinical Klebsiella pneumoniae strain harboring the gene blaOXA48 by reducing its minimum inhibitory concentration (MIC) by 4-fold. In an era where effective inhibitors against OXA-48 carbapenemase are limited, present study addressed this urgent need by rationally designed novel peptides.},
}
@article {pmid40473131,
year = {2025},
author = {Gong, X and Zhu, Y and Ning, X and Zhang, K and Wang, T and Yin, S and Ji, J},
title = {Effect of Ichthyophthirius multifiliis infection on host immunity and microbiota shifts of Takifugu fasciatus.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {107784},
doi = {10.1016/j.micpath.2025.107784},
pmid = {40473131},
issn = {1096-1208},
abstract = {Ichthyophthirius multifiliis (Ich) is a major pathogen responsible for high mortality rates in Takifugu fasciatus aquaculture. Despite its significance, the local and systemic immune responses of pufferfish to Ich infection remain poorly understood. Additionally, the interaction between ectoparasite infection and gut microbiota has not been thoroughly investigated. To address these gaps, we established an Ich infection model in pufferfish through bath administration. RT-PCR confirmed that Ich invades the skin, gill, and fin at 10 days post-infection (dpi) using 5,000 theronts per fish. RT-qPCR analysis revealed immune responses in the spleen, liver, gill, skin, and gut following infection, while H&amp;E staining identified Ich intrusion into the epidermal layer of the skin. RNA-seq analysis showed that pathways such as Th1 and Th2 cell differentiation, legionellosis, and Chagas disease were significantly enriched in the spleen, whereas ECM-receptor interaction, calcium signaling, and PI3K-Akt signaling pathways were enriched in the skin, suggesting that Ich breaches local defenses and activates systemic immune responses. Furthermore, Ich infection reduced the alpha diversity of the gut microbiota, with notable compositional shifts, including a decrease in commensals such as Chryseobacterium and an increase in opportunistic bacteria like Elizabethkingia. These findings enhance our understanding of the intricate interactions between parasite, host, and gut microbiota, providing insights into the immune and microbiome dynamics of Ich infection in pufferfish.},
}
@article {pmid40473125,
year = {2025},
author = {Darwiche, S and Gacesa, R and Ferraro, RB and Alwan, W and Oben, JA and Rashidghamat, E and Long, PF},
title = {Prevalence of skin fungi markedly declines in the lesions of two patients with moderate Hidradenitis Suppurativa.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {107778},
doi = {10.1016/j.micpath.2025.107778},
pmid = {40473125},
issn = {1096-1208},
abstract = {Hidradenitis suppurativa (HS) is a chronic inflammatory disorder affecting hair follicles in intertriginous regions, leading to painful nodules, sinus tracts, and scarring. The pathogenesis of HS is far from clear, but alterations in the bacterial community of the skin microbiome has been debated, yet the potential involvement of fungi - the mycobiome - has received almost no attention. Large areas of skin were sampled for amplicon metagenomics sequencing to negate the inference of low-sequence counts with the objective of examining the provenance of fungi between lesion and lesion-free skin from the same individuals. The DNA from skin swabs was isolated and the V4 region of the 18S rRNA gene was amplified and sequenced. Total fungal counts were inferred from taxonomic assignment of unique operational taxonomic units and absolute numbers then compared between skin sites. There were dramatically lower numbers of fungi in HS lesions with Malassezia dominance, as expected, across samples. This finding suggested, for the first time, that fungal depletion in lesions might be linked to HS pathology through disruption of normal skin barrier function and immunity, potentially due to reduced sebum production essential for fungal growth.},
}
@article {pmid40473107,
year = {2025},
author = {Mascaux, C and Sen, T and Sanchez-Cespedes, M and Ortiz-Cuaran, S and Bossé, Y and Dammeijer, F and Cavic, M and Barr, MP and Arulananda, S and Armisen, R and Berger, AH and Bianchi, F and Carbone, DP and Cerciello, F and Lockwood, WW and Mitsudomi, T and Ohara, S and Politi, K and Qin, S and Roisman, LC and Samstein, R and Skoulidis, F and Tan, AC and Thomas, A and Zhang, J and Wynes, MW and John, T and Tsao, MS and , },
title = {Advances in lung cancer basic and translational research in 2025 - Overview and perspectives focusing on non-small cell lung cancer.},
journal = {Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jtho.2025.05.024},
pmid = {40473107},
issn = {1556-1380},
abstract = {Basic and translational research in lung cancer is a rapidly evolving field with transformational impact in early detection, diagnosis, therapeutic development and personalization of care. Recent advances have greatly increased our understanding in the molecular genomics, proteomics, pathogenesis and cellular biology of this deadly malignancy. The International Association for the Study of Lung Cancer (IASLC) recently formed a Basic and Translational Science (BaTS) Committee to further enhance the scientific leadership of IASLC in thoracic cancer research. This review by members of the committee highlights the breadth of current research in NSCLC, with a focus on molecular risk factors and processes in tumorigenesis, heterogeneity, phenotypic plasticity, metabolic reprograming, immunobiology, the immune microenvironment and microbiome. This review also identifies future research areas that may lead to further improvement in survival outcomes and curative therapies especially for patients with advanced NSCLC.},
}
@article {pmid40473000,
year = {2025},
author = {Carbone, E and Fabrizi, E and Rivabene, R and Cappella, M and Fortini, P and Conti, L and Locuratolo, N and Lorenzini, P and Lacorte, E and Piscopo, P},
title = {Human oral microbiome in aging: a systematic review.},
journal = {Mechanisms of ageing and development},
volume = {},
number = {},
pages = {112080},
doi = {10.1016/j.mad.2025.112080},
pmid = {40473000},
issn = {1872-6216},
abstract = {Studying aging and risk factors associated with chronic non-communicable diseases is increasingly relevant due to the progressive aging of the global population. Risk factors have focused on diet, physical exercise, cognitive activity, and lifestyle habits; however, recent research has begun to explore how the oral microbiome may influence health and contribute to chronic diseases. The aim of our systematic review is to evaluate the link between human oral microbiome and aging. This SR was carried out using PubMed, Cochrane Library, and Embase, identifying 3,490 records, of which 6 met our inclusion/exclusion criteria. These studies were qualitatively assessed using the Revised Risk of Bias Assessment Tool for Nonrandomized Studies of Interventions. Overall, the evidence suggests that while the bacterial and fungal communities remain similar across age groups, there is an increased presence of periodontal pathogens in older subjects. Moreover, bacterial species richness and alpha-diversity decrease with advancing age, though no clear age clustering was observed. Although the reviewed studies offer insights into the association between aging and changes in the oral microbiome, further research is required to address confounding factors, limitations in sample size, and gender differences, in order to better elucidate the role of microbiome alterations in general health.},
}
@article {pmid40472755,
year = {2025},
author = {Chen, M and Xing, L and Gao, S and Guo, Y and Qiu, T and Wang, X and Gao, M},
title = {Metagenomic analysis deciphers airborne pathogens with enhanced antimicrobial resistance and virulence factors in composting facilities.},
journal = {Environment international},
volume = {201},
number = {},
pages = {109569},
doi = {10.1016/j.envint.2025.109569},
pmid = {40472755},
issn = {1873-6750},
abstract = {The composting process has been shown to effectively reduce antimicrobial resistance (AMR) in animal manure, but its influence on surrounding airborne AMR remains unknown, particularly with regard to human-pathogenic antibiotic-resistant bacteria (HPARB). In this study, air and paired compost samples were collected from a full-scale composting facility, and the antibiotic resistome, microbiome, and HPARB were systematically analyzed in both two habitats using metagenomic analysis. Current result uncovered the profiles of HPARB in air, showing that significantly more airborne HPARB were assembled than that in compost samples. Airborne pathogens harboredan increased abundance and diversity of antibiotic resistance genes (ARGs) and virulence factor genes (VFGs) in comparison with compost-borne HPARB. The core antibiotic resistome represents 18.58% of overall ARG subtypes, contributing to 86.31% of ARG abundance. A higher number of enriched core ARGs (2.16- to 13.36-times higher), including mexF, tetW, and vanS, were observed in air samples compared to compost samples. As an important human pathogen, Mycobacterium tuberculosis was prevalent in the air and carried more ARG (6) and VFG (130) subtypes than those in compost. A significantly higher risk score was detected for airborne AMR in the composting facility compared to that in hospital and urban environments. This study revealed the enhanced airborne HPARB through comparative experiments between air and composting habitats. It highlighted the unrecognized AMR risks associated with air in composting site and provided a scientific basis for accurately assessing health outcomes caused by occupational exposure.},
}
@article {pmid40472699,
year = {2025},
author = {Yang, Q and Cao, X and Li, S and Yang, X and Bai, P and Yan, Y and Qi, C and Deng, Z and Wu, B and Song, B},
title = {Chronic ozone exposure induces hippocampal microglia activation by microbial dysbiosis in rat lungs.},
journal = {Ecotoxicology and environmental safety},
volume = {300},
number = {},
pages = {118393},
doi = {10.1016/j.ecoenv.2025.118393},
pmid = {40472699},
issn = {1090-2414},
abstract = {Ozone (O3) pollution has become a significant international public health issue with adverse effects on human health. Recent studies have confirmed that O3 exposure induces neuroinflammation and cognitive dysfunction. It is hypothesized that O3 exposure affects the pulmonary microbiome, triggering inflammatory responses that subsequently contribute to neuroinflammation. After 40 days of O3 exposure in rats, distinct changes in the microbial community were identified using 16S rRNA gene sequencing. This was followed by an assessment of the impact of pulmonary microbiota on serum NETs (neutrophil extracellular traps). Additionally, changes in the hippocampal P2X4R/NLRP3 signaling pathway were investigated following O3 exposure. In vitro experiments were conducted to evaluate the effects of O3 on BV-2 cells. In vivo results indicated that O3 exposure led to an increased abundance of Pseudomonas aeruginosa within the pulmonary microbiota and significantly increased NET levels in rat serum. O3 exposure caused a loose arrangement of hippocampal neurons in rats, resulting in cell atrophy and even death. Compared to controls, O3 exposure significantly upregulated the expression of P2X4R/NLRP3 and pro-inflammatory factors. Similarly, BV-2 cells treated with serum from 1.0 ppm O3-exposed rats exhibited comparable changes. Treatment with a P2X4R inhibitor significantly reduced pathway protein and pro-inflammatory factors expression compared to O3 serum intervention alone. In conclusion, O3 exposure significantly alters the pulmonary microbiome, induces hippocampal damage, and NETs may act as a mediator between the lung and brain axes.},
}
@article {pmid40472561,
year = {2025},
author = {Lin, Z and Qiao, Y and Xu, K and Lu, L and Shu, QY and Tian, S},
title = {The endophytic fungus Serendipita indica reshapes rhizosphere soil microbiota to improve Salix suchowensis growth and phytoremediation.},
journal = {Journal of hazardous materials},
volume = {495},
number = {},
pages = {138620},
doi = {10.1016/j.jhazmat.2025.138620},
pmid = {40472561},
issn = {1873-3336},
abstract = {Soil cadmium (Cd) contamination, a global issue threatening human health, can be mitigated through phytoremediation using plant growth-promoting microorganisms (PGPMs), which enhance heavy metal extraction. Endophyte Serendipita indica promotes plant growth and alleviates abiotic/biotic stress, but its role in reshaping rhizosphere microecology remains unclear. We combined in situ zymography, diffusive equilibration in thin films (DET), and laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) to explore Cd rhizosphere processes. S. indica inoculation significantly increased stems and leaves biomass by 36.52 % and 31.63 %, respectively, and Cd accumulation by 44.30 % in stems and 33.17 % in leaves. DET and zymography mapping showed that S. indica inoculation reduced pH and enhanced enzyme activity in the rhizosphere. LA-ICP-MS mappings revealed that S. indica increased Cd concentration in the root-soil interface and enhanced Cd and phosphorus (P) bioavailability, promoting root uptake and transport to shoots. S. indica inoculation recruited a more complex and stable network, supporting willow growth and Cd absorption. Key strains like Gemmatimonas, Subgroup_10, and Sandaracinus facilitated organic matter degradation, releasing bioavailable P and Cd, thus enhancing the phytoremediation efficiency. In summary, a mutualistic system between S. indica and willow was established, enhancing Cd phytoremediation efficiency by altering rhizosphere microenvironment and microbiome.},
}
@article {pmid40472289,
year = {2025},
author = {Lim, LWZ and Toh, KY and Cook, AR and Lee, JWJ and Lim, JFY},
title = {Public knowledge, awareness and perception of gut microbiome and faecal microbiota transplantation in Singapore: a survey study.},
journal = {Singapore medical journal},
volume = {},
number = {},
pages = {},
pmid = {40472289},
issn = {2737-5935},
abstract = {INTRODUCTION: Despite the exponential increase in microbiome research, knowledge and beliefs about the gut microbiome and faecal microbiota transplantation (FMT) remain unclear. The aim of this study was to identify the extent of knowledge, awareness and perception among the general public regarding the gut microbiome and FMT.<br><br>METHODS: An online questionnaire on knowledge and beliefs about the gut microbiome and FMT was administered to 1831 participants. Data analysis software was used to generate descriptive statistics and explore associations between knowledge and sociodemographic variables.<br><br>RESULTS: Even though only 33% of participants had heard of the gut microbiome, more than 92% had consumed probiotic drinks or supplements. While 85% had not heard of the FMT procedure, 72% of respondents would consider having FMT to treat Clostridioides difficile infection (CDI). Willingness to receive FMT depended mainly on recommendation from healthcare providers (77%). Knowledge and awareness regarding the gut microbiome and FMT were relatively low, despite most participants having prior gut health-related behaviours.<br><br>CONCLUSION: This study identified the public's perceptions of FMT and the potential barriers to its uptake. Insights from the study highlight the need for health education to enhance acceptance of FMT and the importance of using information supported by medical professionals to immunise the public against poorly validated science.},
}
@article {pmid40472245,
year = {2025},
author = {Baeringsdottir, B and Haraldsson, A and Hrafnkelsson, B and Thors, V},
title = {Infant Antibiotic Exposure Is Associated With Increased Risk of Later Childhood Infections, Antibiotic Use and Asthma.},
journal = {The Pediatric infectious disease journal},
volume = {},
number = {},
pages = {},
doi = {10.1097/INF.0000000000004867},
pmid = {40472245},
issn = {1532-0987},
abstract = {BACKGROUND: Antimicrobials have saved millions of lives. Antibiotics are essential in treating infant infections, but may disrupt the gut microbiome and have adverse effects on later health.<br><br>METHODS: This population-based birth cohort study included full-term children born in Iceland from 2010 to 2019 with follow-up for 2-12 years. The cohort was divided into 4 groups according to antibiotic exposure; I: elective cesarean section, II: vaginal birth and maternal intrapartum antibiotics, III: vaginal birth and infants received antibiotics during the first week of life for >48 hours and IV: vaginal birth without antibiotic exposure. Rates of infections, antibiotic use and the risk of asthma later in childhood were calculated.<br><br>RESULTS: Of 43,600 children born in Iceland from 2010 to 2019, 22,393 were included. Group I had 1496 children, group II 3413, group III 356 and group IV 17,128 children. For all antibiotic exposure groups, the risk of infections and antibiotic use was significantly higher (20%-100%), with the largest effect observed for infants treated with antibiotics. This group also had a 2-fold risk of asthma diagnosis when compared with controls (odds ratio: 1.91, P < 0.05).<br><br>CONCLUSIONS: In this cohort study, children with early antibiotic exposure had higher rates of infections and antibiotic use later in childhood compared with controls. Diagnoses of asthma were significantly more common in children with early antibiotic exposure and this effect was most evident after the age of 8 years. The observed late side-effects of antibiotic use, possibly mediated through a disrupted microbiome, should promote a conservative approach to antibiotic treatment in young infants.},
}
@article {pmid40472200,
year = {2025},
author = {Hatch-McChesney, A and Suther, C and Thompson, LA and Radcliffe, PN and Cherian, RV and Liechty, ZS and Stamps, BW and Krieger, S and Nelman-Gonzalez, M and Crucian, B and Diak, D and Mehta, S and Goodson, MS and Barringer, N and Smith, TJ and Karl, JP},
title = {Sex Differences in Immune and Gut Microbiota Responses to Military Training.},
journal = {Medicine and science in sports and exercise},
volume = {},
number = {},
pages = {},
doi = {10.1249/MSS.0000000000003772},
pmid = {40472200},
issn = {1530-0315},
abstract = {PURPOSE: Military training includes multiple stressors that together may increase risk for illness by degrading immune function and altering gut microbiota. However, whether sex differences exist in those responses is undetermined. This study aimed to determine immune and gut microbiota responses during military training and identify sex differences in those responses.<br><br>METHODS: Seventy-two military cadets (33% female) participated in an arduous 17-day training event. Blood, saliva and stool were collected upon beginning (PRE) and completing (POST) training. Immune function was assessed by salivary secretory IgA (SIgA), latent virus reactivation, peripheral leukocyte distribution, circulating cytokines and mitogen-stimulated cytokine profiles. Gut microbiota composition was assessed by 16S rRNA amplicon sequencing.<br><br>RESULTS: Participants experienced a ~ 4% body weight loss and sex-independent increases in concentrations of cortisol, myoglobin, catecholamines and multiple cytokines. The granulocyte-to-lymphocyte ratio increased and SIgA decreased PRE to POST in males but not females (Pinteraction &#x2264; 0.02). Mitogen-stimulated cytokine profiles were generally reduced at POST versus PRE independent of sex. No differences in virus reactivation were observed. Sex differences in gut microbiota responses were limited to Bifidobacterium and Ruminococcus, which increased in males relative to females (log2 fold change (FC) = 2.0-2.4; qinteraction = 0.19). Independent of sex, 24 genera differed at POST versus PRE with Lactobacillus demonstrating the largest decrease (log2FC = -0.90; qtime = 0.02) and Veillonella the largest increase (log2FC = 1.09; qtime = 0.03). Multiple correlations between markers of stress, immune function and gut microbiota composition were observed (q &#x2264; 0.15).<br><br>CONCLUSIONS: Immune redistribution, leukocyte compromise and interrelated changes in gut microbiota composition were evident within this training environment. Those responses demonstrated associations with markers of stress severity but also sex differences suggesting a more pronounced depression of immune function in males.},
}
@article {pmid40472034,
year = {2025},
author = {Noack, C and Jenderny, S and Giez, C and Merza, O and Hofacker, LM and Wittlieb, J and Repnik, U and Bramkamp, M and Ochs, K and Bosch, TCG},
title = {Assembly of a functional neuronal circuit in embryos of an ancestral metazoan is influenced by temperature and the microbiome.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {23},
pages = {e2501225122},
doi = {10.1073/pnas.2501225122},
pmid = {40472034},
issn = {1091-6490},
support = {CRC 1182 C1; CRC 1461 A1//Deutsche Forschungsgemeinschaft (DFG)/ ; HMB//Canadian Institute for Advanced Research (ICRA)/ ; CRC 1461 A1//Deutsche Forschungsgemeinschaft (DFG)/ ; },
mesh = {Animals ; *Microbiota/physiology ; *Hydra/embryology/microbiology/physiology ; *Neurons/physiology ; Temperature ; *Nerve Net/physiology/embryology ; Biological Evolution ; Embryo, Nonmammalian/physiology ; Gap Junctions/physiology ; },
abstract = {Understanding how neural populations emerge to give rise to behavior is a major goal in neuroscience. Here, we explore the self-assembly of neural circuits in Hydra, an organism with a simple nervous system but no centralized information processing, to enhance the understanding of nervous system evolution. We define self-assembly as spontaneous organization of neurons into functional circuits without requiring a prespecified structural template. In this context, the N4 neuronal circuit, which we have previously found to be particularly important in the feeding of the animal, develops in embryos through activity-driven self-assembly, a process in which intrinsic calcium activity drives connectivity and synchronization among spatially distributed neurons over time. Gap junctions and vesicle-mediated communication between neuronal and non-neuronal cells drive rapid assembly, with the embryo's prospective oral region exhibiting the highest neuronal density. An artificial electrical circuit-based model as a biophysically inspired simulation demonstrates dynamic increases in synchronization over time, along with predictions for selective dynamic adaptions of connections. Environmental factors, like temperature and an absent microbiome, modify neural architecture, suggesting the existence of a certain adaptability during neural development. We propose that these fundamental features originated in the last common bilaterian ancestor, supporting the hypothesis that the basic architecture of the nervous system is universal. Since in the natural habitat of Hydra both temperature fluctuations and changes in the microbiome can occur, our work not only illuminates a fundamental developmental process but also may guide environmental and evolutionary studies by explaining how organisms adapt to environmental variations.},
}
@article {pmid40472016,
year = {2025},
author = {MacIntosh, GH and Nuyens, AC and Vickery, JL and Berthold, A and Lloyd, VK},
title = {Epigenetic responses in Borrelia-infected Ixodes scapularis ticks: Over-expression of euchromatic histone lysine methyltransferase 2 and no change in DNA methylation.},
journal = {PloS one},
volume = {20},
number = {6},
pages = {e0324546},
doi = {10.1371/journal.pone.0324546},
pmid = {40472016},
issn = {1932-6203},
mesh = {Animals ; *Ixodes/microbiology/genetics ; *DNA Methylation ; *Epigenesis, Genetic ; *Borrelia burgdorferi/physiology ; *Histone-Lysine N-Methyltransferase/genetics/metabolism ; Lyme Disease/microbiology ; },
abstract = {Borrelia burgdorferi, a tick-vectored spirochete bacteria best known for causing Lyme disease, has been found to induce physiological and behavioural changes in its tick vector that can increase tick fitness and its ability to transmit the bacteria. The mechanism by which this bacterium modulates these changes remains unknown. Epigenetics plays a central role in transducing external and internal microbiome environmental influences to the organism, so we investigated DNA methylation and the expression of a key histone modification enzyme in Borrelia-infected and uninfected Ixodes scapularis ticks. DNA methylation of the pericentromeric tandem repeats family, Ixodes scapularis Repeats (ISR), were assessed by methylated-DNA immunoprecipitation (MeDIP) followed by qPCR of the ISR regions. DNA methylation of the ISR sequences was found. The different repeats had different levels of DNA methylation, however, these levels were not significantly affected by the presence or absence of B. burgdorferi. The epigenetic regulator euchromatic histone lysine methyltransferase 2 (EHMT2) is recognized as having a key role in modulating the organismal stress response to infections. To assess EHMT2 transcription in Borrelia-infected and uninfected ticks, real-time reverse transcriptase PCR was performed. Uninfected ticks had over 800X lower EHMT2 expression than infected ticks. This study is among the first to identify a gene that may be involved in producing epigenetic differences in ticks depending on infection status and lays the groundwork for future epigenetic studies of I. scapularis in response to B. burgdorferi as well as other pathogens that these ticks transmit.},
}
@article {pmid40471941,
year = {2025},
author = {Ritz, T and Rosenkranz, MA and Celedón, JC and Davenport, PW and Djukanovic, R and Feldman, JM and Forsythe, P and Jajour, NN and Vercelli, D and von Leupoldt, A and Wright, RJ},
title = {Asthma: Biomedical and Psychobiological Perspectives for the Disease of the Year 2023.},
journal = {Biopsychosocial science and medicine},
volume = {},
number = {},
pages = {},
doi = {10.1097/PSY.0000000000001410},
pmid = {40471941},
issn = {2998-8756},
abstract = {Substantial knowledge about asthma has accumulated in past decades from biomedical and psychobiological research. This white paper reports on synergistic perspectives for these fields discussed at the first Annual Disease-A-Year Symposium of the American Psychosomatic Society. Progress has been made in identifying mechanical, cellular and molecular mechanisms of asthma and influences of psychosocial factors on development, pathophysiology, and management have been demonstrated. However, much remains to be learned about mechanisms of asthma development, in particular the role of genes and the microbiome, and their interaction with psychosocial factors. Additional psychobiological analysis of immunobiological pathways and pathophysiological features is also needed, as well as integration with asthma phenotypes. Although traditionally viewed as a peripheral disease of the airways, its effect on the central nervous system and cognition have begun to garner attention due to neuroscientific and technological advances. Brain-body interaction are also the focus of airway interoception research, with practical consequences for management of over- and underperception of airway obstruction. An integrative perspective on asthma recognizes societal factors that worsen and consolidate disparities in asthma outcomes and explores mechanisms of building resilience in patients from disadvantages communities. Biomedical treatment with novel monoclonal antibodies promises a personalized medicine approach, while improvements to asthma management trainings have increased disease control and quality of life. Psychobiological and mind-body interventions, such as exercise, breathing training, cognitive behavioral therapy, or meditation techniques, require further exploration in large-scale multicenter trials. Close interdisciplinary collaboration will bring the field closer to the ideal of a holistic biopsychosocial treatment of asthma.},
}
@article {pmid40471835,
year = {2025},
author = {Robinson, LA and Pascual, V},
title = {Recent insights into the role of innate immunity in lupus.},
journal = {Human molecular genetics},
volume = {},
number = {},
pages = {},
doi = {10.1093/hmg/ddaf066},
pmid = {40471835},
issn = {1460-2083},
support = {CORT P50AR070594/AR/NIAMS NIH HHS/United States ; //Center for Lupus Research (VP)/ ; U19 AI082715/AI/NIAID NIH HHS/United States ; },
abstract = {Systemic Lupus Erythematosus (SLE) is a complex autoimmune disorder characterized by loss of self-tolerance to nucleic acids, resulting in multisystem inflammation and organ damage. The genetic underpinning of SLE spans from common risk variants with modest effect sizes to rare monogenic mutations with high penetrance. Recent advances in next-generation sequencing and transcriptomic profiling have illuminated the central role of innate immune pathways in disease pathogenesis. This review synthesizes emerging evidence regarding innate immunity in SLE, with emphasis on toll-like receptor (TLR) signaling and regulatory mechanisms, NLRP3 inflammasome activation, myeloid cell dysregulation, and microbiome-immune interactions. Understanding these pathways provides a foundation for developing targeted therapeutics that may offer precision medicine approaches for this heterogeneous disease.},
}
@article {pmid40471540,
year = {2025},
author = {Zhang, Y and Zhang, K and Song, D and Yan, T and Ma, S and Liu, R and Jin, Y and Gong, H and Yang, L and Wang, X and Liu, S and Wang, C and Zhao, M},
title = {Combination of Rare Sugars L-arabinose, D-mannose, D-xylose, D-allulose, and D-tagatose Alleviates Cognitive Impairment in Mice with Type 2 Diabetes Mellitus.},
journal = {Molecular neurobiology},
volume = {},
number = {},
pages = {},
pmid = {40471540},
issn = {1559-1182},
support = {82071515//National Natural Science Foundation of China/ ; },
abstract = {Herein, the study was conducted to elucidate the impact of a rare sugar complex (RSC) containing L-arabinose, D-mannose, D-xylose, D-allulose, and D-tagatose on cognitive impairment in a Type 2 diabetes mellitus (T2DM) mouse model. Specifically, a diabetes model was established by administering a high-fat diet (HFD) followed by streptozotocin injection. Behavioral performance in T2DM mice was assessed using multiple behavioral tests, including the Morris water maze, Y maze, novel object recognition test, and novel location recognition test. Neuronal damage in the hippocampal region was detected through hematoxylin and eosin staining. Superoxide dismutase (SOD) and malondialdehyde (MDA) constituted key biomarkers for assessing oxidative stress, with SOD indicating antioxidant capacity and MDA reflecting lipid peroxidation. Both were quantified via enzyme-linked immunosorbent assay. Additionally, the types and richness of microorganisms in the feces of each group of mice were analyzed through 16S sequencing of gut microbiota. Behavioral assays demonstrated that T2DM mice exhibited learning and memory impairments, which were notably mitigated by the administration of RSC. SOD activity decreased significantly, whereas MDA levels increased substantially. HE staining revealed that RSC effectively suppressed hippocampal cell apoptosis in T2DM mice. Furthermore, RSC treatment restored the diversity and abundance of gut microbiota in T2DM mice. Collectively, these findings suggest that RSC alleviates cognitive impairment in T2DM mice by reducing cerebral oxidative stress and modulating the intestinal microbiome composition.},
}
@article {pmid40471453,
year = {2025},
author = {Birkeland, E and Bamigbetan, WA and Molven, KD and Thorsby, PM and Gulseth, HL and Aas, AM and Dahl, C},
title = {Can supplements with prebiotic fibres positively influence bone health in type 2 diabetes? Insights from a randomised controlled crossover trial.},
journal = {Archives of osteoporosis},
volume = {20},
number = {1},
pages = {71},
pmid = {40471453},
issn = {1862-3514},
support = {2013-2-267//The DAM Foundation/ ; 36660//Diabetesforbundet/ ; 36660//Mills DA/ ; },
mesh = {Humans ; *Prebiotics/administration &amp; dosage ; *Diabetes Mellitus, Type 2/blood/physiopathology ; Cross-Over Studies ; Male ; Female ; Middle Aged ; Aged ; Double-Blind Method ; *Dietary Supplements ; Calcium/blood ; Vitamin D/blood/analogs &amp; derivatives ; Magnesium/blood ; Bone Remodeling/drug effects ; Biomarkers/blood ; Inulin/administration &amp; dosage ; Gastrointestinal Microbiome ; Fructans ; Collagen Type I/blood ; Procollagen/blood ; Peptides/blood ; Peptide Fragments/blood ; },
abstract = {UNLABELLED: Inulin-type fructans did not significantly improve serum levels of calcium, magnesium, vitamin D, or bone turnover markers in people with type 2 diabetes (T2D). However, interactions between gut microbiota and bone health were suggested, indicating the need for further research in this population.<br><br>BACKGROUND: Evidence suggests that a healthy gut microbiome benefits bone health, especially in immunocompromised populations like the elderly and people with T2D.<br><br>OBJECTIVE: We investigated the effect of prebiotics (inulin-type fructans) on serum concentrations of calcium, magnesium, 25(OH) vitamin D, and the bone turnover markers N-terminal propeptide of type 1 collagen (P1NP), and C-terminal telopeptide of type 1 collagen (CTX-1) in people with T2D.<br><br>DESIGN: Participants (29) were treated for 6&#xa0;weeks with 16&#xa0;g inulin-type fructans and 16&#xa0;g control supplement (maltodextrin) in randomised and double-blind crossover design, with a 4-week washout between treatments.<br><br>RESULTS: Compared to the control, inulin-type fructans did not significantly affect serum concentrations (mean&#x2009;&#xb1;&#x2009;SEM) of calcium (0.05&#x2009;&#xb1;&#x2009;0.02&#xa0;mmol/L vs. 0.02&#x2009;&#xb1;&#x2009;0.03&#xa0;mmol/L, p&#x2009;=&#x2009;0.324), magnesium (0.02&#x2009;&#xb1;&#x2009;0.01&#xa0;mmol/L vs. 0.00&#x2009;&#xb1;&#x2009;0.01&#xa0;mmol/L, p&#x2009;=&#x2009;0.352), 25(OH) vitamin D (-3.60&#x2009;&#xb1;&#x2009;1.94&#xa0;nmol/L vs. -2.00&#x2009;&#xb1;&#x2009;1.97&#xa0;nmol/L, P&#x2009;=&#x2009;0.564), P1NP (0.81&#x2009;&#xb1;&#x2009;0.95 ug/L vs. -0.89&#x2009;&#xb1;&#x2009;0.97 ug/L, p&#x2009;=&#x2009;0.210), or CTX-1 (-0.01&#x2009;&#xb1;&#x2009;0.01 ug/L vs. 0.00&#x2009;&#xb1;&#x2009;0.01 ug/L, p&#x2009;=&#x2009;0.438). However, post hoc analyses of correlations between changes support that cross-talk between the human host and gut microbiota may influence bone health in this population.<br><br>CONCLUSION: This study does not support that inulin-type fructans may improve serum levels of calcium, magnesium, or 25(OH) vitamin D, nor that they affect bone turnover markers in people with T2D over 6&#xa0;weeks. Interactions between microbiota and bone health in this population warrants further investigations. The trial is registered at clinicaltrials.gov (NCT02569684).},
}
@article {pmid40471139,
year = {2025},
author = {Gawish, R and Varada, R and Deckert, F and Hladik, A and Steinbichl, L and Cimatti, L and Milanovic, K and Jain, M and Torgasheva, N and Tanzer, A and De Paepe, K and Van de Wiele, T and Hausmann, B and Lang, M and Pechhacker, M and Ibrahim, N and De Vries, I and Brostjan, C and Sixt, M and Gasche, C and Boon, L and Berry, D and Jantsch, MF and Pereira, FC and Vesely, C},
title = {Filamin A editing in myeloid cells reduces intestinal inflammation and protects from colitis.},
journal = {The Journal of experimental medicine},
volume = {222},
number = {9},
pages = {},
doi = {10.1084/jem.20240109},
pmid = {40471139},
issn = {1540-9538},
support = {57-B28//Austrian Science Fund/ ; V 1025-B//Austrian Science Fund/ ; DOC32-B28//Austrian Science Fund/ ; F8007//Austrian Science Fund/ ; P32678//Austrian Science Fund/ ; //Medical University of Vienna/ ; },
mesh = {*Filamins/genetics/metabolism ; Animals ; *Myeloid Cells/metabolism/pathology ; Humans ; *Colitis/genetics/pathology/prevention &amp; control ; *Inflammation/pathology/genetics ; Mice ; Mice, Inbred C57BL ; Neutrophils/metabolism ; *RNA Editing ; Macrophages/metabolism ; Male ; },
abstract = {Patho-mechanistic origins of ulcerative colitis are still poorly understood. The actin cross-linker filamin A (FLNA) impacts cellular responses through interaction with cytosolic proteins. Posttranscriptional A-to-I editing generates two forms of FLNA: genome-encoded FLNAQ and FLNAR. FLNA is edited in colon fibroblasts, smooth muscle cells, and endothelial cells. We found that the FLNA editing status determines colitis severity. Editing was highest in healthy colons and reduced during murine and human colitis. Mice that exclusively express FLNAR were highly resistant to DSS-induced colitis, whereas fully FLNAQ animals developed severe inflammation. While the genetic induction of FLNA editing influenced transcriptional states of structural cells and microbiome composition, we found that FLNAR exerts protection specifically via myeloid cells, which are physiologically unedited. Introducing fixed FLNAR did not hamper cell migration but reduced macrophage inflammation and rendered neutrophils less prone to NETosis. Thus, loss of FLNA editing correlates with colitis severity, and targeted editing of myeloid cells serves as a novel therapeutic approach in intestinal inflammation.},
}
@article {pmid40470946,
year = {2025},
author = {Wei, Y and Jia, W and Sun, Y and Zhang, T and Miao, H and Wu, Z and Dong, R and Ning, F and Kim, WJ},
title = {Investigating the immunomodulatory effects of honeybee venom peptide apamin in Drosophila platforms.},
journal = {Infection and immunity},
volume = {},
number = {},
pages = {e0013125},
doi = {10.1128/iai.00131-25},
pmid = {40470946},
issn = {1098-5522},
abstract = {Apamin, an 18-amino-acid honeybee venom peptide, although traditionally recognized for its neurotoxic effects, demonstrates potent antimicrobial properties in our research when genetically expressed in Drosophila. This antimicrobial efficacy is independent of its disulfide bonds and is enhanced when the peptide is membrane-tethered. Apamin selectively inhibits pathogenic bacteria, such as Pseudomonas aeruginosa, Enterococcus faecalis, and Escherichia coli, while promoting beneficial bacteria like Lactobacillus plantarum, thereby improving the gut microbiome. This gut-localized antimicrobial activity is associated with increased intestinal stem cell proliferation, midgut acidification, and enteroendocrine cell calcium signaling. Furthermore, apamin's antimicrobial function relies on specific peptidoglycan recognition proteins, particularly PGRP-LA and PGRP-SCs. Apamin expression alone is sufficient to restore the integrity of the gut barrier compromised by stressful conditions. Ultimately, apamin supplementation enhances honeybee gut health in the presence of ingested bacteria. The expression of other honeybee antimicrobial peptides also significantly reduces bacterial infection in flies. Overall, our study provides a comprehensive understanding of honeybee venom peptides and antimicrobial peptides functions, utilizing the Drosophila model system to unravel their mechanisms of action and therapeutic potential.},
}
@article {pmid40470930,
year = {2025},
author = {Ekregbesi, P and Seibert, B and Parish, MA and Flores-Garcia, Y and Creisher, PS and Hoffmann, JP and Liu, JA and Brayton, C and Zavala, F and Klein, SL},
title = {Multi-system dysregulation in placental malaria contributes to adverse perinatal outcomes in mice.},
journal = {Infection and immunity},
volume = {},
number = {},
pages = {e0002125},
doi = {10.1128/iai.00021-25},
pmid = {40470930},
issn = {1098-5522},
abstract = {Sequestration of Plasmodium parasites in the placental vasculature contributes to increased morbidity and mortality in pregnant compared to non-pregnant patients in malaria-endemic regions. In this study, outbred pregnant CD1 mice with semi-allogeneic fetuses were infected with transgenic Plasmodium berghei or mock inoculated by mosquito bite at either embryonic day (E)6 (first trimester-equivalent) or 10 (second trimester-equivalent) and were compared to non-pregnant females. P. berghei-infected mosquitoes had greater biting avidity for E10 dams than uninfected mosquitoes, which was not apparent for E6 dams nor non-pregnant females. Infected E10 dams had greater numbers of parasites than E6 dams in the uterus and spleen, but not in the blood or liver. While parasites were found in placentas, no parasites were present in fetuses. Maternal infection at E6 caused greater maternal morbidity, with greater rates of fetal reabsorption and stillbirths than at E10. Infection at E10 caused adverse offspring outcomes, including growth restriction. To identify possible mechanisms of adverse offspring outcomes, E10 dams were euthanized during peak parasitemia (8 days postinfection [dpi]), and outcomes were compared to mock-infected dams. P. berghei caused significant systemic maternal immune activation with elevated circulating lymphocytes, eosinophils, and neutrophils and splenic cytokine concentrations. P. berghei infection at E10 increased corticosterone and decreased progesterone concentrations, which could contribute to adverse perinatal outcomes through immunomodulation. There were limited changes in the maternal fecal microbiome after P. berghei infection. Mosquito bite infection of outbred dams with P. berghei causes placental malaria and provides a novel, tractable model to investigate therapeutic treatments.},
}
@article {pmid40470429,
year = {2025},
author = {Ahmad, OM and Rukh, S and Dos Santos Pereira, S and Saran, A and Chandran, VI and Muneeb, A and Banderas Echeverry, WM and Shoyoye, M and Akintunde, DM and Hassan, D and Morani, Z and Masood, L},
title = {A Comprehensive Review of the Role of Virulence Factors in Enteropathogenic Escherichia coli-Induced Intestinal Injury.},
journal = {Cureus},
volume = {17},
number = {5},
pages = {e83475},
pmid = {40470429},
issn = {2168-8184},
abstract = {Escherichia coli (E. coli) is a rod-shaped gram-negative bacterium that includes the diarrheagenic strains, an identical group of intestinal pathogens.E. coli diarrhea is transmitted through the feco-oral route, through contaminated food and water. Enteropathogenic E. coli (EPEC) is one of the leading causes of diarrhea in the pediatric age group in developing and developed countries. Depending on the absence or presence of E. coli adherence factor plasmids, they are classified as typical or atypical isolates. The distinguishing feature of EPEC's pathology is the attaching and effacing lesions, which facilitate localized damage by tightly adhering to intestinal epithelial cells, disarranging their surfaces, and effacing microvilli. Typical EPEC possess the locus of enterocyte effacement (LEE), a pathogenicity island, encoding adherence factors, including the Type III Secretion System (T3SS), a needle-like structure injecting effector proteins into host cells. EPEC also have other effector genes like cif or nleC encoded by non-LEE pathogenicity islands, which enable destruction of tight junctions in the host cell. Another key virulence factor is bundle-forming pili (BFP), which aids in the first attachment to enterocytes. Methods like quantitative PCR exist to diagnose EPEC accurately. As of today, no licensed vaccine exists to prevent EPEC infections. Virulence factors for attachment, such as bfpA and intimin, and immunogenic carriers can be potential candidates for vaccine development. Moreover, studies are required to better understand the interaction of EPECwith the intestinal microbiome and immune evasion strategies. This article is aimed at providing a comprehensive review of the epidemiology, transmission, virulence factors, challenges in studying EPEC virulence factors, pathogenesis, host-pathogen interaction, mechanism of intestinal injury, diagnosis, treatment, antibiotic resistance, and vaccination strategy for EPEC, and future research implications. We conducted a comprehensive literature search using credible sources such as PubMed, Google Scholar, and Scopus. We refined our keywords, applied database filters, and assessed citations in the included studies. No meta-analysis, statistical aggregation, or formal evaluation of risk bias was carried out as this review consolidates the literature narratively. High-quality English articles published in reputable peer-reviewed journals from 2010 to 2025 were analyzed, and their findings have been summarized in this comprehensive review.},
}
@article {pmid40470262,
year = {2025},
author = {Fu, F and Yu, Y and Wang, B and Zhao, X and Wang, N and Yin, J and Wu, K and Zhou, Q},
title = {Prostate and urinary microbiomes in prostate cancer development: focus on Cutibacterium acnes.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1562729},
pmid = {40470262},
issn = {2235-2988},
mesh = {Humans ; Male ; *Prostatic Neoplasms/microbiology/pathology ; *Microbiota ; *Prostate/microbiology/pathology ; *Propionibacteriaceae/isolation &amp; purification ; *Urine/microbiology ; },
abstract = {Prostate cancer (PCa) is one of the most prevalent malignancies among men, with its incidence steadily increasing worldwide. Recent advances in microbiome research have opened new avenues for understanding and treating PCa; however, studies focusing specifically on the prostate tissue microbiome remain limited. Evidence suggests that the microbial communities within PCa tissues exhibit significant diversity and regional variability, with certain bacteria potentially contributing to PCa initiation and progression through chronic inflammation. The prostate microbiome comprises not only bacteria but also viruses, fungi, and parasites, and its diversity is influenced by a complex interplay of genetic, environmental, and lifestyle factors. Methodological limitations and sample contamination further complicate the interpretation of microbiome data. The urinary microbiome is similarly diverse and shaped by multiple overlapping influences. Although urine, prostatic fluid, and prostate tissue are anatomically and functionally connected, whether urine and prostatic fluid can accurately reflect the prostate tissue microbiome remains to be conclusively determined. Among the microorganisms detected, Cutibacterium acnes is frequently identified in prostate tissue, urine, and prostatic fluid from PCa patients. This bacterium is known to elicit inflammatory responses through various pathways, potentially impacting tumorigenesis and cancer progression. Nevertheless, findings across studies remain inconsistent. Further research is necessary to elucidate the underlying mechanisms by which the microbiome influences PCa. Such efforts may offer novel insights and strategies for the diagnosis, treatment, and prevention of this disease.},
}
@article {pmid40470258,
year = {2025},
author = {Demirci, M and Gadhave, K},
title = {Editorial: Human microbiome and COVID-19.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1613825},
pmid = {40470258},
issn = {2235-2988},
}
@article {pmid40470050,
year = {2025},
author = {Issilbayeva, A and Sergazy, S and Zhashkeyev, A and Gulyayev, A and Kozhakhmetov, S and Shulgau, Z and Nurgaziyev, M and Nurgaziyeva, A and Zhetkenev, S and Mukhanbetzhanov, N and Jarmukhanov, Z and Mukhanbetzhanova, Z and Vinogradova, E and Zhumadilov, Z and Kushugulova, A and Aljofan, M},
title = {Polyphenol-mediated microbiome modulation in STEMI patients: a pilot study.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1522373},
pmid = {40470050},
issn = {2296-858X},
abstract = {INTRODUCTION: This study investigates the effects of polyphenol supplementation on gut microbiome composition and cardiovascular health in patients with ST-segment elevation myocardial infarction (STEMI).<br><br>METHODS: Double-blind randomized control trial where participants received either polyphenol supplementation or placebo for 3 months, after which composition of the gut microbiome; clinical and laboratory parameters, including TMAO levels and oxidative stress levels, were assessed.<br><br>RESULTS: The stable TMAO levels (from 0.5 [0.2-0.9] to 0.4 [0.3-0.9] &#x3bc;mol, p > 0.05) were observed in the polyphenol group, compared to the increase observed in the placebo group (from 0.5 [0.3-0.6] to 0.7 [0.5-1.4] &#x3bc;mol, p < 0.001). Polyphenol supplementation significantly decreased the Firmicutes/Bacteroidetes ratio (p = 0.04) and increased beneficial bacteria such as Roseburia (p = 0.01), Agathobaculum sp. (p = 0.004), Alistipes finegoldii (p = 0.04) and Sellimonas (p = 0.002). Predicted metabolic pathways analysis supports potential mechanisms linking polyphenol intake to microbiome modulation and TMAO regulation.<br><br>CONCLUSION: Our findings demonstrate that polyphenol supplementation maintains stable TMAO levels by restructuring gut microbiome composition in STEMI patients, evidenced by a more focused microbiome with a significant increase in beneficial butyrate-producing bacteria (Roseburia, Agathobaculum sp., Alistipes finegoldii, and Sellimonas) and a decreased Firmicutes/Bacteroidetes ratio, suggesting microbiome-mediated cardioprotective effects. While promising,l our preliminary findings require further studies with larger cohorts and more advanced sequencing methods to establish their significance for cardiovascular health.<br><br>CLINICAL TRIAL REGISTRATION: ClinicalTrial.gov, identfier: NCT06573892.},
}
@article {pmid40469771,
year = {2025},
author = {Muthumula, CMR and Yanamadala, Y and Gokulan, K and Karn, K and Cunny, H and Sutherland, V and Santos, JH and Khare, S},
title = {Effect of in utero and lactational exposure to antiretroviral therapy on the gut microbial composition and metabolic function in aged rat offspring.},
journal = {Experimental biology and medicine (Maywood, N.J.)},
volume = {250},
number = {},
pages = {10468},
pmid = {40469771},
issn = {1535-3699},
mesh = {Animals ; Female ; *Gastrointestinal Microbiome/drug effects ; Pregnancy ; Male ; *Prenatal Exposure Delayed Effects/microbiology ; *Lactation/drug effects ; Rats ; Fatty Acids, Volatile/metabolism ; *Anti-Retroviral Agents/adverse effects/pharmacology ; Feces/microbiology ; },
abstract = {Despite the highly effective impact of antiretroviral therapy (ART) in reducing mother-to-child transmission of human immunodeficiency virus (HIV), there are concerns of long-term impacts of ART on the health of the offspring. The implications of perinatal exposure to antiviral drugs on the gut bacterial population and metabolic function in the offspring is unclear but may influence health outcomes given the various reported effects of the microbiome in human health. This study aims to gain insight into the potential effect of in utero and lactational exposure to ART on gut microbiota populations and short-chain fatty acids (SCFAs) production in aged rat offspring. Pregnant rats were administered a combination of antiretroviral drugs (abacavir/dolutegravir/lamivudine) at two different dose levels during gestation and throughout lactation, and the fecal bacterial abundance and SCFA levels of the offspring were analyzed when they reached 12 months of age. Our results showed dose-dependent and sex-based differences in fecal microbial abundance at various taxonomic levels. Specifically, we found a decline in Firmicutes in males, and an increase in Actinobacteria among males and females. Furthermore, a sex-specific distribution reorganization of Lactobacillus, Bifidobacterium, and Akkermansia was identified. No significant difference in the concentration of prominent SCFAs and IgA levels were identified. These findings provide preliminary information indicating the need to evaluate perinatal effects of ART more comprehensively on the gut bacterial and metabolic function in future studies, and their potential role in offspring health outcomes.},
}
@article {pmid40469741,
year = {2025},
author = {Qi, JQ and Yuan, HY and Sun, SC and Zama, EF and Tao, BX and Liu, J and Zhang, BH},
title = {Biochar amendment alters rare microbial taxa and enhances wheat growth in alkaline farmland: insights into soil microbiome dynamics.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1563712},
pmid = {40469741},
issn = {1664-302X},
abstract = {INTRODUCTION: Biochar is recognized as a promising soil amendment for maintaining soil fertility and improving soil conditions. Alkaline farmland is widely distributed globally. Soil microbial taxa, including rare, intermediate, and abundant bacteria, fungi, protists, and phoD-harboring microbes, play essential roles in carbon, nitrogen, and phosphorus cycling. However, the impacts of biochar on the community composition of these taxa in alkaline farmland are not well understood. Gaining insights into how the soil microbiome responds to biochar application and its association with crop biomass is crucial for sustainable agriculture. In particular, the responses of rare microbial communities, such as rare protists and phoD-harboring microbial taxa, to biochar and their relationship with crop biomass remain largely unexplored.<br><br>METHODS: In this study, topsoil (0-10 cm) samples were collected from a three-year field experiment in a wheat (Triticum aestivum cv. Jimai 22)-maize (Zea mays cv. Jiyuan 169) rotational cropping system. The experiment included treatments with and without biochar application (CK). Gene abundance of bacterial 16S rRNA and phoD, a gene encoding an alkaline phosphatase involved in phosphorus cycling, was quantified using quantitative polymerase chain reaction (qPCR). The compositions and diversities of bacterial, fungal, protistan, and phoD-harboring microbial communities were analyzed by Illumina MiSeq sequencing.<br><br>RESULTS: Biochar application significantly reduced soil total phosphorus (TP) and ammonium nitrogen (NH4 [+]-N) contents. It increased soil N:P ratios by 19.63%, 2.80%, 23.36%, and 27.10% in B0.5, B1.0, B1.5, and B2.0 treatments, respectively. Soil dissolved organic carbon (DOC) positively correlated with bacterial 16S rRNA gene abundance, while total nitrogen (TN) linked to the ratio of phoD to bacterial 16S rRNA gene abundance and rare protistan taxa. In terms of crop yield, the B1.5 treatment (3.42 t ha[-1]) increased wheat yield by 35% compared to the CK treatment. Mantel test and random forest analyses indicated that rare phoD-harboring, protistan, and fungal communities significantly contributed to wheat growth.<br><br>DISCUSSION: This study offers valuable insights into the effects of biochar on soil microbiomes, especially the responses of abundant, intermediate, and rare taxa. The changes in soil nutrient contents and the correlations between soil properties and microbial communities suggest that biochar can modify the soil environment and microbial structure. The significant contribution of rare microbial communities to wheat growth emphasizes their importance in maintaining agricultural ecosystem health and ensuring sustainable ecosystem services. These findings can guide the rational application of biochar in alkaline farmland to promote sustainable agriculture.},
}
@article {pmid40469735,
year = {2025},
author = {Heisel, T and Gonia, S and Dillon, A and Hoops, SL and Al-Ghalith, GA and Gohl, D and Mukhopadhyay, S and Puopolo, K and Kennedy, P and Sadowsky, MJ and Knights, D and Johnson, AJ and Gerber, JS and Gale, CA},
title = {Gut mycobiome maturation and its determinants during early childhood: a comparison of ITS2 amplicon and shotgun metagenomic sequencing approaches.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1539750},
pmid = {40469735},
issn = {1664-302X},
abstract = {INTRODUCTION: Microbial colonization of the gut in early life is important for the development of metabolism, immunity, and the brain. Fungi and bacteria both colonize the human infant gut. The relatively smaller contribution of fungi to the gut microbiome, as compared to bacteria, has posed technical challenges for the precise characterization of fungal communities (mycobiomes) and limited the ability to longitudinally examine mycobiome development.<br><br>BACKGROUND: The aims of this study were to (1) characterize mycobiome maturation and identify clinical determinants of mycobiome compositional variation during the first 2&#x202f;years of life and (2) compare two sequencing approaches (ITS2 amplicon and whole genome metagenomics) for characterizing mycobiome maturational features. Longitudinal fecal samples and associated clinical metadata were obtained from subjects enrolled as part of the MAGIC (Microbiome, Antibiotics and Growth Infant Cohort) study.<br><br>RESULTS: Overall, fungal richness increased and mycobiome composition changed in a similar ordered pattern during the first 2&#x202f;years of life utilizing either amplicon or metagenomic sequencing approaches. Less resolution of taxa to species and genera levels was observed for the metagenomic dataset. The predominant taxa identified by both sequencing approaches, Candida albicans, Saccharomyces/S. cerevisiae, and Malassezia restricta, each exhibited similar dynamics in abundances and prevalences over the first 2&#x202f;years of life, irrespective of sequencing approach. Antibiotic exposure and breastfeeding status contributed to time-specific mycobiome compositional variation, results that were consistent for both types of sequence datasets. Candida albicans exhibited altered abundance dynamics in association with perinatal antibiotic exposure and birth mode for both sequencing approaches. Post hoc analyses suggested that the birth mode association could be driven by exposure to perinatal antibiotics in children delivered by cesarean section rather than by birth mode itself.<br><br>DISCUSSION: In summary, amplicon and metagenomic sequencing approaches provide generally similar results with respect to mycobiome maturational dynamics and the contribution of clinical variables to variation. Differences in taxa identification by the two approaches likely due to sequence database differences, primer/genome sequence variation, and/or sequencing depth should be taken into consideration.},
}
@article {pmid40469729,
year = {2025},
author = {Sakha, M and Gweyi-Onyango, JP and Masso, C and Baijukya, FP},
title = {Diversity, characteristics, and abundance of native arbuscular mycorrhizal fungi in the semi-arid lands of Eastern Kenya.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1582476},
pmid = {40469729},
issn = {1664-302X},
abstract = {Elucidating the diversity of native arbuscular mycorrhizal (AM) fungi is essential for the sustainable management of semi-arid land ecosystems. This is because they significantly improve plant nutrient uptake and decrease the stress caused by biotic and abiotic factors. In this study, we examined the AM fungal communities and the key drivers influencing their diversity and occurrence in the smallholder farming systems of Eastern Kenya. Soils samples were collected from 34 diverse agricultural fields and AM fungal spores were extracted using wet-sieving and decantation techniques. The spores were quantified, and AM fungal communities were identified based on their morphological characteristics. Statistical data analyses, including relative abundance, the Shannon-Wiener index, analysis of variance (ANOVA), and principal component analysis (PCA), were performed using R software 4.4.0. The results revealed that two AM fungal families dominated the agricultural fields, namely Gigasporaceae (61.0%) and Acaulosporaceae (39.0%). These fungal families comprised a total of five genera, with the following relative abundances: Acaulospora (39.0%), Gigaspora (35.05%), Scutellospora (23.92%), Dentiscutata (1.32%), and Rococetra (0.72%). The AM fungal morpho-species were ranked from 1 to 26 across the five genera. Acaulospora denticulata ranked the highest, with a proportion of 25.19%. The Shannon-Wiener diversity index revealed a higher diversity of AM fungi in agricultural fields with greater spore richness. The PCA showed that the composition of AM fungal communities was strongly related to soil physiochemical characteristics. Dryland farming systems also played a role in AM fungal composition. Overall, the distribution of AM fungal communities across the agricultural fields was lower, implying the need to adopt sustainable dryland farming systems to enhance native AM fungal communities and support the development of context-specific biofertilizers.},
}
@article {pmid40469726,
year = {2025},
author = {Wang, N and Li, X and Weng, H and Zhang, Y and Li, Q and Luo, X and Chen, Y and Dong, Y},
title = {A bibliometric study of global trends in diabetic nephropathy and intestinal flora research.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1577703},
pmid = {40469726},
issn = {1664-302X},
abstract = {BACKGROUND: Diabetic nephropathy is chronic kidney damage caused by diabetes and is one of the most common microvascular complications of diabetes. In diabetic patients, prolonged hyperglycemia leads to progressive damage to kidney structure and function. With the increasing incidence of diabetes, the number of patients with Diabetic Nephropathy is also increasing year by year. At present, there is no drug to cure Diabetic Nephropathy. More and more evidence shows that the development of Diabetic Nephropathy is inseparable from the intestinal axis, and the disorder of intestinal flora is related to the progress of diabetes. Maybe we can explore the pathogenesis of Diabetic Nephropathy from the intestinal flora and find new methods to treat Diabetic Nephropathy.<br><br>METHODS: This article uses CiteSpace VOSviewer and Bibliometrix statistical software explore research hotspots and trends of intestinal flora and Diabetic Nephropathy. The Web of Science Core Collection (WoSCC) was searched for literature from database establishment to December 4, 2024, and ultimately 238 articles were included for quantitative analysis.<br><br>RESULTS: The number of publications has been increasing year by year, reaching its peak in 2024. The high-yield institution is Beijing University of Chinese Medicine, and the most productive country is China. Zhang Yi ranks first in the number of publications by the author. After removing the theme word, inflammation appears the most frequently, followed by oxidative stress. The outbreak hotspots are mainly concentrated in uremic toxin, short chain fatty acid, soy milk, aryl hydrocarbon receptor.<br><br>CONCLUSION: The exploration of the mechanism of action and therapeutic or adjuvant therapeutic targets of the gut microbiome and its metabolites in DN patients may become a research hotspot in the future direction of DN and gut microbiome. Inflammation, oxidative stress, and the production of urinary toxins in DN patients are the directions for researchers to explore the mechanisms related to DN patients and gut microbiome. Aryl hydrocarbon receptor (AhR), Short-chain fatty acids (SCFAs), Traditional Chinese medicine and soy milk provide researchers with treatment ideas for diabetic nephropathy. Exploring the specific mechanisms and therapeutic effects of DN and gut microbiome requires cohort studies and clinical trials for validation.},
}
@article {pmid40469724,
year = {2025},
author = {Zhu, G and Song, H and Duan, M and Wang, J and Luo, J and Yang, S and Wu, F and Jiang, J and Chen, J and Tang, W},
title = {Dietary preferences affect the gut microbiota of three snake species (Squamata: Colubridae).},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1559646},
pmid = {40469724},
issn = {1664-302X},
abstract = {INTRODUCTION: The gut microbiota is an emerging frontier in animal research, and researchers are increasingly transparent about its importance to animal health. Reptiles, particularly snakes, have not received the same attention given to other vertebrates, and the composition of their wild gut microbiome remains understudied.<br><br>METHODS: In this study, the HiSeq high-throughput sequencing platform was used to sequence and analyze the 16S rRNA V4 region of the gut microbiota of three species (Gonyosoma coeruleum, Rhabdophis pentasupralabralis, Rhabdophis tigrinus).<br><br>RESULTS: This study investigated alpha diversity analysis and showed that the gut microbiota richness of RP was significantly higher than that of the other two snakes. The dominant genus of Gonyosoma coeruleum (GC) and Rhabdophis tigrinus (RT) is Cetobacterium, while Enterobacteriaceae; g_uncultured is the dominant genus of Rhabdophis pentasupralabralis (RP). Tree clustering based on Bray-Curtis distances and Jaccard similarity coefficients indicated that the gut microbiota composition of RP and RT was more similar. The unique diet of RP promotes a diverse, competitive gut microbiota, while GC and RT displayed more stable networks linked to shared dietary habits. The functional heat map showed that the predicted functions of the gut microbes of the three snake species were different. These findings suggest that dietary preferences exert a stronger influence on gut microbial composition and function than host genetic background, and distantly related species with similar diets exhibit convergent gut microbiota characteristics.},
}
@article {pmid40469670,
year = {2025},
author = {Lopez Leyva, L and Gonzalez, E and Maurice, CF and Koski, KG},
title = {Milk mineral composition is strongly associated with the human milk microbiome.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1550292},
pmid = {40469670},
issn = {2296-861X},
abstract = {INTRODUCTION: Associations between maternal mineral intake, human milk mineral concentrations, and their interactions with the milk microbiota remain understudied, especially in low- and middle-income countries. To understand potential interactions and gain insight into milk composition dynamics, we explored associations of milk mineral concentrations with maternal mineral intakes and the human milk microbiome in an indigenous Guatemalan community.<br><br>METHODS: In this cross-sectional study, milk samples were collected from 77 Mam-Mayan mothers and classified into early and established lactation. Concentrations of 9 milk minerals were analyzed, and maternal dietary intake was obtained from two 24-h recalls. Microbiome diversity was assessed by 16S rRNA gene sequencing (V5-V6 region). DESeq2 was used for differential abundance analysis. PCA and Spearman's rank correlation explored relationships among milk minerals, maternal mineral intake, and differentially abundant microbial taxa; results with FDR-adjusted p-values < 0.1 were retained.<br><br>RESULTS: Our multifactorial analysis revealed strong associations between milk minerals and the milk microbiome and weak associations with maternal intake. Several maternal intakes (Ca, Se, K, Fe, Mn) and milk mineral concentrations (Ca, Se, K, Mg, Na) were below reference values. In early lactation, milk Fe, Mn, Se, and Cu correlated with differentially abundant taxa, while in established lactation, Fe, Mn, Se, Ca, and Na were correlated. Fe and Mn accounted for 64% of bacterial associations in early lactation and 75% in established lactation. These minerals were correlated with Pseudomonadota (early), Actinomycetota (established), and Bacillota (both), but all species were unique to each stage.<br><br>CONCLUSION: Our findings reveal a complex interplay between milk minerals and the microbiome. Iron, manganese, and selenium were consistently associated with milk bacteria across lactation stages. These correlations may reflect microbial responses to mineral availability. Further longitudinal studies with larger samples are needed to clarify how this interaction influences mineral bioavailability and infant growth.},
}
@article {pmid40469523,
year = {2025},
author = {Wang, YC and Wang, S and Lv, YH and Wang, C},
title = {QSCNAS: A platform for quorum sensing and quenching bacteria analysis in global wastewater treatment plants.},
journal = {iMeta},
volume = {4},
number = {3},
pages = {e70026},
pmid = {40469523},
issn = {2770-596X},
abstract = {This study identifies the potential quorum sensing (QS) bacteria in wastewater treatment plants (WWTPs) and constructs a QS communication network through the establishment of a local QS bacterial database with six languages and the analysis of over 1000 activated sludge microbiome samples collected from 269 WWTPs. The results not only advance the understanding of bacterial communication in WWTPs but also provide a valuable tool for developing regulatory strategies to optimize the functionality of these vital ecosystems.},
}
@article {pmid40469522,
year = {2025},
author = {Wen, T and Liu, YX and Liu, L and Niu, G and Ding, Z and Teng, X and Ma, J and Liu, Y and Yang, S and Xie, P and Zhang, T and Wang, L and Lu, Z and Shen, Q and Yuan, J},
title = {ggClusterNet 2: An R package for microbial co-occurrence networks and associated indicator correlation patterns.},
journal = {iMeta},
volume = {4},
number = {3},
pages = {e70041},
pmid = {40469522},
issn = {2770-596X},
abstract = {Since its initial release in 2022, ggClusterNet has become a vital tool for microbiome research, enabling microbial co-occurrence network analysis and visualization in over 300 studies. To address emerging challenges, including multi-factor experimental designs, multi-treatment conditions, and multi-omics data, we present a comprehensive upgrade with four key components: (1) A microbial co-occurrence network pipeline integrating network computation (Pearson/Spearman/SparCC correlations), visualization, topological characterization of network and node properties, multi-network comparison with statistical testing, network stability (robustness) analysis, and module identification and analysis; (2) Network mining functions for multi-factor, multi-treatment, and spatiotemporal-scale analysis, including Facet.Network() and module.compare.m.ts(); (3) Transkingdom network construction using microbiota, multi-omics, and other relevant data, with diverse visualization layouts such as MatCorPlot2() and cor_link3(); and (4) Transkingdom and multi-omics network analysis, including corBionetwork.st() and visualization algorithms tailored for complex network exploration, including model_maptree2(), model_Gephi.3(), and cir.squ(). The updates in ggClusterNet 2 enable researchers to explore complex network interactions, offering a robust, efficient, user-friendly, reproducible, and visually versatile tool for microbial co-occurrence networks and indicator correlation patterns. The ggClusterNet 2R package is open-source and available on GitHub (https://github.com/taowenmicro/ggClusterNet).},
}
@article {pmid40469520,
year = {2025},
author = {Yu, L and Chen, Z and Yin, S and Guo, Q and Chen, Y and Li, J and Wang, Y and Liu, X and Xu, Z and Zhang, Y and Zhang, Y and Zheng, Z and Chen, K and Ding, Y and Fan, H and Liu, Z and Ding, Y},
title = {Gut-derived Lactobacillus from exceptional responders mitigates chemoradiotherapy-induced intestinal injury through methionine-driven epigenetic modulation.},
journal = {iMeta},
volume = {4},
number = {3},
pages = {e70043},
pmid = {40469520},
issn = {2770-596X},
abstract = {Acute chemoradiotherapy-induced intestinal injury (ACRIII) is a common and debilitating complication in patients with colorectal cancer, significantly impairing both quality of life and treatment outcomes. This study aimed to investigate the role of the gut microbiome in mitigating ACRIII. Through bioinformatics analysis of clinical fecal samples and fecal microbiota transplantation (FMT) experiments in mice, we identified a strong association between a high abundance of Lactobacillus species and the absence of ACRIII. From the fecal samples of rectal cancer patients who achieved complete remission without experiencing ACRIII during chemoradiotherapy, 10 novel Lactobacillus strains were isolated and characterized. Among these, Lacticaseibacillus rhamnosus DY801 exhibited a robust capacity to synthesize methionine through metB. This microbial methionine production modulated methionine metabolism in host gut lymphoid tissue inducer (Lti) cells, without diminishing the therapeutic efficacy of chemoradiotherapy. Supplementation with methionine increased intracellular levels of S-adenosylmethionine and enhanced histone H3 lysine 4 trimethylation (H3K4me3) in Lti cells. These epigenetic modifications led to the suppression of pro-inflammatory cytokines interleukin-17A (IL-17A) and interleukin-22 (IL-22), ultimately reducing ACRIII severity. Our findings suggest that specific Lactobacillus strains derived from patients with exceptional treatment responses may offer a novel therapeutic avenue for preventing or alleviating ACRIII. This microbiome-based approach holds significant potential for improving patient outcomes and enhancing the tolerability of chemoradiotherapy in colorectal cancer.},
}
@article {pmid40469508,
year = {2025},
author = {Zhao, S and Zhong, H and He, Y and Li, X and Zhu, L and Xiong, Z and Zhang, X and Zheng, N and Morgavi, DP and Wang, J},
title = {Leveraging core enzyme structures for microbiota targeted functional regulation: Urease as an example.},
journal = {iMeta},
volume = {4},
number = {3},
pages = {e70032},
pmid = {40469508},
issn = {2770-596X},
abstract = {Microbial communities play critical roles in various ecosystems. Despite extensive research on the taxonomic and functional diversity of microbial communities, effective approaches to regulate targeted microbial functions remain limited. Here, we present an innovative methodology that integrates core enzyme identification, protein structural characterization, regulator virtual screening, and functional validation to achieve precise microbiome functional regulation. As a proof of concept, we focused on the regulation of urea decomposition by the rumen microbiota in ruminants. Through metagenomic analysis, we identified the core urease gene and its corresponding microbial genome (MAG257) affiliated with the unclassified Succinivibrionaceae, and reconstructed its complete gene cluster. Structural analysis of the urease catalytic subunit (UreC) via cryo-electron microscopy (cryo-EM) revealed detailed features of its active site, guiding molecular docking studies that identified epiberberine, a natural compound with potent urease inhibitory activity. Validation in a rumen simulation system demonstrated that epiberberine significantly reduced urea decomposition and enhanced nitrogen utilization. This study establishes a robust framework that combines structural biology and computational screening to achieve targeted microbiome functional regulation, offering a promising tool for microbiome engineering and broader applications in animal productivity, human health, environmental improvement, and biotechnology.},
}
@article {pmid40469507,
year = {2025},
author = {Shen, Y and Qu, W and Song, M and Zhang, T and Liu, C and Shi, X and Xu, X and Jiang, J and Ding, L and Mo, F and Mao, Z and Huang, M and Xu, Z and Chen, J and Shen, E and Ruan, J and Liu, J and Timko, MP and Chen, Y and Fan, L and Zheng, S and Wang, Y},
title = {Single-microbe RNA sequencing uncovers unexplored specialized metabolic functions of keystone species in the human gut.},
journal = {iMeta},
volume = {4},
number = {3},
pages = {e70035},
pmid = {40469507},
issn = {2770-596X},
abstract = {The human body is inhabited by trillions of microorganisms that play a crucial role in health and diseases. Our understanding of the species and functional composition of the human gut microbiome is rapidly expanding, but it is still mainly based on taxonomic profiles or gene abundance measurements. As such, little is known about the species-function heterogeneity and dynamic activities in human microecosystem niches. By applying a novel gut-specific single-microbe ribonucleic acid (RNA) sequencing and analytical framework on three healthy donors with distinct enterotypes, we created a comprehensive transcriptional landscape of the human gut microbiome and dissected functional specialization in 38,922 single microbes across 198 species. We investigated the functional redundancy and complementarity involved in short-chain fatty acids related central carbon metabolism and studied the heterogeneity and covariation of single-microbe metabolic capacity. Comparing the human gut microbiome at different times throughout the day, we were able to map diurnal dynamic activities of the gut microbiome and discovered its association with sub-population functional heterogeneous. Remarkably, using single-microbe RNA sequencing, we systematically dissected the metabolic function heterogeneity of Megamonas funiformis, a keystone species in Asian populations. Together with in vitro and in vivo experimental validations, we proved M. funiformis can effectively improve mineral absorption through exogenous phytic acid degradation, which could potentially serve as a probiotic that reduces malnutrition caused by deficiency of mineral elements. Our results indicated that species-function heterogeneity widely exists and plays important roles in the human gut microbiome, and through single-microbe RNA sequencing, we have been able to capture the transcriptional activity variances and identify keystone species with specialized metabolic functions of possible biological and clinical importance.},
}
@article {pmid40469504,
year = {2025},
author = {Van Den Bossche, T and Armengaud, J and Benndorf, D and Blakeley-Ruiz, JA and Brauer, M and Cheng, K and Creskey, M and Figeys, D and Grenga, L and Griffin, TJ and Henry, C and Hettich, RL and Holstein, T and Jagtap, PD and Jehmlich, N and Kim, J and Kleiner, M and Kunath, BJ and Malliet, X and Martens, L and Mehta, S and Mesuere, B and Ning, Z and Tanca, A and Uzzau, S and Verschaffelt, P and Wang, J and Wilmes, P and Zhang, X and Zhang, X and Li, L and , },
title = {The microbiologist's guide to metaproteomics.},
journal = {iMeta},
volume = {4},
number = {3},
pages = {e70031},
pmid = {40469504},
issn = {2770-596X},
abstract = {Metaproteomics is an emerging approach for studying microbiomes, offering the ability to characterize proteins that underpin microbial functionality within diverse ecosystems. As the primary catalytic and structural components of microbiomes, proteins provide unique insights into the active processes and ecological roles of microbial communities. By integrating metaproteomics with other omics disciplines, researchers can gain a comprehensive understanding of microbial ecology, interactions, and functional dynamics. This review, developed by the Metaproteomics Initiative (www.metaproteomics.org), serves as a practical guide for both microbiome and proteomics researchers, presenting key principles, state-of-the-art methodologies, and analytical workflows essential to metaproteomics. Topics covered include experimental design, sample preparation, mass spectrometry techniques, data analysis strategies, and statistical approaches.},
}
@article {pmid40469040,
year = {2025},
author = {Vogel, SC and Murgueitio, N and Huth, N and Sem, K and Knickmeyer, RC and Short, SJ and Mills-Koonce, R and Propper, C and Wagner, NJ},
title = {Longitudinal associations between the infant gut microbiome and negative affect in toddlerhood.},
journal = {Development and psychopathology},
volume = {},
number = {},
pages = {1-13},
doi = {10.1017/S0954579425100229},
pmid = {40469040},
issn = {1469-2198},
abstract = {The role of the gut microbiome in infant development has gained increasing interest in recent years. Most research on this topic has focused on the first three to four years of life because this is a critical period for developing gut-brain connections. Prior studies have identified associations between the composition and diversity of the gut microbiome in infancy and markers of temperament, including negative affect. However, the specific microbes affected, and the directionality of these associations have differed between studies, likely due to differences in the developmental period of focus and assessment approaches. In the current preregistered study, we examined connections between the gut microbiome, assessed at two time points in infancy (2 weeks and 18 months), and negative affect measured at 30 months of age in a longitudinal study of infants and their caregivers. We found that infants with higher gut microbiome diversity at 2 weeks showed more observed negative affect during a study visit at 30 months. We also found evidence for associations between specific genera of bacteria in infancy and negative affect. These results suggest associations between specific features of the gut microbiome and child behavior may differ based on timing of gut microbiome measurement.},
}
@article {pmid40468884,
year = {2025},
author = {Lee, Y and Ko, YM and Kwak, YS},
title = {Genetic and Nutritional Dynamics of SynCom in Suppressing Apple Fire Blight.},
journal = {The plant pathology journal},
volume = {41},
number = {3},
pages = {380-391},
doi = {10.5423/PPJ.OA.03.2025.0040},
pmid = {40468884},
issn = {1598-2254},
support = {RS-2020-RD009282//Rural Development Administration/ ; RS-2025-00516084//National Research Foundation of Korea/ ; },
abstract = {Fire blight disease, caused by Erwinia amylovora, occurs in apples and other Rosaceae plants and is known to cause significant economic damage. The pathogen usually infects flowers during the reproductive growth period of plants, colonizes, and penetrates by producing exopolysaccharides in the stigma. A synthetic microbial community (SynCom) is an artificial community of microorganisms designed to enhance host viability. To construct SynCom, we attempted to identify and utilize the microbial characteristics of apple trees that are not infected with the pathogen compared to those that are infected. In our previous study, we composed SynCom with strains expected to reduce the density of fire blight pathogens through microbiome analysis, strain isolation, and continuous replacement culture. We are able to observe the disease control effect of the constructed SynCom. However, no study has been conducted to clearly determine the genetic mechanism underlying this effect of the SynCom. Here, we present that potential secondary metabolite candidates and nutritional competition with the pathogen were confirmed as biochemical mechanisms through whole genome analysis of SynCom strains. Additionally, by co-cultivating SynCom with the pathogen in limited nutrient conditions, such as apple blossom extracts, which are susceptible to the pathogen, we confirmed the potential of SynCom treatment to reduce the pathogen densities. This study demonstrates that genetic selection using metagenomics can effectively identify microorganisms with potential functional capabilities.},
}
@article {pmid40468702,
year = {2025},
author = {Yoon, SJ and Han, SK and Kim, TS and Suk, KT and Choi, DH and Kim, YD and Kim, MY and Cheon, GJ and Baik, SK and Kim, DJ},
title = {The crosstalk between gut microbiota and microbiota-derived metabolites in hepatocellular carcinoma.},
journal = {Critical reviews in microbiology},
volume = {},
number = {},
pages = {1-15},
doi = {10.1080/1040841X.2025.2501590},
pmid = {40468702},
issn = {1549-7828},
abstract = {Hepatocellular carcinoma (HCC), one of the leading causes of death worldwide, is a consequence of persistent liver injury, inflammation, and fibrosis. Recent research has demonstrated that the gut-liver axis plays a crucial role in the pathological mechanisms of HCC development. Given the overall paucity of data available, we examined both clinical and animal studies investigating the influence of gut microbiota and their metabolites on the development of HCC in light of current scientific understanding. In this review, we concentrate on the mechanism by which intestinal dysbiosis facilitates the hepatocarcinogenesis pathway and offer a detailed account of the specific pathways involved in the promotion of HCC by the microbiome and its metabolites. Based on this, researchers might extrapolate which strains would be beneficial or harmful to restore gut homeostasis by targeting gut-liver axis in the pathogenesis of HCC.},
}
@article {pmid40468659,
year = {2025},
author = {Hossain, MS and Seo, H and Lee, KA and Ul-Haq, A and Kim, S and Jo, S and Rahim, MA and Tajdozian, H and Ghorbanian, F and Yoon, Y and Barman, I and Shuvo, MSH and Kim, HS and Song, HY},
title = {Microbiome therapeutic PMC72 through reverse translational research in gout.},
journal = {Journal of microbiology (Seoul, Korea)},
volume = {63},
number = {5},
pages = {e2501002},
doi = {10.71150/jm.2501002},
pmid = {40468659},
issn = {1976-3794},
support = {RS-202300219563//National Research Foundation of Korea/ ; //Ministry of Science and ICT/ ; 2020R1I1A-3072680//Ministry of Education/ ; //Soonchunhyang University Research Fund/ ; },
mesh = {Animals ; *Gout/therapy/microbiology/chemically induced ; Humans ; Mice ; *Gastrointestinal Microbiome/drug effects ; Hyperuricemia/chemically induced/therapy ; Uric Acid/blood/metabolism ; Disease Models, Animal ; Translational Research, Biomedical ; Dysbiosis ; Male ; Feces/microbiology ; Febuxostat/therapeutic use ; Oxonic Acid ; Oxidative Stress ; },
abstract = {Gout is an inflammatory arthritis resulting from the deposition of monosodium urate crystals. Urate-lowering therapies for gout have limitations, including side effects and limited efficacy, highlighting the need for novel therapeutic approaches to improve patient outcomes. In this context, our research team conducted a microbiome analysis of fecal samples from healthy individuals and gout patients, identifying Bifidobacterium as a key biomarker. Subsequently, we isolated and identified this strain, B. longum PMC72, and demonstrated its efficacy in a gout mouse model. In potassium oxonate (PO)-induced hyperuricemia mice, PMC72 significantly alleviated nausea, gait disturbances, ankle inflammation, and improved renal health. These effects were associated with marked reductions in oxidative stress markers, including serum uric acid, blood urea nitrogen, hepatic xanthine oxidase, and malondialdehyde (MDA) levels in serum, liver, and joint samples, as well as the downregulation of inflammation and uric acid transport-related gene expression in kidney samples. These benefits were comparable to those treated with Febuxostat, a standard urate-lowering therapy for gout. Furthermore, gut microbiome analysis revealed that PMC72 restored dysbiosis induced by hyperuricemia, contrasting with the reduced microbial diversity observed with febuxostat alone, and showed a complete recovery to eubiosis when combined with Febuxostat. These findings position PMC72 as a promising microbial therapeutic candidate for gout management, demonstrating significant development potential and serving as a benchmark for reverse translational microbiome-based therapeutic research.},
}
@article {pmid40468650,
year = {2025},
author = {Cha, RR and Sonu, I},
title = {Fecal microbiota transplantation: present and future.},
journal = {Clinical endoscopy},
volume = {58},
number = {3},
pages = {352-359},
doi = {10.5946/ce.2024.270},
pmid = {40468650},
issn = {2234-2400},
support = {//Gyeongsang National University Fund/ ; },
abstract = {Fecal microbiota transplantation (FMT) involves transplanting fecal matter from healthy donors into patients with gut dysbiosis to restore microbial balance. It has been proven to be highly effective in treating recurrent Clostridioides difficile infection (CDI), and United States Food and Drug Administration-approved microbiome-based therapies, such as REBYOTA (fecal microbiota live-jslm) and VOWST (fecal microbiota spores live-brpk), offer promising treatment options. Although FMT is widely used to treat recurrent CDI, its use in gastrointestinal and metabolic diseases remains limited. Future research directions include optimizing donor selection, understanding microbial mechanisms, and exploring the potential of FMT for treating other diseases. Ongoing research not only aims to broaden its indications but also improves its safety and efficacy. Emerging therapies such as VE303 (Vedanta) are being studied to refine treatment approaches and expand the use of microbiota-based therapies. Further studies are needed to standardize guidelines, improve patient outcomes, and better define the role of FMT in the treatment of diseases beyond recurrent CDI.},
}
@article {pmid40468453,
year = {2025},
author = {Hu, F and Gebeyew, K and Wu, Z and Chen, B and Jiao, J and Tan, Z and Tian, D and He, Z},
title = {Fat-rich diet promotes microbiome-dependent ATP synthesis in sheep model.},
journal = {Journal of animal science and biotechnology},
volume = {16},
number = {1},
pages = {81},
pmid = {40468453},
issn = {1674-9782},
support = {XDA26040304//Strategic Priority Research Program/ ; XDA26050102//Strategic Priority Research Program/ ; 32072760//National Natural Science Foundation of China/ ; 2022JJ10054//Natural Science Foundation of Hunan Province of China/ ; },
abstract = {BACKGROUND: The ketogenic diet that forces adenosine triphosphate (ATP) production by beta-oxidation of fatty acids instead of carbohydrate glycolysis, has gained consensus on host metabolism. However, the mechanisms how a ketogenic diet alters gastrointestinal microbiome and its downstream consequences on microbial nutrient availability and energy metabolism remain to be elucidated. Here, we used the sheep model fed with fat-rich diet to evaluate the symbiotic microbiome across three regions of the gastrointestinal tract (rumen, ileum, and colon) to gain a comprehensive understanding of the microbial energy metabolism and microbe-mediated ATP biosynthesis.<br><br>RESULTS: Results showed that sheep fed a fat-rich diet had a greater ADG and increased reliance on fat oxidation for fuel utilization. Metagenomics analysis showed the loss of the specialized fiber-degrading bacteria (genus_Fibrobacter) in the rumen and enrichment of genera RUG420 and Eubacterium,&#xa0;which are involved in lipid metabolism and bile acid processing, in the ileum. A significant functional shift related to energy metabolism was shared across three regions of the gastrointestinal microbiomes. These shifts were dominated by glycolysis/gluconeogenesis and TCA cycle in the rumen and by fatty acid degradation and bile acid transformation in the ileum, indicating adaptation to nutrient availability and energy acquisition. Notably, the abundance of substrate-level phosphorylation (SLP) enzymes was significantly increased in the rumen, ileum and colon, while the ATP-producing capacity through electron transport phosphorylation (ETP) by family_Bacteroidaceae in rumen and Acutalibacteraceae in ileum of sheep with fat-rich diet.<br><br>CONCLUSIONS: Altogether, the ATP-related microbiome encoding SLP and ETP in rumen, ileum, and colon contributed 36.95% to the host's weight variation. Our study is the first one demonstrating the microbial potential in the ATP synthesis under the shift in dietary energy source, providing a new perspective on the energy metabolism and precise human macronutrients nutrition.},
}
@article {pmid40468444,
year = {2025},
author = {Tang, Q and Yin, X and Wen, G and Luo, Z and Zhang, L and Tan, S},
title = {Unraveling the composition and function of pig gut microbiome from metagenomics.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {60},
pmid = {40468444},
issn = {2524-4671},
support = {No. [2023] 211//2022 Hunan Province Vocational Education "Chuyi" Action High Level Teacher Team Construction Project/ ; No. [2023] 211//2022 Hunan Province Vocational Education "Chuyi" Action High Level Teacher Team Construction Project/ ; },
abstract = {The gut microbiome plays a crucial role in intestinal maturation, metabolism, and immunoregulation, significantly influencing the host's health and growth performance. This review highlights the use of metagenomic techniques to the composition, function, and dynamic changes of the pig gut microbiota. Research has revealed that environmental and host factors, particularly diet, drive significant variations in microbial composition, which in turn shape host epigenetics through microbial components and metabolites. Furthermore, the strong correlation between the gut microbiota and host health presents opportunities for improving growth performance in the livestock industry.},
}
@article {pmid40468436,
year = {2025},
author = {Kilama, J and Islam, MS and Amat, S},
title = {Bovine ocular microbiome: the next frontier in managing Pinkeye in cattle.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {58},
pmid = {40468436},
issn = {2524-4671},
abstract = {Infectious bovine keratoconjunctivitis (IBK), or pinkeye, represents a significant economic challenge to dairy and beef cattle industries resulting in decreased productivity and increased treatment costs. The current IBK prevention and control strategies in cattle face challenges owing to the multifactorial nature of the disease, the rise of antibiotic resistance in IBK pathogens, and inconsistent efficacy of IBK vaccines. Recent efforts in metagenomic characterization of the eye microbiome in humans and animals, including cattle, have revealed that the ocular surface is colonized by relatively diverse and dynamic microbial community that is essential for maintaining ocular health and can be leveraged to enhance resistance against infectious ocular diseases. In this narrative review, we provide comprehensive insights into the ocular microbiota by summarizing the amplicon and metagenomic sequencing- and culture-based studies conducted in cattle, and by reviewing relevant findings from humans and other animal species. We also explore the potential of the ocular microbiome as a new frontier in managing IBK. Finally, we examine the gut-eye-microbiome axis and discuss its potential contribution in improving the resistance of cattle against IBK.},
}
@article {pmid40468269,
year = {2025},
author = {Li, B and Yang, Y and Xu, B and Song, P and Jiang, F and Gao, H and Cai, Z and Gu, H and Zhang, T},
title = {Comparative macrogenomics reveal plateau adaptation of gut microbiome in cervids.},
journal = {BMC biology},
volume = {23},
number = {1},
pages = {154},
pmid = {40468269},
issn = {1741-7007},
mesh = {*Gastrointestinal Microbiome/genetics ; Animals ; *Deer/microbiology/genetics ; Phylogeny ; Metagenome ; Metagenomics ; *Adaptation, Physiological/genetics ; Energy Metabolism ; Biological Evolution ; },
abstract = {BACKGROUND: Diverse gut microbiota in animals significantly influences host physiology, ecological adaptation, and evolution. However, the specific functional roles of gut microbiota in facilitating host adaptation, as well as the coevolutionary dynamics between microbiota and their hosts, remain largely understudied.<br><br>RESULTS: A total of 41,847 metagenome-assembled genomes and 3193 high-quality species-level genome bins were generated, establishing a comprehensive gut microbiome catalog for cervids in this study. Phylogenetic analysis revealed a coevolutionary relationship between cervids and their gut microbiota. Comparative metagenomic analyses further indicated that the gut microbiota of plateau cervids have undergone genome-level adaptations related to energy metabolism. At the genus level, species-level genome bins from the genera Alistipes and Faecousia in plateau cervids exhibit enhanced energy metabolism capabilities. Structural variations analysis revealed that the insertion and duplications structural variations in the gut microbiota of plateau cervids were significantly enriched in energy metabolism pathways. In contrast, the deletions and contractions in structural variations were predominantly enriched with metabolic pathways involved in the biosynthesis of diverse biochemical molecules.<br><br>CONCLUSIONS: Our study provides a comprehensive gut microbiome catalog of the cervid gut microbiota, revealing the coevolutionary relationship between cervid gut microbiota and hosts. These findings highlight the adaptive genomic evolution of the gut microbiota in contributing to the plateau adaptability of cervids and offer new insights into the mechanisms by which the gut microbiota help hosts adapt to extreme environments.},
}
@article {pmid40468214,
year = {2025},
author = {Yang, X and Chen, H and Wu, L and Guo, X and Xue, D},
title = {Diversity and correlation analysis of microbiomes and metabolites of Sphagnum palustre in various microhabitats.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {761},
pmid = {40468214},
issn = {1471-2229},
support = {2019QZKK0304//Second Tibetan Plateau Scientific Expedition/ ; QNTS202201//Youth Innovation Program of CIB/ ; 2022376//Youth Innovation Promotion Association of the Chinese Academy of Sciences/ ; 2021JDTD011//Youth Science and Technology Innovation Team Program of Sichuan Province of China/ ; },
mesh = {*Microbiota ; *Sphagnopsida/microbiology/metabolism ; Ecosystem ; Soil Microbiology ; Bacteria/genetics/metabolism ; },
abstract = {BACKGROUND: Sphagnum peat mosses are crucial contributors to global carbon sequestration and are a dominant presence in many northern peatland environments. These mosses host a wide variety of microorganisms, which reside within their tissues and on their surfaces. Despite this close association, the connection between these microorganisms and the production of metabolites across different parts of Sphagnum remains unclear.<br><br>RESULTS: This research explored the connection between microbial diversity and metabolite production in various microhabitats of Sphagnum palustre by employing metagenomic and metabolomic techniques. Our results indicate that the S. palustre microbiome composition is more strongly influenced by microhabitat than by geographic location. Microbiome diversity microbiomes related to S. palustre showed a steady decrease from soil to near soil, from X to CAP, and from belowground to aboveground habitats. In contrast, network complexity increased. Species abundance analysis indicated that Proteobacteria was the most prevalent bacterial phylum across CAP, S, Z, and X. Additionally, Ascomycota emerged as the predominant fungal phylum. There were significant differences in nitrogen fixation activity, methane oxidation activity, total nitrogen, and total carbon among different microhabitats. The FAPROTAX analysis revealed differences in the metabolic potential of the carbon (C) and nitrogen (N) cycles across the four microhabitats. LC-MS/MS technology was employed to quantitatively assess metabolites across various S. palustre microhabitats. A total of 3,822 metabolites and 353 differential metabolites were detected, predominantly including lipids, organic acids, and carboxylic acids. The majority of these differential metabolites were associated with metabolic pathways such as carotenoid biosynthesis, steroid biosynthesis, secondary bile acid biosynthesis, as well as the biosynthesis of neomycin, kanamycin, and gentamicin. Correlation analysis revealed both positive and negative relationships between microorganisms and differential metabolites. Methylocystis, which was significantly enriched in X and T, showed a strong positive correlation with differential metabolites in S vs T and Z vs X, but a negative correlation with those in X vs T (p&#x2009;<&#x2009;0.05).<br><br>CONCLUSION: In summary, our study demonstrates that Sphagnum palustre microbiomes are primarily influenced by microhabitats rather than specific environmental conditions at different sites. We identified significant variations in microbial community diversity across various S. palustre microhabitats. Correlation analysis revealed links between microorganisms and differential metabolic processes. This comprehensive investigation of aboveground and belowground microbiomes and metabolites in S. palustre provides new insights into the distribution of microbial communities and metabolites across different microhabitats.},
}
@article {pmid40468177,
year = {2025},
author = {Yang, B and Yue, C and Guo, C and Zheng, M and Yao, X and Xu, J and Huang, S and Yang, M},
title = {Disease-resistant watermelon variety against Fusarium wilt by remodeling rhizosphere soil microenvironment.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {350},
pmid = {40468177},
issn = {1471-2180},
support = {112024AS0100//Natural Science Foundation of Henan Province/ ; },
mesh = {*Rhizosphere ; *Citrullus/microbiology/genetics ; *Soil Microbiology ; *Plant Diseases/microbiology ; *Fusarium/physiology/pathogenicity ; *Disease Resistance ; Soil/chemistry ; Bacteria/classification/genetics/isolation &amp; purification ; Microbiota ; Fungi/classification/genetics/isolation &amp; purification ; Transcriptome ; },
abstract = {BACKGROUND: Rhizosphere microorganisms and their interactions play a critical role in enhancing plant disease resistance. Here, we found that the disease severity of the resistant variety LW025 showed a decreasing trend with the increase in continuous cropping cycles. However, the mechanisms underlying the reduction in disease severity during the continuous cropping of the resistant watermelon variety LW025, particularly its relationship with the rhizosphere microbiome, remain unclear.<br><br>RESULTS: In this study, the transcriptome of different watermelon varieties after continuous planting in pathogen-containing and pathogen-free soils was analyzed. The results showed that only two genes expression showed significant differences in disease-resistant variety between healthy and diseased soils. Subsequently, we analyzed the differences of rhizosphere soil microbial communities after planting different watermelon varieties for three consecutive seasons, as well as the relationship between differential microorganisms and soil physiochemical properties and soil enzyme activity. The results demonstrated continuous cropping of the disease-resistant variety LW025 formed a rhizosphere microbiome different from the initial soil and susceptible variety. Specifically, fungal changes were primarily observed in Ascomycota and Chytridiomycota, while bacterial changes were mainly observed in Cyanobacteria and Gemmatimonadetes. The bacterial functions enriched in the rhizosphere of the resistant variety LW025 after continuous cropping were primarily associated with soil nitrogen cycling. Furthermore, the plant disease index showed a significant positive correlation with the available phosphorus and potassium content in the soil, while exhibiting a significant negative correlation with soil pH and catalase activity.<br><br>CONCLUSIONS: Overall, the reduction in disease severity associated with continuous cropping of the disease-resistant variety LW025 was more closely related to changes in the rhizosphere microecological environment. This study explained the mechanism of the resistant variety LW025 against Fusarium infection, and provided new prospects for the development of technologies based on rhizosphere microecological environment modification to improve the resistance of watermelon to Fusarium wilt.},
}
@article {pmid40468006,
year = {2025},
author = {Sanz, Y and Cryan, JF and Deschasaux-Tanguy, M and Elinav, E and Lambrecht, R and Veiga, P},
title = {The gut microbiome connects nutrition and human health.},
journal = {Nature reviews. Gastroenterology &amp; hepatology},
volume = {},
number = {},
pages = {},
pmid = {40468006},
issn = {1759-5053},
abstract = {The gut microbiome has an undeniable role in mediating the health effects of the diet, given its ability to co-digest nutrients and influence nutrient signalling to multiple organ systems. As a suboptimal diet is a major risk factor for and contributor to disease, understanding the multidirectional interactions between the food we eat, the gut microbiome and the different body organ systems is crucial from a public health perspective. Indeed, this research area is leading to the refinement of nutritional concepts and strategies to optimize health through diet. In this Review, we provide an update on how dietary patterns and food intake shape gut microbiome features, the mode of action of diet-microorganism interactions on the immune, nervous and cardiometabolic systems and how this knowledge could explain the heterogeneity of dietary responses, and support food-based dietary guidelines and medical and precision nutrition. Finally, we discuss the knowledge gaps and research efforts needed to progress towards the integration of microbiome science with more precise dietary advice to leverage the role of nutrition in human health.},
}
@article {pmid40467971,
year = {2025},
author = {Smoliński, J and Czyż, K and Kleszcz, A and Trusz, A and Wyrostek, A and Zajfert, K},
title = {A preliminary study on farmed and free-ranging mouflons core microbiome.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {19555},
pmid = {40467971},
issn = {2045-2322},
mesh = {Animals ; Feces/microbiology ; *Gastrointestinal Microbiome ; Bacteroidetes/genetics/isolation &amp; purification ; *Microbiota ; Firmicutes/genetics/isolation &amp; purification ; Bacteria/genetics/classification ; },
abstract = {The digestive tract of ruminants is populated by a diverse microbiome and is also known as a specific ecosystem. The close relationship between the microbiota and the host digestive system influences development and proper health. The rich microflora of ruminants is often altered by the influence of the environment, diet or individual factors, which in turn affects production rates. The most extensive part of the gastrointestinal tract in terms of microbiology is the large intestine, where bacterial levels increase in the caudal direction. The purpose of this study was to compare the core microbiomes of the feces of farmed and free-ranging mouflons, taking into account differences in housing conditions, as well as their diet and individual variability. The most characteristic clusters for ruminants were studied: Firmicutes and Bacteroidetes, as well as the families Lactobacillaceae and Clostridiaceae. The material for the study consisted of feces collected from 10 farmed and 10 free-ranging mouflons. The experiment was based on demonstrating changes in the levels of the bacteria tested by means of DNA isolation from feces and real-time PCR analysis, taking into account dietary and environmental differences. The results showed that the levels of the Lactobacillaceae and Clostridiaceae families were significantly higher in free-ranging individuals than in farmed ones (p < 0.01). For the Firmicutes and Bacteroidetes phyla, no statistically significant differences were shown. In addition, each mouflon was characterized by an individual composition of the microbiome, which changed through environmental, individual and dietary factors.},
}
@article {pmid40467897,
year = {2025},
author = {Wu, Y and Ehlert, B and Metwally, AA and Perelman, D and Park, H and Brooks, AW and Abbasi, F and Michael, B and Celli, A and Bejikian, C and Ayhan, E and Lu, Y and Lancaster, SM and Hornburg, D and Ramirez, L and Bogumil, D and Pollock, S and Wong, F and Bradley, D and Gutjahr, G and Rangan, ES and Wang, T and McGuire, L and Venkat Rangan, P and Ræder, H and Shipony, Z and Lipson, D and McLaughlin, T and Snyder, MP},
title = {Individual variations in glycemic responses to carbohydrates and underlying metabolic physiology.},
journal = {Nature medicine},
volume = {},
number = {},
pages = {},
pmid = {40467897},
issn = {1546-170X},
support = {R01 DK110186-01//U.S. Department of Health &amp; Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes &amp; Digestive &amp; Kidney Diseases)/ ; P30DK116074//U.S. Department of Health &amp; Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes &amp; Digestive &amp; Kidney Diseases)/ ; F32DK126287//U.S. Department of Health &amp; Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes &amp; Digestive &amp; Kidney Diseases)/ ; R01 DK110186-01//U.S. Department of Health &amp; Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes &amp; Digestive &amp; Kidney Diseases)/ ; P30DK116074//U.S. Department of Health &amp; Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes &amp; Digestive &amp; Kidney Diseases)/ ; 11-23-PDF-76//American Diabetes Association (ADA)/ ; 2T15LM007033//U.S. Department of Health &amp; Human Services | NIH | U.S. National Library of Medicine (NLM)/ ; },
abstract = {Elevated postprandial glycemic responses (PPGRs) are associated with type 2 diabetes and cardiovascular disease. PPGRs to the same foods have been shown to vary between individuals, but systematic characterization of the underlying physiologic and molecular basis is lacking. We measured PPGRs using continuous glucose monitoring in 55 well-phenotyped participants challenged with seven different standard carbohydrate meals administered in replicate. We also examined whether preloading a rice meal with fiber, protein or fat ('mitigators') altered PPGRs. We performed gold-standard metabolic tests and multi-omics profiling to examine the physiologic and molecular basis for interindividual PPGR differences. Overall, rice was the most glucose-elevating carbohydrate meal, but there was considerable interindividual variability. Individuals with the highest PPGR to potatoes (potato-spikers) were more insulin resistant and had lower beta cell function, whereas grape-spikers were more insulin sensitive. Rice-spikers were more likely to be Asian individuals, and bread-spikers had higher blood pressure. Mitigators were less effective in reducing PPGRs in insulin-resistant as compared to insulin-sensitive participants. Multi-omics signatures of PPGR and metabolic phenotypes were discovered, including insulin-resistance-associated triglycerides, hypertension-associated metabolites and PPGR-associated microbiome pathways. These results demonstrate interindividual variability in PPGRs to carbohydrate meals and mitigators and their association with metabolic and molecular profiles.},
}
@article {pmid40467859,
year = {2025},
author = {Ferretti, P and Johnson, K and Priya, S and Blekhman, R},
title = {Genomics of host-microbiome interactions in humans.},
journal = {Nature reviews. Genetics},
volume = {},
number = {},
pages = {},
pmid = {40467859},
issn = {1471-0064},
abstract = {The human microbiome is a complex ecosystem of microorganisms that inhabit the human body and have a crucial role in human health. Microbiome composition is shaped by its interaction with many factors, including human genetics. Advances in genomic technologies are improving the ability to quantify the effect of human genetics on the microbiome through improved heritability studies and microbiome genome-wide association studies (GWAS). Complementary studies using transcriptomic analyses are providing a more comprehensive view of the bidirectional relationship between host gene expression and the microbiome. The resulting insights into the genetic mechanisms driving host-microbiome interactions will ultimately contribute to the development of personalized medicine and targeted therapies.},
}
@article {pmid40467839,
year = {2025},
author = {Chen, YA and Kawashima, H and Park, J and Mohsen, A and Hosomi, K and Nakagata, T and Murakami, H and Nanri, H and Miyachi, M and Kunisawa, J and Mizuguchi, K},
title = {NIBN Japan Microbiome Database, a database for exploring the correlations between human microbiome and health.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {19640},
pmid = {40467839},
issn = {2045-2322},
support = {22AC5002//Ministry of Health, Labour and Welfare/ ; 22AC5002//Ministry of Health, Labour and Welfare/ ; 20AC5004//Ministry of Health, Labour and Welfare/ ; 20AC5004//Ministry of Health, Labour and Welfare/ ; },
mesh = {Humans ; Japan ; *Databases, Factual ; *Gastrointestinal Microbiome ; *Microbiota ; Metadata ; },
abstract = {Recent research has highlighted the substantial impact of gut microbiome on various aspects of human health, such as obesity, inflammation, infectious diseases, and cancer. As a result, gut microbiota composition is increasingly recognized as a potential health indicator and biomarker for disease. Numerous factors, including lifestyle, diet, and physical fitness, are known to shape the composition of the human microbiome. However, a significant challenge in elucidating the relationships between these factors and the gut microbiome lies in needing a comprehensive database that integrates diverse human microbiome profiles with extensive sample metadata. To address this issue, we developed an extensive human microbiome database for healthy individuals. This initiative led to the establishment of the NIBN Japan Microbiome Database (NIBN JMD), one of the largest resources of its kind, encompassing up to 1,000 metadata points and more than 2,000 microbiome samples, including data from longitudinal studies. In this article, we describe the creation and features of NIBN JMD, detailing the data collection, processing, and database implementation. NIBN JMD is publicly accessible at https://jmd.nibn.go.jp/ .},
}
@article {pmid40467588,
year = {2025},
author = {Tajadura-Ortega, V and Chai, W and Roberts, LA and Zhang, Y and Di Maio, A and Decout, AC and Pinheiro, BA and Palma, AS and De Nicola, G and Riaposova, L and Gimeno-Molina, B and Lee, YS and Cao, H and Piskarev, V and Akune, Y and Costa, TRD and Amin, H and Sykes, L and Bennett, PR and Marchesi, JR and Feizi, T and Liu, Y and MacIntyre, DA},
title = {Identification and characterisation of vaginal bacteria-glycan interactions implicated in reproductive tract health and pregnancy outcomes.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {5207},
pmid = {40467588},
issn = {2041-1723},
mesh = {Female ; Humans ; *Vagina/microbiology/metabolism ; Pregnancy ; *Polysaccharides/metabolism ; Bacterial Adhesion/physiology ; Pregnancy Outcome ; *Reproductive Health ; Chondroitin Sulfates/metabolism ; Escherichia coli/metabolism ; Microbiota ; *Bacteria/metabolism ; Lactobacillus/metabolism ; Streptococcus agalactiae/metabolism ; Epithelial Cells/microbiology/metabolism ; },
abstract = {Lactobacillus displacement from the vaginal microbiome associates with adverse health outcomes and is linked to increased risk of preterm birth. Glycans mediate bacterial adhesion events involved in colonisation and infection. Using customised glycan microarrays, we establish glycan interaction profiles of vaginal bacteria implicated in reproductive health. Glycan binding signatures of the opportunistic pathogens Escherichia coli, Fusobacterium nucleatum and Streptococcus agalactiae to oligomannose N-glycans, galactose-terminating glycans and hyaluronic acid, respectively are highly distinct from Lactobacillus commensals. Binding to sulphated glycosaminoglycans by vaginal bacteria is pH dependent, as is binding to neutral and sialic acid-terminating glycans by F. nucleatum. Adhesion of Lactobacillus crispatus, Lactobacillus iners, Gardnerella vaginalis, S. agalactiae and F. nucleatum to vaginal epithelial cells is partially mediated by chondroitin sulphate. S. agalactiae binding to chondroitin sulphate C oligosaccharides is inhibited by L. crispatus. This study highlights glycans as mediators of vaginal bacterial binding events involved in reproductive health and disease.},
}
@article {pmid40467587,
year = {2025},
author = {Xiong, S and Xie, B and Yin, N and Zhu, H and Gao, H and Xu, X and Xiao, K and Cai, X and Sun, G and Sun, X and Cui, Y and Van de Wiele, T and Zhu, Y},
title = {Prenatal exposure to trace elements impacts mother-infant gut microbiome, metabolome and resistome during the first year of life.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {5186},
pmid = {40467587},
issn = {2041-1723},
support = {No. L232076//Natural Science Foundation of Beijing Municipality (Beijing Natural Science Foundation)/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/genetics ; Female ; Pregnancy ; Infant ; *Trace Elements/adverse effects ; *Metabolome/drug effects ; Feces/microbiology ; *Prenatal Exposure Delayed Effects/microbiology/metabolism ; Adult ; Male ; Metagenomics ; Hair/chemistry ; *Maternal Exposure/adverse effects ; Infant, Newborn ; Bacteria/genetics/classification/drug effects ; Copper ; },
abstract = {Infancy is a critical window for the colonization of gut microbiome. However, xenobiotic impacts on gut microbiome development in early life remain poorly understood. Here, we recruit 146 mother-infant pairs and collect stool samples at 3, 6, and 12 months after delivery for amplicon sequencing (N = 353), metagenomics (N = 65), and metabolomics (N = 198). Trace elements in maternal hair samples (N = 119) affect diversity and composition of the infant gut microbiome. Shannon diversity in 3 month-old infants is correlated positively with selenium and negatively with copper, and relative abundance of Bifidobacterium increases under high exposure to aluminum and manganese. During the first year of life, infants and their paired mothers have distinct microbial diversity and composition, and their bacterial community structures gradually approach. here are 56 differential metabolites between the first and second visit and 515 differential metabolites between the second and third visit. The typical profile of antibiotic resistance genes (ARGs) significantly differs between infants and their mothers. High levels of copper and arsenic exposure may induce the enrichment of ARGs in the infant gut. Our findings highlight the dynamics of the gut microbiome, metabolites, and ARG profiles of mother-infant pairs after delivery, associated with prenatal exposure to trace elements.},
}
@article {pmid40467492,
year = {2025},
author = {Tonomura, S and Hattori, Y and Ishibashi, T and Ikeda, S and Noda, K and Chiba, T and Kato, Y and Asano, R and Fukuma, K and Edamoto-Taira, Y and Motooka, D and Inagaki, T and Okazawa, M and Nakamura, S and Koga, M and Toyoda, K and Nomura, R and Nakano, K and Friedland, RP and Takeda, K and Takahashi, R and Ihara, M and Nakaoka, Y},
title = {Oral Pathobiont Streptococcus Anginosus Is Enriched in the Gut of Stroke Patients and Predicts 2-Year Cardiovascular Outcome.},
journal = {Circulation journal : official journal of the Japanese Circulation Society},
volume = {},
number = {},
pages = {},
doi = {10.1253/circj.CJ-24-0872},
pmid = {40467492},
issn = {1347-4820},
abstract = {BACKGROUND: Several cross-sectional studies have implicated gut dysbiosis caused by an abundance of oral commensals in stroke, but the effect on long-term prognosis is still unknown. Therefore, we longitudinally investigated oral pathobionts in the gut and their clinical relevance to stroke.<br><br>METHODS AND RESULTS: We analyzed the salivary and gut microbiomes collected from 189 acute stroke and 55 non-stroke subjects, and found that Streptococcus anginosus was significantly more abundant in both the saliva (median [IQR], 0.01 [0.00-0.14] vs. 0.00 [0.00-0.03], P=0.02) and gut (0.09 [0.00-0.28] vs. 0.00 [0.00-0.02], P<0.001) of the stroke patients compared with their non-stroke counterparts. Network analysis revealed S. anginosus as a central hub in gut dysbiosis. After adjusting for vascular risks, S. anginosus (odds ratio 1.20, 95% confidence interval 1.06-1.36, P<0.01), Anaerostipes hadrus (0.82, [0.73-0.93], P<0.01), and Bacteroides plebeius (0.86, [0.86-0.93], P=0.01) in the gut were independent predictors of stroke. Longitudinally, S. anginosus in the gut was significantly associated with increased rates of death and major cardiovascular events (P=0.04; log-rank test), whereas A. hadrus and B. plebeius were not (P=0.45 and P=0.19). After adjusting for vascular risks, S. anginosus in the gut was a residual risk for increased rates of death and major cardiovascular events (hazard ratio 4.78, 95% confidence interval 1.08-21.18, P=0.04)Conclusions: S. anginosus in the gut may increase the risk of stroke and a poor prognosis.},
}
@article {pmid40467356,
year = {2025},
author = {Messadi, A and Sayhi, S and Ghedira, K and Zaouaoui, C and Arfaoui, B and Khouikhi, S and Rebai, M and Guediche, NEH and Abdelhafidh, N and Louzir, B and Faida, A},
title = {Microbial diversity investigation using 16S metagenomics in Tunisian patients with systemic lupus erythematosus.},
journal = {Revista Argentina de microbiologia},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ram.2025.04.002},
pmid = {40467356},
issn = {0325-7541},
abstract = {Systemic lupus erythematosus (SLE) is a multisystemic autoimmune disease associated with significant morbidity and mortality. It is characterized by a loss of self-immune tolerance and autoantibody production, leading to multiple organ damage. Emerging investigations have confirmed the role of gut microbiota dysbiosis in patients with SLE, although the underlying mechanisms remain unclear to date. In this study, we aim to investigate the bacterial profile of SLE including phylum/class/genus relative abundance and diversity, to compare them with healthy controls and to study the correlation of relative abundance of different patterns with clinical/biological parameters. In this case-control study, the bacterial profile was investigated in 7 SLE patients and 7 healthy controls using 16S metagenomics clustering. The present study reported a low abundance of the class Bacilli (0.58% in SLE vs 1.26% in the controls), the genus Lactobacillus (0.43% vs 0.74%), as well as a higher abundance of the genera Gammaproteobacteria (2.37% vs 0.77%) and Escherichia-Shigella (2.04% vs 0.51%) in SLE samples compared to the controls (p<0.05). We also found an association between the class Betaproteobacteria (4.42% vs 1.57%) and the genus Faecalibacterium (11.34% vs 3.35%) and renal manifestations (p<0.05). The phylum Actinobacteria (0.21% vs 3.8%, p=0.036) and the genus Bifidobacterium levels were lower in active SLE compared to the healthy controls. This study is the first report on the gut microbiota of SLE and the first case-control study in Tunisia and North Africa. We obtained a particular profile of bacterial gut microbiota for the SLE group. We found a specific clustering when compared to the healthy controls.},
}
@article {pmid40467241,
year = {2025},
author = {Alegbeleye, O and Boas, DMV and Sant'Ana, AS},
title = {Harnessing the microbiota of vegetables and ready-to-eat (RTE) vegetables for quality and safety.},
journal = {Food research international (Ottawa, Ont.)},
volume = {214},
number = {},
pages = {116667},
doi = {10.1016/j.foodres.2025.116667},
pmid = {40467241},
issn = {1873-7145},
mesh = {*Vegetables/microbiology/virology ; *Food Microbiology ; *Microbiota ; *Food Safety ; *Fast Foods/microbiology ; Humans ; Bacteria/classification/isolation &amp; purification ; Salads/microbiology ; *Food Quality ; },
abstract = {The microbiota of vegetables and Ready-to-Eat (RTE) vegetable salads can have significant implications for quality and safety. Some microbial groups occurring on vegetables can cause foodborne illnesses, while others can potentially influence the shelf life of vegetables and vegetable salad products. The comprehensive assessment of the microbial structure and diversity of vegetables requires sensitive detection and characterization techniques, and this review discusses some of the strengths and limitations of conventional culture dependent approaches and the promise of some contemporary microbial detection/characterization approaches. Some bacterial groups recovered from vegetables have exhibited resistance to important antibiotics and without adequate safeguards, consumption of vegetables and salad products can potentially contribute to the spread and burden of antibiotic resistance. Studies summarised herein indicate that bacterial groups including Pseudomonas, Erwinia, and Lactic Acid Bacteria which contain common spoilage species are predominant in vegetables. Some possible sources of these bacteria to vegetables include agricultural input and post-harvest handling. Viruses and fungi contribute significantly to shaping microbiota of vegetables but also contain some species that are relevant for public health safety and vegetable shelf-life. Inspite of the relevance of these groups on the phylloshpere of vegetables, there is a comparative dearth of data on the incidence and prevalence of fungal and viral groups on vegetablesComprehensive understanding of the microbial profile of vegetables offers a more accurate assessment of potential food safety, and spoilage risks, and studies should aim to assess the total microbiome of vegetables and vegetable salads.},
}
@article {pmid40467108,
year = {2025},
author = {Ghensi, P and Heidrich, V and Bazzani, D and Asnicar, F and Armanini, F and Bertelle, A and Dell'Acqua, F and Dellasega, E and Waldner, R and Vicentini, D and Bolzan, M and Trevisiol, L and Tomasi, C and Pasolli, E and Segata, N},
title = {Shotgun Metagenomics Identifies in a Cross-Sectional Setting Improved Plaque Microbiome Biomarkers for Peri-Implant Diseases.},
journal = {Journal of clinical periodontology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jcpe.14121},
pmid = {40467108},
issn = {1600-051X},
support = {//Italian Society of Periodontology and Implantology (SIdP)/ ; //Eklund Foundation/ ; //International Team for Implantology (ITI)/ ; /ERC_/European Research Council/International ; //CLC Scientific S.r.l./ ; //PreBiomics S.r.l./ ; },
abstract = {AIM: This observational study aimed to verify and improve the predictive value of plaque microbiome of patients with dental implant for peri-implant diseases.<br><br>MATERIALS AND METHODS: Patients were included in one of the following study groups according to the health status of their dental implants: (a) healthy, (b) affected by mucositis and (c) affected by peri-implantitis. From each patient, submucosal plaque microbiome samples were collected from the considered dental implant and from a contralateral healthy implant/tooth. After shotgun metagenomic sequencing, the plaque microbiome was profiled taxonomically and functionally with MetaPhlAn 4 and HUMAnN 3, respectively. Taxonomic and functional profiles were fed into machine-learning models, which were then evaluated with cross-validation to assess the extent to which the plaque microbiome could be used to pinpoint peri-implant diseases.<br><br>RESULTS: Shotgun metagenomics sequencing was performed for a total of 158 samples spanning 102 individuals. Four-hundred and forty-seven prokaryotic species were identified as part of the peri-implant microbiome, 34% of which were currently uncharacterized species. At the community level, the peri-implant microbiome differed according to the health status of the implant (p&#x2009;&#x2264;&#x2009;0.006 for all pairwise comparisons) but this was site-specific, as healthy contralateral sites showed no discriminating microbiome features. Peri-implantitis microbiomes further showed lower inter-subject variability than healthy plaque microbiomes (p&#x2009;<&#x2009;0.001), while mucositis-associated microbiomes were in the middle of the continuum between health and peri-implantitis. Each health condition was associated with a strong signature of taxonomic and functional microbiome biomarkers (log10 LDA score &#x2265;&#x2009;2.5), 30% and 13% of which represented uncharacterized microbial functions and unknown species, respectively. Distinct Fusobacterium nucleatum clades were associated with implant status, highlighting the subspecies F. nucleatum's functional and phenotypic diversity. Machine-learning models trained on taxonomic or functional plaque microbiome profiles were highly accurate in differentiating clinical groups (AUC&#x2009;=&#x2009;0.78-0.96) and highlighted the extent to which the peri-implant microbiome is associated with peri-implant clinical parameters (AUC&#x2009;=&#x2009;0.79-0.87).<br><br>CONCLUSIONS: Plaque microbiome profiling with shotgun metagenomics revealed consistent associations between microbiome composition and peri-implant diseases. In addition to pointing to peri-implant-associated microbes, warranting further mechanistic studies, we showed high-resolution plaque microbiome evaluation via metagenomics as an effective tool. Its utility within protocols for clinical management of peri-implant diseases should be explored in the future.},
}
@article {pmid40467103,
year = {2025},
author = {Phi Dang, C and Croitoru, K and Turpin, W},
title = {DUOX2-mediated gut barrier dysfunction: a preclinical mechanism in IBD pathogenesis?.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2025-335565},
pmid = {40467103},
issn = {1468-3288},
}
@article {pmid40466870,
year = {2025},
author = {Gurjar, S and Taliyan, R and Kumari, S and Kesharwani, P},
title = {The interplay of triphala and its constituents with respect to metabolic disorders and gut-microbiome.},
journal = {Fitoterapia},
volume = {},
number = {},
pages = {106642},
doi = {10.1016/j.fitote.2025.106642},
pmid = {40466870},
issn = {1873-6971},
abstract = {Ayurveda is based on natural therapeutic methods that focuses on eliminating toxins from the body and enhancing both physical and mental regeneration using herbal remedies. Medicinal plants have significant elemental and therapeutic value. Triphala (TLP) is a highly potent polyherbal Ayurvedic remedy that is widely regarded as one of the most crucial ayurvedic supplements. This study aims to analyze and comprehend the effectiveness and therapeutic value of TLP and its components by summarizing the pertinent literature based on a selection of publications obtained through a focused search of reliable academic resources. The review primarily emphasizes on the ethnomedical and pharmacological effects of TLP, while also providing a probable explanation of the underlying molecular mechanism. TLP is recognized for its antioxidant, anti-inflammatory, immunomodulatory, antibacterial, antimutagenic, hypoglycemic, antineoplastic, chemoprotective, and radioprotective properties. It is also effective against parasitic infections, and other infectious disorders. Although, the mechanisms are not well explored but these activities are also ascribed to alter the gut microbiota composition. Therefore, it is imperative to undertake rigorous systematic study for TLP in order to identify and assess the chemical ingredients which bring about the change either in gut microbiome composition or increase the number of beneficial gut-microbiota. Hence, this review thoroughly examines the pharmacological advantages of Triphala with special emphasis on molecular mechanisms altering the gut-microbiota prior to its potential utilization in clinical environments.},
}
@article {pmid40466780,
year = {2025},
author = {Yang, Y and Abdelfattah, A and Jia, H and Kumar, V and Jiang, Y and Cheng, L},
title = {Enhanced nitrogen removal by Comamonas 110 colonization and bioaugmentation in sequencing batch activated sludge bioreactor.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {132759},
doi = {10.1016/j.biortech.2025.132759},
pmid = {40466780},
issn = {1873-2976},
abstract = {While pure functional strains demonstrate high pollutant removal efficiency, their environmental persistence remains challenging. This study optimized Comamonas 110 inoculation strategies in activated sludge systems, enhancing nitrogen removal efficiency (44 % of nitrogen removal at day 180) and achieving stable colonization (15.22 % abundance at day 180) through 30 % initial dosage combined with operational parameter regulation. Monod modeling and 16S rRNA sequencing revealed Comamonas 110 suppressed Nitrite-Oxidizing Bacteria (NOB) while boosting Ammonia-Oxidizing Bacteria (AOB). Denitrifying enzymes (NAR and NIR) increased significantly in inoculated reactors, attributing to the substantial presence of Comamonas 110. Metagenomics revealed upregulated (tricarboxylic acid) TCA cycle genes and nitrogen metabolism pathways, optimizing electron transfer for denitrification. Concurrently, Extracellular Polymeric Substance (EPS) synthesis-related genes were activated, promoting co-aggregation with native EPS-producing microbes. This study provides new insights into colonization dynamics of bioaugmentation strains through microbiome-environment interplay.},
}
@article {pmid40466732,
year = {2025},
author = {Markey, W and Srinath, H},
title = {The alarming rise of early-onset colorectal cancer.},
journal = {Australian journal of general practice},
volume = {54},
number = {6},
pages = {392-399},
pmid = {40466732},
issn = {2208-7958},
mesh = {Humans ; *Colorectal Neoplasms/epidemiology/diagnosis ; Australia/epidemiology ; Risk Factors ; Incidence ; Age of Onset ; Early Detection of Cancer/methods/trends/statistics &amp; numerical data ; Female ; Mass Screening/methods/trends/statistics &amp; numerical data ; Male ; Middle Aged ; Adult ; },
abstract = {BACKGROUND: Over the past 20 years of the Australian National Bowel Cancer Screening Program, there has been a reduction in Australia's overall rates of colorectal cancer. However, during this same period, there has been a steady rise in the incidence of early-onset colorectal cancer (EOCRC), presenting a new public health issue.<br><br>OBJECTIVE: The aim of this study was to evaluate the literature regarding the rising incidence of EOCRC, highlight the importance of the recent reduction in screening age and document what might be done in a primary healthcare setting.<br><br>DISCUSSION: The increasing incidence of EOCRC has been largely attributed to risk factors including a Western diet, obesity, tobacco use and alcohol intake, which contribute to microbiome dysgenesis and chronic inflammation from an early age. In response, the initial screening age for colorectal cancer was lowered to 45 years from July 2024 via an opt-in system; however, there is evidence to support a further reduction in screening age to 40 years.},
}
@article {pmid40466498,
year = {2025},
author = {Egea, LG and Jiménez-Ramos, R},
title = {Antibiotic pollution alters the microbiome and reduces primary production and growth in the seagrass Cymodocea nodosa (Ucria) Ascherson.},
journal = {Marine environmental research},
volume = {210},
number = {},
pages = {107242},
doi = {10.1016/j.marenvres.2025.107242},
pmid = {40466498},
issn = {1879-0291},
abstract = {Antibiotics are considered a contaminant of emerging concern that can affect marine plants and their associated microbiome. To date, limited information is available about the effects of antibiotic pollution on seagrasses. Here, we conducted a seven-day mesocosm experiment in which we exposed the seagrass Cymodocea nodosa to a cocktail of ampicillin, streptomycin, and amoxicillin (with two total concentration exposure levels of 20 and 200 μg L[-1]). At the end of the incubation, we assessed phyllosphere and rhizosphere microbiome composition, plant growth, and carbon metabolism. We found that the seagrass community switched from a highly autotrophic in control (19.41 mmol C m[-2] d[-1]) to a moderately heterotrophic in the high-exposure treatment (-2.74 mmol C m[-2] d[-1]). This decrease in net community production was attributed to (i) a reduction in photosynthetic pigments (from 20 % to 41 %) due to antibiotic-induced oxidative stress in the seagrass chloroplasts and (ii) a change in the phyllosphere that showed lower species richness and abundance (from x0.3 to x0.7-fold lower) in exposure treatments compared to control. Although most bacterial families showed a reduced relative abundance under antibiotic stress, some taxa, including Pseudoalteromonadaceae, Halomonadaceae, and Cellvibrionaceae, were markedly enriched in the phyllosphere. Our results show that phyllosphere bacterial community is more sensitive to antibiotic pollution in the seawater column than rhizosphere community. Long-term antibiotic stress may also promote the development of seagrass diseases. Overall, our results suggest that antibiotic exposure may reduce seagrass growth and health and may compromise their function as a blue carbon sink.},
}
@article {pmid40466388,
year = {2025},
author = {Memariani, H and Memariani, M and Eskandari, SE and Ghasemian, A and Nour Neamatollahi, A},
title = {The potential role of probiotics and their bioactive compounds in the management of pulmonary tuberculosis.},
journal = {Journal of infection and public health},
volume = {18},
number = {9},
pages = {102840},
doi = {10.1016/j.jiph.2025.102840},
pmid = {40466388},
issn = {1876-035X},
abstract = {The significance of gut microbiota in human health is well recognized, yet its effects on pulmonary infectious diseases like tuberculosis (TB) are not thoroughly comprehended. While anti-TB drugs and preventive strategies are indispensable, the incorporation of adjunct therapies, including probiotics and their bioactive compounds, could provide potential biotherapeutic benefits. This review strives to collate the recent experimental and clinical investigations into the manipulation of the gut microbiome through probiotics, exploring their potential to sustain eubiosis, enhance recovery from TB, and mitigate the adverse effects of anti-TB therapies. The multi-pronged mechanisms by which probiotics act against M. tuberculosis include their immunomodulatory properties, the promotion of autophagy, direct inhibition of the pathogen growth via bacteriocin production, the reduction of adverse effects from anti-TB drugs, and a diminished risk of comorbidities. Future research should prioritize high-quality randomized controlled trials that integrate omics with personalized microbiome-based therapeutic approaches to combat TB.},
}
@article {pmid40466265,
year = {2025},
author = {Chang, S and Song, M and Lee, J and Kim, S and Song, D and Jeon, K and Kim, H and Yang, J and Kim, H and Cho, J},
title = {Stimbiotics help improve intestinal immunity and positively modulate the gut microbiome in broilers with necrotic enteritis.},
journal = {Poultry science},
volume = {104},
number = {8},
pages = {105315},
doi = {10.1016/j.psj.2025.105315},
pmid = {40466265},
issn = {1525-3171},
abstract = {This experiment was conducted to investigate the effect of stimbiotic (STB) in broilers with necrotic enteritis (NE) on nutrient digestibility and gut health. A total of 200 one-day-old Arbor Acres (initial body weight of 44.03 ± 0.28 g) were used in this experiment for 28 days. All broilers were randomly allocated into four treatments, and each experimental group had 10 replicate cages with five broilers per cage. The experiment was conducted in a 2 × 2 factorial designs consisting of two levels of challenge (challenge and non-challenge) and two levels of STB (0 and 0.05 %). All broilers in challenged groups were orally challenged by overdosing with coccidia vaccines (× 10 recommended doses; Livacox® Q). The NE challenge significantly decreased (P < 0.05) nutrient digestibility, interferon-γ, heterophil levels in blood, and villus height:crypt depth (VH:CD) compared to the non-challenge group. Also, the NE challenge significantly lower (P < 0.05) ZO-1 and higher MUC2 gene expression than the non-challenge group. Supplementation of 0.05 % STB with NE challenge significantly increased (P < 0.05) gross energy digestibility and decreased (P < 0.05) the number of oocysts per gram of feces compared to the NE-challenged group. Supplementation of 0.05 % STB significantly increased (P < 0.05) the VH:CD in ileum compared to the non-supplementation group. Also, supplementation of 0.05 % STB is significantly lower (P < 0.05) MUC2 and TLR4 gene expression in ileum than the non-supplementation group. At the genus level, the supplementation of 0.05 % STB with NE challenge significantly decreased (P < 0.05) the abundance of Muribaculaceae compared to the NE-challenged group on d 21. In conclusion, supplementation of 0.05 % STB in a diet could positively regulate the cecal microflora and gene expression of tight junction protein and alleviate the decline in nutrient digestibility caused by NE.},
}
@article {pmid40466051,
year = {2025},
author = {Montgomery, ST and Carr, PG and Caparrós-Martín, JA},
title = {Optimisation of DNA Extraction from Nasal Lining Fluid to Assess the Nasal Microbiome Using Third-Generation Sequencing.},
journal = {American journal of respiratory cell and molecular biology},
volume = {},
number = {},
pages = {},
doi = {10.1165/rcmb.2025-0046MA},
pmid = {40466051},
issn = {1535-4989},
abstract = {Sampling nasal lining fluid (NLF) via nasosorption is minimally invasive and well tolerated, but the feasibility of assessing the nasal microbiome using these samples is unknown. However, low biomass makes airway samples particularly susceptible to issues related to contaminant DNA. For this study, we collected nasal swabs and NLF from adult volunteers. DNA was extracted from a mock microbial community and NLF using a column-based kit (ZymoBIOMICS), a precipitation-based kit (Qiagen), or a previously published precipitation-based method. Quality and quantity of DNA was assessed and short-read 16S rRNA sequencing performed to assess feasibility and extraction bias. An optimised methodology was used to extract DNA from NLF and nasal swabs, and long-read 16S rRNA sequencing performed to compare microbial profiles between NLF and nasal swabs. All extraction methods recovered DNA from the mock community, but only precipitation-based methods yielded sufficient DNA from NLF. Extraction methodologies significantly affected microbial profiles, with mechanical lysis needed to minimize bias. Profiles obtained from NLF and swabs were comparable with long-read sequencing. Our findings demonstrate the feasibility of profiling the nasal microbiome using NLF and validated two extraction methodologies as suitable for full-length 16S rRNA sequencing of low-biomass respiratory samples. Our data demonstrate the importance of unbiased DNA extraction methodologies in low-biomass respiratory samples. Additionally, we demonstrated NLF may be an appropriate surrogate for swabs to assess the nasal microbiome.},
}
@article {pmid40345399,
year = {2025},
author = {Livingston, DBH and Sweet, A and Chowdary, M and Samuel Demissie, M and Rodrigue, A and Pillagawa Gedara, K and Kishore, L and Mahmoodianfard, S and Power, KA},
title = {Diet alters the effects of lipopolysaccharide on intestinal health and cecal microbiota composition in C57Bl/6 male mice.},
journal = {The Journal of nutritional biochemistry},
volume = {144},
number = {},
pages = {109951},
doi = {10.1016/j.jnutbio.2025.109951},
pmid = {40345399},
issn = {1873-4847},
abstract = {Lipopolysaccharide (LPS), a component of the gram-negative bacteria, induces an inflammatory cascade in mice, negatively impacting aspects of the microbiota gut-brain axis (mGBA). Flaxseed (FS), an oilseed enriched in dietary fiber and n3 poly-unsaturated fatty acids, has been shown to partially attenuate LPS-induced systemic and neuroinflammation. In this study, we investigated the impact of FS and FS oil (FO) diets on microbial dysbiosis, biomarkers of intestinal health, hepatic inflammation and oxidative stress, and metabolic homeostasis in male mice, 24-hours post LPS-exposure. Compared to saline-treated mice, LPS mice showed diet-dependent shifts in the cecal microbiome. Most notably, LPS-treated basal diet (BD)-fed mice had reduced Muribaculaceae and Lachnospiraceae, FS-LPS mice had elevated Akkermansia and Enterobacteriaceae, and both the FS-LPS and FO-LPS mice had increased Bacteroides. LPS increased cecal short-chain fatty acid concentrations, the highest of which were found in FS-fed mice. Intestinal health biomarkers were modulated by LPS in a diet-specific manner such that ileal mucous content was elevated in FS- and FO-fed mice, while LPS-induced inflammation (IL-1β) was attenuated in FS-fed mice. On the other hand, LPS-induced hepatic inflammation and oxidative stress, which were not attenuated by FS or FO diets. Bacteroides abundance and serum Il-10 levels, and cecal butyrate concentrations and hippocampal IL-6 mRNA, were negatively correlated in FS-fed mice only, suggesting a potential role of the microbiome in the anti-inflammatory effects of FS post-LPS treatment. Collectively, LPS exposure negatively impacted the cecal microbiome and markers of intestinal, hepatic, and metabolic health, the former being beneficially altered by FS diet.},
}
@article {pmid40465720,
year = {2025},
author = {de Porto, AP and Dylla, NP and Stutz, M and Lin, H and Khalid, M and Mullowney, MW and Little, J and Rose, A and Moran, D and McMillin, M and Burgo, V and Smith, R and Woodson, C and Metcalfe, C and Ramaswamy, R and Lehmann, C and Odenwald, M and Bandealy, N and Zhao, J and Kim, M and Adler, E and Sundararajan, A and Sidebottom, A and Kress, JP and Wolfe, KS and Pamer, EG and Patel, BK},
title = {Fecal metabolite profiling identifies critically ill patients with increased 30-day mortality.},
journal = {Science advances},
volume = {11},
number = {23},
pages = {eadt1466},
doi = {10.1126/sciadv.adt1466},
pmid = {40465720},
issn = {2375-2548},
mesh = {Humans ; *Critical Illness/mortality ; *Feces/microbiology/chemistry ; Male ; Female ; Middle Aged ; *Gastrointestinal Microbiome ; Aged ; Intensive Care Units ; *Metabolome ; Dysbiosis/mortality/microbiology ; Metabolomics/methods ; Prospective Studies ; },
abstract = {Critically ill patients admitted to the medical intensive care unit (MICU) have reduced intestinal microbiota diversity and altered microbiome-associated metabolite concentrations. Metabolites produced by the gut microbiota have been associated with survival of patients receiving complex medical treatments and thus might represent a treatable trait to improve clinical outcomes. We prospectively collected fecal specimens, defined microbiome compositions by shotgun metagenomic sequencing, and quantified microbiota-derived fecal metabolites by mass spectrometry from 196 critically ill patients admitted to the MICU for non-COVID-19 respiratory failure or shock to correlate microbiota features and metabolites with 30-day mortality. Microbiota compositions of the first fecal sample after MICU admission did not independently associate with 30-day mortality. We developed a metabolic dysbiosis score (MDS) that uses fecal concentrations of 13 microbiota-derived metabolites, which predicted 30-day mortality independent of known confounders. The MDS complements existing tools to identify patients at high risk of mortality by incorporating potentially modifiable, microbiome-related, independent contributors to host resilience.},
}
@article {pmid40465653,
year = {2025},
author = {Mengiste, T and Liao, CJ},
title = {Contrasting Mechanisms of Defense Against Biotrophic and Necrotrophic Pathogens, 20 Years Later: What Has Changed?.},
journal = {Annual review of phytopathology},
volume = {},
number = {},
pages = {},
doi = {10.1146/annurev-phyto-121823-031139},
pmid = {40465653},
issn = {1545-2107},
abstract = {Significant advances have been made in understanding mechanisms of plant defense against biotrophic and necrotrophic pathogens. Whole-genome sequencing of these pathogens has uncovered the genetic underpinnings of the distinct and common virulence and defense mechanisms. Necrotrophic pathogens produce toxins, necrosis-inducing proteins, secondary metabolites, and hydrolytic enzymes, and their virulence generates endogenous plant peptides. The recognition of these factors triggers broad-spectrum quantitative resistance. Resistance to specialist, host-specific, toxin-producing pathogens is mediated by the absence of host susceptibility proteins, including nucleotide-binding leucine-rich repeats (NLRs), or by detoxification mechanisms. Biotrophic pathogens utilize distinct virulence strategies, and NLR proteins are critical determinants of resistance, interacting synergistically with other quantitative resistance factors. However, NLRs are ineffective against necrotrophs, which exploit canonical immune responses to establish and promote disease. Immune responses such as hypersensitive cell death and the production of reactive oxygen species and accumulation of hormones exhibit distinct or complex roles in defense against biotrophic and necrotrophic pathogens. Lately, the microbiome has become instrumental in uncovering novel pathogen resistance mechanisms. However, further studies are needed to understand the genes involved in recruiting defense-promoting microbes and their impact on pathogens with distinct virulence. Overall, a comprehensive understanding of mechanisms of resistance to biotrophic and necrotrophic pathogens is crucial for activating or suppressing appropriate host responses.},
}
@article {pmid40465497,
year = {2025},
author = {Shin, R and Kashyap, A and Black, TA and Rashid, RM},
title = {Exploring the Gut Microbiome's Role in Drug-Induced Photosensitivity: A Need for Deeper Investigation.},
journal = {Journal of drugs in dermatology : JDD},
volume = {24},
number = {6},
pages = {e40-e41},
pmid = {40465497},
issn = {1545-9616},
}
@article {pmid40465264,
year = {2025},
author = {Liu, M and Geng, J and Jin, S and Hu, P and Wang, X and Liu, X},
title = {Alterations of the Enteric Virome in Vogt-Koyanagi-Harada Disease.},
journal = {Investigative ophthalmology &amp; visual science},
volume = {66},
number = {6},
pages = {15},
doi = {10.1167/iovs.66.6.15},
pmid = {40465264},
issn = {1552-5783},
mesh = {Humans ; *Uveomeningoencephalitic Syndrome/virology/microbiology ; Male ; Female ; *Virome/genetics ; Adult ; Case-Control Studies ; RNA, Ribosomal, 16S/genetics ; *Gastrointestinal Microbiome ; Middle Aged ; Bacteria/genetics ; Metagenomics ; Young Adult ; },
abstract = {PURPOSE: This study aims to explore the enteric virome characteristics of Vogt Koyanagi Harada (VKH) disease and its potential role in this disease.<br><br>METHODS: Shotgun metagenomic sequencing was used to detect the enteric virome and 16S rRNA to detect the bacteriome in new-onset, untreated patients with VKH (n = 25) and age- and sex-matched healthy controls without autoimmune diseases (n = 25).<br><br>RESULTS: Patients with VKH exhibited different enteric viral communities from healthy controls, characterized by decreased richness of core viral communities (present in > 80% of samples) and increased richness of common viral communities (present in 50%-80% of samples). Notably, within the core virus community, bacteriophage richness was markedly reduced, whereas eukaryotic virus richness significantly increased in patients with VKH. The case-control analysis identified 42 differentially abundant viruses, including a decrease in crAss-like phages, the eukaryotic virus Moumouvirus_moumou, and an enrichment of the Chlamydiamicrovirus_CPG1. Most of the differential phages predominantly targeted bacteria from the phyla Pseudomonadota and Firmicutes. The gut virome-bacteria community correlation analysis revealed a shift in the interactions between the core viruses and bacterial communities. Additionally, Wroclawvirus PA5oct (a Pseudomonas phage) correlated with leukotrichia, a clinically relevant symptom of VKH (P = 0.042). The impact of multiple Pseudomonas phages on the host folate biosynthesis was significantly enhanced in patients with VKH. Moreover, the protein (Earp361-372) encoded by VKH-enriched Pseudomonas was identified to share homology with the melanin antigen gp10044-59.<br><br>CONCLUSIONS: The gut virome of patients with VKH differs significantly from healthy controls, suggesting its disturbance may contribute to gut microbiome imbalance and VKH development.},
}
@article {pmid40465001,
year = {2025},
author = {Ghosh, R and Sil, D and Sharma, R and Kumar, D and Komal, K and Kumar, S and Mahajan, HS and Sharma, M and Kumar, M},
title = {Investigating postbiotics as innovative adjuvants: deciphering the gut-breast connection in breast Cancer therapy, from gut microbiome to personalized medicine.},
journal = {Molecular biology reports},
volume = {52},
number = {1},
pages = {547},
pmid = {40465001},
issn = {1573-4978},
mesh = {Humans ; *Breast Neoplasms/therapy/microbiology/immunology ; *Gastrointestinal Microbiome/drug effects ; Precision Medicine/methods ; Female ; *Probiotics/therapeutic use ; },
abstract = {Breast cancer is the most common and deadly cancer affecting women globally. While traditional treatments - surgery, chemotherapeutic agents, radiotherapy - are used, factors damage their effectiveness: tumor heterogeneity, drug resistance, and non-targeted actions on cancer cells. Postbiotics, a newer category of biotics, confer benefits without living microorganisms and show promise against cancer. This review summarizes the link between gut microbiota and BC, postbiotic mechanisms against cancer, and their potential for personalized medicine. Postbiotics modulate the host immune system and inflammation in BC management. They target apoptotic signaling pathways, such as mitochondrial-dependent and death receptor-dependent pathways, interrupt the cell cycle, inhibit cancer cell growth, and regulate immune responses. In cancer, integrative approaches for therapies include microbiome analysis to provide personalized medical treatment, highlighting the microbiome's impact on cancer. Compared to probiotics, postbiotics have advantages, including better bioavailability, stability, and safety profiles. However, research should continue to address clinical evidence and extended studies in their production and application. The use of postbiotics as adjunctive agents in BC treatment has been highlighted for their potential to enhance standard therapy outcomes.},
}
@article {pmid40464990,
year = {2025},
author = {Peng, Z and Kang, C and Xu, Y and Zhang, C and Zhang, Y and Yan, B and Wang, S and Guo, X and Wan, X and Lv, C and Huang, L and Guo, L and Wang, H},
title = {Effects of Wild and Domesticated Seeds on the Colonization of Rhizosphere Microorganisms in Atractylodes lancea.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {59},
pmid = {40464990},
issn = {1432-184X},
support = {2023YFC3503804//National Key Research and Development Program of China/ ; 2023YFC3503804//National Key Research and Development Program of China/ ; 2023YFC3503804//National Key Research and Development Program of China/ ; 2023YFC3503804//National Key Research and Development Program of China/ ; ZZ18-YO-051, ZZ13-YQ-096//Fundamental Research Funds for the Central Public Welfare Research Institutes/ ; ZZ18-YO-051, ZZ13-YQ-096//Fundamental Research Funds for the Central Public Welfare Research Institutes/ ; ZZ18-YO-051, ZZ13-YQ-096//Fundamental Research Funds for the Central Public Welfare Research Institutes/ ; ZZ18-YO-051, ZZ13-YQ-096//Fundamental Research Funds for the Central Public Welfare Research Institutes/ ; CI2021A03903, CI2021A03905, CI2021B013//Scientific and technological innovation project of China Academy of Chinese Medical Sciences/ ; CI2021A03903, CI2021A03905, CI2021B013//Scientific and technological innovation project of China Academy of Chinese Medical Sciences/ ; CI2021A03903, CI2021A03905, CI2021B013//Scientific and technological innovation project of China Academy of Chinese Medical Sciences/ ; CI2021A03903, CI2021A03905, CI2021B013//Scientific and technological innovation project of China Academy of Chinese Medical Sciences/ ; No: ZYYCXTD-D-202005//Innovation Team and Talents Cultivation Program of National Administration of Traditional Chinese Medicine/ ; No: ZYYCXTD-D-202005//Innovation Team and Talents Cultivation Program of National Administration of Traditional Chinese Medicine/ ; No: ZYYCXTD-D-202005//Innovation Team and Talents Cultivation Program of National Administration of Traditional Chinese Medicine/ ; No: ZYYCXTD-D-202005//Innovation Team and Talents Cultivation Program of National Administration of Traditional Chinese Medicine/ ; },
mesh = {*Rhizosphere ; *Seeds/microbiology/growth &amp; development ; *Soil Microbiology ; *Atractylodes/microbiology/growth &amp; development ; *Microbiota ; *Bacteria/classification/genetics/isolation &amp; purification ; Seedlings/microbiology/growth &amp; development ; Plant Roots/microbiology ; Domestication ; Endophytes/classification/isolation &amp; purification/genetics ; Plant Leaves/microbiology ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The domestication of plant species has played a pivotal role in shaping human civilization, yet it has also contributed to a significant reduction in the genetic diversity of crop varieties. This reduction may have profound implications for the formation and establishment of rhizosphere microbial communities in plants. This study systematically investigates microbiome dynamics during seed development in wild and domesticated Atractylodes lancea. The seeds from both wild and domesticated A. lancea exhibited shared microbial genera, while their communities were changed significantly. However, when A. lancea seeds from wild and domesticated germinated into seedlings under identical microbiological conditions, the leaves and root endophytic microbial and rhizosphere microbiome displayed similar genus. Remarkably, the rhizosphere microbial communities of the seedlings consistently enriched Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium, Paenibacillus, Variovorax, Conexibacter, and norank_f__Micropepsaceae. And this convergence likely arises from the shared chemotype of A. lancea and exposure to identical environmental microbiomes. In summary, this study delineates the transmission processes of A. lancea seed endophytes and identifies the dynamic patterns of microbial shifts during its development from seed to seedling. These findings contribute to a broader understanding of plant-microbe interactions and the role of microbial ecology in crop improvement.},
}
@article {pmid40464955,
year = {2025},
author = {Wang, Y and Li, Z},
title = {Mendelian randomization analysis unveils causal relationships between skin microbiota and osteomyelitis.},
journal = {Archives of dermatological research},
volume = {317},
number = {1},
pages = {797},
pmid = {40464955},
issn = {1432-069X},
mesh = {Humans ; *Osteomyelitis/microbiology/genetics/epidemiology ; Mendelian Randomization Analysis ; *Skin/microbiology ; *Microbiota/genetics ; Genome-Wide Association Study ; Polymorphism, Single Nucleotide ; Skin Microbiome ; },
abstract = {BACKGROUND: Osteomyelitis results principally from endo-/exogenous bacterial infections, whose incidence that complicating bone injuries reaches approximately 30%, with the risk of disability and teratogenicity. Skin microbiota has been found to be clinically linked to osteomyelitis, but substantial evidence is lacking.<br><br>METHODS: Mendelian randomization (MR) was applied to unveil the causality between human skin microbiome and osteomyelitis. Genetic data of 1,656 skin microbiota samples were obtained from genome-wide association studies (GWAS), with the outcome of osteomyelitis from UK Biobank (UKB) database.<br><br>RESULTS: Two sample MR confirmed 12 skin microbiota strains that possessed significant causality strength with osteomyelitis, in which asv013 [S. epidermidis] (&#x3b2;&#x2009;=&#x2009;0.061, P&#x2009;=&#x2009;0.027), Genus propionibacterium (&#x3b2;&#x2009;=&#x2009;0.065, P&#x2009;=&#x2009;0.021), Family micrococcaceae (&#x3b2;&#x2009;=&#x2009;0.086, P&#x2009;=&#x2009;0.004), asv003 [Staphylococcus (unc.)] (&#x3b2;&#x2009;=&#x2009;0.065, P&#x2009;=&#x2009;0.027), and asv004 [Corynebacterium (unc.)] (&#x3b2;&#x2009;=&#x2009;0.070, P&#x2009;=&#x2009;0.016) were drivers of osteomyelitis, whilst the leaving asv037 [C. Glutamicum] (&#x3b2; = -0.041, P&#x2009;=&#x2009;0.004), asv021 [Micrococcus (unc.)] (&#x3b2; = -0.059, P&#x2009;=&#x2009;0.019), asv063 [Finegoldia (unc.)] (&#x3b2; = -0.037, P&#x2009;=&#x2009;0.038), Order clostridiales (&#x3b2; = -0.043, P&#x2009;=&#x2009;0.013), Class betaproteobacteria (&#x3b2; = -0.061, P&#x2009;=&#x2009;0.004), Family clostridiales (&#x3b2; = -0.061, P&#x2009;=&#x2009;0.002), and Order clostridiales (&#x3b2; = -0.063, P&#x2009;=&#x2009;0.023) could be perceived as protective factors. No heterogeneity or pleiotropy in sensitivity analyses were observed, hinting the robustness of the MR findings.<br><br>CONCLUSION: This study preliminarily clarified the causal effect of skin microbiome on osteomyelitis. Strains that may significantly trigger or suppress the outcome of osteomyelitis were figured out, which may provide promising insights for the genesis and progression of osteomyelitis, thereby benefiting relevant clinical prevention and treatment.},
}
@article {pmid40464915,
year = {2025},
author = {Kim, R and Oh, S and Woo, KA and Shin, CM and Park, KU and Lee, JY},
title = {Blood microbiome signatures in the REM sleep behavior disorder-Lewy body disease continuum.},
journal = {Journal of neural transmission (Vienna, Austria : 1996)},
volume = {},
number = {},
pages = {},
pmid = {40464915},
issn = {1435-1463},
abstract = {Although systemic inflammation triggered by alterations in microbiota from various body sites has been proposed as a potential mechanism underlying Lewy body diseases (LBDs), the association between the blood microbiome and LBDs remains uncertain. This study aimed to investigate the blood microbiome profiles across the REM sleep behavior disorder (RBD)-LBD continuum and to explore their potential as biomarkers reflecting disease phenotypes and clinical severity. Blood samples were collected from 106 patients across the RBD-LBD continuum, including 41 with isolated RBD (iRBD), 45 Parkinson's disease with probable RBD, and 20 dementia with Lewy bodies with probable RBD, as well as from 94 healthy controls. All patients were evaluated with the Movement Disorder Society-Unified Parkinson's Disease Rating Scale (MDS-UPDRS) and comprehensive neuropsychological tests. Microbiome taxonomic compositions were analyzed using 16 S rRNA metagenomic sequencing. Significant microbial shifts were observed in the RBD-LBD continuum group compared to controls, with reduced microbial alpha diversity and distinct beta diversity patterns. Specifically, the genus Stenotrophomonas was enriched, while the genera Acetobacter, Enhydrobacter, and Lactobacillus were depleted in the RBD-LBD continuum group. The combined model using these genera demonstrated high predictive accuracy for the RBD-LBD continuum, with the area under the receiver-operating-characteristic curve (AUC) of 0.970 (95% confidence interval [CI]: 0.950-0.980). This model also successfully distinguished the iRBD subgroup from controls, achieving an AUC of 0.956 (95% CI, 0.914-0.987). Alpha and beta diversity were significantly associated with MDS-UPDRS Parts I and II scores in the RBD-LBD continuum group. Our findings suggest that patients within the RBD-LBD continuum may share specific blood microbiome signatures.},
}
@article {pmid40464747,
year = {2025},
author = {Zhu, H and Jin, S and Fan, S and Liu, W and Wang, Y and Ha, J and Lu, Y and Li, Z and Mi, M and Zhang, J and Liu, W and Yixi, L and Feng, F and Xu, J},
title = {Compare Phellodendri Chinensis Cortex before and after salt-water processing to ameliorate diabetic nephropathy via metabolomics and microbiome analysis.},
journal = {The Journal of pharmacy and pharmacology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jpp/rgaf033},
pmid = {40464747},
issn = {2042-7158},
support = {XZ202401ZR0004//Natural Science Foundation of Tibet Autonomous Region/ ; 300224080210//Tibet University of Tibetan Medicine School-Level Scientific Research Project/ ; 30022506016//2025 Central Support Fund for Local University Development/ ; },
abstract = {OBJECTIVES: The study aims to investigate the therapeutic effects and the underlying mechanisms of Phellodendri Chinensis Cortex (PC) and its salt-water processed form (SPC) on diabetic nephropathy (DN).<br><br>METHODS: Histopathological examination, biochemical evaluation immunohistochemistry/immunofluorescence assay were used to compare the effects of PC and SPC on DN. Intestinal microbiota was sequenced by 16S rDNA, serum differential metabolites were identified by UPLC-Q/TOF-MS to elucidate the mechanism.<br><br>RESULTS: PC and SPC could improve renal function, reduce blood glucose, proteinuria, inflammation, and oxidative stress, and restoring gut microbiota homeostasis in DN rats, with SPC showing superior efficacy. PC influenced 8 metabolites, primarily in glycerolipid metabolism and pentose and glucuronate interconversions, whereas SPC affected 30 metabolites, predominantly in pathways closely associated with glucose and lipid metabolism, including pentose and glucuronate interconversions, ether lipid metabolism and glycerophospholipid metabolism. Correlation analysis identified specific gut microbiota, such as Enterobacteriaceae, Muribaculaceae, and Lachnospiraceae, as highly correlated with the metabolic effects induced by PC and SPC.<br><br>CONCLUSION: The study provides evidence that PC and SPC have a beneficial effect on DN, with SPC exhibiting enhanced therapeutic potential. Furthermore, SPC could better restore gut microbiota diversity and structure, and improved glucose and lipid metabolism.},
}
@article {pmid40464639,
year = {2025},
author = {Zhang, Q and Liu, Y and Li, Y and Bai, G and Pang, J and Wu, M and Li, J and Zhao, X and Xia, Y},
title = {Implications of gut microbiota-mediated epigenetic modifications in intestinal diseases.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2508426},
doi = {10.1080/19490976.2025.2508426},
pmid = {40464639},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Epigenesis, Genetic ; Animals ; Dysbiosis/microbiology/therapy ; DNA Methylation ; Fecal Microbiota Transplantation ; Prebiotics/administration &amp; dosage ; *Intestinal Diseases/microbiology/genetics/therapy ; Probiotics ; Inflammatory Bowel Diseases/microbiology/genetics/therapy ; Colorectal Neoplasms/microbiology/genetics ; },
abstract = {Intestinal diseases are highly prevalent, affecting millions worldwide and significantly contributing to global morbidity. The treatment of complex disorders, such as inflammatory bowel disease (IBD) and colorectal cancer (CRC), remains challenging due to multifactorial etiologies, diverse patient responses, and the limitations of current therapeutic strategies. Although the gut microbiota clearly plays a role in regulating the onset of intestinal diseases, few studies have explored the epigenetic factors by which the microbiota contributes to disease development. Here, the latest insights into the molecular mechanisms underlying the bidirectional influence between gut microbiota and epigenetic modifications are discussed, including DNA methylation, histone modifications, non-coding RNAs, and N6-methyladenosine (m[6]A). Importantly, mechanistic studies based on animal models or human cells have demonstrated that the gut microbiota, and other environmental factors, influence targeted gene expression and activate immune pathways through host epigenetic dysregulation, which are closely associated with the development of IBD and CRC. Furthermore, potential microbiome interventions, including probiotics, prebiotics and postbiotics, fecal microbiota transplantation (FMT), dietary modifications, and phage therapy, have been proposed as innovative therapeutic strategies to correct these abnormal epigenetic patterns associated with the diseases. Overall, addressing microbiome dysbiosis and its epigenetic consequences presents a promising frontier in the treatment of intestinal diseases, offering the potential to not only restore microbial balance but also provide more targeted and personalized therapeutic strategies for better patient outcomes.},
}
@article {pmid40464558,
year = {2025},
author = {Ruan, Y and Zhu, T and Yang, R and Su, F and An, C and Hu, Z and Li, X and Li, Y and Chen, P and Shao, X and Qin, J and Chen, H and Chen, R},
title = {Donor-derived microbial engraftment and gut microbiota shifts associated with weight loss following fecal microbiota transplantation.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0012025},
doi = {10.1128/aem.00120-25},
pmid = {40464558},
issn = {1098-5336},
abstract = {Fecal microbiota transplantation (FMT) is a promising treatment for microbiota dysbiosis and may provide metabolic benefits for obesity. However, its mechanisms and variability in clinical outcomes remain poorly understood. This 12-week multicenter, single-arm study evaluated the efficacy of FMT for weight loss and explored the role of donor-derived microbial engraftment and functional shifts in mediating weight loss among overweight and obese individuals. Twenty-three participants (body mass index ≥24 kg/m[2]) without diabetes received three biweekly FMT sessions via a nasojejunal tube. Fecal samples from participants and donors were analyzed using metagenomic sequencing. By week 12, 52% of participants were classified as responders, achieving significant weight loss of ≥5% from baseline, with an average weight loss of 7.98 ± 2.69 kg (P < 0.001). In contrast, non-responders lost 2.90 ± 1.89 kg (P < 0.001). Responders exhibited a significantly higher proportion of donor-derived microbial strains post-FMT compared to non-responders (37.8% vs 15.2%, P = 0.020). Notably, key taxa, including Phascolarctobacterium (P = 0.034) and Acidaminococcaceae (P = 0.012), increased significantly in abundance in responders post-FMT, indicating successful microbial engraftment as a critical determinant of therapeutic success. These findings suggest that FMT is a viable intervention for weight loss in obese individuals. Successful donor-derived microbial engraftment strongly correlates with weight loss efficacy, highlighting the potential of microbiota-targeted therapies in obesity management and providing insights into the mechanisms underlying FMT outcomes.IMPORTANCEPrior research indicates that fecal microbiota transplantation (FMT) is a promising treatment for diseases related to microbiota imbalance, potentially providing metabolic benefits for obesity. However, the specific role of donor-derived microbial engraftment in driving clinical efficacy has remained unclear. In this study, we evaluated the efficacy of FMT in promoting weight loss and explored the role of donor-derived bacterial strains in this process. Our findings demonstrate that the successful engraftment of specific donor-derived taxa, such as Phascolarctobacterium and Acidaminococcaceae, is strongly associated with significant weight loss. This highlights the critical interplay between donor microbiota and recipient gut environment. These findings underscore the potential of microbiota-targeted therapies as a novel strategy for obesity management.CLINICAL TRIALSThis study is registered with the Chinese Clinical Trial Registry as ChiCTR1900024760.},
}
@article {pmid40464499,
year = {2025},
author = {Zhang, X and Wan, L and Zheng, Y and Ai, Y},
title = {Gut Barrier, Microbial Metabolites, and Immune Homeostasis in Autoimmune Hepatitis: From Molecular Mechanisms to Strategies.},
journal = {Frontiers in bioscience (Landmark edition)},
volume = {30},
number = {5},
pages = {27747},
doi = {10.31083/FBL27747},
pmid = {40464499},
issn = {2768-6698},
support = {RCTJ202429//The Youth Talent Support Program of the Anhui Provincial Association for Science and Technology/ ; 8180050//National Natural Science Foundation of China Youth Project/ ; Z2023280/2023PTCM12//Technology project of China Three Gorges University/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; *Hepatitis, Autoimmune/immunology/microbiology/metabolism/therapy ; *Homeostasis/immunology ; Animals ; Probiotics/therapeutic use ; *Intestinal Mucosa/metabolism/immunology/microbiology ; Dysbiosis ; Bile Acids and Salts/metabolism ; },
abstract = {Autoimmune hepatitis (AIH) is a chronic immune-mediated inflammatory liver disease characterized by recurring immune-triggered hepatic injury. While scientists have yet to fully elucidate the precise triggers of AIH, contemporary research indicates that both gut microbiota and their metabolic products significantly influence AIH progression. These factors contribute to multiple mechanisms, including compromised intestinal barrier function, altered microbial and metabolite trafficking, and disrupted immune balance, leading to inflammatory responses. This review begins by exploring the intestinal microbial populations and their byproducts linked to AIH. It highlights how disrupted gut flora compromises intestinal immune defenses, enables bacterial migration from the gut to hepatic tissue, and induces liver inflammatory responses. Research validates that metabolic products from microbes, such as short-chain fatty acids (SCFAs), bile acids (BAs), and specific amino acids (glutamine, cysteine, tryptophan, and branched-chain variants, among others), interact with immune cell populations. These interactions, coupled with immune cell modifications, contribute to AIH progression. Our review identifies promising treatment strategies, including the use of probiotic supplementation, engineered prebiotic compounds, microbiota transfer procedures, and specific medications targeting gut microorganisms and their byproducts. These approaches could potentially reduce immune-triggered hepatic damage, offering potential new avenues for AIH management.},
}
@article {pmid40464118,
year = {2025},
author = {Zepeda-Rivera, MA and Dewhirst, FE and Bullman, S and Johnston, CD},
title = {Addressing controversy in Fusobacterium nomenclature: what exactly does "F. nucleatum" refer to?.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2514797},
doi = {10.1080/19490976.2025.2514797},
pmid = {40464118},
issn = {1949-0984},
mesh = {*Terminology as Topic ; Humans ; *Fusobacterium/classification/genetics ; *Fusobacterium Infections/microbiology ; *Fusobacterium nucleatum/classification/genetics ; },
abstract = {The F. nucleatum group (sensu lato) is historically composed of four subspecies (F. nucleatum subsp. animalis, F. nucleatum subsp. nucleatum, F. nucleatum subsp. polymorphum, F. nucleatum subsp. vincentii). Although F. nucleatum sensu lato members are typically associated with oral disease, they have recently been shown to disseminate to the gastrointestinal tract and are associated with adverse health conditions such as inflammatory bowel disease and colorectal cancer (CRC). A growing debate over the nomenclature applied to Fusobacterium taxonomy has resulted in different names for these lineages, shifting them from their historic subspecies designations to distinct species names (F. animalis, F. nucleatum, F. polymorphum, F. vincentii). This shift in naming scheme can lead to potentially significant confusion as "F. nucleatum" can now refer to both the group (sensu lato) and a distinct lineage (sensu stricto; historically F. nucleatum subsp. nucleatum). For example, the substantial body of literature documenting the involvement of "F. nucleatum" (sensu lato) in CRC is seemingly contradicted by recent analyses showing that "F. nucleatum" (sensu stricto) is not enriched in CRC. However, this apparent contradiction is due only to changes in the updated Fusobacterium naming scheme. Furthermore, discrepancies arising from this nomenclature shift can obscure the crucial role of other lineages in tumor biology, particularly that of F. nucleatum subsp. animalis/F. animalis. Thus, the adoption of this nomenclature reclassification without careful consideration risks misleading non-experts and sparking misinterpretation of scientific literature and discourse. Here we elaborate on the challenges of the updated Fusobacterium nomenclature scheme, propose tentative suggestions to improve accuracy and clarity, and call for a broader research community effort to discuss and implement a unified approach moving forward.},
}
@article {pmid40463962,
year = {2025},
author = {Liu, RP and Senior, A and Bao, Z and Koay, YC and Holmes, A and O'Sullivan, JF},
title = {Multi-organ multi-omic and gut microbiome markers of fat and sucrose dietary oversupply in cardiometabolic disease.},
journal = {iScience},
volume = {28},
number = {4},
pages = {111887},
pmid = {40463962},
issn = {2589-0042},
abstract = {Cardiometabolic disease is the greatest challenge facing global health. Increasingly, evidence suggests that Western diet comprising an over-supply of energy from fat and sucrose leads to obesity, insulin resistance, hypertension, and cardiovascular disease. Traditional preclinical animal studies of cardiometabolic disease often adopt a reductionist approach, focusing on individual components. To overcome this, we comprehensively assessed cardiometabolic phenotypes- anthropometric, physiological, and metabolic- along with the molecular changes consequent upon fat or sucrose dietary oversupply, or both in male C57BL/6J mice. Molecular assessment included measurement of the gut microbiome and several metabolite pools including plasma, heart, liver, and gut contents (cecal and fecal). In these mice, we identified key changes across phenotypes, metabolites, microbiota, and their interrelationship, and synthesized all the data into four distinct phenogroups that explain the variance across cardiometabolic parameters. These phenogroups provide insight into inter-organ regulation of Western diet-dependent cardiometabolic phenotypes, highlighting important avenues for further study.},
}
@article {pmid40463520,
year = {2025},
author = {Patel, SM and Farirai, J and Patel, MZ and Boiditswe, S and Tawe, L and Lekalake, S and Matshaba, M and Steenhoff, AP and Arscott-Mills, T and Feemster, KA and Shah, SS and Thielman, N and Cunningham, CK and David, LA and Murdoch, DM and Kelly, MS},
title = {Alterations of the upper respiratory microbiome among children living with HIV infection in Botswana.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.1101/2022.12.19.22283664},
pmid = {40463520},
abstract = {Children living with HIV (CLWH) are at high risk of colonization and infection by bacterial respiratory pathogens, though this risk can be reduced by other microbes in the upper respiratory microbiome. The impact of HIV infection on development of the upper respiratory microbiome during childhood is poorly understood, and we sought to address this knowledge gap by identifying associations between HIV infection and the nasopharyngeal microbiomes of children in Botswana. We enrolled Batswana CLWH (<5 years) and age- and sex-matched HIV-exposed, uninfected (HEU) and HIV-unexposed, uninfected (HUU) children in a cross-sectional study. We used shotgun metagenomic sequencing to compare the nasopharyngeal microbiomes of children by HIV status. Among the 143 children in this study, HIV infection and HIV-associated immunosuppression were associated with alterations in nasopharyngeal microbiome composition, including lower abundances of Corynebacterium species associated with respiratory health. These findings suggest that the upper respiratory microbiome may contribute to the high risk of bacterial respiratory infections among CLWH.},
}
@article {pmid40463507,
year = {2025},
author = {Seidi, S and Raz, A and Maleki-Ravasan, N and Forouzan, E and Karimian, F and Sebbane, F and Sohrabi, A and Esmaeili, S and Mostafavi, E},
title = {The interplay between species and locations shapes vector fleas microbial communities in plague foci: pathogens rather than symbionts?.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1568103},
pmid = {40463507},
issn = {2235-2988},
mesh = {Animals ; *Siphonaptera/microbiology ; *Plague/transmission/microbiology/epidemiology ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Symbiosis ; *Insect Vectors/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; Iran/epidemiology ; Humans ; Bartonella/isolation &amp; purification/genetics ; High-Throughput Nucleotide Sequencing ; Yersinia pestis ; DNA, Bacterial/genetics ; Phylogeny ; },
abstract = {Besides causing allergies from their bites, fleas transmit the most notorious zoonotic pathogen, Yersinia pestis. They also harbor commensal bacteria in their guts. Here, the microbial communities of fleas were characterized using 16S rRNA Next-Generation Sequencing to understand microbial interactions and functions in areas with historical plague-outbreaks in Iran with the ultimate idea of managing flea-borne diseases. Meriones persicus, Xenopsylla buxtoni and Bartonella spp. were identified as the dominant host, vector and bacterium, respectively. Six bacteria Bartonella, Sphingomonas, Wolbachia, Cardinium, Rickettsia and Ralstonia were identified as the most abundant genera in the microbiome of five flea species. More detailed surveys revealed substantial intrageneric variations (e.g. nine phylotypes for Bartonella) and the diverse nature (from biofilm-forming human pathogens to insect reproductive manipulators, and environmental microbes) for the bacteria studied. The fleas microbiome is largely affected by species and to a lesser extent by location, and circulates by both horizontal and vertical transmissions. The prevalence of Bartonella spp. infection in fleas highlights the potential to explore One Health approaches, particularly in addressing travel-related and zoonotic disease risks. Environmental drivers-such as climate change, habitat alteration, and host dynamics-shape flea microbiomes and influence disease risk, while concerns about antimicrobial resistance further complicate control efforts. Our findings advocate for coordinated strategies that combine public health education, ecological monitoring, and global collaboration to sustainably manage flea-borne diseases.},
}
@article {pmid40463443,
year = {2025},
author = {Huang, X and Liu, Y and Jiang, F and Xin, L and Wang, Z and Hua, Z and Wang, C and Zhang, L and Yu, J},
title = {Exploring the research progression and evolutionary trends of gut microbiome and hypertension: a bibliometric analysis.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1530857},
pmid = {40463443},
issn = {1664-302X},
abstract = {Hypertension is one of the most common cardiovascular diseases, with multiple underlying mechanisms. The gut microbiome, as one of the most important microbial communities in the human body, plays a significant role in the development of various diseases, including hypertension. While numerous studies have explored the relationship between gut microbiome and hypertension from different perspectives, there has been no bibliometric study in this field. Therefore, a bibliometric analysis is crucial for accurately assessing and summarizing the current research status. The analysis indicates that the number of publications in this field has steadily increased in recent years, with China and the United States leading in development. The journal Nutrients has the highest number of published papers, and Marques, Francine Z is a prominent figure with significant contributions and influence in this field. Co-occurrence and trend analysis suggest that the main research hotspots include the relationship between gut microbiome and hypertension, mechanisms by which gut microbiome promotes hypertension, and new therapeutic strategies targeting gut microbiome to improve hypertension. Future research trends may focus on expanding new metabolites or measurement techniques, building databases of human and animal gut microbiota and their metabolites, and developing new drugs targeting gut microbiota for hypertension. In summary, this study visually demonstrates the dynamic changes in research hotspots, revealing new patterns and focuses in the field, and aims to provide new insights for clinical work on hypertension.},
}
@article {pmid40463440,
year = {2025},
author = {Deshpande, SP and Sujith, S and Jobby, R and Rajasekharan, SK and Ravichandran, V and Solomon, AP},
title = {The gut microbiome: an emerging epicenter of antimicrobial resistance?.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1593065},
pmid = {40463440},
issn = {1664-302X},
abstract = {The human gut is one of the most densely populated microbial environments, home to trillions of microorganisms that live in harmony with the body. These microbes help with digestion and play key roles in maintaining a balanced immune system and protecting us from harmful pathogens. However, the crowded nature of this ecosystem makes it easier for harmful bacteria to acquire antimicrobial resistance (AMR) genes, which can lead to multidrug-resistant (MDR) infections. The rise of MDR infections makes treatments harder, leading to more extended hospital stays, relapses, and worse outcomes for patients, ultimately increasing healthcare costs and environmental strain. Since many MDR infections are challenging to treat, nosocomial infection control protocols and infection prevention programmes are frequently the only measures in our hands to stop the spread of these bacteria. New approaches are therefore urgently required to prevent the colonization of MDR infections. This review aims to explore the current understanding of antimicrobial resistance pathways, focusing on how the gut microbiota contributes to AMR. We have also emphasized the potential strategies to prevent the spread and colonization of MDR infections.},
}
@article {pmid40463435,
year = {2025},
author = {Strokach, A and Zoruk, P and Boldyreva, D and Morozov, M and Olekhnovich, E and Veselovsky, V and Babenko, V and Selezneva, O and Zakharevich, N and Larin, A and Koldman, S and Koldman, V and Odorskaya, M and Yunes, R and Pavlov, V and Kudryavtseva, A and Danilenko, V and Klimina, K},
title = {Comparative evaluation of sequencing technologies and primer sets for mouse gut microbiota profiling.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1584359},
pmid = {40463435},
issn = {1664-302X},
abstract = {BACKGROUND: Advancements in sequencing technologies, such as Illumina and Oxford Nanopore Technologies (ONT), have significantly improved microbiome research. However, variations in sequencing platforms, primer selection, and DNA quality may influence microbial diversity assessments, particularly in studies of gut microbiota. This study systematically evaluates these factors in mouse gut microbiota analysis, comparing 16S rRNA gene sequencing and metagenome sequencing (MS) across both platforms.<br><br>RESULTS: Our findings highlight the critical influence of primer selection on 16S rRNA sequencing results, with certain primer combinations detecting unique taxa that others miss. Despite these variations in taxonomic resolution, all tested primer sets consistently revealed significant differences between experimental groups, indicating that key microbial shifts induced by bacterial cultures remain detectable regardless of primer choice. A comparative analysis of Illumina and ONT 16S rRNA sequencing revealed notable differences in microbial diversity profiling, with ONT capturing a broader range of taxa. In contrast, MS on both platforms showed a high degree of correlation, indicating that ONT sequencing errors have minimal impact on taxonomic diversity estimations. Furthermore, the type of extracted DNA (high molecular weight vs. standard DNA) had little on microbial diversity outcomes, underscoring the robustness of these sequencing technologies.<br><br>CONCLUSION: These results highlight the advantages and limitations of different sequencing strategies in microbiota research. While 16S rRNA sequencing remains a cost-effective tool for assessing bacterial diversity, MS provides superior taxonomic resolution and more precise species identification. Our study advocates for a hybrid approach that combines multiple sequencing technologies to achieve a more comprehensive and accurate representation of microbial communities.},
}
@article {pmid40463434,
year = {2025},
author = {Asgharzadeh, S and Pourhajibagher, M and Bahador, A},
title = {The microbial landscape of tumors: a deep dive into intratumoral microbiota.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1542142},
pmid = {40463434},
issn = {1664-302X},
abstract = {Microorganisms in the human body play crucial roles in various health and disease processes. Research indicates that diverse bacterial species are implicated in numerous cancer types. Apart from its involvement in cancer initiation and progression, the microbiome holds promise as a biomarker for diagnosing cancer, assessing risk, and determining prognosis. Intratumoral microbes profoundly impact tumor biology by regulating the initiation and progression of tumors and modulating their response to chemotherapy, radiotherapy, and immunotherapy. A deeper understanding of the role of the intratumoral microbiome in cancer requires further investigation into its effects and underlying mechanisms. This review delves into the significance of intratumoral bacteria in cancer initiation, progression, and metastasis, their impact on cancer treatment outcomes, and Approaches Employed for Profiling the Intratumoral Microbiome.},
}
@article {pmid40463375,
year = {2025},
author = {Fredericks, MN and Kolodner, Z and Waalkes, A and Sawatzki, K and Hao, L and Long, DR and Penewit, K and Midkiff, CC and McCormick, CJ and Beraki, S and Edlefsen, PT and Barrow, J and Greninger, AL and Gale, M and Blair, RV and Salipante, SJ and Fuller, DH and O'Connor, MA},
title = {SIV/SARS-CoV-2 coinfection in rhesus macaques impacts viral shedding, host immunity, the microbiome, and viral evolution.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1587688},
pmid = {40463375},
issn = {1664-3224},
mesh = {Animals ; Macaca mulatta ; *Virus Shedding ; *COVID-19/immunology/virology ; *SARS-CoV-2/immunology/physiology/genetics ; *Simian Immunodeficiency Virus/immunology/physiology ; *Simian Acquired Immunodeficiency Syndrome/immunology/virology ; *Coinfection/immunology/virology ; Disease Models, Animal ; *Microbiota/immunology ; Antibodies, Viral/immunology/blood ; },
abstract = {People living with HIV (PLWH) have an increased risk of severe COVID-19, including prolonged viral shedding and emergence of mutations. To investigate the simian immunodeficiency virus (SIV) macaque model for HIV/SARS-CoV-2 coinfection, seven SIV+ rhesus macaques were co-infected with SARS-CoV-2. COVID-19 in all macaques was mild. SARS-CoV-2 replication persisted in the upper, but not the lower respiratory tract for 14 days post-infection. Animals showed impaired generation of anti-SARS-CoV-2 antibodies and T-cells. Animals also displayed transient changes in microbial communities in the upper airway and gastrointestinal tract. Evidence of SARS-CoV-2 evolution was observed in the upper respiratory tract. This study demonstrates that SIV/SARS-CoV-2 coinfection in rhesus macaques recapitulates aspects of COVID-19 in PLWH. We show that SIV impairs anti-SARS-CoV-2 immunity, potentially leading to prolonged viral shedding, altered pathogenesis, and viral evolution. This highlights the importance of HIV status in COVID-19 and supports the use of this model for HIV/SARS-CoV-2 coinfection.},
}
@article {pmid40463287,
year = {2025},
author = {Mahant, AM and Fong, V and Gromisch, M and Hunte, R and Michael, I and Aguilan, JT and Murphy, K and Keller, MJ and Herold, BC},
title = {Neutralizing Activity of Cervicovaginal Secretions against Herpes Simplex Virus is Mediated by Mucosal IgG and Viral Glycoprotein E and Adversely Impacted by Vaginal Dysbiosis.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.05.15.654401},
pmid = {40463287},
issn = {2692-8205},
abstract = {Genital herpes simplex virus (HSV) recurrences are more common in women with bacterial vaginosis (BV). Prior studies demonstrated that genital tract secretions exhibit variable neutralizing activity against HSV, independent of serostatus, but the relationship of this activity to the vaginal microbiome and underlying mechanisms have not been defined. To test the hypothesis that cervicovaginal antiviral activity is lower in women with BV, we took advantage of cervicovaginal lavage (CVL) available from two studies conducted among women with symptomatic BV and healthy controls. CVL obtained from women with BV had significantly less antiviral activity than controls (p< 0.001). Inhibitory activity correlated negatively and most strongly with Shannon diversity index (p<0.0001). The innate activity did not differ comparing HSV-seropositive versus seronegative participants and no HSV-specific antibodies were detected in CVL. Activity was enriched in the immunoglobulin fraction but was lost when IgG (but not IgA) was depleted. Increasing doses of an anti-glycoprotein E (gE) monoclonal antibody overcame the neutralizing activity, suggesting that interactions between the Fc region of IgG and gE, a viral Fc gamma receptor (FcγR), contribute. Consistent with this notion, CVL had less HSV inhibitory activity against a gE-null virus. Glycan analysis demonstrated a decrease in mature glycans in IgG from CVL with low antiviral activity and treatment of CVL with peptide N-glycanase F, which cleaves N-glycans in IgG, resulted in a loss of HSV inhibitory activity. We speculate that glycosidases elaborated by anaerobic bacteria cleave Fc glycans, resulting in decreased affinity for gE and a reduction in protective activity. IMPORTANCE: This study provides a mechanistic link for the increased risk of HSV infection and replication in the setting of symptomatic bacterial vaginosis and asymptomatic vaginal dysbiosis. Independent of Fab antigen specificity, the Fc region of mucosal IgG may neutralize HSV by binding to glycoprotein E, a viral Fc receptor. Vaginal dysbiosis leads to a loss of Fc glycans and a concomitant decrease in this innate antiviral activity. These findings suggest that viral Fc receptors, previously thought to function only in immune evasion, may also play a protective role. The results highlight the importance of developing and implementing strategies to protect against vaginal dysbiosis.},
}
@article {pmid40463244,
year = {2025},
author = {Alqudah, S and DeLucia, B and Osborn, LJ and Markley, RL and Bobba, V and Preston, SM and Thambidurai, T and Nia, LH and Fulmer, CG and Sangwan, N and Nemet, I and Claesen, J},
title = {Gut microbial conversion of dietary elderberry extract to hydrocinnamic acid improves obesity-associated metabolic disorders.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.05.18.654739},
pmid = {40463244},
issn = {2692-8205},
abstract = {Obesity-associated metabolic disorders such as type 2 diabetes mellitus and metabolic dysfunction associated fatty liver disease are major global health concerns, yet current pharmacological treatments often present with major side-effects. Dietary interventions including polyphenol-rich foods offer a promising complementary option for obesity amelioration, but their efficacy is dependent on specific gut microbial metabolism and the underlying molecular mechanisms mostly remain elusive. Here, we demonstrated that dietary elderberry (Eld) extract abrogates the effects of an obesogenic diet in a gut microbiota-dependent manner, by preventing insulin resistance and reducing hepatic steatosis in mice. We developed a targeted, quantitative liquid chromatography-tandem mass spectrometry method for detection of gut bacterial polyphenol catabolites and identified hydrocinnamic acid as a key microbial metabolite, enriched in the portal vein plasma of Eld supplemented animals. Next, we showed that hydrocinnamic acid potently activates hepatic AMP-activated protein kinase α, explaining its role in improved liver lipid homeostasis. Furthermore, we uncovered the metabolic pathway cumulating in hydrocinnamic acid production in the common gut commensal Clostridium sporogenes . Our characterization of hydrocinnamic acid as a diet-derived, and microbiota-dependent metabolite with insulin-sensitizing and anti-steatotic activities will contribute to microbiome-targeted dietary interventions to prevent and treat obesity-associated metabolic diseases.},
}
@article {pmid40463208,
year = {2025},
author = {Mulay, SA and Vishnivetskaya, TA and Hochanadel, LH and Klingeman, DM and Lloyd, KG and Pelletier, DA and Podar, M},
title = {BONCAT-Live for isolation and cultivation of active environmental microbes.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.05.14.654084},
pmid = {40463208},
issn = {2692-8205},
abstract = {UNLABELLED: In diverse environments, microbes drive a myriad of processes, from geochemical and nutrient cycling to interspecies interactions, including in association with plants and animals. Their physiological state is dynamic and impacted by abiotic and biotic conditions, responding to environmental fluctuations by changes in cellular metabolism, according to their genetic potential. Molecular, cellular and genomic approaches can identify and measure microbial responses and adaptation to environmental changes in native communities. However, isolating the individual microbes that respond to specific changes has been difficult. To address that, we implemented BONCAT-Live, by integrating bio-orthogonal non-canonical amino acid tagging (BONCAT) in diverse native communities, with isolation and cultivation of cells responding to specific stimuli, at different time scales. In frozen Arctic permafrost samples, we identified and isolated dormant bacteria that become active after thawing under native or nutrient enriched conditions. From a Populus tree rhizosphere, we isolated strains that thrive under high concentrations of root exudates that act as defense compounds and nutrients. In the human oral microbiome, we identified and isolated bacteria that rapidly proliferated when exposed to metabolites provided by the host or other co-occurring microbes. Further characterization of isolated bacterial strains will provide opportunities for in depth determination of how these microbes adapt to changes in their environments, individually and as part of model communities.<br><br>IMPORTANCE: Dynamic microbial activity transforms environments and impacts health and disease in associations with plants and animals, including humans. Identifying the contribution of individual microbes to those processes in real time has not been generally compatible with their selective cultivation. BONCAT-Live tracks which microbes in environmental samples are translationally active and couples it with single cell isolation and cultivation. By studying the response of individual community member to specific natural or induced physical or chemical changes in the environment and culturing those organisms, BONCAT-Live enables further insights into microbial metabolic strategies, community dynamics and environmental adaptations.},
}
@article {pmid40463026,
year = {2025},
author = {Fulcher, JA and Newman, K and Pham, B and Li, F and Cho, GD and Elliott, J and Tobin, NH and Shoptaw, S and Gorbach, PM and Aldrovandi, GM},
title = {Comparison of oral and gut microbiome highlights role of oral bacteria in systemic inflammation in HIV.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.05.16.654362},
pmid = {40463026},
issn = {2692-8205},
abstract = {BACKGROUND: Chronic HIV-1 infection is associated with increased inflammation-related comorbidities, despite effective viral suppression with antiretroviral therapy. While the role of the gut microbiome in inflammation is well-studied, the contribution of the oral microbiome remains less clear. This study investigates the relationship between the oral and gut microbiomes in driving systemic inflammation in persons with HIV.<br><br>METHODS: This cross-sectional study utilized archived samples from 198 participants (99 with HIV and 99 without HIV). Oral microbiome composition was analyzed via 16S rRNA sequencing and systemic inflammatory biomarkers were measured using multiplex assays. Gut microbiome data from previous studies were integrated for comparative analyses. Bacterial inflammatory potential was assessed through in vitro co-culture and epithelial barrier permeability assays.<br><br>RESULTS: The oral microbiome in HIV was characterized by increased Veillonella, Capnocytophaga , and Megasphaera , and several decreased genera including Fusobacterium . Using PERMANOVA, we found that the oral microbiome was a significant driver of cytokine variation in HIV compared to the gut microbiome, and identified specific associations with oral Veillonella and Megasphaera . We found no differences in anti- Veillonella parvula serum IgG by HIV status, but IgG titers did correlate with microbial translocation markers sCD14 and LBP in HIV. In vitro studies demonstrated that Veillonella parvula increased oral epithelial barrier permeability and induced monocyte activation.<br><br>CONCLUSIONS: The oral microbiome, particularly Veillonella parvula , may contributes to systemic inflammation in HIV through mechanisms involving epithelial barrier disruption, oral translocation, and monocyte activation.},
}
@article {pmid40462952,
year = {2025},
author = {Zhou, H and Chen, J and Zhang, X},
title = {BMDD: A Probabilistic Framework for Accurate Imputation of Zero-inflated Microbiome Sequencing Data.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.05.08.652808},
pmid = {40462952},
issn = {2692-8205},
abstract = {UNLABELLED: Microbiome sequencing data are inherently sparse and compositional, with excessive zeros arising from biological absence or insufficient sampling. These zeros pose significant challenges for downstream analyses, particularly those that require log-transformation. We introduce BMDD (BiModal Dirichlet Distribution), a novel probabilistic modeling framework for accurate imputation of microbiome sequencing data. Unlike existing imputation approaches that assume unimodal abundance, BMDD captures the bimodal abundance distribution of the taxa via a mixture of Dirichlet priors. It uses variational inference and a scalable expectation-maximization algorithm for efficient imputation. Through simulations and real microbiome datasets, we demonstrate that BMDD outperforms competing methods in reconstructing true abundances and improves the performance of differential abundance analysis. Through multiple posterior samples, BMDD enables robust inference by accounting for uncertainty in zero imputation. Our method offers a principled and computationally efficient solution for analyzing high-dimensional, zero-inflated microbiome sequencing data and is broadly applicable in microbial biomarker discovery and host-microbiome interaction studies. BMDD is available at: https://github.com/zhouhj1994/BMDD .<br><br>AUTHOR SUMMARY: Understanding the microbes living in and on our bodies-the microbiome-relies on analyzing complex sequencing data. However, these data often contain many zeros, either because a microbe is truly absent or simply missed due to insufficient sampling. These missing values make it hard to accurately analyze microbial patterns and identify important differences between groups, especially for methods that work on a log scale. To address this, we developed a new method called BMDD that uses a more realistic model to impute the zeros. Unlike existing tools that assume each microbe follows an unimodal abundance distribution, BMDD allows for microbes to follow a bimodal distribution, so they could behave differently in different conditions. It provides not just a single guess, but a range of possible values to better reflect the uncertainty. Our testing shows that BMDD more accurately recovers the true microbial profiles and improves the ability to detect meaningful differences between groups. This method can help researchers gain clearer insights into how the microbiome affects health and disease.},
}
@article {pmid40462927,
year = {2025},
author = {Imes, AM and Pavelsky, MN and Badal, K and Kamp, DL and Briseño, JL and Sakmar, T and Vogt, MA and Nyholm, SV and Heath-Heckman, EAC and Grasse, B and Septer, AN and Mandel, MJ},
title = {Euprymna berryi as a comparative model host for Vibrio fischeri light organ symbiosis.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.01.10.632448},
pmid = {40462927},
issn = {2692-8205},
abstract = {UNLABELLED: Functional studies of host-microbe interactions benefit from natural model systems that enable exploration of molecular mechanisms at the host-microbe interface. Bioluminescent Vibrio fischeri colonize the light organ of the Hawaiian bobtail squid, Euprymna scolopes , and this binary model has enabled advances in understanding host-microbe communication, colonization specificity, in vivo biofilms, intraspecific competition, and quorum sensing. The hummingbird bobtail squid, Euprymna berryi, can be generationally bred and maintained in lab settings and has had multiple genes deleted by CRISPR approaches. The prospect of expanding the utility of the light organ model system by producing multigenerational host lines led us to determine the extent to which the E. berryi light organ symbiosis parallels known processes in E. scolopes . However, the nature of the E. berryi light organ, including its microbial constituency and specificity for microbial partners, have not been examined. In this report, we isolate bacteria from E. berryi animals and tank water. Assays of bacterial behaviors required in the host, as well as host responses to bacterial colonization, illustrate largely parallel phenotypes in E. berryi and E. scolopes hatchlings. This study reveals E. berryi to be a valuable comparative model to complement studies in E. scolopes .<br><br>IMPORTANCE: Microbiome studies have been substantially advanced by model systems that enable functional interrogation of the roles of the partners and the molecular communication between those partners. The Euprymna scolopes-Vibrio fischeri system has contributed foundational knowledge, revealing key roles for bacterial quorum sensing broadly and in animal hosts, for bacteria in stimulating animal development, for bacterial motility in accessing host sites, and for in vivo biofilm formation in development and specificity of an animal's microbiome. Euprymna berryi is a second bobtail squid host, and one that has recently been shown to be robust to laboratory husbandry and amenable to gene knockout. This study identifies E. berryi as a strong symbiosis model host due to features that are conserved with those of E. scolopes , which will enable extension of functional studies in bobtail squid symbioses.},
}
@article {pmid40462844,
year = {2025},
author = {Morra, M and Marradi, D and Gandini, L and Ivagnes, V and Ottolini, G and Bovio, A and Jabali, G and Maraschi, L and Dada, IA and Chawanda, TV and Gorla, M and Tarasiuk, O and Mocchetti, C and Soluri, MF and Boccafoschi, F and Sblattero, D and Cotella, D},
title = {A non-hypothesis-driven practical laboratory activity on functional metagenomics: "fishing" protein-coding DNA sequences from microbiomes.},
journal = {Frontiers in bioengineering and biotechnology},
volume = {13},
number = {},
pages = {1602982},
pmid = {40462844},
issn = {2296-4185},
abstract = {Practical laboratory of the most functional metagenomics courses focuses on activities aimed at providing specific skills in bioinformatics through the analysis of genomic datasets. However, sequence-based analyses of metagenomes should be complemented by function-based analyses, to provide evidential knowledge of gene function. A "true" functional metagenomic approach relies on the construction and screening of metagenomic libraries - physical libraries that contain DNA cloned from metagenomes of various origin. The information obtained from functional metagenomics will help in future annotations of gene function and serve as a complement to sequence-based metagenomics. Here, we describe a simple protocol for the construction of a metagenomic DNA library, optimized and tested by a team of undergraduate biotechnology students. This protocol is based on a technique developed in our laboratory and currently used for research. Using this protocol, libraries of protein domains can be quickly generated, from the DNA of any intron-less genome, such as those of bacteria or phages. Therefore, these libraries provide a valuable platform for training students in various validation tools, including computational methods - for example, metagenome assembly, functional annotation - and proteomics techniques, including protein expression and analysis. By varying the biological source and validation pipeline, this approach offers virtually limitless opportunities for innovative thesis research projects.},
}
@article {pmid40462511,
year = {2025},
author = {Qian, LM and Wang, SX and Zhou, W and Qin, ZX and Wang, YN and Zhao, Q and Xu, RH},
title = {Individualized metagenomic network model for colorectal cancer diagnosis: insights into viral regulation of gut microecology.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {3},
pages = {},
doi = {10.1093/bib/bbaf208},
pmid = {40462511},
issn = {1477-4054},
support = {Y-HR2020QN-0474//Beijing Xisike Clinical Oncology Research Foundation/ ; 84000-31630002//Sun Yat-sen University clinical research 5010 program/ ; CIRP-SYSUCC-0004//Cancer Innovative Research Program of Sun Yat-sen University Cancer Center/ ; 2019-I2M-5-036//CAMS Innovation Fund for Medical Sciences (CIFMS)/ ; 82173128//National Natural Science Foundation of China/ ; 81930065//National Natural Science Foundation of China/ ; 82321003//National Natural Science Foundation of China/ ; },
mesh = {*Colorectal Neoplasms/diagnosis/virology/microbiology/genetics ; Humans ; *Gastrointestinal Microbiome ; *Metagenomics/methods ; *Metagenome ; Dysbiosis/virology ; },
abstract = {The role of gut microbiota, especially viruses, in colorectal cancer (CRC) pathogenesis remains unclear. This study investigated the interplay between gut microbiota and CRC development. We developed a viral/bacterial sequence analysis pipeline to reanalyze gut metagenomic datasets from eight CRC studies. A multisample co-occurrence network was constructed to delineate microbiota species interconnections. Our analysis confirmed dysbiosis in CRC patients and revealed enrichment of viral species, particularly those hosted by Lactococcus and Escherichia. These viruses were identified as central hubs in the multikingdom interaction network. We developed a network-based model using single sample networks (SSN) that distinguished CRC patients from controls with an area under the curve (AUC) of 0.93. Models combining relative abundance and SSN assessment achieved an AUC of 0.97, outperforming SSN-based models without viral data. This study highlights the crucial role of viruses in the gut microbiome network and their potential as targets for CRC prevention and intervention. Our approach offers a new perspective on noninvasive diagnostic criteria for CRC.},
}
@article {pmid40462354,
year = {2025},
author = {Li, X and Xu, L and Demaree, B and Noecker, C and Bisanz, JE and Weisgerber, DW and Modavi, C and Turnbaugh, PJ and Abate, AR},
title = {Microbiome Single Cell Atlases Generated with a Commercial Instrument.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e2409338},
doi = {10.1002/advs.202409338},
pmid = {40462354},
issn = {2198-3844},
support = {//Florida State University Start-up fund/ ; COA7000-138420-7030928-45-A73H5//UCSF Benioff Center for Microbiome Medicine (BCMM) Trainee Pilot Award/ ; R01HG008978//Foundation for the National Institutes of Health/ ; U01AI129206//Foundation for the National Institutes of Health/ ; R01AI149699//Foundation for the National Institutes of Health/ ; R01EB019453//Foundation for the National Institutes of Health/ ; R01HL122593//Foundation for the National Institutes of Health/ ; R01AT011117//Foundation for the National Institutes of Health/ ; F32GM140808//Foundation for the National Institutes of Health/ ; },
abstract = {Single-cell sequencing is useful for resolving complex systems into their composite cell types and computationally mining them for unique features that are masked in pooled sequencing. However, while commercial instruments have made single-cell analysis widespread for mammalian cells, analogous tools for microbes are limited. Here, EASi-seq (Easily Accessible Single microbe sequencing) is presented. By adapting the single-cell workflow of the commercial Mission Bio Tapestri instrument, this method allows for efficient sequencing of individual microbial genomes. EASi-seq allows tens of thousands of microbes to be sequenced per run and, as it is shown, can generate detailed atlases of human and environmental microbiomes. The ability to capture large genome datasets from thousands of single microbes provides new opportunities in discovering and analyzing species subpopulations. To facilitate this, a companion bioinformatic pipeline is developed that clusters genome by sequence similarity, improving whole genome assembly, strain identification, taxonomic classification, and gene annotation. In addition, the integration of metagenomic contigs with the EASi-seq datasets is demonstrated to reduce capture bias and increase coverage. EASi-seq enables high-quality single-cell genomic sequencing for microbiome samples using a simple workflow run on a commercially available platform.},
}
@article {pmid40462248,
year = {2025},
author = {García-Sánchez, JC and Rovito, SM},
title = {Differences in composition and potential function of the bacterial communities of cave- and surface-dwelling Mexican salamanders.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {56},
pmid = {40462248},
issn = {2524-4671},
support = {Problemas Nacionales FOINS 2015 #721//Consejo Nacional de Humanidades, Ciencias y Tecnolog&#xed;as/ ; Problemas Nacionales FOINS 2015 #721//Consejo Nacional de Humanidades, Ciencias y Tecnolog&#xed;as/ ; },
abstract = {Caves are a challenging environment for many organisms to inhabit, and many cave-dwelling animals are endemic to particular cave systems. Microorganisms in caves have been shown to have a high biosynthetic capacity, likely as a result of intense biological interactions to deal with resource scarcity. Although cave salamanders have been studied extensively in other parts of the world, they have received relatively little attention in Mexico. Declines of some cave-dwelling species may be due to outbreaks of fungal disease, and a better understanding of their cutaneous microbiome could help with future conservation efforts in the face of disease outbreaks. We characterized the cutaneous microbiome of 11 cave-dwelling Mexican salamanders and their relatives from surface environments using high-throughput 16S amplicon sequencing. We expected cave salamanders to have a more diverse microbiome containing more bacteria with potential antifungal capacity compared to forest salamanders. We also estimated networks of associations between bacteria to test the hypothesis that there are more positive associations in caves. Finally, we used a bioinformatic approach to see if bacteria in caves potentially have more metabolic pathways associated with microbial communication as a result of more intense biological interactions in caves. Although we do not find higher skin bacterial diversity in caves compared to forests, we do find differences in microbiome composition between environments, more positive associations between bacteria, and a slightly higher number of metabolic pathways associated with microbial communication in caves. Our results provide some support for an impact of the cave environment on the skin microbiome of Mexican salamanders.},
}
@article {pmid40462245,
year = {2025},
author = {Min, X and Aldar, and Jian, G},
title = {Dietary Supplementation With Mannitol Regulates the Rumen and Intestinal Microbiome, Immune Function, and Antioxidant Capacity of Grazed Mongolian Sheep.},
journal = {Animal science journal = Nihon chikusan Gakkaiho},
volume = {96},
number = {1},
pages = {e70074},
doi = {10.1111/asj.70074},
pmid = {40462245},
issn = {1740-0929},
support = {2020LH03011//Natural Science Foundation of Inner Mongolia Autonomous Region/ ; 2023LHMS03047//Natural Science Foundation of Inner Mongolia Autonomous Region/ ; 2022JBQN088//Fundamental Research Funds for the Inner Mongolia Normal University/ ; },
mesh = {Animals ; *Mannitol/administration &amp; dosage/pharmacology ; *Rumen/microbiology/metabolism/immunology ; Sheep/immunology/microbiology/metabolism/physiology ; *Gastrointestinal Microbiome/drug effects ; *Antioxidants/metabolism ; *Dietary Supplements ; *Diet/veterinary ; *Animal Nutritional Physiological Phenomena ; Animal Feed ; Fermentation/drug effects ; *Intestines/microbiology ; },
abstract = {This study aimed to investigate the short-term effects of mannitol supplementation on grazing Mongolian sheep, including ruminal and intestinal microbiome, serum biochemical parameters, and immune and antioxidant functions. Ten sheep were randomly divided into control and experimental groups (n = 5) receiving without or with 10 g/kg mannitol, respectively. After 20 days, including a 5-day adaptation, mannitol did not affect the average daily gain and rumen fermentation but significantly altered microbial composition, as evidenced by principal coordinates' analysis. The abundances of genera including Rikenellaceae_RC9_gut_group increased notably in the rumen, and those of Alistipes and Norank_f_Muribaculaceae increased in intestine with mannitol supplementation. Mannitol increased the serum concentrations of total protein, albumin, retinol-binding protein, paraoxonase, and total cholesterol and decreased alanine aminotransferase levels. Mannitol also increased the levels of immunoglobulins, interleukins, tumor necrosis factor, interferon, and complements and antioxidant enzyme activities while reducing malondialdehyde and hydrogen peroxide concentrations. The serum total protein positively correlated with Rikenellaceae_RC9_gut_group and Alistipes while negatively correlated with superoxide dismutase and specific microbial genera. Taken together, mannitol supplementation reshapes ruminal and intestinal microbial communities, improving serum biomarkers, immune responses, and antioxidant defenses in grazing Mongolian sheep. These findings offer insights into novel feeding strategies for the management of grazing sheep.},
}
@article {pmid40462143,
year = {2025},
author = {Kindtler, NL and Sheikh, S and Zervas, A and Ellegaard-Jensen, L and Feld, L and Scheel, M and Jiménez, FC and da Fonseca, RR and Laursen, KH and Jacobsen, CS and Ekelund, F},
title = {Small sample amounts from rhizosphere of barley maintain microbial community structure and diversity revealed by total RNA sequencing.},
journal = {Plant methods},
volume = {21},
number = {1},
pages = {79},
pmid = {40462143},
issn = {1746-4811},
abstract = {Total RNA sequencing is a crucial technique in microbial ecology for profiling active microbial communities in various environments, including the rhizosphere. Since total RNA sequencing yields both 16 S and 18 S ribosomal RNA (rRNA), it is effective for taxonomic profiling of the full microbial community in a sample. However, the effectiveness of this approach with limited initial sample amounts remains unclear. In this study, we grew barley in a growth system designed for highly controlled plant experiments using an inert growth medium inoculated with a soil microbiome. Our objectives were two-fold: firstly, to test the feasibility of extracting total RNA from the rhizosphere of barley grown in an inert growth medium consisting of sand and perlite. Secondly, we aimed to address the challenge of extracting comprehensive taxonomic information from minimal amounts of rhizosphere samples from barley plants, using three different amounts of freeze-dried rhizosphere material: 10, 40, and 200 mg. We showed that although smaller sample amounts yielded lower concentrations of extracted RNA, this did not significantly influence the diversity or composition of the rhizosphere microbiome as indicated by SSU rRNA. Our results demonstrate that total RNA sequencing, focusing on SSU rRNA, robustly captures the taxonomic diversity of active rhizosphere microbial communities, even in small initial sample amounts. Effective use of smaller samples opens new possibilities for detailed studies in environments where sample quantity is limited. We also conclude that the growth system applied in this experiment is suitable for highly controlled plant experiments focusing on total RNA extraction from the rhizosphere.},
}
@article {pmid40462080,
year = {2025},
author = {Kobayashi, Y and Fujiwara, N and Murakami, Y and Ishida, S and Kinguchi, S and Haze, T and Azushima, K and Fujiwara, A and Wakui, H and Sakakura, M and Terayama, K and Hirawa, N and Isozaki, T and Yasuzaki, H and Takase, H and Yano, Y and Tamura, K},
title = {Visualizing fatigue mechanisms in non-communicable diseases: an integrative approach with multi-omics and machine learning.},
journal = {BMC medical informatics and decision making},
volume = {25},
number = {1},
pages = {204},
pmid = {40462080},
issn = {1472-6947},
mesh = {Humans ; *Machine Learning ; Female ; *Noncommunicable Diseases ; Male ; Middle Aged ; *Fatigue/metabolism/etiology/genetics/microbiology ; Saliva/chemistry ; Adult ; *Metabolomics ; Microbiota ; Biomarkers ; Aged ; Multiomics ; },
abstract = {BACKGROUND: Fatigue is a prevalent and debilitating symptom of non-communicable diseases (NCDs); however, its biological basis are not well-defined. This exploratory study aimed to identify key biological drivers of fatigue by integrating metabolomic, microbiome, and genetic data from blood and saliva samples using a multi-omics approach.<br><br>METHODS: Metabolomic, microbiome, and single nucleotide polymorphisim analyses were conducted on saliva and blood samples from 52 patients with NCDs. Fatigue dimensions were assessed using the Multidimensional Fatigue Inventory and correlated with biological markers. LightGBM, a gradient boosting algorithm, was used for fatigue prediction, and model performance was evaluated using the F1-score, accuracy, and receiver operating characteristic area under the curve using leave-one-out cross-validation. Statistical analyses included correlation tests and multiple comparison adjustments (p&#x2009;<&#x2009;0.05; false discovery rate&#x2009;<0.05). This study was approved by the Yokohama City University Hospital Ethics Committee (F230100022).<br><br>RESULTS: Plasmalogen synthesis was significantly associated with physical fatigue in both blood and saliva samples. Additionally, homocysteine degradation and catecholamine biosynthesis in the blood were significantly associated with mental fatigue (Holm p&#x2009;<&#x2009;0.05). Microbial imbalances, including reduced levels of Firmicutes negativicutes and Patescibacteria saccharimonadia, correlated with general and physical fatigue (r&#x2009;=&#x2009;-&#x2009;0.379, p&#x2009;=&#x2009;0.006). Genetic variants in genes, such as GPR180, NOTCH3, SVIL, HSD17B11, and PLXNA1, were linked to various fatigue dimensions (r range:&#x2009;-0.539-0.517, p&#x2009;<&#x2009;0.05). Machine learning models based on blood and salivary biomarkers achieved an F1-score of approximately 0.7 in predicting fatigue dimensions.<br><br>CONCLUSION: This study provides preliminary insights into the potential involvement of alterations in lipid metabolism, catecholamine biosynthesis disruptions, microbial imbalances, and specific genetic variants in fatigue in patients with NCDs. These findings lay the groundwork for personalized interventions, although further validation and model refinement across diverse populations are needed to enhance the prediction performance and clinical applicability.},
}
@article {pmid40461936,
year = {2025},
author = {Liao, GY and Dai, S and Bae, E and Singh, S and Klug, J and Pettan-Brewer, C and Ladiges, W},
title = {Morphological features of the domestic house cricket (Acheta domesticus) for translational aging studies.},
journal = {GeroScience},
volume = {},
number = {},
pages = {},
pmid = {40461936},
issn = {2509-2723},
support = {R01 AG057381/AG/NIA NIH HHS/United States ; },
abstract = {Aging alters morphology and locomotor function in diverse organisms, yet standardized model systems for studying these changes remain limited to a relatively few species. Here, we present a comprehensive analysis of age- and sex-dependent morphological variations in house crickets (Acheta domesticus), integrating refined husbandry protocols to enhance reproducibility and translational relevance. To ensure data consistency, we implemented a standardized husbandry framework incorporating self-determined photoperiods, co-housing both sexes, and controlled diet and hydration strategies. We observed progressive increases in body weight, length, and appendage dimensions with age, with pronounced sexual dimorphism emerging post-maturity. Structural adaptations, including increased femoral volume and cross-sectional area, suggest compensatory mechanisms for age-related declines in muscle efficiency, while reduced hind leg-to-body length ratios indicate potential biomechanical constraints on locomotion. Furthermore, antennal growth patterns highlight prolonged sensory investment, potentially offsetting declining mobility in aging individuals. Our results underscore the necessity of harmonizing environmental conditions in gerontological research, as variations in lighting, substrate availability, and microbiome exposure may significantly impact physiological resilience and behavioral fidelity. Future work should explore the influence of microbiome diversity on lifespan and stress resilience while refining methodologies for cricket rearing from egg to adulthood. By bridging invertebrate and vertebrate aging research, this study positions house crickets as a scalable, high-throughput animal model for investigating age-related functional decline, behavioral plasticity, and lifespan-extending interventions. Integrating behavioral assays, biomechanical analyses, and molecular markers of aging will further elucidate the interplay between morphology, function, health, and longevity, advancing the utility of crickets in comparative geroscience.},
}
@article {pmid40461881,
year = {2025},
author = {Yang, L and Wei, W and Wang, Y and Kuai, W and Xu, L},
title = {Causal relationship between gut microbiota and hepatocellular carcinoma: a two-sample Mendelian randomization and case-control study.},
journal = {Discover oncology},
volume = {16},
number = {1},
pages = {994},
pmid = {40461881},
issn = {2730-6011},
support = {23JCYBJC00950//the Natural Science Foundation of Tianjin/ ; 23JCYBJC00950//the Natural Science Foundation of Tianjin/ ; 23JCYBJC00950//the Natural Science Foundation of Tianjin/ ; 23JCYBJC00950//the Natural Science Foundation of Tianjin/ ; 23JCYBJC00950//the Natural Science Foundation of Tianjin/ ; TJYXZDXK-059B//Tianjin Key Medical Discipline(Specialty) Construction Project/ ; TJYXZDXK-059B//Tianjin Key Medical Discipline(Specialty) Construction Project/ ; TJYXZDXK-059B//Tianjin Key Medical Discipline(Specialty) Construction Project/ ; TJYXZDXK-059B//Tianjin Key Medical Discipline(Specialty) Construction Project/ ; TJYXZDXK-059B//Tianjin Key Medical Discipline(Specialty) Construction Project/ ; TJWJ2022XK034//Tianjin Health Science and Technology Project Key Discipline Special/ ; TJWJ2022XK034//Tianjin Health Science and Technology Project Key Discipline Special/ ; TJWJ2022XK034//Tianjin Health Science and Technology Project Key Discipline Special/ ; TJWJ2022XK034//Tianjin Health Science and Technology Project Key Discipline Special/ ; TJWJ2022XK034//Tianjin Health Science and Technology Project Key Discipline Special/ ; },
abstract = {BACKGROUND: Accumulating evidence from both observational studies and clinical trials has established a connection between the gut microbiome and hepatocellular carcinoma (HCC). Nevertheless, the causal relationship between gut microbes and hepatocellular carcinoma remains ambiguous.<br><br>METHODS: The principal study method employed was Mendelian randomization (MR). The exposure group included 7738 samples from the MiBioGen Consortium Gut Microbiota Genome-Wide Association Study (GWAS), whereas the outcome group included 8,885,115 single nucleotide polymorphisms (SNPs) from the IEU OpenGWAS project database of hepatocellular carcinoma (HCC). Utilizing the MR-Egger regression, weighted median (WME), and weighted mode (WM) as supplemental methods for inverse variance weighting (IVW), the main basis was IVW. Additional sensitivity, pleiotropy, and heterogeneity tests were performed. To confirm the MR results, sequencing data from a case-control study were used. We enrolled 29 patients with HBV-HCC who were hospitalized at Tianjin Second People's Hospital between October 2022 and August 2023, and chose 21 healthy employees as controls.<br><br>RESULTS: IVW analysis showed that gut Clostridia (OR&#x2009;=&#x2009;0.554, 95%CI: 0.361-0.850, p&#x2009;=&#x2009;0.007), Clostridiales (OR&#x2009;=&#x2009;0.554, 95%CI: 0.361-0.850, p&#x2009;=&#x2009;0.007), and Dorea (OR&#x2009;=&#x2009;0.679, 95%CI: 0.479-0.964, p&#x2009;=&#x2009;0.030) were protective factors against HCC. Gut Desulfovibrio piger (OR&#x2009;=&#x2009;1.304, 95%CI: 1.080-1.499, p&#x2009;=&#x2009;0.004), Bacteroides ovatus (OR&#x2009;=&#x2009;1.304, 95%CI: 1.046-1.626, p&#x2009;=&#x2009;0.018), Bacteroides stercoris (OR&#x2009;=&#x2009;1.714, 95%CI: 1.183-2.483, p&#x2009;=&#x2009;0.004), and Paraprevotella xylaniphila (OR&#x2009;=&#x2009;1.256, 95%CI: 1.003-1.573, p&#x2009;=&#x2009;0.047) were risk factors for HCC. A case-control study demonstrated that the relative abundances of gut Clostridia, Clostridiales, and Dorea were significantly higher in healthy controls than in patients with HCC. Conversely, the relative abundance of Bacteroides stercoris was lower in healthy controls than in patients with HCC.<br><br>CONCLUSION: This study showed that gut Clostridia, Clostridiales, and Dorea were associated with a reduced risk of HCC, whereas gut Bacteroides stercoris was the exact opposite.<br><br>CONCLUSION: This study demonstrated that gut Clostridia, Clostridiales, and Dorea were linked to a decreased HCC risk, while gut Bacteroides stercoris was linked to an increased HCC risk.},
}
@article {pmid40461820,
year = {2025},
author = {Piccinno, G and Thompson, KN and Manghi, P and Ghazi, AR and Thomas, AM and Blanco-Míguez, A and Asnicar, F and Mladenovic, K and Pinto, F and Armanini, F and Punčochář, M and Piperni, E and Heidrich, V and Fackelmann, G and Ferrero, G and Tarallo, S and Nguyen, LH and Yan, Y and Keles, NA and Tuna, BG and Vymetalkova, V and Trompetto, M and Liska, V and Hucl, T and Vodicka, P and Bencsiková, B and Čarnogurská, M and Popovici, V and Marmorino, F and Cremolini, C and Pardini, B and Cordero, F and Song, M and Chan, AT and Derosa, L and Zitvogel, L and Huttenhower, C and Naccarati, A and Budinska, E and Segata, N},
title = {Pooled analysis of 3,741 stool metagenomes from 18 cohorts for cross-stage and strain-level reproducible microbial biomarkers of colorectal cancer.},
journal = {Nature medicine},
volume = {},
number = {},
pages = {},
pmid = {40461820},
issn = {1546-170X},
support = {101045015//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 825410//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; CGCATF-2023/100036//Cancer Research UK (CRUK)/ ; CGCATF-2023/100041//Cancer Research UK (CRUK)/ ; 1OT2CA297205-01//U.S. Department of Health &amp; Human Services | NIH | NCI | Division of Cancer Epidemiology and Genetics, National Cancer Institute (National Cancer Institute Division of Cancer Epidemiology and Genetics)/ ; OT2CA297680//U.S. Department of Health &amp; Human Services | NIH | NCI | Division of Cancer Epidemiology and Genetics, National Cancer Institute (National Cancer Institute Division of Cancer Epidemiology and Genetics)/ ; },
abstract = {Associations between the gut microbiome and colorectal cancer (CRC) have been uncovered, but larger and more diverse studies are needed to assess their potential clinical use. We expanded upon 12 metagenomic datasets of patients with CRC (n = 930), adenomas (n = 210) and healthy control individuals (n = 976; total n = 2,116) with 6 new cohorts (n = 1,625) providing granular information on cancer stage and the anatomic location of tumors. We improved CRC prediction accuracy based solely on gut metagenomics (average area under the curve = 0.85) and highlighted the contribution of 19 newly profiled species and distinct Fusobacterium nucleatum clades. Specific gut species distinguish left-sided versus right-sided CRC (area under the curve = 0.66) with an enrichment of oral-typical microbes. We identified strain-specific CRC signatures with the commensal Ruminococcus bicirculans and Faecalibacterium prausnitzii showing subclades associated with late-stage CRC. Our analysis confirms that the microbiome can be a clinical target for CRC screening and characterizes it as a biomarker for CRC progression.},
}
@article {pmid40461716,
year = {2025},
author = {Mora-Godínez, S and de la Garza, AL and Tamez-Rivera, O and Senés-Guerrero, C and Carrizales-Sánchez, AK and García-Rivas, G and Hernández-Brenes, C},
title = {Lipidomic signatures linked to gut microbiota alterations in children and adolescents with type 2 diabetes mellitus and metabolic syndrome.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {19427},
pmid = {40461716},
issn = {2045-2322},
support = {875797//Consejo Nacional de Humanidades, Ciencias y Tecnolog&#xed;as/ ; },
mesh = {Humans ; *Diabetes Mellitus, Type 2/microbiology/metabolism/blood ; *Gastrointestinal Microbiome ; Child ; *Metabolic Syndrome/microbiology/metabolism/blood ; Adolescent ; Male ; Female ; *Lipidomics/methods ; *Lipids/blood ; Biomarkers/blood ; Body Mass Index ; },
abstract = {Youth-onset type 2 diabetes mellitus (T2DM) has an aggressive clinical course and is usually preceded by obesity and metabolic syndrome (MetS). Lipids have emerged as potential biomarkers for studying metabolic risk factors and predicting disease progression. An untargeted lipidomic analysis by liquid chromatography-mass spectrometry was performed in thirty pediatric subjects with T2DM and MetS and a healthy group. Plasma lipids were associated with obesity, metabolic risk factors, inflammatory biomarkers, and gut microbiota. A total of 375 lipid species were annotated. MetS and T2DM groups had increased levels of phosphocholines (15-18), phosphoinositols (2-3), sphingomyelins (2-3), and triglycerides (1-4), and lower plasmalogens (2-6) and lysophospholipids (1-2). Phosphocholines, phosphoinositols, sphingomyelins, and triglycerides positively correlated with metabolic risk factors such as body mass index (BMI), waist and hip circumference, triglycerides, glucose, insulin, and HOMA-IR. Ceramides were significantly higher in MetS and T2DM in regression analysis, adjusted for BMI, age, and sex, and only increased with higher BMI in the healthy group. Significant positive correlations were observed for phosphocholines and phosphoinositols with species from the phyla Pseudomonadota and Bacillota, like Weissella cibaria and Enterobacter hormaechei, and the latter species with ceramides. This study provides novel evidence on the role of plasma lipids in the pathophysiology of MetS and T2DM in children and adolescents and their associations with gut microbial species. These findings documented opportunities for developing therapeutic strategies, such as dietary interventions and microbiome modulation, to mitigate the burden of metabolic diseases in pediatric populations.},
}
@article {pmid40461630,
year = {2025},
author = {Koch, M and Lado, S and Bodner-Adler, B and Carlin, G and Pacífico, C and Bauer, C and Cartwright, R and Seki, D and Steininger, C and Makristathis, A and Umek, W},
title = {Women suffering from overactive bladder syndrome exhibit a higher urethral viral abundance compared to healthy controls: a pilot study.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {19484},
pmid = {40461630},
issn = {2045-2322},
support = {1815//OeNB Jubil&#xe4;umsfonds/ ; },
mesh = {Humans ; Female ; *Urinary Bladder, Overactive/virology/microbiology ; Pilot Projects ; Middle Aged ; *Urethra/virology/microbiology ; Microbiota ; Case-Control Studies ; Prospective Studies ; Adult ; Phylogeny ; Aged ; Bacteria/genetics ; Virome ; *Viruses/genetics/isolation &amp; purification/classification ; High-Throughput Nucleotide Sequencing ; },
abstract = {The interactions between the human bacterial microbiome and essential bodily functions are well established for organ systems such as the oral cavity, gut, and female reproductive tract. However, the urinary microbiome, particularly its viral component, remains largely unexplored. Emerging evidence suggests that the urinary microbiome may play a significant role in the development of overactive bladder syndrome (OAB). This study aims to fill this knowledge gap by investigating the potential link between the urethral virome and female overactive bladder syndrome, and by aligning these findings with the bacterial microbiome. Prospective pilot study including 15 patients with overactive bladder syndrome and five controls. Current urinary tract infection and antibiotic therapy within the last two months were ruled out and controls were matched to cases by age and body mass index. Urethral swabs (Copan eSwab[®] urethra) were taken from each participant at one single time point. Subsequent viral isolation, purification, and enrichment were conducted using the ViPEP method. Next-generation sequencing was performed on pooled samples, followed by bioinformatic analysis to identify and classify viral contigs. Phylogenetic analysis was conducted to assess genetic relationships among identified viral sequences. The bacterial microbiome was analyzed by sequencing of the variable V3-4 region of the eubacterial 16 S rDNA gene on the Illumina MiSeq platform. We identified twenty-one viruses and bacteriophages only in pooled urethral swab samples of the OAB group, but no valid detections were retained in the control group after analysis. The most abundant human virus in urethral swab samples was human papilloma virus, whereas the most abundant bacteriophages belong to the family of Siphoviridae. In the bacterial microbiome analysis, we identified statistically higher levels of Veillonella and Bacteroides in OAB samples. Results of this pilot study suggest a difference in the urethral virome between women with OAB and healthy controls. When looking deeper into the detected virus families and species, we might postulate a unique microbial pattern of OAB patients. This pattern suggests an interplay of immunosuppression, autoimmune processes and a larger diversity of bacterial and viral microbes. Current evidence strongly suggests a disturbance of the healthy microbiome of the urogenital tract in patients with OAB, leading to subclinical chronic inflammation and thus typical OAB symptoms. Further research should focus on interventions aimed at restoring a healthy microbiome in OAB patients to mitigate inflammation and improve symptom control.},
}
@article {pmid40461557,
year = {2025},
author = {Buchmann, C and Rudolph, S and Neff, J and Steinmetz, Z},
title = {Impact of polyacrylic acid as soil amendment on soil microbial activity under different moisture regimes.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {19422},
pmid = {40461557},
issn = {2045-2322},
mesh = {*Acrylic Resins/chemistry/pharmacology ; *Soil Microbiology ; *Soil/chemistry ; Hydrogen-Ion Concentration ; Water/chemistry ; Carbon Dioxide ; Microbiota/drug effects ; },
abstract = {Polyacrylic acid (PAA), a synthetic superabsorbent polymer (SAP), enhances the maximum water holding capacity (WHCmax), soil structural stability, and aeration of soil but may simultaneously affect soil microbiome by altering soil properties. However, its effects on microbial activity under different moisture regimes remain insufficiently understood. We examined the impact of PAA on soil microbial activity in a sand and loam treated with PAA at three concentrations (25, 250, 2500 mg kg[- 1] dry soil) either incubated under constant moisture or subjected to ten drying-rewetting cycles. During incubation, soil WHCmax, pH, and soil microbial activity via headspace CO2 and MicroResp assay were measured. PAA increased WHCmax in both soils, yet its effectiveness decreased in loam under static conditions. Initially, PAA acidified both soils, with pH shifts persisting in sand but dissipating in loam after one week. Drying-rewetting cycles counteracted acidification and partially maintained PAA swelling. In sand, high PAA concentrations consistently suppressed microbial respiration across substrate groups, whereas in loam, microbial responses were modulated by moisture dynamics: drying-rewetting enhanced, while static moisture reduced SIR under PAA treatment. Overall, PAA altered soil microbial activity in a concentration-, soil type-, and moisture-dependent manner, emphasizing the dual role of SAPs in improving soil water retention while potentially impairing microbial-mediated soil functions over time.},
}
@article {pmid40461531,
year = {2025},
author = {Marzouk, NH and Rashwan, HH and El-Hadidi, M and Ramadan, R and Mysara, M},
title = {Proinflammatory and GABA eating bacteria in Parkinson's disease gut microbiome from a meta-analysis prospective.},
journal = {NPJ Parkinson's disease},
volume = {11},
number = {1},
pages = {145},
pmid = {40461531},
issn = {2373-8057},
abstract = {Parkinson's disease (PD) is the second most common neurodegenerative disorder, characterized by motor dysfunction coupled with gastrointestinal disturbances. Recent studies implicate the gut microbiome with the development of PD, yet pinpointing the exact microbial players is still to be determined. This meta-analysis is the first to consolidate five homogenous case-control studies, covering the same variable regions of the 16S rRNA of 1007 fecal samples. Utilizing our unified pipeline, we identified several key players potentially contributing to PD. Our findings reveal higher microbial diversity characterized by elevated levels GABA consuming species particularly Evtepia gabavorous, contributing to neuronal excitability. We also report the abundance of the proinflammatory Klebsiella variicola and the H2S-producing Streptococcus anginosus bacteria, potentially promoting α-synuclein accumulation in the brain. This comprehensive analysis highlights the potential of gut microbiota as a biomarker and a therapeutic strategy to mitigate the progression of PD, possibly facilitating diagnosis and enhancing patient outcomes.},
}
@article {pmid40461526,
year = {2025},
author = {Kutos, S and Bennett, RE and Santos, D and Botero-Delgadillo, E and Muletz-Wolz, CR},
title = {Soil and cherry bacterial communities predict flavor on coffee farms.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {19387},
pmid = {40461526},
issn = {2045-2322},
mesh = {*Soil Microbiology ; *Coffea/microbiology ; *Microbiota ; *Bacteria/genetics/classification/isolation &amp; purification ; *Coffee/microbiology ; Farms ; *Prunus avium/microbiology ; *Taste ; Colombia ; },
abstract = {Coffee (Coffea arabica) is a popular beverage worldwide with increasing value placed on sensory qualities as specialty markets grow. Plant-associated microbiomes have emerged as a potential but poorly understood driver of coffee flavor that may interact with other environmental and farm management factors. To determine if coffee plant-associated bacteria are linked with flavor, we collected 320 soil and 320 coffee cherry samples from 22 farms in Cundinamarca, Colombia that varied in farm management system (shade vs. sun-grown) and in flavor (presence vs. absence of a specialty flavor profile). We found, using amplicon sequencing, that soil and cherry bacterial communities differed between sun and shade farms and between farms that did and did not produce specialty flavored coffee, with shade + flavor farms notably distinct. Flavor presence was predicted by the abundance of multiple bacterial strains in soils and cherries, but correlations with flavor differed between sun and shade systems. These bacterial taxa correlated with coffee flavor may guide future efforts to optimize farms for specialty quality characteristics. Overall, the observed complex relationships between plant-associated bacteria and coffee flavor will likely require that initiatives seeking to optimize microbiomes for quality outcomes be tailored to individual farm systems and local conditions.},
}
@article {pmid40461483,
year = {2025},
author = {Li, X and Jin, R and Wang, Z and Niu, C and Song, Z and Liu, X and Huang, J and Zhang, H and Qian, X and Gao, F and Wang, S and Yu, C and Sun, L and Huang, Y and Zheng, L and Wang, G and Sun, Y and Yang, X and Bao, Y and Li, J},
title = {TSP50 deficiency in neural stem cells aggravates colitis in mice by altering intestinal microbiome.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {93},
pmid = {40461483},
issn = {2055-5008},
support = {No. SZSM202311023//Sanming Project of Medicine in Shenzhen/ ; No. ynkt2021-zz38//Guangdong High-level Hospital Construction Fund of Shenzhen Children's Hospital/ ; No. 202101011196JC, 20210101198JC//the Research Foundation of Jilin Provincial Science and Technology Development/ ; No. 135131002//the Fundamental Research Funds for the Central Universities/ ; GZC20240236//the Postdoctoral Fellowship Program of CPSF/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; Mice ; *Neural Stem Cells/metabolism ; *Colitis/microbiology/pathology/genetics ; Intestinal Mucosa/microbiology/metabolism ; Acetylcholine/metabolism ; Disease Models, Animal ; Male ; Mice, Inbred C57BL ; Acetylcholinesterase/metabolism ; Inflammatory Bowel Diseases/microbiology ; },
abstract = {Inflammatory bowel disease (IBD) is a complex disease characterized by persistent chronic inflammation of the gastrointestinal tract and periodic episodes. Despite the increasing number of related studies, the detailed pathogenesis of IBD has not been elucidated. In recent years, host-microbiota interactions in the pathogenesis of IBD have received extensive attention. Testes-specific protease 50 (TSP50) is a potential risk gene for IBD, but whether it can affect the susceptibility of colitis by regulating the gut microbiome is still unclear. Here, we showed that TSP50 deficiency in neural stem cells (NSCs) aggravated colitis in mice by altering intestinal microbiome. Mechanistically, TSP50 maintained the level of neurotransmitter acetylcholine (ACh) by degrading acetylcholinesterase (AChE), thereby maintaining intestinal mucosa and intestinal microecological homeostasis and reducing the susceptibility to colitis. These findings provide a new perspective on the interaction between host and commensal microbiota, which may be beneficial for developing potential therapeutic strategies for IBD.},
}
@article {pmid40461354,
year = {2025},
author = {Yao, RA and Berrin, JG and McKee, LS and Bissaro, B},
title = {Fungal cell walls: the rising importance of carbohydrate-active enzymes.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2025.05.001},
pmid = {40461354},
issn = {1878-4380},
abstract = {As the interface between the fungal cell and its surroundings, the fungal cell wall (FCW) plays an essential physiological role in a myriad of biological processes. It provides support, protection, and enables material exchange with the environment, playing a key role in microbiome and host-microbe interactions. The fact that FCWs are mainly composed of complex carbohydrates makes carbohydrate-active enzymes (CAZymes) the main players in FCW remodelling and degradation. Despite the biological importance of these processes, our understanding of the underlying enzymology remains limited. In this review, we discuss the role of FCW-active CAZymes in various contexts, including fungal physiology, pathogenesis, human gut microbiomes, and the global carbon cycle, while highlighting knowledge gaps and potential applications in agriculture, biotechnology, and health.},
}
@article {pmid40461059,
year = {2025},
author = {Laiola, M and Koppe, L and Larabi, A and Thirion, F and Lange, C and Quinquis, B and David, A and Le Chatelier, E and Benoit, B and Sequino, G and Chanon, S and Vieille-Marchiset, A and Herpe, YE and Alvarez, JC and Glorieux, G and Krukowski, H and Geert, HRB and Raes, J and Fouque, D and Massy, ZA and Ehrlich, SD and Stengel, B and Wagner, S and , },
title = {Toxic microbiome and progression of chronic kidney disease: insights from a longitudinal CKD-Microbiome Study.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2024-334634},
pmid = {40461059},
issn = {1468-3288},
abstract = {BACKGROUND: The gut microbiota has been linked to non-communicable diseases, including chronic kidney disease (CKD). However, the relationships between gut microbiome composition changes, uraemic toxins (UTs) accumulation, and diet on CKD severity and progression remain underexplored.<br><br>OBJECTIVE: To characterise relationships between gut microbiome composition and functionality, UTs diet, and CKD severity and progression, as well as assess microbial contributions to UTs accumulation through mice faecal microbiota transplantation (FMT).<br><br>DESIGN: This study profiled the gut microbiome of 240 non-dialysis patients with CKD (CKD-REIN cohort) using shotgun metagenomics, with follow-up in 103 patients after 3 years, with comparisons with healthy volunteers from the Milieu Int&#xe9;rieur cohort. A multiomics approach identifies features associated with CKD severity (and progression), with validation in an independent Belgian cohort. Experimental models used FMT to test CKD gut microbiome effects on UTs and kidney fibrosis. Changes in gut microbiome over time were evaluated, and the impact of diet on these changes was assessed.<br><br>RESULTS: Compared with matched healthy controls, patients with CKD exhibited gut microbiota alteration, with enrichment of UT precursor-producing species. Patients with severe CKD exhibited higher UT levels and greater enrichment of UT (precursor)-producing species in the microbiota than patients with moderate CKD. Over time, UT (precursor)-producing species increased, and a plant-based low protein diet appeared to mitigate these changes. FMT from patients with CKD to antibiotic-treated CKD model mice increased serum UT levels and exacerbated kidney fibrosis.<br><br>CONCLUSIONS: This study highlights the role of the microbiome and UTs in CKD, suggesting a potential therapeutic target to slow disease progression.},
}
@article {pmid40460904,
year = {2025},
author = {Zhou, X and Ma, J and Qiao, M and Wang, Y and Cao, ZH and Su, JQ and Xie, WY and O'Connor, P and Li, G},
title = {Converting pig manure into biochar mitigates the antibiotic resistance of vegetable endophytes.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {381},
number = {},
pages = {126587},
doi = {10.1016/j.envpol.2025.126587},
pmid = {40460904},
issn = {1873-6424},
abstract = {Manure applications can facilitate the transmission of antibiotic resistance genes (ARGs) from the soil to the plant microbiome, with detrimental effects on human health through the food chain. Interventions to mitigate the spread of ARGs from animal waste to plants are essential for food safety. We previously demonstrated that converting composted manure into biochar can effectively mitigate the spread of ARGs into soil. However, it remains unclear whether compost-derived biochar can decrease the spread of ARGs in the vegetable endosphere. In this study, a pot experiment involving pakchoi (Brassica chinensis) was conducted to investigate the effects of compost-derived biochar on endophytic ARGs and the pakchoi microbiome. A total of 99 ARGs and 7 mobile genetic elements (MGEs) were identified in endophytes via high-throughput quantitative PCR. Compared with the compost amendment, the application of biochar produced from composted pig manure significantly decreased the diversity of ARGs and MGEs in vegetable endophytes. The abundance of ARGs, MGEs, and bacteria closely related to known pathogens in roots treated with biochar was much lower than that in roots treated with compost, but was similar to that in the control treatment. Fertilizer treatments influenced endophytic bacterial community assembly, while bacterial communities played an important role in shaping ARG profiles. Overall, the transmission of ARGs from animal waste to endophytic microbiomes in vegetables can be effectively mitigated using biochar derived from manure.},
}
@article {pmid40460898,
year = {2025},
author = {Palma, G and Bruzzese, F and Meo, C and de Nigris, F},
title = {Raf kinase inhibitor protein modulator of gut microbiota and immunotherapy responses in cancer.},
journal = {Biochimica et biophysica acta. Reviews on cancer},
volume = {},
number = {},
pages = {189364},
doi = {10.1016/j.bbcan.2025.189364},
pmid = {40460898},
issn = {1879-2561},
abstract = {Cancer progression and the therapeutic efficacy of targeted treatments are increasingly recognized to be influenced by the gut microbiota (GM). This is particularly evident in the context of immunotherapies, as the composition of the GM can modulate the immune system through different mechanisms. Emerging evidence suggests that Raf kinase inhibitor protein (RKIP), a well-established tumor suppressor, may shape the GM by regulating immune and inflammatory pathways. Altered RKIP expression within tumors can reprogram the tumor microenvironment and microbiota composition, ultimately influencing the response to immunotherapy. In this review, we explore the complex interplay between RKIP, downstream pathway, the microbiota, and immunotherapy. Drawing from both preclinical and clinical studies, we examine how RKIP and kinase inhibitors change microbial composition and immune modulation, and how these interactions affect immunotherapeutic outcomes. A deeper understanding of these mechanisms could guide the development of more effective cancer treatment strategies and highlight the microbiome's potential role in shaping immunotherapy responses.},
}
@article {pmid40460824,
year = {2025},
author = {Gogokhia, L and Tran, N and Grier, A and Nagayama, M and Xiang, G and Funez-dePagnier, G and Lavergne, A and Ericsson, C and Ben Maamar, S and Zhang, M and Battat, R and Scherl, E and Lukin, DJ and Longman, RS},
title = {Donor composition and fiber promote strain engraftment in a randomized controlled trial of fecal microbiota transplant for ulcerative colitis.},
journal = {Med (New York, N.Y.)},
volume = {},
number = {},
pages = {100707},
doi = {10.1016/j.medj.2025.100707},
pmid = {40460824},
issn = {2666-6340},
abstract = {BACKGROUND: Fecal microbiota transplantation (FMT) is an emerging treatment for ulcerative colitis (UC), but the impact of prebiotic fiber on FMT efficacy for UC is unclear. We performed a randomized, double-blind, placebo-controlled clinical trial to examine the efficacy of FMT with and without dietary fiber supplementation in patients with UC.<br><br>METHODS: 27 patients with mild to moderate UC were randomized to receive a single FMT or placebo with or without psyllium fiber supplementation for 8 weeks. The primary outcome was clinical response at week 8, and secondary outcomes included endoscopic improvement and clinical remission. Metagenomic sequencing of fecal DNA was analyzed to determine taxonomic profiles and donor strain engraftment.<br><br>FINDINGS: The trial was terminated early due to manufacturer discontinuation of FMT product. FMT induced clinical response, remission, and endoscopic improvement in UC patients compared to placebo (p < 0.05), but fiber did not improve clinical outcomes of FMT. Recipient microbiome composition post-FMT shifted toward donor composition in responders and non-responders, but the durability of this change was stronger in responders. Clinical response and durable change in microbiome composition following FMT was donor dependent. Strain tracking analysis also demonstrated a donor-dependent variability in the rate of successful engraftment and identified a consortium of engrafted bacteria associated with treatment response or fiber supplementation.<br><br>CONCLUSIONS: Single-dose FMT demonstrated clinical efficacy for mild to moderate UC compared to placebo but revealed no benefit of fiber supplementation. These results highlight proof of concept that donor selection and prebiotic fiber can shape strain-level engraftment. This study was registered at ClinicalTrials.gov: NCT03998488.<br><br>FUNDING: National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Diseases (R01 DK128257, to R.S.L.).},
}
@article {pmid40460635,
year = {2025},
author = {Cui, J and Ding, W and Li, S and Wu, X and Wang, J and Su, Q and Qi, J and Sun, X and Fu, J},
title = {Insights into the synergistic mechanisms of citric acid in detoxifying cadmium in tall fescue.},
journal = {Journal of hazardous materials},
volume = {494},
number = {},
pages = {138693},
doi = {10.1016/j.jhazmat.2025.138693},
pmid = {40460635},
issn = {1873-3336},
abstract = {Tall fescue (Festuca arundinacea) can potentially be utilized as an accumulator species for cadmium (Cd) phytoremediation, whereas Cd toxicity can be alleviated by citric acid (CA). This study systematically explored the mechanisms of CA in reducing the toxicity of Cd to tall fescue from morph-physiological, biochemical, ecological and bioinformatics perspectives. Results showed that CA enhanced energy via the tricarboxylic acid cycle and increased antioxidants through the phenylpropanoid and amino acids metabolic pathways, thereby stabilizing photosynthesis and improving Cd tolerance in tall fescue. Morphologically, CA widened root cell wall by increasing lignin, hemicellulose and pectin, leading to enhanced Cd adsorption and restricted Cd migration. Fungal nutrient types were specifically recruited, including 34 Cd-resistant fungi contributing to detoxify Cd. CA-altered soil environments interacted with root exudates, which chelated Cd and showed a strong correlation with Cd-resistant fungi. Synergistic interactions through five pathways for CA-mediated Cd detoxification among root exudates, soil factors, and microbes were disclosed, with fungi contributing the most (17.6 %). Collectively, this study revealed the CA alleviated Cd toxicity through a synergistic interaction network across multiple dimensions. The identified metabolites, microbes and soil factors could serve as indicators for future research on Cd detoxification in other crops or perennial grasses.},
}
@article {pmid40460625,
year = {2025},
author = {Xie, H and Wang, X and Cui, L and Chen, R and Zhao, R and Yu, Y and Chen, D and Yu, YL and Li, B and Li, YF},
title = {Life-long impacts of nanoplastics to rice plant (Oryza sativa L.): Decreased grain yield with perturbed metallome and soil microbiome.},
journal = {Journal of hazardous materials},
volume = {494},
number = {},
pages = {138787},
doi = {10.1016/j.jhazmat.2025.138787},
pmid = {40460625},
issn = {1873-3336},
abstract = {Approximately 367 million metric tons of plastic were produced globally in 2020, and it is projected that the global plastic waste will reach around 12,000 metric tons by 2050. Plastic waste can be fragmented into nanoplastics (NPs). Despite their widespread presence in the environment and even within the human body, the long-term risks of NPs to plants, animals, and humans remain poorly understood. This study investigated the life-long impacts of nano polyethylene terephthalate (nPET) on rice (Oryza sativa L.), which is a staple food for a significant portion of the global population. We found that nPET exposure at environmentally relevant concentrations negatively affected rice growth, compromising grain quality and yield. nPET exposure disrupted the metallome, interfered with chlorophyll synthesis, and induced oxidative stress in rice plants. Additionally, nPET exposure influenced soil health, as evidenced by increased soil organic matter (SOM) during the tillering and flowering stages. The soil microbial community were significantly perturbed, with distinct β-diversity observed between nPET-exposed and control soils, including variations in species abundance at the phylum and family levels. Moreover, nPET exposure affected soil microbiota involved in carbon, nitrogen, and sulfur cycles, with specific species capable of degrading PET being identified. Overall, exposure to environmentally relevant concentrations of nPET led to reduced rice grain yield and compromised soil health, characterized by perturbed metallome and soil microbiome. Therefore, effective management of NPs in soils is urgently needed to ensure food safety and soil health.},
}
@article {pmid40460541,
year = {2025},
author = {Kang, MG and Kwak, MJ and Kang, A and Park, J and Lee, DJ and Mun, J and Kim, S and Mun, D and Lee, W and Choi, H and Seo, E and Choi, Y and Jeong, KC and Oh, S and Kim, J and Kim, Y},
title = {Metagenome-based microbial metabolic strategies to mitigate ruminal methane emissions using Komagataeibacter-based symbiotics.},
journal = {The Science of the total environment},
volume = {987},
number = {},
pages = {179793},
doi = {10.1016/j.scitotenv.2025.179793},
pmid = {40460541},
issn = {1879-1026},
abstract = {Global warming increasingly threatens organisms in equatorial regions, where temperatures often exceed physiological limits. Rumen methanogens are a major biological source of anthropogenic methane, a potent greenhouse gas. Therefore, ruminal methane mitigation strategies that preserve animal productivity are urgently needed. Our In vitro analysis of Holstein steer rumen fluid-integrating gas production, volatile fatty acid (VFA) profiles, and metagenomic data-demonstrated that kombucha, a fermented beverage, effectively reduces methane emissions by modulating ruminal fermentation. Rumen fluid was incubated for 60 h under three treatments (control, 3-NOP, and kombucha). During the initial 30 h, kombucha reduced methane by 15.07 % compared to the control but was 17.54 % higher than 3-NOP. In the subsequent 30 h, kombucha achieved sustained reductions of 34.72 % versus the control and 26.28 % versus 3-NOP, highlighting its uniquely sustained methane-reducing effect. A metagenomics-guided screening and in vitro validation identified Komagataeibacter intermedius SLAM-NK6B as a key strain underlying the methane-reducing effect of kombucha. The genome of SLAM-NK6B encodes biosynthetic gene clusters for cellulose, malate, citrate, and methanobactin-metabolites that can modulate the rumen microbiota. SLAM-NK6B supplementation reduced methanogen abundance by 53.32 % and increased hydrogen pressure, shifting microbial metabolism. Excluding acetate, VFA production increased significantly, with propionate levels elevated by 15.39-43.81 %. Metagenomic data further indicated activation of alternative hydrogen sink pathways, including citrate-to-propionate and malate-to-propionate conversions. This study proposes a novel microbial metabolic strategy for methane mitigation, enabling both methane reduction and enhanced fermentation efficiency. Such metabolic guidance of the rumen microbiome offers a sustainable approach to low-emission ruminant production.},
}
@article {pmid40460378,
year = {2025},
author = {Tokumaru, T and Toyama, T and Nakade, Y and Ogura, H and Oshima, M and Nakagawa, S and Mita, M and Miyagawa, T and Kitajima, S and Hara, A and Sakai, N and Shimizu, M and Iwata, Y and Wada, T},
title = {Effects of sake lees intake on fecal uremic toxins, plasma D-alanine, constipation, and gut microbiome in healthy adults: A single-arm clinical trial.},
journal = {PloS one},
volume = {20},
number = {6},
pages = {e0325482},
pmid = {40460378},
issn = {1932-6203},
mesh = {Humans ; *Constipation/diet therapy/blood/microbiology ; *Gastrointestinal Microbiome ; Middle Aged ; Male ; Female ; *Feces/chemistry/microbiology ; Adult ; *Uremic Toxins/metabolism/analysis ; *Alanine/blood ; Pilot Projects ; Indoles/analysis ; },
abstract = {BACKGROUND: Sake lees consumption has the potential to reduce uremic toxins by influencing the gut microbiome. To lay the groundwork for a clinical trial targeting chronic kidney disease (CKD) patients, we conducted a pilot study to explore the relationship between sake lees intake and changes in fecal uremic toxin levels among individuals with constipation. D-alanine, a renoprotective component of sake lees, was also evaluated.<br><br>METHODS: This single-arm, before and after study lacked a control group. Participants met the diagnostic criteria for chronic constipation. They consumed 25 or 50&#x2009;g of sake lees daily for 6 weeks. The primary endpoint was the change in fecal indole levels from baseline. Secondary endpoints included changes in plasma D-alanine, Constipation Scoring System (CSS) scores, and the composition of the fecal microbiome.<br><br>RESULTS: Eight participants, with a mean age of 46 years, completed the study. Percentage changes in fecal indole levels were +42%,&#x2009;+&#x2009;52%, and -6% at weeks 2, 4, and 6, respectively. Plasma D-alanine levels showed percentage changes of +39%,&#x2009;+&#x2009;24%, and +38% at the same time points. CSS scores improved from 9.2 to 6.8 by week 2 and remained stable after week 4. The proportion of the phylum Firmicutes in the gut microbiome increased slightly from 53% at baseline to 57% by week 6.<br><br>CONCLUSION: Sake lees intake may reduce fecal uremic toxins, elevate plasma D-alanine levels, alleviate constipation, and modify the gut microbiome. However, future studies are needed to confirm these effects in patients with CKD.},
}
@article {pmid40460250,
year = {2025},
author = {Voermans, B and Gerdes, V and Nieuwdorp, M},
title = {Gut microbiota alterations and their role in the pathophysiology of obesity following bariatric surgery.},
journal = {Expert review of endocrinology &amp; metabolism},
volume = {},
number = {},
pages = {1-15},
doi = {10.1080/17446651.2025.2512551},
pmid = {40460250},
issn = {1744-8417},
abstract = {INTRODUCTION: Obesity is a global epidemic associated with significant health risks, including type 2 diabetes, cardiovascular diseases, and metabolic disorders. Bariatric surgery remains the gold standard for achieving significant and sustained weight loss. This narrative review was created using literature searches in PubMed, Web of Science, and Scopus.<br><br>AREAS COVERED: Bariatric surgery induces shifts in gut microbiota composition, with changes in alpha and beta diversity and alters microbial phyla, such as Bacillota, Bacteroidota, Actinomycetota, Pseudomonadota, and Verrucomicrobiota. Genera and species belonging to these groups that have been associated with the pathophysiology of obesity are reported altered as well. These microbial changes, particularly after Roux-en-Y gastric bypass surgery, are generally linked to cardiometabolic improvements to gut hormone profiles and bile acid metabolism.<br><br>EXPERT OPINION: This review focuses on the changes in gut microbiota following Roux-en-Y gastric bypass (RYGB) and sleeve gastrectomy (SG), highlighting longitudinal human studies. Despite conflicting results, some genera, such as Veillonella, Streptococcus, and Akkermansia muciniphila, show consistent increases post-surgery and may serve as markers of metabolic improvements. The predominance of facultative anaerobes suggests a shift in the gut environment post-surgery. These findings are mainly associations and could be further developed into treatment with the use of next-generation probiotics.},
}
@article {pmid40460162,
year = {2025},
author = {Loganathan, T and Doss C, GP},
title = {Gut microbiota and its influence on the Gut-Brain axis in comparison with chemotherapy patients and cancer-free control data in Breast cancer-A computational perspective.},
journal = {PloS one},
volume = {20},
number = {6},
pages = {e0324742},
pmid = {40460162},
issn = {1932-6203},
mesh = {Humans ; *Breast Neoplasms/drug therapy/microbiology ; *Gastrointestinal Microbiome/drug effects/genetics ; Female ; RNA, Ribosomal, 16S/genetics ; Middle Aged ; Adult ; Case-Control Studies ; *Brain ; Bacteria/genetics/classification ; },
abstract = {Breast cancer (BC) continues to be a major cause of cancer-related illness and death among women worldwide. Traditional treatments include surgery, radiation, hormone therapy, and chemotherapy, but these approaches often face challenges due to variability in patient response and adverse effects. This study investigated the relationship between gut microbiome diversity, community composition, and pathway analysis in women undergoing chemotherapy for BC (During Treatment-DT) compared to cancer-free controls (CFC). Using 16S rRNA amplicon sequencing, the study assessed alpha and beta diversity. Results showed differences in microbiome composition between DT and CFC samples, with Firmicutes being highly abundant in both groups. Core microbiome and correlation analysis at the phylum and genus levels identified significant microbiota. Specifically, the abundance of genera such as Pseudomonas and Akkermansia decreased, while Ruminococcus and Allistipes increased, as determined by statistical and machine learning approaches. Disease associations were examined based on KO abundance, identifying links to conditions such as autism spectrum disorder, Clostridium difficile infection, chronic kidney disease, and multiple sclerosis. Key KEGG pathways enriched in DT and CFC groups included the two-component system, tyrosine metabolism, and the pentose phosphate pathway. Conversely, dysbiosis or the presence of pathogenic bacteria (Ruminococcus) associated with the SOX8 gene could lead to chemoresistance, altered metabolic pathways, and increased toxicity. These findings underscore the potential implications for treatment outcomes and personalized medicine.},
}
@article {pmid40460149,
year = {2025},
author = {Dodson, B and Suner, T and Haar, ELV and Han, YW},
title = {Oral Microbiome and Adverse Pregnancy Outcomes.},
journal = {American journal of reproductive immunology (New York, N.Y. : 1989)},
volume = {93},
number = {6},
pages = {e70107},
doi = {10.1111/aji.70107},
pmid = {40460149},
issn = {1600-0897},
support = {R01DE029532//National Institute of Dental and Craniolfacial Research/ ; R01CA292464/CA/NCI NIH HHS/United States ; },
mesh = {Humans ; Female ; Pregnancy ; *Microbiota/immunology ; Pregnancy Outcome ; *Mouth/microbiology ; *Fusobacterium nucleatum ; *Pregnancy Complications, Infectious/microbiology/immunology ; Premature Birth/microbiology ; Fatty Acids, Omega-3/therapeutic use ; Placenta/microbiology/immunology ; Animals ; },
abstract = {Intrauterine infection plays a pivotal role in adverse pregnancy outcomes including preterm birth, stillbirth, neonatal sepsis, and pregnancy-associated hypertension and diabetes. Development of culture-independent microbial detection technologies have greatly advanced our knowledge of microbes implicated in intrauterine infection. Increasing evidence demonstrates the involvement of oral bacteria, especially Fusobacterium nucleatum, in adverse pregnancy outcomes. This review summarizes the oral bacteria detected in intrauterine cavity, their route of dissemination and consequences, and the use of omega-3 fatty acids to suppress microbial-induced placental inflammation.},
}
@article {pmid40460144,
year = {2025},
author = {Alley, AW and Łaniewski, P and Bruno, GT and Moffitt, DV and Arani, G and Farland, LV and Herbst-Kralovetz, MM},
title = {Vaginal Microbiome Dominated by Lactobacillus Positively Impacts Clinical Pregnancy in Patients With Frozen Embryo Transfers.},
journal = {American journal of reproductive immunology (New York, N.Y. : 1989)},
volume = {93},
number = {6},
pages = {e70108},
doi = {10.1111/aji.70108},
pmid = {40460144},
issn = {1600-0897},
mesh = {Humans ; Female ; Pregnancy ; *Vagina/microbiology ; *Embryo Transfer ; Adult ; *Microbiota ; *Lactobacillus/physiology/genetics ; Prospective Studies ; Cryopreservation ; RNA, Ribosomal, 16S/genetics ; Cohort Studies ; },
abstract = {PROBLEM: There is evidence that the bacterial microbiome of the female reproductive tract affects fertility outcomes, but the findings are conflicting, and studies are lacking in racially and ethnically diverse populations.<br><br>METHOD OF STUDY: In this prospective cohort study, vaginal swabs were collected from 87 female patients at time of frozen embryo transfer (FET) after oral estradiol preparation of the endometrium. The primary outcome was an ultrasound demonstrating a viable intrauterine pregnancy. 16s rRNA gene sequencing was performed on the swabs to compare the vaginal microbiome between those who achieved a viable pregnancy compared to those who did not.<br><br>RESULTS: A total of 87 patients participated in the study, of whom 25% (22/87) reported a race other than White and 17% (15/87) identified as Hispanic. There were 55 patients who achieved clinical pregnancy. Patients who achieved pregnancy had a significantly higher prevalence of Lactobacillus-dominant profiles: 67% (37/55) compared with 41% (13/32) of the nonpregnant group (p = 0.024), with a relative risk of pregnancy of 1.52 [1.05, 2.20]. Nonpregnant patients exhibited more Enterobacteriacae and other opportunistic pathogens. Hispanic patients in the study cohort demonstrated decreased clinical pregnancy rates (p = 0.021) and lower Lactobacillus dominance (p = 0.01) compared to non-Hispanic White women.<br><br>CONCLUSIONS: This study suggests that a vaginal microbiome predominated by Lactobacillus is associated with successful embryo implantation and early establishment of pregnancy after FET. Decreased Lactobacillus dominance may contribute to reproductive outcome disparities among Hispanic women. These findings support the consideration of the female reproductive microbiome in the evaluation and treatment of infertility.},
}
@article {pmid40459942,
year = {2025},
author = {Woestmann, F and Strubl, S and Farowski, F and Arjune, S and Tsakmaklis, A and Todorova, P and Späth, MR and Brodesser, S and Baar, T and Grundmann, F and Vehreschild, MJGT and Müller, RU},
title = {The Gut Microbiome in Autosomal Dominant Polycystic Kidney Disease: A Cross-Sectional Study.},
journal = {Kidney360},
volume = {},
number = {},
pages = {},
doi = {10.34067/KID.0000000836},
pmid = {40459942},
issn = {2641-7650},
abstract = {BACKGROUND: Changes in gut microbiota signatures have been associated with chronic kidney disease and nephrolithiasis and may thus be a factor explaining variability of outcome in ADPKD. We aimed to characterize the intestinal microbiome in a cross-sectional study of patients with ADPKD and to explore the potential impact of microbiome signatures on PKD disease progression.<br><br>METHODS: This observational cross-sectional pilot study recruited 25 patients from the AD(H)PKD patient cohort and 12 healthy, age- and sex matched control subjects. The gut microbiome was analyzed by 16S rRNA gene profiling of stool samples. Bacteria-derived serum uremic toxins were measured using liquid chromatography coupled to tandem mass spectrometry. Microbiome data was correlated with age, kidney function, and markers of PKD disease progression like Mayo classification and arterial hypertension <35 years of age.<br><br>RESULTS: Patients with ADPKD displayed a significantly decreased abundance of Actinobacteria including probiotic Bifidobacteriaceae and significantly increased abundance of Enterobacteriaceae. Those findings were independent of kidney function. Most notably, Streptococcaceae were significantly overrepresented in patients with Mayo Classes 1D and 1E compared to 1A-1C. Additionally, early onset of hypertension (< 35 years of age) was associated with an increased abundance of Proteobacteria and a decreased abundance of Tannerelleaceae. Furthermore, patients with ADPKD revealed an increased abundance of Peptococcaceae with increasing age and declining kidney function. Finally, serum uremic toxin levels were significantly increased in patients with ADPKD, highly correlating with eGFR.<br><br>CONCLUSIONS: This pilot study suggests relevant changes in gut microbiota signatures of patients with ADPKD which might be associated with rapid disease progression. These findings indicate that composition of the gut microbiota could potentially contribute to disease progression of ADPKD and the individual disease variability. Further investigation is warranted to assess the gut microbiota as a potential therapeutic target in ADPKD.},
}
@article {pmid40459917,
year = {2025},
author = {Ricci, S and Duplessis, M and Royer, I and Talbot, G and Martineau, C and Poulin-Laprade, D and Petri, RM},
title = {Assessment of microbial composition across the quebec dairy farm-scape.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxaf132},
pmid = {40459917},
issn = {1365-2672},
abstract = {AIMS: The aim of this preliminary study was to evaluate the shared composition and structure of the microbiome between cow feces, milk, manure, and soil samples across dairy farms in Quebec.<br><br>METHODS AND RESULTS: Analysis of the prokaryotic 16S, eukaryotic 18S, and fungal ITS rRNA genes was used to detect community structures, diversities, and spatial compositions, alongside potential contamination routes. Community structures of prokaryotic, eukaryotic and fungal microbiomes were significantly different between niches and could be separated based on mean temperature. Bacteria and eukaryotes showed the highest diversity in fecal samples, whereas fungi were most diverse in soil. Percent of amplicon sequence variants (ASVs) shared between feces, manure and the other matrices varied among microbial markers, with the highest values for fungi. The contamination route prediction also identified the highest probability of transmission of fungi using the ITS marker.<br><br>CONCLUSIONS: Sample type had the greatest influence on microbiome structure, although temperature had an impact on microbial composition of soil and manure samples. Results elucidate interactions at the animal-environment interface, informing the need for a better understanding of fungal transfer and seasonal variability.},
}
@article {pmid40459913,
year = {2025},
author = {Naghshineh, N and Kutos, S and Lewis, JD and Barnes, EM},
title = {Reorganization of bacterial community network structure in the eastern redback salamander (Plethodon cinereus) and its soil reservoir across a gradient of land use.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiaf057},
pmid = {40459913},
issn = {1574-6941},
abstract = {The eastern redback salamander Plethodon cinereus is prevalent in the urbanized northeastern USA and exhibits low susceptibility to the fungal pathogen Batrachochytrium dendrobatidis (Bd). Disease resistance is partially attributed to Bd-inhibitory microbes in the P. cinereus cutaneous microbiome, but less is known regarding the associations that structure these bacterial communities. This is an essential area of study as shifts in microbial associations may influence community stability and function, driving differences in disease tolerance. Here, we analyzed the networks of the soil and salamander skin core bacterial communities along a 65-km urbanization gradient originating in New York City. We leveraged network analysis tools that help account for the biases inherent in 16S rRNA amplicon datasets, finding that soil networks were the most complex and stable, but complexity and stability increased with urbanization intensity in salamander networks. The network of Bd positive salamanders was also more complex and stable than that of Bd negative salamanders. While stress and complexity are thought to be destabilizing, our results suggest that prolonged exposure to environmental degradation may promote larger, stable co-occurring populations of microbes on hosts. This network analysis work generated hypotheses with experimental applicability, ultimately having the potential to enhance conservation management efforts.},
}
@article {pmid40459906,
year = {2025},
author = {Manzoor, M and Suryavanshi, MV and Mujeeburahiman, M and Arun, AB and Miller, AW and Shouche, YS and Rekha, PD},
title = {Urine microbiome profiles in patients with different types of kidney stones.},
journal = {FEMS microbiology letters},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsle/fnaf054},
pmid = {40459906},
issn = {1574-6968},
abstract = {Kidney stone disease (KSD) is a multifactorial condition influenced by systemic and extrinsic factors, including diet, genetics, metabolic disorders, and microbial and environmental factors. Although preliminary evidence links the urinary microbiome (UMB) to stone formation, its role in different stone types remains unclear. We analysed UMB in patients with four distinct types of kidney stones (calcium oxalate, struvite, uric acid, and mixed composition). Urine samples from patients with KSD and controls were analysed using 16S rRNA gene sequencing. Patients with KSD exhibited distinct microbiota compositions, with increased abundances of Corynebacterium, Prevotella, and Staphylococcus than controls. The abundance of Dongia and Stenotrophomonas was higher in pure-stone formers than in mixed-stone formers (p < 0.05). Calcium oxalate stone formers had elevated levels of Pseudomonas and Dongia and reduced levels of Peptoniphilus than controls (p < 0.05). No significant differences in microbial diversity were observed between groups. Microbial composition correlated with blood and urine parameters, suggesting a potential influence on metabolic health and stone formation. These findings underscore the important role of UMB in KSD and provide valuable insights into its involvement in disease development and new opportunities for microbiome-based therapeutic strategies.},
}
@article {pmid40459760,
year = {2025},
author = {Zhao, Y and Liu, W and Hu, Y},
title = {Beyond the tumor: the gut microbiome as a key player in immunotherapy efficacy and resistance.},
journal = {Naunyn-Schmiedeberg's archives of pharmacology},
volume = {},
number = {},
pages = {},
pmid = {40459760},
issn = {1432-1912},
abstract = {Cancer immunotherapy aims to use the immune system of the body for improved therapeutic effects on tumors. Currently, one of the more encouraging interventions under evaluation involves the use of immune checkpoint blockade, which offers longer benefit periods and greater patient tolerance than previous interventions for solid malignancies. Nevertheless, a majority of patients never respond or gradually acquire resistance; hence, a suboptimal effect of the therapy ensues. Resistance to such treatments may arise from tumor-specific factors, host factors, and environmental influences. There is growing evidence that the gut microbiome is an important modulator not only of the efficacy of these treatments but also of toxicities. Current studies are focused on the identification of key microbial profiles from both preclinical and clinical samples associated with immunotherapeutic response and antitumor activities. Elucidation of this complex interaction may provide ways to modulate gut microbial communities to improve patient outcomes. The current review addresses the components responsible for resistance against immune checkpoint inhibitors and highlights the crucial linkage between gut microbiome-immune interactions. We further summarize some recent clinical findings and explore prospective avenues for research in this evolving area of cancer treatment.},
}
@article {pmid40459724,
year = {2025},
author = {Vijayaganapathi, A and Mohanasrinivasan, V},
title = {A Review of Next-Generation Probiotics-As a Gateway to Biotherapeutics.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {40459724},
issn = {1867-1314},
abstract = {Next-generation probiotics (NGPs) represent a promising advancement in microbial therapeutics, offering targeted and personalized interventions for various health disorders. Unlike traditional probiotics, NGPs focus on specific bacterial strains with enhanced functional properties, achieved through genetic engineering and next-generation sequencing technologies. Their applications span gastrointestinal disorders, metabolic syndromes, immune-related conditions, skin diseases, oral health, and animal well-being. NGPs contribute to gut microbiome modulation, metabolic regulation, and immune system enhancement, demonstrating therapeutic potential in clinical studies. Regulatory challenges persist, as NGPs fall under different legal classifications worldwide, necessitating rigorous safety assessments, including whole-genome sequencing to evaluate virulence and antibiotic resistance. Clinical trials continue to validate their efficacy in diverse conditions, emphasizing the need for standardized guidelines. Furthermore, novel probiotic delivery systems, including microdevices and targeted coatings, are being explored to improve bacterial viability and colonization in the gut. Identifying new probiotic strains with enhanced survival capabilities and elucidating their mechanisms of action remain critical for advancing probiotic science. Cost-effectiveness and commercialization of NGPs present opportunities for broader healthcare integration, with increasing research supporting their role in disease prevention and treatment. This review highlights the multifaceted potential of NGPs and the challenges that must be addressed for their successful implementation in modern healthcare.},
}
@article {pmid40459557,
year = {2025},
author = {Talbert, JA and Spicer, SK and Manning, SD and Gaddy, JA and Townsend, SD},
title = {Human Milk Oligosaccharides Mediate the Host-Microbe Interface in a Model Vaginal Community.},
journal = {ACS infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1021/acsinfecdis.5c00295},
pmid = {40459557},
issn = {2373-8227},
abstract = {Group B Streptococcus (GBS) is an opportunistic bacterium that can cause severe infection during gestation, leading to adverse pregnancy outcomes and neonatal disease. As current treatments only decrease chances of early onset neonatal disease without impacting the risk of chorioamnionitis, preterm birth, or late-onset disease, novel therapeutics are needed. Here, we demonstrate that human milk oligosaccharides (HMOs) positively modulate cocultures of GBS and Lactobacillus spp., common inhabitants of a healthy vaginal microbiome, across in vitro, ex vivo, and in vivo experiments. HMOs shift the total cell population in vitro to favor Lactobacillus, which was qualitatively visualized via scanning electron microscopy. Lactobacillus adherence to EpiVaginal tissues was also increased with HMOs during coinoculation with GBS. Using an in vivo mouse model of reproductive GBS infection, Lactobacillus crispatus and HMOs prevented ascending infection, reducing bacterial burden in both the placenta and fetus. L. crispatus alone reduced the burden in all reproductive tissues tested except the vagina. Together, these results highlight the benefit of pre- and probiotic treatment to potentially reduce GBS colonization during gestation.},
}
@article {pmid40459422,
year = {2025},
author = {Bar-El, L and Veisman, I and Simons, M and Delpra, C and King, CR and Gubbels, A},
title = {Gut feeling: understanding the endometriosis-digestive link to enhance patient care and symptom control.},
journal = {Current opinion in obstetrics &amp; gynecology},
volume = {},
number = {},
pages = {},
doi = {10.1097/GCO.0000000000001041},
pmid = {40459422},
issn = {1473-656X},
abstract = {PURPOSE OF REVIEW: Endometriosis is a chronic inflammatory condition that frequently presents with gastrointestinal (GI) symptoms that overlap with disorders such as irritable bowel syndrome, inflammatory bowel disease, and gastroparesis, leading to diagnostic delays. Recent research highlights the intricate relationship between endometriosis and gut health, including the role of microbiota, hormonal influences, and immune dysregulation. This review explored these mechanisms and their clinical implications for enhancing diagnosis and management strategies.<br><br>RECENT FINDINGS: Recent studies have suggested that hormonal fluctuations, prostaglandin dysregulation, and gut microbiota alterations contribute to GI symptoms in endometriosis. The microbiota-gut-brain axis has been implicated in disease progression, with dysbiosis influencing systemic inflammation and estrogen metabolism. Additionally, endometriotic lesions directly infiltrating the bowel can mimic GI disorders. Multidisciplinary care models, including gastroenterologists and gynecologists, are increasingly being recognized as essential for accurate diagnosis and care. Emerging therapies such as microbiome-targeted interventions, dietary modifications, and novel biomarkers offer promising avenues for improving patient outcomes.<br><br>SUMMARY: Recognizing the gut-endometriosis connection is crucial for reducing diagnostic delays and optimizing treatment strategies. Future research should focus on refining noninvasive diagnostic tools, exploring microbiome-based therapies, and enhancing interdisciplinary collaboration to improve patient care.},
}
@article {pmid40459257,
year = {2025},
author = {Tang-Wing, C and Mohanty, I and Bryant, M and Makowski, K and Melendez, D and Dorrestein, PC and Knight, R and Caraballo-Rodríguez, AM and Allaband, C and Jenné, K},
title = {Correction for Tang-Wing et al., "Impact of diet change on the gut microbiome of common marmosets (Callithrix jacchus)".},
journal = {mSystems},
volume = {},
number = {},
pages = {e0032725},
doi = {10.1128/msystems.00327-25},
pmid = {40459257},
issn = {2379-5077},
}
@article {pmid40459209,
year = {2025},
author = {Tang, Z and Tan, W and Li, R and Weng, L and Chen, X and Xi, B and Lv, D},
title = {Advances in Rhizosphere Microbiome and Rhizosphere Immunity Effect: A Review.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c02003},
pmid = {40459209},
issn = {1520-5118},
abstract = {Rhizosphere immunity, an emerging concept, involves complex interactions among plant roots, rhizospheric microbiota, and the soil environment that collectively safeguard plant health. Although extensively studied, the mechanisms driving rhizosphere immunity remain insufficiently elucidated. Rhizosphere microbes enhanced plant immunity through colonization, ISR/SAR induction, and interactions with root exudates and endophytes, triggering defense signals, producing antimicrobials, and modulating host metabolism. Organic and bioorganic fertilizers enhanced these effects by reshaping microbial communities, enriching beneficial taxa, and indirectly promoting resistance via improved nutrient cycling and soil health. Synthetic microbial communities (SynComs) have been developed to stabilize and enhance biocontrol. Four scalable SynComs design strategies have emerged: reductionist approaches for mechanistic insight, antagonistic combinations, core microbiome-based assemblies using keystone taxa, and resource competition to outcompete pathogens. Together, these approaches offer scalable solutions to construct stable and functional SynComs that enhance rhizosphere immunity. Future efforts should focus on translating rhizosphere immunity into agriculture by elucidating microbiome-plant-soil interactions and optimizing long-term soil management.},
}
@article {pmid40459094,
year = {2025},
author = {Dahl, MB and Brachmann, S and Söllinger, A and Schnell, M and Ahlers, L and Wutkowska, M and Hoff, KJ and Nath, N and Groß, V and Wang, H and Weil, M and Piecha, M and Schaffer, M and Jensen, C and Kuss, AW and Gall, C and Wimmer, E and Pribasnig, T and Tveit, AT and Sigurdsson, BD and Schleper, C and Richter, A and Urich, T},
title = {Quantifying Soil Microbiome Abundance by Metatranscriptomics and Complementary Molecular Techniques-Cross-Validation and Perspectives.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {e14130},
doi = {10.1111/1755-0998.14130},
pmid = {40459094},
issn = {1755-0998},
support = {21-17322M//The Czech Science Foundation/ ; BO 5559/1-1//Deutsche Forschungsgemeinschaft/ ; INST 292/146-1 FUGB//Deutsche Forschungsgemeinschaft/ ; UR198/7-1//Deutsche Forschungsgemeinschaft/ ; 813114//HORIZON EUROPE European Innovation Council/ ; //Research Council of Norway/ ; },
abstract = {Linking meta-omics and biogeochemistry approaches in soils has remained challenging. This study evaluates the use of an internal RNA extraction standard and its potential for making quantitative estimates of a given microbial community size (biomass) in soil metatranscriptomics. We evaluate commonly used laboratory protocols for RNA processing, metatranscriptomic sequencing and quantitative reverse transcription polymerase chain reaction (qRT-PCR). Metatranscriptomic profiles from soil samples were generated using two library preparation protocols and prepared in triplicates. RNA extracted from pure cultures of Saccharolobus solfataricus was added to the samples as an internal nucleic acid extraction standard (NAEstd). RNA reads originating from NAEstd were identified with a 99.9% accuracy. A remarkable replication consistency between triplicates was seen (average Bray-Curtis dissimilarity 0.03 ± 0.02), in addition to a clear library preparation bias. Nevertheless, the between-sample pattern was not affected by library type. Estimates of 16S rRNA transcript abundance derived from qRT-PCR experiments, NAEstd and a previously published quantification method of metatranscriptomics (hereafter qMeTra) were compared with microbial biomass carbon (MBC) and nitrogen (MBN) extracts. The derived biomass estimates differed by orders of magnitude. While most estimates were significantly correlated with each other, no correlation was observed between NAEstd and MBC extracts. We discuss how simultaneous changes in community size and the soils nucleic acid retention strength might hamper accurate biomass estimation. Adding NAEstd has the potential to shed important light on nucleic acid retention in the substance matrix (e.g., soil) during extraction.},
}
@article {pmid40458610,
year = {2025},
author = {Liao, M and Cai, J and Zhu, F and Lan, Y and Xu, T and Guo, J and Xue, Q and Wen, Y and Zou, F and Zhang, Y and Zhang, S and Yan, Y and Ai, J and Cui, J and Zhang, W},
title = {Meta-transcriptomics Reveals Dysbiosis of the Respiratory Microbiome in Older Adults with Long COVID.},
journal = {Research (Washington, D.C.)},
volume = {8},
number = {},
pages = {0720},
pmid = {40458610},
issn = {2639-5274},
abstract = {Limited research has investigated the connection between long COVID (LC) and the respiratory microbiome, particularly in older adults. This study aimed to characterize the respiratory microbiome of older LC patients (with an average age of 65 years old), through meta-transcriptomic sequencing of 201 individual samples. Marked differences in microbial diversity were observed between LC and non-LC patients, including disruptions in both pathogenic bacteria and fungi. Importantly, viral taxa, such as Herpes simplex virus type 1 and Human coronavirus 229E, were more frequently detected in LC patients, indicating the vulnerability of LC patients to viral infections. Functional annotation at the expression level revealed notable differences in microbial metabolism with alterations observed in pathways related to tryptophan-serotonin metabolism in LC patients. These findings underscore the altered microbial landscape, especially in older adults who developed LC, and fill the gap for the potentially clinical roles played by the respiratory microbiome.},
}
@article {pmid40458521,
year = {2025},
author = {Moreland, RB and Brubaker, L and Wolfe, AJ},
title = {Polymicrobial urine cultures: reconciling contamination with the urobiome while recognizing the pathogens.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1562687},
pmid = {40458521},
issn = {2235-2988},
mesh = {Humans ; *Urinary Tract Infections/microbiology/diagnosis ; *Coinfection/microbiology/diagnosis ; *Urine/microbiology ; *Microbiota ; *Bacteria/isolation &amp; purification/classification ; Bacteriuria/microbiology/diagnosis ; Female ; Pregnancy ; },
abstract = {Polymicrobial or mixed urine cultures of more than one predominant microbe confound clinical urinary tract infection diagnosis. The current College of American Pathologists clinical laboratory standard states that a urine sample cultured with more than two isolates with >10,000 colony forming units/ml is to be considered contaminated. However, the presence of urinary sample bacteria in individuals without urinary symptoms (referred to as asymptomatic bacteriuria) is common especially in older people and in pregnant individuals. Furthermore, the discovery of an indigenous urinary microbiome (urobiome) in healthy humans throughout life from shortly after birth to death conflicts with the long-standing notion that urine derived from sterile filtered blood should be sterile above the urethral sphincter. Polymicrobial infections are not consistent with Koch's postulates that a single pathogen is causal for disease. In this review, we will discuss current standards of contamination, how to reconcile the sterility of urine with the existence of the urobiome, a history of polymicrobial infections, and why re-examining current practices is essential for the practice of medicine, improving quality of life, and potentially saving lives. .},
}
@article {pmid40458403,
year = {2025},
author = {Burke, OM and Frerichs, VR and Garcia, DF and Stone, RC and Lev-Tov, H and Czarnowicki, T and Keane, RW and Ojeh, N and Marjanovic, J and Pastar, I and Tomic-Canic, M and de Rivero Vaccari, JP and Sawaya, AP},
title = {The impact of innate immunity and epigenetics in the pathogenesis of hidradenitis suppurativa.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1593253},
pmid = {40458403},
issn = {1664-3224},
mesh = {Humans ; *Hidradenitis Suppurativa/immunology/genetics/etiology/microbiology ; *Immunity, Innate/genetics ; *Epigenesis, Genetic/immunology ; Inflammasomes/immunology/metabolism ; Animals ; DNA Methylation ; Microbiota/immunology ; Dysbiosis/immunology ; },
abstract = {Hidradenitis Suppurativa (HS) is a chronic multifactorial inflammatory skin disease with a debilitating impact on quality of life. Here, we review the complex interplay of innate and adaptive immune dysregulation in HS pathogenesis, in the context of microbial dysbiosis, genetic predisposition, cellular dysfunction and epigenetic factors. Hyperactivation of the innate system triggered by follicular occlusion leads to a cascade of activated signaling pathways leading to persistent inflammation as the disease progresses. This immune hyperactivation is further complicated by microbiome dysbiosis, which is associated with dysregulation of inflammasomes and altered expression of host antimicrobial peptides. Keratinocytes, fibroblasts, macrophages, and neutrophils exhibit altered functions, and contribute to the inflammatory cascade and disease chronicity in HS. Epigenetic mechanisms including DNA methylation, histone modifications, and non-coding RNAs modulate immune responses and contribute to aberrant cytokine and chemokine expression that drive the persistent inflammatory state in HS pathogenesis. We highlight the need for future research to explore the concept of epigenetic memory in epidermal stem cells and inflammasome activation to gain a better understanding of these mechanisms and pave the way for development of future novel therapeutic targets and strategies to disrupt the persistent chronic inflammation cycle in this debilitating condition.},
}
@article {pmid40458398,
year = {2025},
author = {Yan, W and Zhang, K and Guo, J and Xu, L},
title = {Bile acid-mediated gut-liver axis crosstalk: the role of nuclear receptor signaling in dynamic regulation of inflammatory networks.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1595486},
pmid = {40458398},
issn = {1664-3224},
mesh = {Humans ; *Bile Acids and Salts/metabolism/immunology ; *Receptors, Cytoplasmic and Nuclear/metabolism ; Signal Transduction ; Animals ; *Liver/metabolism/immunology ; *Gastrointestinal Microbiome/immunology ; *Inflammation/metabolism/immunology ; Receptors, G-Protein-Coupled/metabolism ; Non-alcoholic Fatty Liver Disease/metabolism/immunology ; },
abstract = {Bile acids (BAs) are critical mediators of metabolic and immune regulation, influencing both liver and intestinal function. Their homeostasis, maintained through the enterohepatic circulation, is pivotal for immune-metabolic balance. BAs activate key receptors, including Farnesoid X Receptor (FXR) and TGR5, to modulate inflammation. FXR exerts anti-inflammatory effects by suppressing NF-κB signaling and cytokine production, whereas TGR5 primarily regulates NLRP3 inflammasome activation. Dysregulated BA signaling, driven by microbial dysbiosis, exacerbates inflammatory diseases like non-alcoholic fatty liver disease (NAFLD) and inflammatory bowel disease (IBD). This review explores the intricate roles of BAs in inflammation, highlighting the microbiome's influence on BA metabolism and immune responses. Understanding the BA-immune axis offers new therapeutic avenues for modulating inflammation and improving clinical outcomes in inflammatory diseases.},
}
@article {pmid40458201,
year = {2025},
author = {Siddiqui, DA and Tsai, YC and Giron Bastidas, J and Jazaeri, MS and Kotsakis, GA},
title = {Utilizing a naturopathic mouthwash with selective antimicrobial effects against multispecies oral biofilms for prevention of dysbiosis.},
journal = {Frontiers in oral health},
volume = {6},
number = {},
pages = {1529061},
pmid = {40458201},
issn = {2673-4842},
abstract = {INTRODUCTION: Oral rinses intended for the prevention and treatment of periodontal diseases have traditionally focused on bactericidal effects. This study evaluates the efficacy of a naturopathic mouthwash containing plant attenuations and propolis against common gram- pathogenic and gram+ commensal oral species in comparison to conventional antiseptic oral rinses.<br><br>METHODS: Streptoccoccus oralis, Streptococcus gordonii, Veillonella parvula, Fusobacterium nucleatum, and Porphyromonas gingivalis were cultured and treated with naturopathic StellaLife&#xae; VEGA&#xae; Oral Rinse (SL), 0.12% chlorhexidine gluconate (CHX), LISTERINE&#xae; COOL MINT&#xae; mouthwash (LIS), or phosphate-buffered saline (PBS) as negative control. Firstly, planktonic bacterial growth was assessed through optical density measurements and colony-forming unit (CFU) counts. Subsequently, a 4-species or clinical ex vivo multispecies biofilm was used to evaluate antibiofilm effects through selective agar plating and fluorescence in situ hybridization (FISH) or live-dead biofilm imaging, respectively. Lastly, cytocompatibility to oral rinses was tested using a 3D human fibroblast spheroid model.<br><br>RESULTS: SL significantly inhibited the growth of disease-associated F. nucleatum and P. gingivalis 12 and 120 h, respectively, after treatment, while exhibiting lower toxicity toward commensal S. oralis, S. gordonii, and V. parvula vs. LIS or CHX (all p < 0.05). Correspondingly, in 4-species biofilms, selective agar plating and FISH-staining showed decreased abundance of F. nucleatum and P. gingivalis after 4 h recovery following SL treatment vs. PBS control while maintaining a robust commensal biofilm of S. oralis and V. parvula. In contrast, CHX or LIS treatment demonstrated non-selective killing, leading to sparse biofilms with residual F. nucleatum and P. gingivalis. When tested against clinical ex vivo multispecies biofilms, all oral rinses showed significant antibiofilm effects (all p < 0.001), disrupting biofilm structure and reducing bacterial viability. Lastly, 3D human fibroblast spheroids treated with CHX or LIS displayed greater cytotoxicity with detachment of cellular debris from the spheroid mass, while spheroids exposed to SL exhibited minimal cell death with cellular viability maintained across the spheroid structure.<br><br>DISCUSSION: The SL homeopathic rinse demonstrated selective action on oral bacteria, preferentially reducing pathogen bacterial load while preserving commensal species with high cytocompatibility. Future validation in human studies is needed to assess its selective antimicrobial activity to maintain a eubiotic oral microbiome and explore broader applications in oral health.},
}
@article {pmid40458149,
year = {2025},
author = {Silva, JCC and Lucy, MC},
title = {Reanalysis of 2 metritis studies demonstrates different patterns of postpartum uterine infection for primiparous versus multiparous cows.},
journal = {JDS communications},
volume = {6},
number = {3},
pages = {362-367},
pmid = {40458149},
issn = {2666-9102},
abstract = {Metritis typically has a greater incidence in primiparous compared with multiparous cows. In separate studies with similar design, we noted that primiparous and multiparous cows responded differently to a model developed to induce metritis via the intrauterine infusion of a bacterial challenge of Fusobacterium necrophorum, Trueperella pyogenes, and Escherichia coli. To understand the difference between primiparous and multiparous cows, we reanalyzed the relative abundance of bacteria genera within the vaginal microbiome during the first 2 wk postpartum from the 2 previous studies for primiparous and multiparous cows. We conducted a first reanalysis of primiparous and multiparous cows that received an identical challenge dose (10[6] cfu of each pathogen) and a second reanalysis that compared all primiparous and multiparous cows that were or were not diagnosed with metritis regardless of challenge dose (0, 10[3], 10[6], or 10[9] cfu per pathogen). The challenge model resulted in clinical metritis in both primiparous and multiparous cows, although some control cows (0 dose) developed metritis and, conversely, some bacterial challenge cows failed to develop metritis. Importantly, cows that contracted metritis had increased and sustained relative abundance of key metritis pathogens including Fusobacterium, Porphyromonas, Helcococcus, and Trueperella after calving regardless of parity. We unexpectedly found, however, that primiparous cows that did not develop metritis had a different bacterial profile (based on 16S ribosomal gene sequencing as well as bacterial culture) compared with multiparous cows that did not develop metritis. In primiparous nonmetritis cows, the relative abundance of the genera Fusobacterium, Porphyromonas, Helcococcus, and Trueperella was almost identical to primiparous metritis cows during the first week postpartum, but the relative abundances in nonmetritis cows decreased rapidly thereafter. The relative abundance of the same genera in nonmetritis multiparous cows did not increase or increased to a lesser extent postpartum. The different patterns of infection for nonmetritis primiparous (initial increase in relative abundance [wk 1] followed by a decrease [wk 2]) compared with nonmetritis multiparous cows (stable and low-level relative abundance for 2 wk postpartum) was found when the analysis included only challenge cows (10[6] cfu dose) or all cows regardless of dose. We found different patterns of infection for primiparous compared with multiparous cows. This observation may explain lesser incidence of metritis in multiparous compared with primiparous cows.},
}
@article {pmid40457766,
year = {2025},
author = {Pu, F and Liu, Y and Ahmed, FZ and Wang, X and Green, D and Zhang, H},
title = {Advancing antihypertensive drug development.},
journal = {British journal of pharmacology},
volume = {},
number = {},
pages = {},
doi = {10.1111/bph.70063},
pmid = {40457766},
issn = {1476-5381},
support = {//N/A/ ; },
abstract = {Hypertension affects more than a billion individuals worldwide and remains a major cause of cardiovascular morbidity and mortality. Despite advances in therapies, optimal blood pressure control remains elusive for many patients because of treatment resistance, adverse effects, and adherence challenges. This review highlights innovative approaches in hypertension management. Aldosterone synthase inhibitors (ASIs) and non-steroidal mineralocorticoid receptor antagonists improve blood pressure control and offer cardiorenal benefits while reducing adverse effects including hyperkalaemia. Endothelin receptor antagonists show promise in resistant hypertension by addressing vasoconstrictive pathways. RNA-based therapies, like zilebesiran, provide a novel approach to suppress angiotensinogen, offering durable antihypertensive effects with less frequent dosing. Additional advances include AT2 receptor agonists, ACE2/Angiotensin-(1-7)/MAS receptor activators and NAD[+] boosting compounds, which target key mechanisms of vascular dysfunction and ageing-related hypertension. Gut microbiome-targeted therapies and fixed-dose combination pills are also discussed for their potential to enhance blood pressure control and patient adherence. These emerging therapies not only aim to lower blood pressure but also address underlying pathophysiological mechanisms, offering a precision-focussed approach to treatment. By critically analysing these developments, this review provides insights into how novel strategies can overcome existing challenges in hypertension management, reduce the global disease burden and improve patient outcomes.},
}
@article {pmid40457749,
year = {2025},
author = {Navalpur Shanmugam, NK and Zamudio, F and Vijaya Kumar, DK and Barrett, KA and VanDoren, R and Chen, M and Barr, OM and Watson, S and Lin, CJ and Eimer, WA and Jorfi, M and Choi, SH and Moir, RD and Tanzi, RE},
title = {Acute experimental colitis in 5xFAD Alzheimer's disease mice leads to enhanced monocyte infiltration into the brain accompanied by reduced β-amyloid deposition.},
journal = {Alzheimer's &amp; dementia : the journal of the Alzheimer's Association},
volume = {21},
number = {6},
pages = {e70292},
doi = {10.1002/alz.70292},
pmid = {40457749},
issn = {1552-5279},
support = {//Cure Alzheimer's Fund/ ; },
mesh = {Animals ; *Alzheimer Disease/metabolism/pathology ; *Colitis/chemically induced/pathology/metabolism ; Mice ; *Amyloid beta-Peptides/metabolism ; *Monocytes/metabolism/pathology ; *Brain/metabolism/pathology ; Disease Models, Animal ; Mice, Transgenic ; Gastrointestinal Microbiome ; Dextran Sulfate ; Dysbiosis ; },
abstract = {INTRODUCTION: Emerging evidence has connected Alzheimer's disease (AD) to systemic inflammation, intestinal abnormalities, and altered gut microbiota, highlighting the significance of the gut-brain axis. Here, we investigated the impact of acute experimental colitis (acute colitis) on AD pathology.<br><br>METHODS: Acute colitis was induced in 2-month-old 5xFAD mice using dextran sodium sulfate (DSS) to assess the effects of intestinal inflammation on the microbiome, systemic inflammation, neuroinflammation, and beta-amyloid deposition.<br><br>RESULTS: Induction of acute colitis in 5xFAD mice led to microbial dysbiosis and systemic inflammation. As a result, monocyte infiltration was observed in the brain accompanied by reduced cerebral beta-amyloid deposition and increased beta-amyloid efflux into the bloodstream.<br><br>DISCUSSION: Increased infiltration of monocytes and elevated beta-amyloid release into the bloodstream could both be responsible for the reduced beta-amyloid deposition in 5xFAD mice following acute colitis. These results further highlight an important connection between gut-induced peripheral inflammation and the progression of AD.<br><br>HIGHLIGHTS: Microbial dysbiosis occurs as a result of acute colitis in 5xFAD mice. Acute colitis in 5xFAD mice affects beta-amyloid deposition. Increased IL-2 and IL-6 cytokine levels in the hippocampus of 5xFAD colitis mice. Colitis in 5xFAD mice increases serum proinflammatory cytokine levels and endotoxins. Acute colitis in 5xFAD mice increases monocyte infiltration and serum beta-amyloid.},
}
@article {pmid40457720,
year = {2025},
author = {Cortizo, DL and Casarin, RCV and Paz, HES and Stolf, CS and Monteiro, MF and Labate, MTV and Casati, MZ and Dib, LL},
title = {Microbiome and Metaproteome of Craniofacial Implant Regions in Health and Disease.},
journal = {Oral diseases},
volume = {},
number = {},
pages = {},
doi = {10.1111/odi.15398},
pmid = {40457720},
issn = {1601-0825},
support = {//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; //Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; },
abstract = {BACKGROUND: Craniofacial defects from cancer surgery led to functional, aesthetic, and psychological challenges. Rehabilitation with craniofacial implants addresses these issues by improving prosthesis retention through osseointegration and providing predictable cosmetic results. However, maintaining a healthy transcutaneous region is essential for implant longevity.<br><br>OBJECTIVE: Evaluation of the microbial community and host response around extraoral implants.<br><br>METHODS: In an intrasubject control study design, 12 cancer patients who had undergone oculofacial rehabilitation with implant-supported prostheses were included. Biofilm and peri-implant fluid samples were collected from the transcutaneous region of healthy and diseased implants. Microbiome profiling was conducted through DNA sequencing of the V3-V4 region of the 16S rRNA gene, and proteome analysis was performed using liquid chromatography-tandem mass spectrometry.<br><br>RESULTS: Differentially abundant species were observed, with Streptococcus intermedius being the most abundant in diseased areas, followed by Corynebacterium diphtheriae and Prevotella bivia. Metaproteomic analysis revealed distinct protein expression patterns between the groups, with increased activation of proinflammatory responses and inactivation of anti-inflammatory responses in the diseased group.<br><br>CONCLUSION: The study demonstrated an increased abundance of pathogenic bacterial community accompanied by an imbalanced immune response, thereby highlighting host-microbial factors that can influence the success of osseointegration and facial rehabilitation.},
}
@article {pmid40457634,
year = {2025},
author = {Qian, G and Chen, X and Liu, G and Yu, J and Zhong, S and Yang, J and Sun, Y and Zhou, J},
title = {Exploring the etiology of colitis: insights from gut microbiota research.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2512010},
doi = {10.1080/19490976.2025.2512010},
pmid = {40457634},
issn = {1949-0984},
mesh = {*Gastrointestinal Microbiome ; Humans ; *Dysbiosis/microbiology/complications ; *Colitis/microbiology/etiology/pathology/immunology ; Animals ; Bacteria/metabolism/classification/genetics ; },
abstract = {Colitis represents a significant global health concern, with its incidence rising annually in recent years. Despite the unclear specifics of its pathogenic mechanisms, dysbiosis of the intestinal microbiota is recognized as a major factor contributing to various forms of colitis. This article examines the mechanisms through which alterations in intestinal microbiota contribute to the pathogenesis of several common types of colitis. These mechanisms predominantly involve disruption of barrier function, aberrant immune responses, and damage induced by microbial metabolites. This review offers insights that enhance the understanding of colitis pathogenesis.},
}
@article {pmid40457484,
year = {2025},
author = {Jin, J and Liu, S and Zhou, Q and Fang, Z and Lin, Y and Xu, S and Feng, B and Zhuo, Y and Luo, H and Liu, X and Wu, D and Che, L},
title = {Cinnamaldehyde supplementation in sows and their offspring: effects on colostrum and milk composition, performance, redox status and intestinal health.},
journal = {Journal of animal science and biotechnology},
volume = {16},
number = {1},
pages = {79},
pmid = {40457484},
issn = {1674-9782},
support = {CARS-35//Earmarked Fund for China Agriculture Research System/ ; 2023YFD1300802//National Key Research and Development Program of China/ ; },
abstract = {BACKGROUND: Maternal nutrition significantly influences offspring development. This study investigated the effects of maternal or post-weaning cinnamaldehyde (CA) supplementation in sows and their offspring on reproductive performance and health. Sixty sows, selected based on body condition score and parity, were randomly allocated to control or CA (500 mg/kg) diets from d 107 of gestation to d 24 of lactation. At weaning, 128 piglets were assigned to four groups (n = 8) based on weight and source litter for a 21-d experiment. The four groups were CON-CON (both sow and piglet on CON), CON-CA (sow on CON, piglet on CA), CA-CON (sow on CA, piglet on CON), and CA-CA (both sow and piglet on CA).<br><br>RESULTS: Maternal CA supplementation tended to improve body weight (+&#x2009;15%, P&#x2009;=&#x2009;0.09) and average daily gain (+&#x2009;21%, P&#x2009;=&#x2009;0.07) of suckling piglets, along with increased levels of milk IgG (P&#x2009;=&#x2009;0.01) and IgM (P&#x2009;=&#x2009;0.02), colostrum crude fat (P&#x2009;=&#x2009;0.01), and plasma glutathione peroxidase (GSH-Px)&#xa0;activity&#xa0;(P = 0.02) at farrowing. Moreover, maternal CA supplementation significantly improved plasma antioxidant capacity, expressions of intestinal barrier and anti-inflammatory genes, and gut microbiota structure of piglets at the end of suckling. Additionally, maternal CA supplementation increased the apparent total tract digestibility (ATTD) of crude protein (P&#x2009;<&#x2009;0.01), gross energy (GE;&#xa0;P&#x2009;=&#x2009;0.03), and dry matter (P&#x2009;=&#x2009;0.01), improved jejunal sucrase activity (P&#x2009;<&#x2009;0.01), villus height (P&#x2009;=&#x2009;0.03), the ratio of villi height to crypt depth (P&#x2009;=&#x2009;0.02), and the expressions of intestinal barrier and anti-inflammatory genes in post-weaning piglets. Furthermore, post-weaning CA supplementation tended to decrease diarrhea scores of piglets during d 14-21 and increased the ATTD of GE (P&#x2009;=&#x2009;0.02), activities of jejunal sucrase (P&#x2009;=&#x2009;0.02), plasma catalase (P&#x2009;=&#x2009;0.01), and total superoxide dismutase (P&#x2009;<&#x2009;0.01) in piglets.<br><br>CONCLUSION: Maternal CA supplementation tended to increase the growth rate and weaning weight of suckling piglets, associated with improved antioxidant capacity and milk composition. Moreover, maternal CA supplementation or post-weaning CA supplementation improved nutrient digestibility, redox status, and intestinal function-related parameters of weaned piglets.},
}
@article {pmid40457479,
year = {2025},
author = {Wu, X and Liu, X and Tan, H and Song, J and Ma, S and Tan, Y},
title = {Longitudinal change and causal relationship between gut microbiota and gestational diabetes mellitus.},
journal = {Diabetology &amp; metabolic syndrome},
volume = {17},
number = {1},
pages = {188},
pmid = {40457479},
issn = {1758-5996},
support = {82360665//the National Natural Science Foundation of China/ ; 2024JJ7406//the Natural Science Foundation of Hunan Province/ ; 24A0383//the Scientific Research Project of Education Department of Hunan Province/ ; 202401000932//the Research Project on Teaching Reform of ordinary Colleges and Universities in Hunan Province/ ; 202401000932//the Research Project on Teaching Reform of ordinary Colleges and Universities in Hunan Province/ ; 202401000932//the Research Project on Teaching Reform of ordinary Colleges and Universities in Hunan Province/ ; 2024JGYB206//the Degree and Graduate Education Reform Research Project in Hunan Province/ ; 2024JGYB206//the Degree and Graduate Education Reform Research Project in Hunan Province/ ; 2024JGYB206//the Degree and Graduate Education Reform Research Project in Hunan Province/ ; },
abstract = {BACKGROUND: Recent studies have increasingly shown the connection between gut microbiome and gestational diabetes mellitus (GDM). However, most studies only focused on a single time point during pregnancy.<br><br>METHODS: We conducted a nested case-control study in a follow-up cohort, recruiting 52 patients with GDM and 52 healthy controls. 16&#xa0;S rRNA sequencing was used to explore gut microbiota profiles at early, middle, and late trimesters during pregnancy. Mendelian randomization analysis was performed to investigate the causal relationship between gut microbiota and GDM.<br><br>RESULTS: Diversity analysis revealed no difference in the overall gut microbiota composition between the two groups, however, we found 16 differential gut microbiota during pregnancy. Trend analysis revealed significant alterations during pregnancy in the relative abundance of Odoribacter, Ruminococcus gnavus group, Erysipelatoclostridium, and Erysipelotrichaceae UCG-003 in the control group, and of Ruminococcaceae UCG-002 and Odoribacter in the GDM group across three time points. Five genera of gut microbiota were found to be correlated with several blood glucose indicators. Additionally, Mendelian randomization analysis confirmed causal relationships between Prevotella 9, Methanobrevibacter, and GDM.<br><br>CONCLUSIONS: Significant alterations in the relative abundance of Ruminococcaceae UCG-002 and Odoribacter were observed throughout the three trimesters of pregnancy in women with GDM. Elevated levels of Prevotella 9 in early trimester were causally associated with an increased risk of GDM, while Methanobrevibacter exhibited protective effects.},
}
@article {pmid40457432,
year = {2025},
author = {Du, L and Wang, B and Wang, X and Wang, L and Wang, R and Zhang, Y and Hong, Z and Han, X and Wang, Y},
title = {Gastrointestinal exposure to silica nanoparticles induced Alzheimer's disease-like neurotoxicity in mice relying on gut microbiota and modulation through TLR4/NF-κB and HDAC.},
journal = {Journal of nanobiotechnology},
volume = {23},
number = {1},
pages = {406},
pmid = {40457432},
issn = {1477-3155},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Silicon Dioxide/toxicity/chemistry ; Mice ; *Nanoparticles/toxicity/chemistry ; *Alzheimer Disease/metabolism/chemically induced ; NF-kappa B/metabolism ; Mice, Inbred C57BL ; *Toll-Like Receptor 4/metabolism ; *Histone Deacetylases/metabolism ; Male ; Gastrointestinal Tract/drug effects ; Oxidative Stress/drug effects ; Brain/drug effects/metabolism ; Signal Transduction/drug effects ; },
abstract = {BACKGROUND: Silica nanoparticles (SiO2 NPs) are widely used in the food and pharmaceutical industries and dramatically increase the health risks associated with gastrointestinal exposure. However, the neurotoxicological effects and mechanisms of exposure to SiO2 NPs and their relationship with the gut microbiome require further in-depth investigation. Here, we performed a systematic assessment of the toxicity of gavage containing 20 nm SiO2 NPs to C57BL/6 J mice.<br><br>RESULTS: After 14&#xa0;weeks administration, we comprehensively discovered that gastrointestinal exposure to SiO2 NPs led to mice Alzheimer's disease (AD)-like neurotoxicity, including A&#x3b2; accumulation, cognitive impairment, oxidative stress burden, and neuroinflammation, which was microbiota-gut-brain axis-dependent and proven using a low-load gut-bacteria experiment and antibiotic treatment. Mechanistically, gastrointestinal exposure to SiO2 NPs disrupted intestinal homeostasis. Specifically, the total faecal short-chain fatty acid (SCFA) levels were reduced as analysed by 16S rRNA gene sequencing and liquid chromatography mass-spectrometry (LC-MS) analysis. The reduced SCFA content damaged the integrity of gut-brain axis by increasing gut permeability, which may have caused metabolite redistribution, brain basement membrane dissolution, activated the neuroinflammation signalling pathway TLR4/NF-&#x3ba;B, and interfered with HDAC3 and HDAC1/OGG1 pathways.<br><br>CONCLUSIONS: We showed for the first time that gastrointestinal exposure to SiO2 NPs depends on the gut microbiome and causes neurological and cognitive impairment via gut-brain axis information transmission. These findings suggest that the gut microbiota, as a mediator between intestinal and brain information communications, contributes to gastrointestinal exposure to SiO2 NPs-induced neurotoxicity. The health risks of exposure to SiO2 NPs should be recognised, and addressing strategies should be extensively reconsidered.},
}
@article {pmid40457130,
year = {2025},
author = {Chu, NHS},
title = {Dietary Manipulation on Gut Microbiome in Patients with Diabetes and Colorectal cancer.},
journal = {Current nutrition reports},
volume = {14},
number = {1},
pages = {75},
pmid = {40457130},
issn = {2161-3311},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Colorectal Neoplasms/microbiology/diet therapy ; *Diabetes Mellitus, Type 2/microbiology/diet therapy/complications ; Dysbiosis/microbiology/diet therapy ; *Diet ; },
abstract = {PURPOSE OF REVIEW: This review aims to investigate the relationship between dietary changes and the microbiome in patients with diabetes and colorectal cancer (CRC). The link between CRC and type 2 diabetes is momentous, as individuals with diabetes have a 40-60% higher risk of developing CRC and often experience lower survival rates. However, limited studies explore how diabetes may contribute to the progression to CRC through changes in the microbiome. By clarifying these connections, this review summarizes mechanisms in type 2 diabetes and CRC through microbiota pathways, presenting evidence from clinical trials regarding nutritional interventions for treating both conditions. We will focus on how nutritional components can alter the gut microbiome, highlighting the potential role of nutritional adjustments as adjuvant therapy for patients with diabetes who are facing precancerous or cancerous conditions.<br><br>RECENT FINDINGS: There is growing evidence about the interactions between the microbiome and the causes of diabetes and CRC. Both conditions are characterised by changes in the gut microbiome, known as dysbiosis, which involves alterations in specific bacteria, such as Bifidobacterium, Bacteroides, Akkermansia, Faecalibacterium, Ruminococcus, and Fusobacterium. It is important to consider dietary modifications to address dysbiosis, malnutrition, glycemic variability, and inflammation underlying these conditions. Consuming a higher amount of fermentable carbohydrates alongside a lower amount of fermentable proteins can positively influence the microenvironment that regulates insulin secretion and bile acids, as well as an increase in short-chain fatty acids. This may be beneficial for patients with diabetes and CRC. However, it is also important to consider potential interactions between food and medication as well as gastrointestinal tolerability.},
}
@article {pmid40457129,
year = {2025},
author = {Tiwari, VK and Vishwakarma, A and Verma, D and Sharma, M},
title = {Microbial diversity analysis of municipal solid waste landfills soils of Delhi (NCR) and plastic dump sites of Uttar Pradesh region of India and their function prediction for plastic degrading enzymes.},
journal = {World journal of microbiology &amp; biotechnology},
volume = {41},
number = {6},
pages = {187},
pmid = {40457129},
issn = {1573-0972},
mesh = {India ; *Soil Microbiology ; *Bacteria/classification/genetics/enzymology/isolation &amp; purification/metabolism ; *Waste Disposal Facilities ; RNA, Ribosomal, 16S/genetics ; Biodegradation, Environmental ; Solid Waste ; *Plastics/metabolism ; Phylogeny ; Biodiversity ; DNA, Bacterial/genetics ; Microbiota ; Soil/chemistry ; },
abstract = {Municipal solid waste landfills are rich in plastic waste, fostering a unique microbial ecosystem distinct from natural habitats. This study aimed to investigate the microbial diversity at four landfill and plastic dump sites using a 16S rDNA metataxanomics approach, and to predict their potential for plastic degradation. Environmental DNA was isolated and analyzed through Illumina MiSeq sequencing. The results revealed a dominant presence of Pseudomonadota (47%) across all sites, with key genera including Streptomyces, Galbibacter, Alcanivorax, and OM190. The most abundant species were unclassified Chloroflexi bacterium, Galbibacter marinus, Gracilimonas amylolytica, and Teredinibacter sp. Alpha diversity analysis showed the highest species richness in plastic dump site in Utrathia (Lucknow), followed by Ghazipur landfill Site (Delhi), with low evenness across the bacterial communities. Beta diversity analysis, using Bray-Curtis and PCA, indicated distinct microbial profiles for each site. The PICRUSt analysis identified 402 genes related to nine enzyme categories involved in plastic degradation. Pearson correlation network analysis of top 1% genera highlighted positive associations between genera like Galbibacter, Alcanivorax, Thioalkalimicrobium, Idiomarina and Pseudomonas with peroxygenase enzyme. This study underscores the microbial diversity and functional potential of landfill microbes in plastic degradation, contributing to our understanding of the plastisphere microbiome in landfill environments.},
}
@article {pmid40457025,
year = {2025},
author = {Elkrief, A and Pidgeon, R and Maleki Vareki, S and Messaoudene, M and Castagner, B and Routy, B},
title = {The gut microbiome as a target in cancer immunotherapy: opportunities and challenges for drug development.},
journal = {Nature reviews. Drug discovery},
volume = {},
number = {},
pages = {},
pmid = {40457025},
issn = {1474-1784},
abstract = {The gut microbiome has a critical role in shaping the patient's immune response and influencing the efficacy of anticancer immunotherapy. Emerging evidence suggests that modulating the gut microbiome through interventions such as faecal microbiota transplantation, probiotics, prebiotics and lifestyle modifications may enhance therapeutic outcomes. Consequently, drug development efforts in immuno-oncology have expanded to explore microbiome-based therapeutic strategies. In this Review, we examine the rationale for targeting the microbiome in cancer treatment, highlighting key advances in clinical microbiome characterization and their implications for immunotherapy. We discuss findings from recent clinical trials evaluating microbiome-based interventions and address the challenges associated with translating these approaches into clinical practice. Finally, we outline future directions for the development and integration of microbiome-targeted therapies in oncology, with a focus on optimizing efficacy, safety and patient stratification strategies.},
}
@article {pmid40457019,
year = {2025},
author = {Yoon, SM and Ki, CS and Song, JS},
title = {CleanSeqU algorithm for decontamination of catheterized urine 16S rRNA sequencing data.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {19270},
pmid = {40457019},
issn = {2045-2322},
mesh = {*RNA, Ribosomal, 16S/genetics ; Humans ; *Algorithms ; *Decontamination/methods ; Microbiota/genetics ; Female ; Vagina/microbiology ; Sequence Analysis, DNA/methods ; *Urine/microbiology ; },
abstract = {Contamination in low-biomass samples, such as urine, presents a major challenge for 16S rRNA gene sequencing, as extraneous DNA from reagents and the environment often obscures microbial signals. Existing in silico decontamination algorithms face limitations in accurately identifying and removing these contaminants. To address this issue, we developed CleanSeqU, a novel decontamination algorithm designed to enhance the accuracy of 16S rRNA gene sequencing data for catheterized urine samples. This approach is grounded in the principle that the compositional pattern of potential contaminant taxa remains similar between biological samples and blank controls. Also, the algorithm identifies potential contaminants based on ecological plausibility and custom blacklist. We evaluated CleanSeqU's performance using vaginal microbiome dilution experiments as a proxy for low-biomass urine samples and compared it to the Decontam, Microdecon, and SCRuB algorithm. CleanSeqU consistently outperformed Decontam, Microdecon, and SCRuB across various contamination levels, with superior accuracy, F1-scores, and reduced beta-dissimilarity. CleanSeqU improved specificity and positive predictive value by correctly identifying and removing a higher number of contaminant amplicon sequence variants (ASVs). Furthermore, the reduced alpha diversity in the decontaminated datasets suggests more precise contaminant elimination. With its practical use of a single blank extraction control per batch and adjustable decontamination rules, CleanSeqU provides an efficient and scalable solution that delivers accurate microbial profiles. Our findings highlight its potential to significantly advance urine microbiome research by delivering more accurate microbial profiles.},
}
@article {pmid40456950,
year = {2025},
author = {Kocharovskaya, Y and Delegan, Y and Sevostianov, S and Bogun, A and Demin, DV},
title = {Metagenomic Analysis of Pulp and Paper Wastes and Prospects for Their Self-purification.},
journal = {Current microbiology},
volume = {82},
number = {7},
pages = {320},
pmid = {40456950},
issn = {1432-0991},
mesh = {*Paper ; *Metagenomics ; Lignin/metabolism ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; *Industrial Waste/analysis ; Biodegradation, Environmental ; *Microbiota ; High-Throughput Nucleotide Sequencing ; },
abstract = {Thousands of tons of waste accumulate, as a result of the activities of the pulp and paper industry, which is often stored in the form of dumps. However, intensifying the use of lignocellulose for more efficient bioremediation remains highly challenging. Therefore, the study of microbiomes with potentially desirable characteristics for the decomposition of pulp and paper wastes is currently an important task. In this study, a comprehensive assessment of the microbiota biodiversity of these dumps was carried out using high-throughput, high-resolution sequencing. In study 472 million high-quality clean reads assembled into 6,413,337 contigs with a total length of 4306 Mb, of which 3,633,174 open reading frames (ORFs) were identified. The core microbiome was composed of four phyla from Proteobacteria, Actinobacteria, Bacteroidetes, and Verrucomicrobia. Representatives of phylum Proteobacteria prevailed in samples. Annotation using the KEGG database in the Metabolism category resulted in 654,234 ORFs and 5138 ORFs encoding enzymes/proteins involved in degradation of lignocellulose which formed main pool of the wastes. By use of the created database, the search for lignocellulose degradation genes showed that genera Shewanella, Achromobacter, and Delftia covered significant part of the reads. The results indicate that the established microbiome of local landfills can be considered as an important source for improving lignocellulose bioremediation, provided that lignocellulosic fungi are sufficiently active. In whole, these new data can be used as a scientific basis to form an efficient eco-biotechnology for auto-remediation of pulp and paper industry waste.},
}
@article {pmid40456902,
year = {2025},
author = {Guo, HB and Zhao, JC and Liu, WY and Bi, YD and Sibirina, LA and Yu, XD},
title = {Microbiome analysis for artificially establishing the symbiotic relationship between Hebeloma hiemale and Quercus mongolica.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {19273},
pmid = {40456902},
issn = {2045-2322},
support = {2022-MS-418//Natural Science Foundation of Liaoning Province/ ; 2024-MSLH-344//Natural Science Foundation of Liaoning Province/ ; 32370008//National Natural Science Foundation of China/ ; },
mesh = {*Quercus/microbiology ; *Symbiosis ; *Microbiota ; *Mycorrhizae/physiology/genetics ; Soil Microbiology ; Rhizosphere ; *Hebeloma/physiology ; Bacteria/genetics/classification ; },
abstract = {Ectomycorrhizae (ECM) play a critical role in enhancing plant growth and health. However, the influence of artificially established ectomycorrhizal symbioses on the structure and function of rhizosphere microbial communities remains inadequately understood. In this study, a symbiotic relationship between Hebeloma hiemale and Quercus mongolica was established to investigate the influence of ECM on soil microbial communities in the rhizosphere of the host plant. High-throughput sequencing revealed that H. hiemale inoculation altered the evenness of both the fungal and bacterial communities and reduced the diversity of the bacterial community relative to the blank control. In particular, several bacterial genera with an enhanced capacity for nutrient cycling, contaminant degradation, and host plant protection were enriched following H. hiemale inoculation. Shifts in fungal community structure suggest potential benefits for the host plant, including reduced cadmium uptake, enhanced mercury remediation, and increased protection against pathogens. Our results highlight the complex interactions between ECM and rhizosphere microbial communities to enable a better understanding of the importance of multi-species relationships in plant-microbe symbioses and their ecological implications.},
}
@article {pmid40456878,
year = {2025},
author = {Ng, RWY and Chen, Z and Yang, L and Wong, OWH and Leung, ASY and Tsui, KW and Kwok, NMW and Tang, LHY and Cheung, PMH and Chan, PKS and Ip, M},
title = {Association between attention-deficit/hyperactivity disorders and intestinal disorders: A systematic review and Meta-analysis.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {19278},
pmid = {40456878},
issn = {2045-2322},
support = {CUHK 24115121//Hong Kong Special Administrative Region, China/ ; },
mesh = {Humans ; *Attention Deficit Disorder with Hyperactivity/complications/epidemiology/microbiology ; *Intestinal Diseases/epidemiology/complications ; Gastrointestinal Microbiome ; *Irritable Bowel Syndrome/epidemiology ; Risk Factors ; },
abstract = {Patients with attention-deficit hyperactivity disorder (ADHD) reported significantly more constipation and flatulence than healthy controls. An altered gut microbiome can be associated with gastrointestinal symptoms. However, comprehensive information about associated risk of intestinal disorders and ADHD remains limited. A systematic review of the literature was therefore conducted to investigate the association between ADHD and different types of intestinal disorders. A total of 11 studies with 3,851,163 unique individuals, including 175 806 individuals with ADHD and 3 675 357 individuals without ADHD were included. The pooled OR of intestinal disorders for individuals with ADHD was 1.25 (95%CI, 0.75-2.07). A significant positive association was found between ADHD and irritable bowel syndrome (IBS) (OR 1.63 [95% CI 1.45-1.83]). Studies conducted in Eastern Mediterranean Region yielded a summary OR estimate that was higher than summary OR estimates in studies conducted in Region of the Americas, European Region and Western Pacific Region (3.03 [1.53-5.99] vs. 2.20 [1.05-4.63], 1.04 [0.44-2.41], 0.68 [0.25-1.87]), with p value 0.053, indicating a trend towards significance. High heterogeneity was observed. Our study supports association between ADHD and increased risk of IBS. Our study suggests an altered gut microbiome is the potential link that bridges gap between ADHD and intestinal disorder.},
}
@article {pmid40456853,
year = {2025},
author = {Xu, R and Nicol, MP and Cheema, AS and McEachran, JL and Warden, AH and Perrella, SL and Gridneva, Z and Geddes, DT and Stinson, LF},
title = {The human milk microbiome is minimally associated with breastfeeding practices.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {19308},
pmid = {40456853},
issn = {2045-2322},
mesh = {Humans ; *Milk, Human/microbiology ; *Breast Feeding ; *Microbiota ; Female ; Adult ; RNA, Ribosomal, 16S/genetics ; Infant ; Bacteria/genetics/classification ; },
abstract = {The human milk microbiome is dominated by typical oral and skin bacteria, suggesting that bacterial communities from the infant mouth and maternal skin contribute to the development of the human milk microbiome. It is postulated that breastfeeding characteristics, such as breastfeeding frequency and duration, could lead to different levels of exposure to oral and skin bacteria, and subsequently, altered bacterial profiles in human milk. To investigate the associations between breastfeeding characteristics and the human milk microbiome, this study analysed milk samples collected from 56 participants at 3 months postpartum by full-length 16 S rRNA gene sequencing. Breastfeeding characteristics (breastfeeding frequency, total 24 h breastfeeding duration, and 24 h milk removal volume) were recorded by the participants using the 24 h test weighing protocol. The milk microbiome was largely robust to breastfeeding practices, with only one association detected between breastfeeding characteristics and the milk microbiome. Duration of breastfeeding from the sampled breast (per 24 h) was weakly positively associated with the relative abundance of Streptococcus salivarius (P = 0.035). No associations with alpha nor beta diversity were detected. In conclusion, variations in breastfeeding characteristics do not have a major impact on the composition or diversity of the human milk microbiome.},
}
@article {pmid40456836,
year = {2025},
author = {Özcan, E and Yu, KB and Dinh, L and Lum, GR and Lau, K and Hsu, J and Arino, M and Paramo, J and Lopez-Romero, A and Hsiao, EY},
title = {Author Correction: Dietary fiber content in clinical ketogenic diets modifies the gut microbiome and seizure resistance in mice.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {5090},
doi = {10.1038/s41467-025-60533-7},
pmid = {40456836},
issn = {2041-1723},
}
@article {pmid40456745,
year = {2025},
author = {Taubenheim, J and Kadibalban, AS and Zimmermann, J and Taubenheim, C and Tran, F and Rosenstiel, P and Aden, K and Kaleta, C},
title = {Metabolic modeling reveals a multi-level deregulation of host-microbiome metabolic networks in IBD.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {5120},
pmid = {40456745},
issn = {2041-1723},
support = {EXC2167//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; FOR5042//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 01ZX1902A//Bundesministerium f&#xfc;r Bildung und Forschung (Federal Ministry of Education and Research)/ ; 01ZX1915A//Bundesministerium f&#xfc;r Bildung und Forschung (Federal Ministry of Education and Research)/ ; 2020_EKCS.11//Else Kr&#xf6;ner-Fresenius-Stiftung (Else Kroner-Fresenius Foundation)/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Inflammatory Bowel Diseases/metabolism/microbiology ; *Metabolic Networks and Pathways ; NAD/metabolism ; Metabolome ; Phospholipids/metabolism ; Polyamines/metabolism ; Amino Acids/metabolism ; Tryptophan/metabolism ; Models, Biological ; Homeostasis ; Male ; Female ; Transcriptome ; *Host Microbial Interactions ; Metabolomics ; },
abstract = {Inflammatory bowel diseases (IBDs) are chronic disorders involving dysregulated immune responses. Despite the role of disrupted host-microbial interaction in the pathophysiology of IBD, the underlying metabolic principles are not fully understood. We densely profiled microbiome, transcriptome and metabolome signatures from longitudinal IBD cohorts before and after advanced drug therapy initiation and reconstructed metabolic models of the gut microbiome and the host intestine to study host-microbiome metabolic cross-talk in the context of inflammation. Here, we identified concomitant changes in metabolic activity across data layers involving NAD, amino acid, one-carbon and phospholipid metabolism. In particular on the host level, elevated tryptophan catabolism depleted circulating tryptophan, thereby impairing NAD biosynthesis. Reduced host transamination reactions disrupted nitrogen homeostasis and polyamine/glutathione metabolism. The suppressed one-carbon cycle in patient tissues altered phospholipid profiles due to limited choline availability. Simultaneously, microbiome metabolic shifts in NAD, amino acid and polyamine metabolism exacerbated these host metabolic imbalances. Leveraging host and microbe metabolic models, we predicted dietary interventions remodeling the microbiome to restore metabolic homeostasis, suggesting novel therapeutic strategies for IBD.},
}
@article {pmid40456658,
year = {2025},
author = {Wang, ZY and Zhong, YJ and Wang, YF and Xie, NH and Zhang, Y and Jiang, ZY and Shi, RJ and Liang, XL},
title = {Ecological functions of plant-beneficial microbiomes and their application prospects in sustainable agriculture.},
journal = {Ying yong sheng tai xue bao = The journal of applied ecology},
volume = {36},
number = {5},
pages = {1553-1566},
doi = {10.13287/j.1001-9332.202504.036},
pmid = {40456658},
issn = {1001-9332},
mesh = {*Microbiota/physiology ; *Soil Microbiology ; *Agriculture/methods ; Mycorrhizae/physiology ; Bacteriophages/physiology ; *Crops, Agricultural/growth &amp; development/microbiology ; *Ecosystem ; Symbiosis ; Sustainable Development ; Plant Development ; },
abstract = {Soil microbial communities form dynamic interaction networks with plants, which influence growth, development, stress tolerance, and ecological adaptability of plants. In recent years, the roles of beneficial micro-biomes, including plant growth-promoting rhizobacteria (PGPR), arbuscular mycorrhizal fungi (AMF), and plant-associated bacteriophages, in agricultural ecosystems have received increasing attention. Beneficial microorganisms can facilitate soil nutrient release, secrete plant hormones, and regulate signaling pathways, thereby establishing symbiotic relationships with plant for healthy host growth. They also play crucial roles in enhancing plant tolerance to salinity, drought, and pest-related stresses. Bacteriophages, as integral components of plant microbiomes, exhibit potential ecological functions, such as modulating host metabolism, boosting plant resistance, and maintaining microbial community balance. However, the mechanisms through which plant-associated microbiomes influence plant physiological traits remain less understood. The application of exogenous microorganisms in agriculture faces many challenges, such as competition from native microbiomes, environmental adaptability, and functional stabi-lity. We summarized the ecological functions of plant-beneficial microbiomes, including bacteriophages, in agricultural systems, highlighting their synergistic roles in soil health maintenance, nutrient cycling optimization, biodiversity conservation, and reducing reliance on chemical inputs. Furthermore, we discussed the complex mechanisms underlying plant-microbiome-environment interactions and proposed strategies for optimizing microbiome functions to promote sustainable development of agriculture and ensuring food security and ecological balance.},
}
@article {pmid40456421,
year = {2025},
author = {Talukdar, D and Raju, YJ and Jana, P and Sharma, K and Babele, P and Kothidar, A and Ahrodia, T and Narendrakumar, L and Shyam, KR and Singh, U and Tanwar, S and Harle, S and Chaudhuri, S and Raghavan, S and Wadhwa, N and Mukherjee, S and Bhatnagar, S and Das, B and , },
title = {Genomic insights into the potency and functional roles of Lactobacillus species in term and preterm births.},
journal = {Genomics},
volume = {},
number = {},
pages = {111063},
doi = {10.1016/j.ygeno.2025.111063},
pmid = {40456421},
issn = {1089-8646},
abstract = {The vaginal microbiome, typically dominated by Lactobacillus species, plays a key role in reducing the risk of preterm birth (PTB) by protecting against infections. In this study, we sequenced 133 Lactobacillus genomes isolated from the reproductive tracts of pregnant Indian women. Genomic analysis identified genes linked to pathogen resistance and anti-inflammatory functions. Further proteome analysis of cell-free supernatant revealed antimicrobial properties, including lysin and bacteriocin, while antibacterial tests confirmed their ability to inhibit reproductive tract pathogens. These findings suggest that Lactobacillus strains protect against harmful microbes, potentially reducing infection risks and PTB. This Lactobacillus consortium holds promise for developing biotherapeutics aimed at improving maternal health.},
}
@article {pmid40456384,
year = {2025},
author = {Nayyar, J and Bedu-Ferrari, C and Patangia, D and Hurley, E and Feeley, L and Ross, RP and Stanton, C and Brady, P},
title = {Gut and oral microbial profile associations to oral cancer.},
journal = {Journal of dentistry},
volume = {},
number = {},
pages = {105848},
doi = {10.1016/j.jdent.2025.105848},
pmid = {40456384},
issn = {1879-176X},
abstract = {The human microbiome is widely known to be associated with health and disease. The oral microbiome has been linked with oral diseases and infections, though not many studies have explored the relation between oral and gut microbiome with oral cancer based on lesion histology METHODS: This study uniquely explores the oral and gut microbiota in 30 participants (n=30) divided into three groups based on histology; Benign (B) (n=15), Potentially Malignant (PM) (n=8), and Malignant (M) (n=7) oral lesions. Using shotgun metagenomic sequencing, we analysed microbiota profiles to determine their potential as biomarkers for oral malignancy RESULTS: Distinct gut microbial profiles were observed between Benign and Malignant groups and the association of specific microbes in oral saliva, such as Haemophilus parainfluenzae, Veillonella parvula, Fusobacterium nucleatum and Rothia mucilaginosa were strongly associated with malignancy CONCLUSION: The data from this exploratory study suggest that oral and gut microbiomes could act as possible biomarkers and aid in early detection and assessment of oral cancer risk. With regard to potentially malignant lesions, future research could study individual Oral Potentially Malignant Disorders (OPMDs) as distinct entities due to the wide variation in clinical and histological presentation. Further research is required to develop definitive biomarkers in both potentially malignant and malignant oral lesions CLINICAL SIGNIFICANCE: While smoking and alcohol are known risk factors for oral cancer, a biomarker such as the saliva/stool microbiome profile could help identify a risk indicator or a potential risk factor. Additionally such a biomarker could help identify patients with OPMDs that are likely to undergo malignant transformation.},
}
@article {pmid40456365,
year = {2025},
author = {Zhao, X and Overbeek, LV and Burgess, CM and Holden, N and Brennan, F and Johannessen, GS and Allende, A and Höfte, M and Cottyn, B and Pothier, JF and Schikora, A and Uyttendaele, M},
title = {Human Pathogenic Microorganisms in Fresh Produce Production: Lessons Learned When Plant Science Meets Food Safety.},
journal = {Journal of food protection},
volume = {},
number = {},
pages = {100551},
doi = {10.1016/j.jfp.2025.100551},
pmid = {40456365},
issn = {1944-9097},
abstract = {To enhance control of human pathogenic microorganisms in plant production systems, an EU COST Action (HUPLANTcontrol CA16110) was initiated, bringing together microbiologists in food, environmental and plant microbial ecology. This article summarizes the outcomes of multiple workshops and the four main lessons learned: (i) many terminologies need further explanation to facilitate multidisciplinary communication on the behavior of human pathogens from pre-harvest plant production to post-harvest food storage, (ii) the complexity of bacterial taxonomy pushes microbial hazard identification for greater resolution of characterisation (to subspecies, or even strain level) needing a multi-method approach, (iii) hazard characterisation should consider a range of factors to evaluate the weight of evidence for adverse health effects in humans, including strain pathogenicity, host susceptibility, and the impact of the plant, food, or human gut microbiome, (iv) a wide diversity of microorganisms in varying numbers and behaviours co-exist in the plant microbiome, including good (beneficial for plant or human health), bad (established human or plant pathogens) or ugly (causing spoilage or opportunistic disease). In conclusion, active listening in communication and a multi-perspective approach are the foundation for every successful conversation when plant science meets food safety.},
}
@article {pmid40456300,
year = {2025},
author = {Gao, F and Wang, C and Cao, Z and Zhang, X and Xi, W and Liu, Y and Zhan, X and Jia, M and Gou, N and Yu, L and Zhang, Y and Guo, Y and Wang, W and Zhu, F and Ma, X and Gao, Y},
title = {Nod2 deficiency exacerbates schizophrenia-related alterations in offspring of maternal immune activation in a sex-dependent manner.},
journal = {Brain, behavior, and immunity},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.bbi.2025.05.030},
pmid = {40456300},
issn = {1090-2139},
abstract = {INTRODUCTION: Schizophrenia is a severe mental disorder with a complex etiopathogenesis involving both genetic and environmental risk factors. Evidence suggests that immune dysregulation plays a key role in its development, with maternal immune activation (MIA) during pregnancy identified as a significant environmental contributor. However, not all maternal infections result in schizophrenia-like outcomes, indicating that genetic susceptibility may render some individuals more vulnerable to MIA. Nucleotide-binding oligomerization domain-containing protein 2 (NOD2), an intracellular receptor, plays a crucial role in maintaining the balance between intestinal microbiota and immune responses, but its precise role in gut-brain interactions during neurodevelopment remain unclear.<br><br>METHODS: To investigate the interaction between MIA and Nod2 deficiency, we evaluated behavioral and physiological phenotypes in Nod2[-/-] mice exposed to poly(I:C)-induced MIA. In addition to immune responses, we analyzed maternal gut microbiota and the transmission of microbiota between mothers and offspring. Given the role of the gut-brain axis in schizophrenia, we conducted intestinal immunofluorescence staining, organoid cultures, and RNA sequencing of fetal brains to assess gut injury and neuroimmune changes in the brain. Male and female offspring were analyzed separately.<br><br>RESULTS: Dual exposure led to schizophrenia-like behaviors in a sex-specific manner, as well as brain development disruptions, compromised gut integrity, reduced intestinal organoid-forming capacity, and altered gut microbiota composition. Importantly, maternal gut microbiota disturbances, coupled with microbial transmission to offspring, appear to increase schizophrenia risk with potential long-term behavioral consequences.<br><br>CONCLUSION: This study underscores the intricate interplay of genetic, environmental, and microbiome factors, offering a valuable model for investigating the complex pathophysiology of neurodevelopmental disorders.},
}
@article {pmid40455948,
year = {2025},
author = {Azzolino, D and Felicetti, A and Santacroce, L and Lucchi, T and Garcia-Godoy, F and Passarelli, PC},
title = {The emerging role of oral microbiota: A key driver of oral and systemic health.},
journal = {American journal of dentistry},
volume = {38},
number = {3},
pages = {111-116},
pmid = {40455948},
issn = {0894-8275},
mesh = {Humans ; *Microbiota/physiology ; *Oral Health ; Dysbiosis/microbiology ; *Mouth/microbiology ; *Mouth Diseases/microbiology ; },
abstract = {PURPOSE: To describe the existing literature on the emerging role of the oral microbiota in shaping both oral and systemic health.<br><br>METHODS: A narrative review was performed. PubMed, EMBASE and Scopus databases were searched for relevant articles published in the English language.<br><br>RESULTS: The oral microbiota plays a crucial role in both oral and systemic health, yet its composition and functions have been underexplored compared to the gut microbiota. The oral cavity harbors a diverse range of microorganisms, including bacteria, fungi, viruses, archaea, and protozoa, which interact within biofilms to influence oral health. The microbiome is influenced by various factors such as diet, oral hygiene, smoking, alcohol consumption, socioeconomic status, pregnancy, and genetics. Dysbiosis in the oral microbiota has been linked to a range of oral diseases, including dental caries, periodontal diseases, oral candidiasis, and even oral cancer. Additionally, oral bacteria can impact systemic health, with emerging associations to cardiovascular disease, respiratory conditions, and various cancers. Effective management of oral dysbiosis involves strategies such as mouthwashes, dietary modifications, and supplementation with probiotics and prebiotics, which can modulate the microbiota, enhance immune responses, and reduce pathogenic growth.<br><br>CLINICAL SIGNIFICANCE: Oral microbiota dysbiosis, beyond its role in mediating oral diseases, is emerging as a driver of a range of systemic health conditions, including cardiovascular disease, respiratory conditions, and various cancers. A holistic approach combining regular oral hygiene, balanced nutrition, and microbiome-targeted interventions is essential for maintaining oral health and potentially preventing associated systemic diseases.},
}
@article {pmid40455875,
year = {2025},
author = {Mussa, FM and Joachim, A and Moshiro, R and Masoud, SS and Addo, MM and Pagel, J and Krumkamp, R and Kobbe, R and Salim, N},
title = {A study protocol for neonatal sepsis and gut microbiomics among preterm infants admitted at Muhimbili National Hospital, Tanzania.},
journal = {PloS one},
volume = {20},
number = {6},
pages = {e0325099},
doi = {10.1371/journal.pone.0325099},
pmid = {40455875},
issn = {1932-6203},
mesh = {Humans ; Tanzania/epidemiology ; Infant, Newborn ; *Neonatal Sepsis/microbiology/epidemiology ; *Infant, Premature ; *Gastrointestinal Microbiome ; Prospective Studies ; Female ; Male ; Dysbiosis/microbiology ; },
abstract = {BACKGROUND: Neonatal mortality remains high in many low- and middle-income countries (LMICs), with neonatal sepsis and antimicrobial resistance (AMR) posing significant threats to newborns, particularly in sub-Saharan Africa (SSA). Tanzania is among the countries with the highest neonatal mortality rates, with sepsis being a major contributor. Gut dysbiosis has been identified as a risk factor for neonatal sepsis in high-income countries, due to factors like abundance of pathogenic bacteria, decrease in microbiome diversity, intestinal barrier defects and bacterial translocation. Understanding gut dysbiosis in the local setting and its role in sepsis development may offer new prevention strategies, such as probiotics for high-risk preterm infants.<br><br>OBJECTIVES: This prospective neonatal cohort, established at Muhimbili National Hospital (MNH) in Dar es Salaam, Tanzania, aims to analyze the gut microbiome of preterm infants and explore associations with neonatal late-onset sepsis (LOS). Additionally, data on bacterial pathogens of bloodstream infections and AMR prevalence will be identified. Secondary endpoints include clinical LOS, sepsis-related death, death from any cause, and hospital discharge outcomes.<br><br>METHODS: Eligible preterm neonates (28 + 0 to <34 weeks of gestational age, birth weight&#x2009;&#x2265;&#x2009;1000g) will be recruited with maternal consent. Socio-demographic and clinical data, microbiological details of blood pathogens, and a set of fresh frozen fecal samples during the 28 days observation period will be collected. The study targets a sample size of 1350 participants and we expect 72-135 culture-proven LOS during a study period of 18 months. Fecal samples will undergo next-generation sequencing (NGS) to analyze microbial community functions in comparison to matched controls.<br><br>DISCUSSION: This collaborative study between universities in Tanzania and Germany, aims to analyze the neonatal microbiome in relation to sepsis development and AMR of blood culture isolates to enhance neonatal sepsis care, improve diagnostics and treatment. The project will offer insights into potential therapeutic strategies for the future, promote academic exchange, capacity building and research on African microbiomes.},
}
@article {pmid40455399,
year = {2025},
author = {Qayyum, H and Raziq, MF and Manzoor, H and Zaidi, SSA and Ali, A and Kayani, MUR},
title = {Efficient De Novo Assembly and Recovery of Microbial Genomes from Complex Metagenomes Using a Reduced Set of k-mers.},
journal = {Interdisciplinary sciences, computational life sciences},
volume = {},
number = {},
pages = {},
pmid = {40455399},
issn = {1867-1462},
abstract = {De novo assembly and genome binning are fundamental steps for genome-resolved metagenomics analyses. However, the availability of limited computational resources and extensive processing time limit the broader application of these analyses. To address these challenges, the optimization of the parameters employed in these processes can improve the effective utilization of available metagenomics tools. Therefore, this study tested three sets of k-mers (default, reduced, and extended) for their efficiency in metagenome assembly and suitability in recovering metagenome-assembled genomes. The results demonstrate that the reduced set of k-mers outperforms the other two sets in computational efficiency and the quality of results. The assemblies from the default set are comparable with those from the reduced set; however, less complete and highly contaminated metagenome-assembled genomes are obtained at the expense of higher processing time. The extended set of k-mers yields less contiguous but computationally expensive assemblies. This set takes approximately 3-times more processing time than the reduced k-mers and recovers the lowest proportions of high and medium-quality metagenome-assembled genomes. Contrarily, the reduced set produces better assemblies, substantially improving the number and quality of the recovered metagenome-assembled genomes in significantly reduced processing time. Validation of the reduced k-mer set on previously published metagenome datasets further demonstrates its effectiveness not only for human metagenomes but also for the metagenomes of environmental origin. These findings underscore that the reduced k-mer set is optimal for efficient metagenome analyses of varying complexities and origins. This optimization of the k-mer set used in metagenome assemblers significantly reduces computational time while improving the quality of the assemblies and recovered metagenome-assembled genomes. This efficient solution will facilitate the widespread application of genome-resolved analyses, even in resource-limited settings, and help the recovery of better-quality metagenome-assembled genomes for downstream analyses.},
}
@article {pmid40455162,
year = {2025},
author = {Pathania, A},
title = {Diverse Facets of Nonhuman Sequences in Read Outputs of the Human Next-Generation Sequencing Data and Their Relevance with Viruses.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2927},
number = {},
pages = {251-258},
pmid = {40455162},
issn = {1940-6029},
mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Viruses/genetics ; Genome, Human ; Microbiota/genetics ; Sequence Analysis, DNA/methods ; Genomics/methods ; Computational Biology/methods ; },
abstract = {In human genomic studies, on average, 10% of next-generation sequencing (NGS) reads fail to align with the human reference genome. These unmapped reads vary across samples and have three main potential sources. First, they could represent contamination introduced during sample processing or from the sequencing technology itself. Second, these sequences might originate from microorganisms, like viruses, bacteria, and fungi, that have coevolved with humans and residing within humans. These natural inhabitants of the human body make up the human microbiota. During taking the human cell samples, the microbiota of the surroundings can infect the human samples. Third, these reads could come from active or dormant pathogens residing in the taken human cell samples, like viruses. Research shows that the composition of these microbial species changes with the health and condition of human tissues. In this study, author proposes that unmapped reads may serve as indicators of the pathological state of various tissues and cell types. An outline is marked for experimental approaches to test these ideas and explore the potential of these reads as diagnostic markers.},
}
@article {pmid40455096,
year = {2025},
author = {Bai, J and Zeng, Q and Ni, Y and Yi, X and Xie, Y and Wu, Y and Wu, Z and Chen, H and Yang, A},
title = {Synbiotic Combination of Lactiplantibacillus plantarum and Fructo-Oligosaccharide Alleviates Soy Protein-Induced Food Allergies in Mice by Modulating the Gut Microbiota and Its Metabolisms.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c00728},
pmid = {40455096},
issn = {1520-5118},
abstract = {Oral administration of synbiotics is a highly effective approach to improve food allergies through the modulation of gut microbiota. Therefore, the effects of synbiotics composed of Lactiplantibacillus plantarum (Lp) and fructo-oligosaccharide (FOS) on soybean-sensitized mice were explored in this study focusing on the gut microbiota and metabolisms. The results indicated that Lp-FOS intervention significantly alleviated allergic symptoms, reduced the IgE, IgG1, and mMCP-1 levels, restored the balance of Th1/Th2 and Tregs/Th17, and enhanced intestinal barrier integrity. 16S rDNA microbiome sequencing revealed that Lp-FOS increased the Lachnospiraceae and Lactobacillus proportions and reduced the Desulfovibrionaceae and Muribaculaceae proportions. Nontargeted metabolomics further demonstrated that Lp-FOS improved gut metabolic disorders by modulating key pathways involved in amino acid metabolism, cofactor and vitamin metabolism, and lipid metabolism, with a notable enhancement in tryptophan metabolism. Collectively, this study confirmed that Lp-FOS could mitigate soybean allergy by regulating the immune system, gut microbiota, and metabolic pathway. This study will offer novel insights into developing synbiotic-based interventions against food allergies.},
}
@article {pmid40454876,
year = {2025},
author = {Hung, CT and Kern, J and Trsan, T and Panda, SK and Laury, M and Jain, U and Colonna, M and Stappenbeck, TS and Liu, TC},
title = {Transgenerational Obesity Modulation of Gut Mucosal Immunity.},
journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology},
volume = {39},
number = {11},
pages = {e70678},
pmid = {40454876},
issn = {1530-6860},
support = {DK136829//HHS | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)/ ; DK125296//HHS | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)/ ; DK124274//HHS | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)/ ; DK126699//HHS | National Institutes of Health (NIH)/ ; AT009714//HHS | National Institutes of Health (NIH)/ ; },
mesh = {Animals ; *Obesity/immunology ; *Immunity, Mucosal ; Female ; Mice ; Gastrointestinal Microbiome/immunology ; Diet, High-Fat/adverse effects ; *Intestinal Mucosa/immunology ; Paneth Cells/immunology/pathology ; Male ; Mice, Inbred C57BL ; Intraepithelial Lymphocytes/immunology ; Diet, Western/adverse effects ; },
abstract = {The prevalence of obesity in the United States has continued to increase over the past several decades. A growing concern is that transgenerational effects of obesity negatively impact physiologic functions. We showed that consumption of a high fat, high sugar "Western" diet (WD) decreased the density of both gut innate (Paneth cells) and adaptive immune cells (intraepithelial lymphocytes; IEL). We asked whether consumption of WD impacts gut mucosal immunity in the offspring. WD-mediated Paneth cell loss was reversible, whereas IEL loss was not. However, the overall composition of the fecal microbiome and response to infection were defined by the diet consumed by the progeny. Therefore, offspring from obese dams can prevent gut immunity impairment by consuming a healthy diet.},
}
@article {pmid40454874,
year = {2025},
author = {Pfister, CA and Berlinghof, J and Bogan, M and Cardini, U and Gobet, A and Hamon-Giraud, P and Hart, J and Jimenez, N and Siegel, A and Stanfield, E and Vallet, M and Leblanc, C and Rousseau, C and Thomas, F and Stock, W and Dittami, SM},
title = {Evolutionary history and association with seaweeds shape the genomes and metabolisms of marine bacteria.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0099624},
doi = {10.1128/msphere.00996-24},
pmid = {40454874},
issn = {2379-5042},
abstract = {UNLABELLED: Seaweeds harbor a rich diversity of bacteria, providing them with metabolic resources and a surface for attachment and biofilm development. The host's unique environment potentially shapes the bacterial genomes and promotes adaptations for a symbiotic lifestyle. To investigate whether the genomes of seaweed-associated bacteria are genetically and metabolically distinct from their close free-living relatives in seawater, we compared both the seaweed-associated and free-living counterparts of 72 bacterial genera across 16 seaweed hosts using whole-genome sequences or high-quality metagenome-assembled genomes. While taxonomic affiliation strongly influenced genome characteristics such as GC content, gene number, and size, host association had a lower effect overall. A reduced genome size was suggested only in Nereocystis luetkeana-associated microbes, while only Ascophyllum nodosum-associated bacteria had an increased GC content. Metabolic adaptations were indicated from the genomes of seaweed-associated bacteria, including enriched pathways for B vitamin production, complex carbohydrate utilization, and amino acid biosynthesis. In particular, Flavobacteriia showed the most pronounced differences between host-associated and free-living strains. We further hypothesized that bacteria associated with seaweed might have evolved to complement their host's metabolism and tested this inference by analyzing the genomes of both the seaweed Ectocarpus subulatus and its 28 bacterial associates but found no evidence for such complementarity. Our analyses of 72 paired bacterial genomes highlighted significant metabolic differences in seaweed-associated strains with implications for carbon, nitrogen, and sulfur cycling in the coastal ocean.<br><br>IMPORTANCE: We hypothesized that the unique environment of seaweeds in coastal oceans shapes bacterial genomes and promotes a symbiotic lifestyle. We compared the genomes of bacteria isolated from seaweed with bacteria from the same genus found free-living in seawater. For genome features that included the number of genes, the size of the genome, and the GC content, taxonomy was of greater importance than bacterial lifestyle. When we compared metabolic abilities, we again found a strong effect of taxonomy in determining metabolism. Although several metabolic pathways differed between free-living and host-associated bacteria, this was especially prominent for Flavobacteriia in the phylum Bacteroidota. Notably, bacteria living on seaweeds had an increased occurrence of genes for B vitamin synthesis, complex carbohydrate use, and nitrogen uptake, indicating that bacterial genomes reflect both their evolutionary history and the current environment they inhabit.},
}
@article {pmid39530534,
year = {2024},
author = {Kao, D and Wong, K and Jijon, H and Moayyedi, P and Franz, R and McDougall, C and Hotte, N and Panaccione, R and Semlacher, E and Kroeker, KI and Peerani, F and MacDonald, KV and Xu, H and Narula, N and Turbide, C and Marshall, DA and Madsen, KL},
title = {Preliminary Results From a Multicenter, Randomized Trial Using Fecal Microbiota Transplantation to Induce Remission in Patients With Mild-to-Moderate Crohn's Disease.},
journal = {The American journal of gastroenterology},
volume = {120},
number = {6},
pages = {1334-1344},
pmid = {39530534},
issn = {1572-0241},
support = {PJT 148913/CAPMC/CIHR/Canada ; PJT 148913/CAPMC/CIHR/Canada ; },
mesh = {Humans ; *Fecal Microbiota Transplantation/methods ; *Crohn Disease/therapy ; Male ; Female ; Remission Induction/methods ; Adult ; Double-Blind Method ; Middle Aged ; Quality of Life ; Colonoscopy ; Treatment Outcome ; Canada ; Severity of Illness Index ; },
abstract = {INTRODUCTION: Fecal microbiota transplantation (FMT) has shown promise at inducing remission in ulcerative colitis. This study is the first of its kind to evaluate the efficacy and safety of FMT at inducing remission in Crohn's disease (CD).<br><br>METHODS: This double-blind, placebo-controlled trial was conducted in 3 Canadian academic centers; randomized patients with mild-to-moderate CD received FMT or placebo. The first treatment was administered by colonoscopy followed by weekly oral capsules for 7 weeks. Primary end point was clinical and endoscopic remission at week 8. Secondary outcomes included clinical and endoscopic response, adverse events, and health-related quality of life using generic and disease-specific instruments.<br><br>RESULTS: From July 2017 to June 2021, 21 and 13 patients were randomized to FMT and placebo groups, respectively. The trial terminated early due to futility. At week 8, 0% (0/15) of patients in the FMT group versus 8.3% (1/11) in the placebo group reached the primary end point of combined clinical and endoscopic remission as per protocol analysis. There were no differences between the groups in clinical or endoscopic responses. One patient in each group had worsening of CD. Although both groups experienced statistically significant improvements in health-related quality of life, only the FMT group had a significant decrease in activity impairment. Although there were no significant changes in microbial diversity or composition, patients who achieved clinical response became more similar to their donors in stool microbial composition.<br><br>DISCUSSION: FMT was not effective at inducing clinical and endoscopic remission in CD using the FMT regimen in this study. Future studies may use other strategies to enhance treatment response, including longer intervention, antibiotic pretreatment, optimized donor-recipient pairing, and concomitant anti-inflammatory diet, and biologic or small molecule therapies.},
}
@article {pmid40454840,
year = {2025},
author = {Li, Z and Yin, Z and Chen, W and Wang, Z},
title = {Impact of Gut and Reproductive Tract Microbiota on Estrogen Metabolism in Endometriosis.},
journal = {American journal of reproductive immunology (New York, N.Y. : 1989)},
volume = {93},
number = {6},
pages = {e70109},
doi = {10.1111/aji.70109},
pmid = {40454840},
issn = {1600-0897},
mesh = {Humans ; *Endometriosis/microbiology/immunology/metabolism ; Female ; *Estrogens/metabolism ; *Gastrointestinal Microbiome/immunology ; *Dysbiosis/immunology ; Animals ; *Microbiota ; },
abstract = {BACKGROUND: The incidence of endometriosis is rising, particularly among younger populations, yet current diagnostic and therapeutic approaches remain limited. This highlights the urgent need for novel diagnostic tools and effective treatments. Recent studies have shown that intestinal and reproductive tract bacterial dysbiosis is closely associated with the development of endometriosis and plays a key role in the regulation of estrogen metabolism.<br><br>OBJECTIVES: This review aims to provide a comprehensive overview of the mechanisms of the microbiota's role in regulating estrogen levels and influencing the development and progression of endometriosis, providing important insights into the diagnosis and management of the disease.<br><br>CONCLUSIONS: Microbial changes not only promote estrogen imbalance by regulating &#x3b2;-glucuronidase activity, but also respond to estrogen imbalance by affecting the expression of metabolites such as short-chain fatty acids and lipopolysaccharides. In addition, significant fluctuations in estrogen levels also affect the composition of the microbial community. Both factors jointly lead to changes in the immune microenvironment of endometriosis.},
}
@article {pmid40454811,
year = {2025},
author = {Millard, SA and Vendrov, KC and Young, VB and Seekatz, AM},
title = {Host origin of microbiota drives functional recovery and Clostridioides difficile clearance in mice.},
journal = {mBio},
volume = {},
number = {},
pages = {e0110825},
doi = {10.1128/mbio.01108-25},
pmid = {40454811},
issn = {2150-7511},
abstract = {UNLABELLED: Colonization resistance provided by the gut microbiota is essential for resisting both initial Clostridioides difficile infection (CDI) and potential recurrent infection (rCDI). Although fecal microbiota transplantation (FMT) has been successful in treating rCDI by restoring microbial composition and function, mechanisms underlying the efficacy of standardized stool-derived products remain poorly understood. Using a combination of 16S rRNA gene-based and metagenomic sequencing alongside metabolomics, we investigated microbiome recovery following FMT from human and murine donor sources in a mouse model of rCDI. We found that a human-derived microbiota was less effective in clearing C. difficile compared to a mouse-derived microbiota, despite recovery of taxonomic diversity, compositional changes, and bacterial functions typically associated with clearance. Metabolomic analysis revealed deficits in secondary metabolites compared to those that received murine FMT, suggesting a functional remodeling between human microbes in their new host environment. Collectively, our data revealed additional environmental, ecological, or host factors to consider in FMT-based recovery from rCDI.<br><br>IMPORTANCE: Clostridioides difficile is a significant healthcare-associated pathogen, with recurrent infections presenting a major treatment challenge due to further disruption of the microbiota after antibiotic administration. Despite the success of fecal microbiota transplantation (FMT) for the treatment of recurrent infection, the mechanisms mediating its efficacy remain underexplored. This study reveals that the effectiveness of FMT may be compromised by a mismatch between donor microbes and the recipient environment, leading to deficits in key microbial metabolites. These findings highlight additional factors to consider when assessing the efficacy of microbial-based therapeutics for C. difficile infection (CDI) and other conditions.},
}
@article {pmid40454553,
year = {2025},
author = {Liu, Y and Gates, AD and Liu, Z and Duque, Q and Schmidt, SS and Chen, MY and Hamilton, CD and O'Toole, GA and Haney, CH},
title = {In vitro biofilm formation by a beneficial bacterium partially predicts in planta protection against rhizosphere pathogens.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf114},
pmid = {40454553},
issn = {1751-7370},
abstract = {Plant roots form associations with beneficial and pathogenic soil microorganisms. Although members of the rhizosphere microbiome can protect against pathogens, the mechanisms are poorly understood. We hypothesized that the ability to form a biofilm on the root surface is necessary for the exclusion of pathogens; however, it is not known if the same biofilm formation components required in vitro are necessary in vivo. Pseudomonas brassicacearum WCS365 is a beneficial strain that is phylogenetically closely related to an opportunistic pathogen Pseudomonas sp. N2C3 and confers protection against N2C3 in the rhizosphere. We used this plant-mutualist-pathogen model to screen collections of P. brassicacearum WCS365 increased attachment mutants (iam) and surface attachment defective (sad) transposon insertion mutants that form increased or decreased biofilm on abiotic surfaces, respectively. We found that whereas the P. brassicacearum WCS365 mutants had altered biofilm formation in vitro, only a subset of these mutants lost protection against N2C3. Non-protective mutants those involved in large adhesion protein (LapA) biosynthesis, flagellar synthesis and function, and O-antigen biosynthesis. We found that the inability of P. brassicacearum WCS365 mutants to grow in planta, and the inability to suppress pathogen growth, both partially contributed to loss of plant protection. We did not find a correlation between the extent of biofilm formed in vitro and pathogen protection in planta indicating that biofilm formation on abiotic surfaces may not fully predict pathogen exclusion in planta. Collectively, our work provides insights into mechanisms of biofilm formation and host colonization that shape the outcomes of host-microbe-pathogen interactions.},
}
@article {pmid40454482,
year = {2025},
author = {Koletic, C and Mrad, A and Martin, A and Devkota, S},
title = {Diet's impact on gut microbial assemblage in health and disease.},
journal = {The Journal of clinical investigation},
volume = {135},
number = {11},
pages = {},
doi = {10.1172/JCI184319},
pmid = {40454482},
issn = {1558-8238},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Diet ; Animals ; Chronic Disease ; },
abstract = {The gut microbiome has been linked to everything from human behavior to athletic performance to disease pathogenesis. And yet, few universal truths have emerged regarding how the microbiome exerts its effects or responds to the host environment except for one: gut microbiota are exquisitely sensitive to human diets. What we eat from birth onward shapes our gut microbiome composition and function, and this is likely an evolutionarily conserved interaction that benefits the microbe and often the host. However, modern diets and lifestyles have created discordance between our slowly evolving human genome and rapidly adaptable microbiome, and have been implicated in the rise of chronic diseases over the past 75 years. Diet and microbiome interactions have been reviewed extensively, so here we focus on areas of microbiome research that have most illuminated natural and disruptive dietary forces over time in humans, and where we may have opportunities to restore the natural balance of host with microbes in our modern world.},
}
@article {pmid40454480,
year = {2025},
author = {Lynch, LE and Lahowetz, R and Maresso, C and Terwilliger, A and Pizzini, J and Melendez Hebib, V and Britton, RA and Maresso, AW and Preidis, GA},
title = {Present and future of microbiome-targeting therapeutics.},
journal = {The Journal of clinical investigation},
volume = {135},
number = {11},
pages = {},
doi = {10.1172/JCI184323},
pmid = {40454480},
issn = {1558-8238},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Probiotics/therapeutic use ; *Phage Therapy/trends/methods ; Bacteriophages ; Animals ; },
abstract = {A large body of evidence suggests that single- and multiple-strain probiotics and synbiotics could have roles in the management of specific gastrointestinal disorders. However, ongoing concerns regarding the quality and heterogeneity of the clinical data, safety in vulnerable populations, and the lack of regulation of products containing live microbes are barriers to widespread clinical use. Safety and regulatory issues must be addressed and new technologies considered. One alternative future strategy is the use of synthetic bacterial communities, defined as manually assembled consortia of two or more bacteria originally derived from the human gastrointestinal tract. Synthetic bacterial communities can model functional, ecological, and structural aspects of native communities within the gastrointestinal tract, occupying varying nutritional niches and providing the host with a stable, robust, and diverse gut microbiota that can prevent pathobiont colonization by way of colonization resistance. Alternatively, phage therapy is the use of lytic phage to treat bacterial infections. The rise of antimicrobial resistance has led to renewed interest in phage therapy, and the high specificity of phages for their hosts has spurred interest in using phage-based approaches to precisely modulate the microbiome. In this Review, we consider the present and future of microbiome-targeting therapies, with a special focus on early-life applications, such as prevention of necrotizing enterocolitis.},
}
@article {pmid40454369,
year = {2025},
author = {Dong, Y and Zhang, Z and Zhu, Z and Hu, T and Chen, J and Teng, L and Liu, Z},
title = {Interactions between host sex and seasonal changes shape the gut microbial communities of wild blue sheep (Pseudois nayaur).},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1553622},
pmid = {40454369},
issn = {1664-302X},
abstract = {The construction of gut microbial communities in wildlife is influenced by both environmental factors and host genetic background. However, the mechanisms through which these factors interact to shape microbial communities remain poorly understood. In this study, we systematically sampled fecal specimens from male and female wild blue sheep across different seasons in Helan Mountain Nature Reserve and analyzed them using 16S rRNA gene sequencing. The objective was to investigate seasonal changes and interactions between sex and season on the gut microbial communities of blue sheep. Our results revealed that Firmicutes and Bacteroidetes were the dominant phyla across all groups, and the ten most abundant genera remain stable across both sexes and seasons. Alpha diversity (Chao1, two-way ANOVA, p = 0.001) and Beta diversity (PCoA, Anosim, R = 0.5410, p = 0.001) analyses further confirmed that seasonal and sex-specific interactions significantly shape the microbial community structure. Notably, the gut microbiomes of male and female blue sheep exhibited distinct response patterns to seasonal changes. LEfSe analysis (LDA > 3) identified 20 microbial taxa with significant seasonal differences, some of which showed sex-specific seasonal variation. These findings highlight the critical role of host sex in modulating the adaptation of gut microbial communities to seasonal environmental stresses. This study provides new insights into the ecological and evolutionary mechanisms of wildlife gut microbiomes and offers a scientific basis for sex-based wildlife conservation strategies.},
}
@article {pmid40454365,
year = {2025},
author = {Shadab, M and Samanta, SK and Baruah, J and Deka, S and Raj, G and Talukdar, NC},
title = {Comparative analysis of endophytic bacterial localization and microbiome diversity in plant varieties under varied growth conditions through microscopic imaging and sequencing techniques.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1568209},
pmid = {40454365},
issn = {1664-302X},
abstract = {INTRODUCTION: Intracellular colonization by endophytic bacteria (EB) is a relatively new and less explored aspect of plant microbiome research. In this study, we investigated the presence and localization of EB in Nicotiana tabacum var. Podali and Vigna radiata var. Pratap using SYTO9 (S9) and Propidium Iodide (PI) staining.<br><br>METHODOLOGY: Confocal Laser Scanning Microscopy (CLSM) was used to visualized bacterial localization, MitoTracker Deep Red (MDR) was used to confirm non- overlapping mitochondrial staining. Time-lapse imaging was employed to observe bacterial motility. For microbial community profiling next-generation sequencing (NGS) of the 16S rRNA gene was conducted to analyze bacterial diversity and composition.<br><br>RESULTS: Confocal laser scanning microscopy (CLSM) revealed S9-labelled live bacteria located close to the nucleus in Podali tissues and suspension cultures, while PI selectively stained dead cells. MitoTracker Deep Red (MDR) confirmed that there was no overlap with mitochondrial staining. Interestingly, time-lapse imaging captured the movement of bacteria within the cells, indicating possible bacterial motility. EB were observed in both in vitro and field-grown Podali plants, whereas they were detected only in field-grown Pratap plants. Next-generation sequencing revealed that Podali harbored a much higher bacterial diversity, with 37 bacterial families identified mainly from Burkholderiaceae and Enterobacteriaceae. In contrast, Pratap plants showed lower diversity, with only 10 bacterial families, dominated by Rhizobiaceae.<br><br>CONCLUSION: This study is among the first to report intracellular EB localization in these plant varieties and demonstrates how environmental conditions and growth methods can influence the composition of plant-associated microbiomes.},
}
@article {pmid40454183,
year = {2025},
author = {Moradzad, M and Moloudi, MR and Abdollahi, A and Fakhari, S and Vahabzadeh, Z},
title = {TMAO promotes metabolic dysfunction-associated fatty liver disease (MAFLD) development through long-non coding RNA- highly upregulated liver cancer (HULC).},
journal = {Journal of diabetes and metabolic disorders},
volume = {24},
number = {1},
pages = {131},
pmid = {40454183},
issn = {2251-6581},
abstract = {OBJECTIVES: Trimethylamine N-oxide (TMAO) is related to the pathogenesis of Metabolic dysfunction-associated fatty liver disease (NAFLD). However, the molecular mechanism of how TMAO causes MAFLD development is still unclear. The present study attempted to investigate whether TMAO contributes to MAFLD development through HULC in a cellular model of MAFLD.<br><br>METHODS: HepG2 cells were cultured and induced in a fatty liver cell model. HULC knockdown was induced using the CRISPR/Cas13 system. Fatty liver cells were exposed to TMAO concentrations (75&#xb5;M and 300&#xb5;M) before and after HULC knockdown. RT-qPCR was used to evaluate the expression of the target genes. Apoptosis was assessed using Annexin V-FITC and PI staining. Statistical analyses included ANOVA and post-hoc tests.<br><br>RESULTS: TMAO upregulated the expression of HULC, followed by P38MAPK overexpression (P value&#x2009;<&#x2009;0.05). Upon HULC knockdown, TMAO could not change P3MAPK expression and its downstream targets, including TNF&#x3b1;, IL-6, and PNPPLA3 in fatty liver cells. Additionally, TMAO significantly induced apoptosis in the fatty acid cellular model (P value&#x2009;<&#x2009;0.05).<br><br>CONCLUSION: In conclusion, the results of this study provide evidence of the TMAO/HULC/P38MAPK axis involvement in the pathogenesis of MAFLD by increasing the expression of genes involved in inflammation and fibrosis. Our data suggests that TMAO reduction could be a therapeutic target in MAFLD through gut microbiome modulation.},
}
@article {pmid40454151,
year = {2025},
author = {Khiabani, A and Khalilabadi, RM and Valandani, HM and Khoshnegah, Z and Khanahmad, A and Shahraki, H and Nezamabadipour, N and Farsinejad, A and Rahimlou, M},
title = {Gut microbiome alterations in immune thrombocytopenia: a systematic review of current evidence.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1511612},
pmid = {40454151},
issn = {2296-858X},
abstract = {BACKGROUND: Immune thrombocytopenia (ITP) is an autoimmune disorder characterized by immune-mediated platelet destruction and impaired platelet production. Recent evidence suggests a role for gut microbiome dysbiosis in autoimmune diseases, but its association with ITP remains unclear. This systematic review explores the potential link between the gut microbiome and ITP pathophysiology.<br><br>METHODS: We conducted a comprehensive search in five databases (MEDLINE, Scopus, Web of Science, Cochrane Library, Embase) from 1980 to July 2024, adhering to PRISMA 2020 guidelines. Studies assessing the gut microbiome in patients with ITP were included. The primary outcome was alterations in gut microbiota composition, and study selection was performed in three phases, with discrepancies resolved through consensus.<br><br>RESULTS: From 480 studies screened, 12 met the inclusion criteria. The studies revealed significant alterations in gut microbiota composition, particularly at the phylum level. An increase in Bacteroidetes and Proteobacteria was observed in some studies, while others reported a decrease in these phyla. Firmicutes showed inconsistent results across studies. Alpha and beta diversity analysis also yielded conflicting results, with some studies reporting decreased diversity, while others found no significant difference or an increase.<br><br>CONCLUSION: The results suggest a potential link between gut microbiota dysbiosis and ITP, though findings remain inconsistent across studies. Further well-designed research is needed to clarify the role of the microbiome in ITP, with implications for novel therapeutic approaches.},
}
@article {pmid40453723,
year = {2025},
author = {Zou, B and Zhao, D and Zhou, S and Kang, JX and Wang, B},
title = {Insight into the effects of Omega-3 fatty acids on gut microbiota: impact of a balanced tissue Omega-6/Omega-3 ratio.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1575323},
pmid = {40453723},
issn = {2296-861X},
abstract = {Emerging evidence suggests that Omega-3 polyunsaturated fatty acids (PUFAs) are essential structural and functional nutrients that significantly influence the composition and function of the gut microbiota, a key mediator of host health. Although evidence suggests that increasing tissue Omega-3 levels through dietary intervention may optimize gut microbiota-host interaction through modulation of composition, metabolite production, and the intestinal mucus barrier, some studies have reported inconsistent findings regarding these protective effects. Studies indicate that a high Omega-6/Omega-3 ratio appears to attenuate the beneficial effects of Omega-3 supplementation on microbial diversity and abundance, while a balanced ratio fosters a more favorable microbiome profile. This review comprehensively highlights the potential effects of differential endogenous Omega-6/Omega-3 ratios on the gut microbiota-modulating capacity of Omega-3 PUFAs, which should be incorporated as a mandatory monitoring indicator in future clinical investigations. These insights provide a new direction for further optimizing the clinical application of Omega-3 PUFAs in chronic disease prevention and treatment.},
}
@article {pmid40453336,
year = {2025},
author = {Lai, X and He, Z and Wang, S and Zhang, F and Wang, H and Wang, X and Liu, S and Yan, L},
title = {Bacterial wilt pathogen induced spatial shifts of root-associated microbiome and metabolome of potatoes.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1577123},
pmid = {40453336},
issn = {1664-462X},
abstract = {INTRODUCTION: Plant root-associated microbiomes play an important role in plant health, yet their responses to bacterial wilt remain unclear poorly understood.<br><br>METHODS: This study investigated spatial variations in microbiome and metabolome composition across three root-associated niches-root-surrounding soil, rhizosphere, and endosphere-of healthy and Ralstonia solanacearum-infected potato plants. A total of 36 samples were analyzed, with microbial diversity assessed by full-length 16S rRNA and ITS sequencing, and metabolic profiles characterized using LC-QTOF-MS.<br><br>RESULTS: Alpha diversity analysis revealed that bacterial diversity in healthy plants was consistently higher than in diseased plants, progressively increasing from the root-surrounding soil to the rhizosphere, and most notably in the endosphere, where the Shannon index declined from 5.3 (healthy) to 1.2 (diseased). In contrast, fungal diversity was lower in diseased plants in the root-surrounding soil and rhizosphere, but significantly elevated in the endosphere, suggesting niche-specific microbial responses to pathogen stress. Beta diversity confirmed significant microbiome restructuring under pathogen stress (R&#xb2; > 0.5, p = 0.001). Taxonomic analysis showed over 98% dominance of Proteobacteria in the diseased endosphere, where Burkholderia, Pseudomonas, and Massilia enriched in healthy plants were significantly reduced. R. solanacearum infection promotes the enrichment of Fusarium species in both the rhizosphere and endosphere. Metabolomic analysis revealed extensive pathogen-induced metabolic reprogramming, with 299 upregulated and 483 downregulated metabolites in the diseased endosphere, including antimicrobial metabolites such as verruculogen and aurachin A. Network analysis identified XTP as a central metabolite regulating microbial interactions, whereas antimicrobial metabolites exhibited targeted pathogen suppression. O2PLS analysis revealed that pathogen-induced antimicrobial metabolites (e.g., Gentamicin X2, Glutathionylspermine) were associated with Clostridia and Ketobacter in diseased plants, while nucleotide-related compounds (e.g., XTP) correlated with Rhodomicrobium and others, indicating infection-driven microbial adaptation and metabolic restructuring.<br><br>DISCUSSION: These findings provide insights into pathogen-driven disruptions in root microbiomes and suggest potential microbiome engineering strategies for bacterial wilt management.},
}
@article {pmid40453286,
year = {2025},
author = {Semiz, V and Aksoy, RA and Altun, Z},
title = {Oral Microbiome-Mediated Carcinogenesis in Oral Cavity Cancer: A Narrative Review.},
journal = {Cureus},
volume = {17},
number = {4},
pages = {e83242},
pmid = {40453286},
issn = {2168-8184},
abstract = {The global impact of oral cavity cancer (OCC) is substantial, given its five-year survival rate of nearly 50%. Tobacco, alcohol, and betel nut consumption are primary risk factors, but OCC can also develop in individuals without these exposures. Recent studies increasingly indicate that the oral microbiome may contribute to the pathogenesis of OCC, especially in the context of poor oral hygiene and periodontal disease. The oral microbiome consists of hundreds of bacterial and fungal species, influenced by factors such as smoking, alcohol, diet, and medications. Smoking disrupts microbial balance and epithelial barriers, contributing to dysbiosis. Studies have linked periodontal pathogens like Porphyromonas gingivalis, Fusobacterium nucleatum, and Treponema denticola to OCC, while certain Streptococcus species may have protective effects. Microbial alterations are observed in both OCC and precancerous lesions, suggesting a role in early carcinogenesis. The oral microbiome may facilitate carcinogenesis through multiple interrelated mechanisms, including the generation of carcinogenic byproducts (e.g., nitrosamines, acetaldehyde, hydrogen sulfide), persistent inflammatory signaling, immune evasion, resistance to apoptosis, and the activation of epithelial-mesenchymal transition pathways. These factors contribute to DNA damage, genomic instability, and tumor progression. A deeper understanding of how the oral microbiome influences OCC may offer novel strategies for both prevention and clinical management. Future research should focus on microbiome-targeted interventions to reduce OCC risk and improve clinical outcomes.},
}
@article {pmid40453238,
year = {2025},
author = {Jin, J and Liu, S and Peng, X and Wang, C and Zhou, Q and Fang, Z and Lin, Y and Xu, S and Feng, B and Zhuo, Y and Zhao, H and Wu, D and Che, L},
title = {Effects of dietary cinnamaldehyde supplementation in the perinatal period on reproductive performance, milk composition, redox status and gut microbiota of sows.},
journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)},
volume = {21},
number = {},
pages = {97-106},
pmid = {40453238},
issn = {2405-6383},
abstract = {Improving sow health during the perinatal period is crucial for reproductive performance. Cinnamaldehyde (CA), a naturally occurring compound, is known for its anti-inflammatory, antioxidant, and gut microbiota-modulating properties. This study evaluated the effects of dietary CA supplementation during the perinatal period on reproductive performance, milk composition, redox status, and gut microbiota of sows. Forty DanBred sows were randomly divided into two groups and fed either a basal (CON) diet or the basal diet supplemented with 1 g/kg CA from day 107 of gestation to day 7 of lactation. The results showed that dietary CA supplementation decreased farrowing duration (-78 min, P = 0.031) and tended to increase the concentrations of crude fat (P = 0.070) and dry matter (P = 0.078) in colostrum. Additionally, CA increased plasma glucose (P = 0.012) and decreased non-esterified fatty acid (NEFA) and triglyceride (TG) concentrations (P < 0.05) at farrowing. CA also reduced malondialdehyde (MDA) concentration (P = 0.048) and tended to increase plasma total superoxide dismutase activity (P = 0.084) at farrowing. Furthermore, CA supplementation increased the average daily gain (ADG) of piglets during days 15 to 21 of lactation (P = 0.040) and tended to increase the average daily feed intake (ADFI) of sows during days 8 to 14 of lactation (P = 0.059). Gut microbiota analysis revealed that CA increased the relative abundances of g_Roseburia, s_Ruminococcus_flavefaciens, g_UCG_012, f_p_251_o5, and o_Lachnospirales at farrowing, along with increased fecal propionate (P = 0.027) and butyrate contents (P = 0.057). Correlation analysis indicated that the relative abundances of g_Roseburia and o_Lachnospiraceae were positively correlated with plasma glucose, while the relative abundances of s_Ruminococcus_flavefaciens and g_UCG_012 were negatively correlated with plasma TG concentration, and o_Lachnospirales abundance was negatively correlated with plasma NEFA concentration at farrowing. Additionally, plasma MDA concentration was positively correlated with mean birth interval, and glutathione peroxidase activity was positively correlated with ADFI. In conclusion, dietary CA supplementation during the perinatal period can shorten farrowing duration, improve colostrum composition, and enhance the growth rate of suckling piglets in late lactation, likely due to its positive effects on energy metabolism, redox status, and gut microbiota around parturition.},
}
@article {pmid40453237,
year = {2025},
author = {Xie, X and Cao, Y and Li, Q and Li, Q and Yang, X and Wang, R and Zhang, X and Tan, Z and Lin, B and Wang, M},
title = {Mitigating enteric methane emissions: An overview of methanogenesis, inhibitors and future prospects.},
journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)},
volume = {21},
number = {},
pages = {84-96},
pmid = {40453237},
issn = {2405-6383},
abstract = {Enteric methane emissions account for approximately 17% of global anthropogenic greenhouse gas emissions and represent 2% to 12% of energy losses from energy intake in ruminants. To reduce these emissions and accelerate the achievement of carbon neutrality, it is critical to understand the factors driving methanogenesis in the rumen and develop effective methane mitigation strategies. Methanogenesis inhibitors, when used in conjunction with nutritional and breeding management strategies, are widely regarded as effective additives for optimizing rumen function, enhancing nutrient utilization and reducing enteric methane emissions. The field of inhibitor development is evolving rapidly under increasing mitigation pressure, necessitating continual review to guide the understanding of their mechanisms of action, effectiveness, risk and potential for widespread use in ruminant production systems. This review compiles data from 78 peer-reviewed in vivo studies conducted over the past 5 years, focusing on 10 inhibitors, which demonstrates 5% to 75% in daily methane emission reduction, 2% to 70% in methane yield reduction, and 11% to 74% in methane intensity reduction. Among the inhibitors, macroalgae are the most effective, achieving 22% to 75% of methane reductions, followed by small targeted molecule inhibitors 3-nitrooxypropanol (3-NOP) with 13% to 62% of methane reductions. Additionally, this review discusses the mechanisms underlying these mitigation strategies, their impact on animal productivity performance, the barriers to their widespread adoption, and directions for future research. Special attention is given to the effects of these inhibitors on rumen hydrogen partial pressure and other metabolic pathways, as improper use may adversely affect nutrient utilization, overall metabolism and animal performance. Future mitigation efforts should focus on the developing next-generation inhibitors that precisely target methanogenic archaea and the methanogenesis pathway. These novel inhibitors must meet on a principle of safety for the host animals, human health and environment, and be economically viable and technically supported with efficiency in achieving long-term mitigation with minimal lifecycle carbon footprints.},
}
@article {pmid40453233,
year = {2025},
author = {Garg, K and Booth, R and Cobey, A and Gilbert, L and Ozdemir, A},
title = {Diagnostic and Therapeutic Challenges in Lyme Disease and Co-Infections: Unraveling Neuropsychiatric and Neurological Complexities-A Comprehensive Case Series Analysis.},
journal = {Integrative medicine (Encinitas, Calif.)},
volume = {24},
number = {3},
pages = {10-27},
pmid = {40453233},
issn = {1546-993X},
abstract = {BACKGROUND/OBJECTIVES: Lyme disease (LD) and its co-infections present significant diagnostic and treatment challenges due to their complex interplay with neurological symptoms, immune responses, autoimmune reactions, and mental health conditions. Standard two-tier LD testing often fails to detect cases, necessitating expanded serologic and functional testing. Following CARE Guidelines, this case series examines ten clinical narratives of LD, highlighting the limitations of standard diagnostic methods, the potential benefits of specialized testing, and the need for an effective paradigm for LD management.<br><br>METHODS: A multidisciplinary approach grounded in integrative medicine was adopted. Diagnostic methods included advanced serological panels (e.g., TICKPLEX[&#xae;]), co-infection testing, functional immune markers, Cunningham Panel testing for neuropsychiatric Lyme presentations, and imaging. Treatments included traditional antibiotics, botanical antimicrobials (Cryptolepis, Artemisinin, Biocidin), mitochondrial and neuroprotective support (CoQ10, NAD+, magnesium), nutritional therapies, detox support, immune system support protocols, pulsed electromagnetic field therapy, and methylene blue protocols.<br><br>RESULTS: The findings from this case series demonstrate the heterogeneity of LD manifestations across different ages, genders, and backgrounds. Compared to promising specialized testing, standard laboratory tests often misdiagnose LD and its co-infections as Parkinson's disease, multiple sclerosis, lupus, autism, and psychiatric disorders. Furthermore, integrating diverse treatment modalities, including combination and rotational antibiotic therapy, IV ceftriaxone for neurological cases, detoxification support (glutathione IV, vitamin C IV), and immune modulation with intravenous immunoglobulin, helped manage symptoms. Herxheimer reactions were effectively managed with antioxidant and detox therapies. Patients receiving long-term maintenance therapies, including herbal antimicrobials and gut microbiome support, showed fewer relapses.<br><br>CONCLUSIONS: This case series advocates for a holistic, patient-centered approach. It emphasizes the necessity of comprehensive diagnostics that consider external factors, including post-vaccine symptom exacerbations, immune dysregulation, personalized treatment strategies, and ongoing research to improve LD management. These findings provide an evidence-based framework for physicians to integrate conventional and natural medicine strategies to optimize LD care.},
}
@article {pmid40452949,
year = {2025},
author = {Artru, F and Hernández-Gea, V},
title = {Rifaximin in the spotlight: Are we ready to target the microbiome?.},
journal = {JHEP reports : innovation in hepatology},
volume = {7},
number = {5},
pages = {101360},
pmid = {40452949},
issn = {2589-5559},
}
@article {pmid40452928,
year = {2025},
author = {Silva-Andrade, C and Hernández, S and Saa, P and Perez-Rueda, E and Garrido, D and Martin, AJ},
title = {A machine-learning approach for predicting butyrate production by microbial consortia using metabolic network information.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e19296},
pmid = {40452928},
issn = {2167-8359},
mesh = {*Machine Learning ; *Butyrates/metabolism ; *Microbial Consortia/physiology ; *Metabolic Networks and Pathways ; Humans ; Gastrointestinal Microbiome ; *Bacteria/metabolism/genetics ; Algorithms ; },
abstract = {Understanding the behavior of microbial consortia is crucial for predicting metabolite production by microorganisms. Genome-scale network reconstructions enable the computation of metabolic interactions and specific associations within microbial consortia underpinning the production of different metabolites. In the context of the human gut, butyrate is a central metabolite produced by bacteria that plays a key role within the gut microbiome impacting human health. Despite its importance, there is a lack of computational methods capable of predicting its production as a function of the consortium composition. Here, we present a novel machine-learning approach leveraging automatically generated genome-scale metabolic models to tackle this limitation. Briefly, all consortia made of two up to 13 members from a pool of 19 bacteria with known genomes, including at least one butyrate producer from a pool of three known producer species, were built and their (maximum) in silico butyrate production simulated. Using network-derived descriptors from each bacteria, butyrate production by the above consortia was used as training data for various machine learning models. The performance of the algorithms was evaluated using k-fold cross-validation and new experimental data, displaying a Pearson correlation coefficient exceeding 0.75 for the predicted and observed butyrate production in two bacteria consortia. While consortia with more than two bacteria showed generally worse predictions, the best machine-learning models still outperformed predictions from genome-scale metabolic models alone. Overall, this approach provides a valuable tool and framework for probing promising butyrate-producing consortia on a large scale, guiding experimentation, and more importantly, predicting metabolic production by consortia.},
}
@article {pmid40452867,
year = {2025},
author = {Labarre, A and Guitard, E and Tossing, G and Parker, JA},
title = {Suppression of har-1/CHCHD10 phenotypes for ALS-FTD therapy discovery.},
journal = {microPublication biology},
volume = {2025},
number = {},
pages = {},
pmid = {40452867},
issn = {2578-9430},
abstract = {Mutations in CHCHD10 are linked to a variety of neurodegenerative diseases, including amyotrophic lateral sclerosis and frontotemporal dementia (ALS-FTD). The Caenorhabditis elegans orthologue of CHCHD10 is har-1 , and we investigated whether har-1 mutants could be used for therapeutic discovery in ALS-FTD. Our results show that the small molecule pioglitazone and the probiotic Lacticaseibacillus rhamnosus HA-114 can alleviate har-1 mutant phenotypes. These findings suggest that har-1 mutants are suitable for modifier screens and could be adapted for high-throughput drug screening and microbiome studies to aid in discovering therapies for ALS-FTD.},
}
@article {pmid40452786,
year = {2025},
author = {Yan, L and Wu, F and Jiao, J and Maimaiti, A and Li, Y and Shao, L and Liang, Q and Xiong, X and Qin, Z},
title = {Stomatobaculum longum-Derived Extracellular Vesicles Enhance Oral Squamous Cell Carcinoma Malignancy Through BRCA1/EXO1/TP53BP1 Modulation.},
journal = {International journal of nanomedicine},
volume = {20},
number = {},
pages = {6659-6674},
pmid = {40452786},
issn = {1178-2013},
mesh = {Humans ; *Extracellular Vesicles/metabolism ; *Mouth Neoplasms/microbiology/pathology/metabolism ; Animals ; Cell Proliferation ; Tumor Suppressor p53-Binding Protein 1/metabolism ; Cell Line, Tumor ; BRCA1 Protein/metabolism ; *Carcinoma, Squamous Cell/pathology/microbiology/metabolism ; Mice ; Mice, Nude ; Female ; Male ; RNA, Ribosomal, 16S/genetics ; Signal Transduction ; Microbiota ; },
abstract = {BACKGROUND: Oral squamous cell carcinoma (OSCC) is a common malignancy among Asian populations, and emerging evidence suggests that oral microbiota dysbiosis may play a role in its pathogenesis. This study investigates the role of the oral microbiome, particularly Stomatobaculum longum (S. longum), in OSCC progression and explores the underlying molecular mechanisms involving bacterial extracellular vesicles (EVs).<br><br>METHODS: 16S rRNA sequencing was conducted on tumor and adjacent non-tumor tissues from OSCC patients to identify microbial composition. In vitro and in vivo experiments were used to evaluate the effects of S. longum on OSCC proliferation and cell cycle progression. GW4869, an inhibitor of EVs' release, was applied to validate the EVs-mediated mechanisms. Extracellular vesicles from S. longum (SBL-EVs) were isolated using ultracentrifugation and characterized by transmission electron microscopy (TEM) and nanoparticle tracking analysis (NTA). High-throughput sequencing and functional assays were performed to identify signaling pathways regulated by SBL-EVs.<br><br>RESULTS: Tumor tissues exhibited a significant enrichment of S. longum compared to non-tumor tissues. S. longum promoted OSCC proliferation and cell cycle progression both in vitro and in vivo, which was reversed by GW4869 treatment. SBL-EVs were successfully isolated and characterized, and they were found to promote OSCC progression by activating the BRCA1/EXO1/TP53BP1 signaling axis.<br><br>CONCLUSION: This study demonstrates the oncogenic role of S. longum in OSCC, mediated through EVs-dependent regulation of the BRCA1/EXO1/TP53BP1 pathway. Targeting bacterial EVs or their downstream signaling may represent a novel therapeutic strategy for OSCC.},
}
@article {pmid40452779,
year = {2025},
author = {Watanabe, C},
title = {Plasma Treatment - Results of Skin Microbiome Analysis.},
journal = {Clinical, cosmetic and investigational dermatology},
volume = {18},
number = {},
pages = {1269-1279},
pmid = {40452779},
issn = {1178-7015},
abstract = {PURPOSE: Skin health is deeply linked with the balance of resident bacteria, and a disturbance in this balance can readily cause skin problems. Sterilization with plasma treatment offers potential to improve symptoms in patients with acne vulgaris or atopic dermatitis. The aim of this study was to examine the antibacterial effect of plasma and analyze the correlation between changes in the balance of resident skin bacteria and clinical symptoms following plasma treatment in patients with acne vulgaris or atopic dermatitis.<br><br>PATIENTS AND METHODS: Five patients each with acne vulgaris or atopic dermatitis of moderate severity were treated with plasma irradiation of their face (including lesions) using a nitrogen plasma device called NeoGen Plasma Skin Regeneration. Changes in the resident flora were assessed before and after irradiation using next-generation sequencing.<br><br>RESULTS: At 24&#xa0;hours, the proportion of Propionibacterium acnes decreased from 31.2% to 16.2%, and Staphylococcus epidermidis increased from 10.8% to 11.7%; in patients with atopic dermatitis, Staphylococcus aureus decreased from 4.2% to 2.1%. Across all 10 patients, there was a significant increase in Simpson's Index (P=0.045), indicating improvement of the microbiome balance of resident bacteria.<br><br>CONCLUSION: Plasma treatment had a sterilization effect and improved microbiome balance. Larger studies are therefore warranted.},
}
@article {pmid40452652,
year = {2025},
author = {Naqib, A and Ahmad, I and McDonald, Z and Kalinin, S and Rocha, J and Tandon, A and Rayala, R and Feferman, L and Chlipala, GE and Chen, H and Lindeblad, M and Rubinstein, I and Green, S and van Breemen, R and Feinstein, DL},
title = {Alterations in the cecal microbiome of New Zealand White rabbits due to the long-acting anticoagulant rodenticide brodifacoum.},
journal = {Toxicology communications},
volume = {9},
number = {1},
pages = {},
pmid = {40452652},
issn = {2473-4306},
abstract = {Long-acting anti-coagulant rodenticides (LAARs) are well characterized with respect to inhibition of vitamin K1 synthesis and effects on blood coagulation. However, the effects of LAARs on the microbiome have not been explored. We administered brodifacoum (BDF), one of the more potent LAARs, to adult male New Zealand White rabbits, and carried out 16S RNA sequencing on cecal samples collected after different times. Samples were also obtained from rabbits treated with the bile sequestrant cholestyramine (CSA) which accelerates BDF clearance from the body, and from CSA-only treated rabbits. Changes at both the phylum and genus levels in relative abundance were observed after 2- and 3-days exposure to BDF. The majority of those microbiota changes were prevented by co-treatment with CSA. Identification of metabolic pathways potentially altered by BDF using Picrust2 identified several L-arginine-related pathways. Exposure to BDF caused increases in plasma L-arginine concentration as well as nitrites, suggesting increased activity of nitric oxide synthase. We also observed increases due to BDF in plasma concentrations of L-arginine-related molecules including L-citrulline, L-ornithine, and methylated L-arginines. These results demonstrate that LAAR poisoning can induce microbiome dysbiosis and influence metabolic pathways and metabolites involved in inflammation and vasodilation.},
}
@article {pmid40452584,
year = {2025},
author = {Zhang, W and Ge, Y and Yao, L and Yan, Q and Wei, J and Yin, Y and Liu, B},
title = {Changes of Microbiome in Human Papillomavirus Infection and Cervical Cancer: A Systematic Review and Meta-Analysis.},
journal = {Cancer reports (Hoboken, N.J.)},
volume = {8},
number = {6},
pages = {e70246},
doi = {10.1002/cnr2.70246},
pmid = {40452584},
issn = {2573-8348},
support = {2023-ZD-89//Lanzhou Science and Technology Bureau/ ; 24JRRA360//Natural Science Foundation of Gansu Province/ ; GSWSKY2021-026//Health Commission of Gansu Province/ ; },
mesh = {Humans ; *Uterine Cervical Neoplasms/microbiology/virology/pathology ; Female ; *Papillomavirus Infections/microbiology/virology/complications ; *Microbiota/genetics ; Vagina/microbiology ; Papillomaviridae/isolation &amp; purification ; High-Throughput Nucleotide Sequencing ; },
abstract = {BACKGROUND AND OBJECTIVES: We aimed to conduct a systematic review and meta-analysis of high-throughput sequencing studies to assess changes in microbiome alpha, beta diversity, and composition differences in patients with human papillomavirus (HPV) infection and cervical cancer.<br><br>METHODS: The PubMed, Embase, Web of Science, and Cochrane Library databases were systematically searched to include original studies. The effect size estimates with a 95% confidence interval were combined using a random effects model. The meta-analysis was performed using the Stata MP16 software.<br><br>RESULTS: A total of 64 studies were included, with a meta-analysis of the diversity index performed on a subset of seven studies. Microbial diversity of patients infected with HPV was observed to be significantly different from that of healthy controls (CHAO index: 95% CI 0.42, 5.03, I[2]&#x2009;=&#x2009;99.18%, p&#x2009;<&#x2009;0.05). Subgroup analysis based on the sample collection region showed a significant difference between vaginal microbiota of the treatment group and control group, as measured by the Shannon index (95% CI 0.12, 0.97, I[2]&#x2009;=&#x2009;67.09%, p&#x2009;<&#x2009;0.05). Further, subgroup analysis of samples sequenced with the primer pair for the V3-V4 region showed a statistically significant difference in alpha diversity (Shannon index: 95% CI 0.28, 0.72, I[2]&#x2009;=&#x2009;0.00%, p&#x2009;<&#x2009;0.05) between treatment and control groups. The microbial diversity varied between patients with inferior cervical lesions (low-grade squamous intraepithelial lesion) and healthy controls (Shannon index: 95% CI 0.02, 0.58, I[2]&#x2009;=&#x2009;0.00%, p&#x2009;<&#x2009;0.05). The bacterial marker genera differed at each cervical lesion stage. Gardnerella was prevalent during the HPV infection stage, but its proportion decreased after the occurrence of cervical lesions. In contrast, the proportions of Prevotella, Porphyromonas, and Dialister increased during the cervical cancer stages.<br><br>CONCLUSIONS: Patients with simple HPV infections frequently exhibit unstable microbial diversity and are influenced by various factors. The microbial environment continues to change after the occurrence of cervical lesions and is correlated with the severity of cervical lesions.},
}
@article {pmid40452402,
year = {2025},
author = {Gohmann, L and Cusick, JA and Demas, GE and Wellman, CL},
title = {Maternal Stress and Maternal Microbiome Manipulations Remodel Offspring Medial Prefrontal Cortex in a Sex-Dependent Manner.},
journal = {Developmental neurobiology},
volume = {85},
number = {3},
pages = {e22971},
doi = {10.1002/dneu.22971},
pmid = {40452402},
issn = {1932-846X},
support = {T32HD049336/NH/NIH HHS/United States ; IOS-1656414//National Science Foundation/ ; },
mesh = {Animals ; *Prefrontal Cortex/growth &amp; development/pathology/drug effects ; Female ; *Stress, Psychological/pathology/physiopathology ; Male ; Pregnancy ; *Prenatal Exposure Delayed Effects/physiopathology/pathology ; *Sex Characteristics ; Dendrites/pathology ; *Microbiota/physiology/drug effects ; Anti-Bacterial Agents/pharmacology ; Phodopus ; Cricetinae ; Pyramidal Cells/pathology ; },
abstract = {Maternal stress and disruptions of the maternal microbiome during development can have profound organizational effects on the brain and behavior of offspring. We have previously demonstrated that these manipulations have marked, sex-dependent effects on aggressive behavior in Siberian hamsters, Phodopus sungorus. Given that the prelimbic cortex is sensitive to stress and may play a role in modulating social behaviors, here we investigated how maternal stress and disruption of the microbiome during pregnancy may affect the development of the prelimbic cortex in offspring. Pregnant hamsters were exposed to either a broad-spectrum antibiotic, social stress, combined treatments, or no manipulation (i.e., control). Adult offspring (PND 107-115) were euthanized, brains were stained using Golgi histology, and apical and basilar dendritic lengths of pyramidal cells in the prelimbic cortex were quantified. Our data indicate that maternal stress and microbiome manipulation have a sex-dependent effect on offspring dendritic morphology. Maternal stress increased apical dendritic length in female but not male offspring relative to controls. However, the combination of maternal stress and maternal antibiotics ameliorated the effect of stress alone. Thus, maternal stress and disruption of the microbiome interact to produce lasting changes in the prefrontal cortex of female offspring. Such changes may contribute to the behavioral effects of these manipulations.},
}
@article {pmid40452334,
year = {2025},
author = {Ryser, FS and Demeter, T and Pijuan, JB and Shambat, SM and Brühlmann, C and Mauthe, T and Hilty, M and Soyka, MB and Steiner, UC and Brugger, SD},
title = {Dupilumab Treatment Is Associated With Clinical Improvement and a Shift Toward a Health-Associated Nasal Passage Microbiota in Diffuse Type 2 Chronic Rhinosinusitis.},
journal = {Allergy},
volume = {},
number = {},
pages = {},
doi = {10.1111/all.16600},
pmid = {40452334},
issn = {1398-9995},
support = {211422//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; //Urs C Steiner (UCS)/ ; },
abstract = {BACKGROUND: Nasal microbiota composition of patients with diffuse type 2 chronic rhinosinusitis with nasal polyps (CRSwNP) is altered compared to healthy individuals. Dupilumab, an anti-IL-4Rα-mAb, modulates type 2 inflammation, but the effect on microbiota composition in CRSwNP is unknown. The aim of this study was to investigate longitudinal effects of dupilumab on the nasal passage and gastrointestinal microbiota in patients with diffuse type 2 CRSwNP.<br><br>METHODS: Twenty-seven patients with diffuse type 2 CRSwNP treated with dupilumab 300&#x2009;mg subcutaneously every 2&#x2009;weeks, 10 untreated patients with CRSwNP, and 11 healthy controls were included. Nasal and stool samples were collected at Days 0, 28, 90, and 180 posttreatment of the treated CRSwNP group and at Days 0 and 28 of untreated CRSwNP and healthy controls. The samples were analyzed using 16S rRNA gene amplicon sequencing (V3/V4).<br><br>RESULTS: In CRSwNP patients, the most abundant genera in nasal passage microbiota were Corynebacterium and Staphylococcus. Cutibacterium and Lawsonella were less abundant in CRSwNP at baseline compared to healthy controls. Dupilumab treatment was associated with increased relative abundances in the nasal passage of genera such as Lawsonella, Corynebacterium, and Dolosigranulum. Microbial diversity of the gastrointestinal microbiota in CRSwNP at baseline was significantly higher than in healthy controls. There were no changes in gastrointestinal microbiota during dupilumab treatment.<br><br>CONCLUSION: Dupilumab treatment was associated with a shift in the nasal passage bacterial microbiota toward that of healthy controls, whereas the composition of gastrointestinal microbiota did not change. These findings suggest that nasal passage microbiota composition is influenced by the underlying inflammatory endotype.},
}
@article {pmid40452151,
year = {2025},
author = {Turetsky, MR and Weston, DJ and Cox, WD and Petro, C and Shaw, AJ},
title = {The challenging but unique eco-evolutionary aspects of Sphagnum moss.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.70233},
pmid = {40452151},
issn = {1469-8137},
abstract = {Sphagnum is emerging as a useful system for advancing knowledge at the interface between ecology and evolutionary biology. Here, we explore: the importance of the Sphagnum microbiome to ecosystem structure and function; the value of naturally occurring genetic variation within Sphagnum populations; and the ongoing process of speciation and ecological divergence in the genus. Recent advances in understanding the molecular genetics underpinning cyanobacteria associations with Sphagnum's living and hyaline cells make this a rich area for future research, including implications for carbon and nitrogen exchange. We review niche differentiation in Sphagnum, underlying functional traits, and phylogenetic conservation. More knowledge is needed about naturally occurring variation within Sphagnum species, including trait plasticity and variation between sexes, to explore broader issues such as the mechanisms underpinning metabolism and its consequences for microbiomes as well as how we can most effectively use Sphagnum in restoration and other ecological problem solving. We use newly resolved phylogenetic relationships within the S. magellanicum complex to illustrate its potential for studying ecologically driven speciation. Our review focuses on the unique challenges in using Sphagnum as an eco-evolutionary system but also offers insights into emerging questions across genetics, physiological traits, ecological function, and biogeochemical cycling.},
}
@article {pmid40452061,
year = {2025},
author = {Sagor, MS and Islam, T and Tamanna, NT and Bappy, MKI and Danishuddin, and Haque, MA and Lackner, M},
title = {The functional landscape of the appendix microbiome under conditions of health and disease.},
journal = {Gut pathogens},
volume = {17},
number = {1},
pages = {38},
pmid = {40452061},
issn = {1757-4749},
abstract = {Traditionally regarded as a vestigial organ, the appendix is now being reevaluated for its significant function in health and nutrition of humans. Serving as a "safe house" for beneficial, desired gut bacteria, the appendix is protected by resilient biofilms that create a secure environment. This makes the appendix a"basin" for gut microbiota (GM), replenishing the microbial population following disruptions from infections, antibiotic use, or inflammatory bowel disease (IBD). Beyond simply hosting bacteria, the appendix has an active role in functions of the immune system. Disruption of the Appendix Microbiome (AM), such as through appendectomy, was found to result in lowered diversity of gut microorganisms and an increased risk of various diseases. The potential therapeutic applications of the AM are a particularly promising area of research. The appendix's unique microbial environment and its impact on immunity open new avenues for treatments. These include modulating GM to improve cancer treatment outcomes, mitigating IBD, regulating metabolic pathways in obesity and diabetes, influencing neurotransmitter production in neurological disorders, and addressing cardiovascular and autoimmune diseases. This review highlights the appendix's transformation from a misunderstood organ to a critical component of gut health and immunity. It explores the function of the human appendix as a resilient reservoir for desired microorganisms, and its role in disease progression. Furthermore, it examines the potential therapeutic applications of AM, presenting exciting opportunities for future research and treatment innovations.},
}
@article {pmid40452057,
year = {2025},
author = {Francioli, D and Kampouris, ID and Kuhl-Nagel, T and Babin, D and Sommermann, L and Behr, JH and Chowdhury, SP and Zrenner, R and Moradtalab, N and Schloter, M and Geistlinger, J and Ludewig, U and Neumann, G and Smalla, K and Grosch, R},
title = {Microbial inoculants modulate the rhizosphere microbiome, alleviate plant stress responses, and enhance maize growth at field scale.},
journal = {Genome biology},
volume = {26},
number = {1},
pages = {148},
pmid = {40452057},
issn = {1474-760X},
support = {031B0514A- E//Bundesministerium f&#xfc;r Bildung und Forschung/ ; 031B0514A- E//Bundesministerium f&#xfc;r Bildung und Forschung/ ; 031B0514A- E//Bundesministerium f&#xfc;r Bildung und Forschung/ ; 031B0514A- E//Bundesministerium f&#xfc;r Bildung und Forschung/ ; 031B0514A- E//Bundesministerium f&#xfc;r Bildung und Forschung/ ; 031B0514A- E//Bundesministerium f&#xfc;r Bildung und Forschung/ ; 031B0514A- E//Bundesministerium f&#xfc;r Bildung und Forschung/ ; 031B0514A- E//Bundesministerium f&#xfc;r Bildung und Forschung/ ; 031B0514A- E//Bundesministerium f&#xfc;r Bildung und Forschung/ ; 031B0514A- E//Bundesministerium f&#xfc;r Bildung und Forschung/ ; 031B0514A- E//Bundesministerium f&#xfc;r Bildung und Forschung/ ; 031B0514A- E//Bundesministerium f&#xfc;r Bildung und Forschung/ ; 031B0514A- E//Bundesministerium f&#xfc;r Bildung und Forschung/ ; 031B0514A- E//Bundesministerium f&#xfc;r Bildung und Forschung/ ; 031B0514A- E//Bundesministerium f&#xfc;r Bildung und Forschung/ ; },
mesh = {*Zea mays/microbiology/growth &amp; development ; *Rhizosphere ; *Microbiota ; *Stress, Physiological ; Bacillus ; Plant Roots/microbiology ; Soil Microbiology ; *Agricultural Inoculants/physiology ; },
abstract = {BACKGROUND: Field inoculation of crops with beneficial microbes is a promising sustainable strategy to enhance plant fitness and nutrient acquisition. However, effectiveness can vary due to environmental factors, microbial competition, and methodological challenges, while their precise modes of action remain uncertain. This underscores the need for further research to optimize inoculation strategies for consistent agricultural benefits.<br><br>RESULTS: Using a comprehensive, multidisciplinary approach, we investigate the effects of a consortium of beneficial microbes (BMc) (Pseudomonas sp. RU47, Bacillus atrophaeus ABi03, Trichoderma harzianum OMG16) on maize (Zea mays cv. Benedictio) through an inoculation experiment conducted within a long-term field trial across intensive and extensive farming practices. Additionally, an unexpected early drought stress emerged as a climatic variable, offering further insight into the effectiveness of the microbial consortium. Our findings demonstrate that BMc root inoculation primarily enhanced plant growth and fitness, particularly by increasing iron uptake, which is crucial for drought adaptation. Inoculated maize plants show improved shoot growth and fitness compared to non-inoculated plants, regardless of farming practices. Specifically, BMc modulate plant hormonal balance, enhance the detoxification of reactive oxygen species, and increase root exudation of iron-chelating metabolites. Amplicon sequencing reveals shifts in rhizosphere bacterial and fungal communities mediated by the consortium. Metagenomic shotgun sequencing indicates enrichment of genes related to antimicrobial lipopeptides and siderophores.<br><br>CONCLUSIONS: Our findings highlight the multifaceted benefits of BMc inoculation on plant fitness, significantly influencing metabolism, stress responses, and the rhizosphere microbiome. These improvements are crucial for advancing sustainable agricultural practices by enhancing plant resilience and productivity.},
}
@article {pmid40452048,
year = {2025},
author = {Erdrich, S and Jayasinghe, T and Vuyisich, M and Toma, R and Gelissen, I and Harnett, JE},
title = {Characterisation of the Oral Microbiome in Women With Fibromyalgia: An Observational Case-Control Study.},
journal = {European journal of pain (London, England)},
volume = {29},
number = {6},
pages = {e70051},
doi = {10.1002/ejp.70051},
pmid = {40452048},
issn = {1532-2149},
mesh = {Humans ; *Fibromyalgia/microbiology ; Female ; Case-Control Studies ; *Microbiota/physiology ; Middle Aged ; Adult ; *Mouth/microbiology ; *Oral Health ; Saliva/microbiology ; },
abstract = {BACKGROUND: Fibromyalgia is a complex disorder, associated with a range of symptoms, not least of which is chronic, widespread pain. Although several reports have brought the role of oral health in systemic diseases into recent focus, the oral microbiome in fibromyalgia is unexplored. The aim of this study was to compare oral health and the oral microbiome in women with fibromyalgia with that of age-matched controls.<br><br>METHODS: This observational case-control study recruited adult non-smoking, non-diabetic women meeting American College of Rheumatology (ACR) 2016 fibromyalgia criteria and age-matched controls living in New Zealand. Metatranscriptomic data from salivary samples were evaluated for differences at phyla, genus and species level, with adjustment for age, BMI and added dietary sugar intake. Results were examined against self-reported oral health.<br><br>RESULTS: No differences were seen in richness or diversity of oral species between the fibromyalgia (n&#x2009;=&#x2009;106) and control (n&#x2009;=&#x2009;52) groups. Women with fibromyalgia had significantly lower scores on measures of oral health, which were associated with subtle shifts in the core oral microbiome. Several oral genera were significantly correlated with oral health scores (q&#x2009;&#x2264;&#x2009;0.05). Higher relative abundance of the periopathogens Prevotella denticola and Solobacterium moorei was apparent in women with fibromyalgia.<br><br>CONCLUSION: Significant differences in oral health and the oral microbiome were seen in women with fibromyalgia. This novel discovery presents an intriguing hypothesis that invites deeper investigation into the interaction between oral health and the oral microbiome in this population, and whether these influence the aetiology and/or symptoms of fibromyalgia in women.<br><br>SIGNIFICANCE: This study presents the first evidence of altered oral microbiome in women with fibromyalgia, revealing significant disparities in oral health and the microbiome. The observed overabundance of periopathogens and the underrepresentation of commensals compared to a control group suggest intriguing potential links between the oral microbiome and fibromyalgia symptoms. These findings indicate that enhancing oral health may have broader implications for disease management and lay a robust foundation for further exploration of oral-systemic interactions in fibromyalgia.},
}
@article {pmid40451966,
year = {2025},
author = {Wei, Z and Li, J and Wang, X and Wang, X and Zhao, D},
title = {A Mendelian randomization and animal study on the causal relationship between gut microbiota and ischemic stroke.},
journal = {Journal of thrombosis and thrombolysis},
volume = {},
number = {},
pages = {},
pmid = {40451966},
issn = {1573-742X},
support = {20220505042ZP//Jilin Scientific and Technological Development Program/ ; },
abstract = {A growing body of evidence points to a strong link between ischemic stroke and the gut microbiome. Given the wide diversity present in gut microbiota, this research intends to employ advanced and thorough data to investigate the causative relationship between gut microbiota and ischemic stroke. We performed a two-sample study using Mendelian randomization to clarify the causal connection between gut microbiota and ischemic stroke. The GISCOME network encompassed 6,021 individuals with ischemic stroke, primarily of European descent. A total of 473 gut microbial taxa were extracted from the genome-wide association study catalog. The research involved a forward Mendelian randomization approach(gut microbiota as exposure, ischemic stroke as outcome). A variety of analytical techniques were applied, including inverse variance weighting, Weighted Median, MR-Egger, Weighted Mode, and Simple Mode. Following this, a sensitivity analysis was performed to confirm the reliability of our findings. Rats underwent treatment using a middle cerebral artery occlusion model, and after 7 days, stool samples were collected for 16s sequencing to assess changes in gut microbiota and to compare these with the Mendelian randomization results. Our analysis suggests a potential causal association between gut microbiota and ischemic stroke. Through forward causal analysis, relationships of causality between 20 different gut microbial taxa and ischemic stroke were unveiled. Findings from 16s sequencing indicated that there was an overlap of 6 gut microbial taxa with the results of Mendelian randomization. The results of our research indicate a direct link between gut microbiota and ischemic stroke, offering possible direction for upcoming clinical trials.},
}
@article {pmid40451466,
year = {2025},
author = {Osogo, AK and Muyekho, F and Were, H and Okoth, P},
title = {Deciphering common bean (Phaseolus Vulgaris L.) microbiome assemblages reveal mechanistic insights into host-pathogen-microbiome interactions.},
journal = {Genomics},
volume = {},
number = {},
pages = {111064},
doi = {10.1016/j.ygeno.2025.111064},
pmid = {40451466},
issn = {1089-8646},
abstract = {Common bean (Phaseolus vulgaris L.) is the primary source of proteins and nutrients in most households in sub-Saharan Africa. However, production of this crop is constrained by several biotic factors. While research on common bean plant-pathogen interactions has predominantly focused on binary relationships, the diversity of microbes naturally inhabiting plant tissues and their interactions has often been overlooked. Recent findings, however, show that these resident microbes actively contribute to plant defense mechanisms, rather than merely acting as passive bystanders. This study aimed to document and explore potential interactions within the common bean microbiome assemblages through field investigations in selected locations across the western regions of Kenya. Common bean leaf samples were collected from farmer's fields along motorable roads 3-5 km apart. Shotgun metagenomic analysis identified a diverse range of microorganisms, including bacteria, fungi, yeast, phytoplasmas, viruses, and bacteriophages, across multiple taxonomic levels-spanning 4 Kingdoms, 136 Phyla, 168 Classes, 360 Orders, 792 Families, 2039 Genera, and 6130 Species-both epiphytic and endophytic, and pathogenic or non-pathogenic. Pseudomonadota consistently showed the highest taxonomic annotation for antimicrobial-resistant organisms, highlighting its central role in resistance across the studied area. The sequences obtained were mapped to the EggNOG, CAZy, and KEGG databases to explore, assign, and predict gene functions. The EggNOG database emphasized the importance of "Replication, recombination, and repair" processes in maintaining genomic stability, along with amino acid transport, energy production, and metabolism. CAZy analysis revealed a significant presence of glycosyltransferases, particularly from GT1 and GT32 families, and noted the role of enzymes like Glycoside Hydrolases in plant defense against pathogens. KEGG pathway analysis underscored the central role of metabolic processes such as energy metabolism, translation, and carbohydrate metabolism. Key pathways linked to plant defense and resilience, including 2-oxocarboxylic acid metabolism, amino acid biosynthesis, and secondary metabolite biosynthesis, were identified. These findings underscore the role of metabolic and enzymatic processes in strengthening plant defenses and stress tolerance while laying the groundwork for multidisciplinary research to advance sustainable agriculture and food safety.},
}
@article {pmid40451282,
year = {2025},
author = {Zhang, Y and Song, W and Zhou, L and Wei, S and Xu, L and Li, X and Yu, J},
title = {Bacteria-metabolite butyrate boosts anti-PD1 efficacy in colorectal cancer patient-derived organoids through activating autologous tumour-infiltrating GNLY [+]CD8[+] T cells.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2025-335306},
pmid = {40451282},
issn = {1468-3288},
}
@article {pmid40450938,
year = {2025},
author = {Hou, Y and Jia, R and Zhou, L and Zhang, L and Wei, S and Li, B and Zhu, J},
title = {Alterations in microbial-mediated methane, nitrogen, sulfur, and phosphorus cycling within paddy soil induced by integrated rice-fish farming.},
journal = {Journal of environmental management},
volume = {388},
number = {},
pages = {126056},
doi = {10.1016/j.jenvman.2025.126056},
pmid = {40450938},
issn = {1095-8630},
abstract = {Rice paddies are crucial ecosystems, supporting dense microbial populations and playing a significant role in global food security. Integrated rice-fish farming has been recognized as an important agricultural production pattern to enhance agro-ecosystem stability and food productivity. Using metagenomic sequencing, we compared the microbial-mediated soil CH4, N, S, and P cycles in integrated rice-fish farming versus traditional rice monoculture, exploring their potential coupling mechanisms within microbes. Integrated rice-fish farming has significantly impacted these microbial-mediated cycles in paddy soil, altering the overall functional diversity, sum abundance, and microbial host diversity for the CH4, N, S, and P cycling genes. Specifically, it suppressed the denitrification, assimilatory nitrate reduction (ANR), assimilatory sulfate reduction (ASR), thiosulfate oxidation, organic phosphoester hydrolysis, and two-component system pathways and most of their associated functional genes, while enhanced the acetoclastic methanogenesis and the reduction of tetrathionate to thiosulfate processes. Compared to traditional rice monoculture, integrated rice-fish farming resulted in metagenome-assembled genomes (MAGs) with fewer and more isolated biogeochemical cycling genes, lacking potential couplings among multi-element cycles. Additionally, this farming approach increased the soil nutrient levels including the total carbon (TC), total organic carbon (TOC), total nitrogen (TN), total sulfur (TS), and total phosphorus (TP) concentrations, which have been identified as the most crucial factors driving the alterations in microbial functional genes/pathways involved in biogeochemical cycling processes in our study. Overall, integrated rice-fish farming dynamically altered the microbial-mediated CH4, N, S, and P cycles and their potential couplings within microbes through promoting the soil nutrient levels, which could favor rice growth, thus maintaining food security and providing refined knowledge for maintaining soil sustainability.},
}
@article {pmid40450783,
year = {2025},
author = {Rajput, V and Pramanik, R and Nannaware, K and Shah, P and Bhalerao, A and Jain, N and Shashidhara, LS and Kamble, S and Dastager, S and Dharne, M},
title = {Metagenomics based longitudinal monitoring of antibiotic resistome and microbiome in the inlets of wastewater treatment plants in an Indian megacity.},
journal = {The Science of the total environment},
volume = {986},
number = {},
pages = {179691},
doi = {10.1016/j.scitotenv.2025.179691},
pmid = {40450783},
issn = {1879-1026},
abstract = {The growing threat of antimicrobial resistance (AMR) poses a significant global challenge, undermining advancements in healthcare, agriculture, and life expectancy. Despite its critical importance, data on population-level AMR trends, including seasonal and temporal variations, remain scarce. In this study, we conducted metagenomic analysis on 190 wastewater samples collected monthly from December 2022 to December 2023 in Pune, India, to assess the diversity, dynamics, and co-occurrence of AMR determinants. Using nanopore shotgun sequencing, we generated 87.86 Gbp of data, enabling the taxonomic classification of 157 bacterial phyla and 3291 genera. Proteobacteria dominated the microbial community, with notable seasonal shifts, including increased Streptococcus abundance correlating with SARS-CoV-2 viral surges in March 2023. We identified 637 distinct antimicrobial resistance genes (ARGs) associated with 29 antibiotic classes, with multidrug, macrolide-lincosamide-streptogramin, beta-lactams, and tetracyclines genes being the most prevalent, particularly within WHO priority pathogens such as Enterobacteriaceae and Pseudomonas. Temporal normalization of ARG abundance revealed significant seasonal variability, peaking during winter, potentially driven by increased antibiotic use for respiratory infections. The integration of viral load data with AMR trends highlighted complex interactions between viral outbreaks and AMR dissemination. This study demonstrates the potential of wastewater surveillance as an early warning system for AMR, providing valuable insights into environmental and community resistance dynamics. Our results underscore the importance of integrated AMR surveillance to inform public health strategies aimed at mitigating the global AMR threat.},
}
@article {pmid40450648,
year = {2025},
author = {Aswinanand, B and Haridevamuthu, B and Guru, A and Arockiaraj, J},
title = {The impact of climate, weather, seasonal transitions, and diurnal rhythms on gut microbiota and immune homeostasis.},
journal = {Antonie van Leeuwenhoek},
volume = {118},
number = {7},
pages = {86},
pmid = {40450648},
issn = {1572-9699},
mesh = {*Gastrointestinal Microbiome/physiology/immunology ; Humans ; *Homeostasis ; Seasons ; *Circadian Rhythm ; *Climate Change ; *Weather ; },
abstract = {The influence of meteorological environmental factors such as climate change, weather alterations, seasonal transitions, and diurnal cycles on human health is becoming increasingly evident, particularly through their modulation of the gut microbiome and immune homeostasis. The human gut microbiota maintains immune homeostasis and regulates various physiological and metabolic functions by producing metabolites like short-chain fatty acids (SCFAs), bile acids (BAs), indole derivatives (IDs), choline metabolites (CMs), and bacterial vitamins (BVs). Climate change disrupts this gut microbiome's impact through the gut-liver axis, which has been linked to the occurrence of fatty liver diseases. Temperature fluctuations, such as cold exposure, impair the gut microbiota's ability to respond to adaptive thermogenesis by disrupting the Firmicutes to Bacteroides ratio, affecting insulin sensitivity. In contrast, high temperatures support the increase in Proteobacterial populations, leading to greater gut permeability, allowing pathogens to trigger inflammation, oxidative stress, and immune dysregulation. In summer, an increase in Firmicutes contributes to weight gain and obesity, and in contrast, in winter, a rise in Bacteroides exacerbates conditions like rheumatoid arthritis (RA). High humidity also affects the Bacteroides/Firmicutes ratio by increasing and contributing to Bacteroides-driven inflammation. Conversely, lower humidity levels impair the mucosal defense mechanisms, increasing infection susceptibility and gut barrier dysfunction. Alterations in diurnal cycles are also linked to conditions like type 2 diabetes (T2D) and inflammatory bowel disease (IBD), by affecting the gut microbiome. Overall, the review emphasizes the crucial role of these factors in maintaining immune homeostasis through gut microbiome composition, highlighting the importance of understanding these influences for targeted interventions that restore gut health, particularly in relation to meteorologically driven environmental factors.},
}
@article {pmid40450635,
year = {2025},
author = {Oh, S and An, S and Park, K and Lee, S and Han, YM and Koh, SJ and Lee, J and Gim, H and Kim, D and Seo, H},
title = {Gut Microbial Signatures in Long COVID: Potential Biomarkers and Therapeutic Targets.},
journal = {Infectious diseases and therapy},
volume = {},
number = {},
pages = {},
pmid = {40450635},
issn = {2193-8229},
support = {2022R1A2C1010356//National Research Foundation of Korea/ ; RS-2023-00227939//National Research Foundation of Korea/ ; },
abstract = {INTRODUCTION: Following severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) infection, symptoms can persist for more than 12 weeks in over 10% of patients in a condition known as long coronavirus disease (COVID). Gut microbiota dysbiosis is correlated with long COVID, but the specific relationship between long COVID and the gut microbiome remains unclear. Here, we aimed to investigate connections between the gut microbiota and long COVID severity.<br><br>METHODS: Fecal samples were collected from 31 patients with long COVID, 14 with COVID-19 but not long COVID, and 23 healthy controls. The mean interval between COVID-19 diagnosis and sample collection was 65.5&#xa0;(range: 13.0-110.3)&#xa0;weeks for patients with long COVID and 74.8&#xa0;(range: 50.7-110.4)&#xa0;weeks for positive control group. Gut microbiota composition was analyzed using 16S rRNA gene sequencing. Patient-reported outcomes were used to comprehensively assess long COVID symptom severity.<br><br>RESULTS: Symptom severity was higher in patients with severe initial infections and significantly correlated with serum triglyceride, fasting blood glucose, and high-density lipoprotein-cholesterol levels. Results showed distinct microbial profiles in patients with long COVID. Leuconostoc, Actinomyces, and Granulicatella were significantly enriched, and they accurately distinguished patients with long COVID from controls, indicating their potential as long COVID biomarkers. Particular gut bacteria were significantly correlated with certain systemic, gastrointestinal, otolaryngologic, and visual symptoms. Parabacteroides, Eubacterium ventriosum group, and Rothia abundance was correlated with blood biomarkers that influence long COVID development, including total and low-density lipoprotein cholesterol and basophil levels.<br><br>CONCLUSIONS: The gut microbial signature of patients with long COVID differed from that of healthy controls. Certain microbial genera showed significant differences between patients with long COVID and controls, suggesting potential as preliminary biomarkers and therapeutic targets for long COVID pending validation in larger studies.},
}
@article {pmid40450306,
year = {2025},
author = {Lu, J and Petri, RM and MacIsaac, JL and Collins, SA},
title = {Novel insight into the impact of black soldier fly larvae meal and protease on cecal microbiome, SCFAs, and excreta composition in laying hens.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {55},
pmid = {40450306},
issn = {2524-4671},
abstract = {BACKGROUND: Insect farming represents a sustainable loop that recycles organic wastes back to the food chain while requiring minimal inputs such as land and water. Insect products are not only low in environment footprint, but also nutrient-dense and contain health-promoting bioactives. Black soldier fly larvae meal (BSFLM) stands out as an excellent source of protein and chitin, and the latter is a polysaccharide associated with promoting gut health. A 20-week feeding trial evaluated the effects of three dietary inclusion levels of BSFLM (0%, 6.5%, and 13%), with and without protease enzyme (Concentrase-P) supplementation, on two commercial laying hen strains: Lohmann Brown-Lite (brown hens) and Lohmann LSL-Lite White (white hens). The two strains of 52-week-old hens (mean weight = 2.2 kg) were housed in one production room, with each strain distributed across 36 conventional cages (5 birds per cage). Each treatment was randomly assigned to six cages (n = 6). At the end of the trial, cecal microbiome, SCFA production and excreta composition were studied.<br><br>RESULTS: White hens exhibited a distinct cecal microbiome compared to brown hens (p&#x2009;<&#x2009;0.05), characterized by enhanced diversity, increased relative abundance of Actinobacteriota, and an altered cecal SCFA profile with increased butyric acid and reduced acetic acid levels (p&#x2009;<&#x2009;0.05). Independent from strain, both 6.5% and 13% BSFLM inclusion promoted cecal microbial richness and evenness, shifting the community to produce more acetic acid and less butyric acid (p&#x2009;<&#x2009;0.05). Excreta analysis showed significantly higher concentrations and daily excretion of nitrogen, ammoniacal nitrogen and non-ammoniacal nitrogen in both strains on the 13% BSFLM diet. Concentrase-P supplementation effectively ameliorated the elevated nitrogen and ammoniacal nitrogen excretion linked to the 13% BSFLM diet, despite having minimal effects on the cecal microbiome and SCFA production.<br><br>CONCLUSION: Our study provides a novel perspective on the enhanced cecal microbiome diversity in laying hens fed high levels of BSFLM, linking it to suboptimal protein digestion and an undesired increase in protein fermentation, which we have demonstrated can be partially addressed by protease supplementation. Our findings highlight the need to consider interactions between host nutrition, gut microbiome, and sustainability when evaluating novel feed ingredients.},
}
@article {pmid40450182,
year = {2025},
author = {Wang, C and Dong, T and Rong, X and Yang, Y and Mou, J and Li, J and Ge, J and Mu, X and Jiang, J},
title = {Microbiome in prostate cancer: pathogenic mechanisms, multi-omics diagnostics, and synergistic therapies.},
journal = {Journal of cancer research and clinical oncology},
volume = {151},
number = {6},
pages = {178},
pmid = {40450182},
issn = {1432-1335},
support = {82172230//the National Natural Science Foundation of China/ ; 21ZGY29//the Changchun Scientific and Technological Development Program/ ; 3R218FM83430//Life Spring AKY Pharmaceuticals/ ; 20240205001YY//the Jilin Scientific and Technological Development Program/ ; 2017F014//the Jilin Health Service Capacity Improvement Program/ ; },
mesh = {Humans ; *Prostatic Neoplasms/microbiology/therapy/diagnosis/pathology ; Male ; *Microbiota ; Metagenomics/methods ; Multiomics ; },
abstract = {BACKGROUND: Prostate cancer (PCa) is a leading cause of cancer-related deaths in men, with the microbiome emerging as a significant factor in its development and progression. Understanding the microbiome's role could provide new insights into PCa pathogenesis and treatment.<br><br>OBJECTIVE: This review aims to explore the interactions between the microbiome and PCa, focusing on microbial imbalances and their effects on immune responses, inflammation, and hormone levels. It also discusses advanced research techniques and the potential for microbiome modulation in PCa management.<br><br>METHODS: The review synthesizes current literature on the microbiome's role in PCa, highlighting differences in microbial composition between cancerous and healthy prostate tissues. It examines techniques such as high-throughput sequencing and metagenomics and explores the mechanisms through which the microbiome influences PCa.<br><br>CONCLUSIONS: The review reveals substantial microbial differences in prostate tissues of PCa patients compared to healthy individuals, indicating a potential link between microbiome alterations and disease progression. It highlights the promise of microbiome-based strategies for diagnosis and treatment and underscores the need for further research into personalized, microbiome-centric approaches for PCa management.},
}
@article {pmid40450070,
year = {2025},
author = {Wang, T and Wang, G and Wu, M and Lan, H and Liu, J and Gong, H and Zheng, X},
title = {Maternal β-carotene supplementation improves offspring growth, development, immunity, and intestinal microbiota in chickens via immune-mediated and microbial-mediated maternal effects.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {19149},
pmid = {40450070},
issn = {2045-2322},
support = {20220203096SF//the Technology Development Plan Program of Jilin Province/ ; 2021YFD2101003-2//the National Key R&amp;D Program of China/ ; 32472995//the National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Chickens/growth &amp; development/immunology/microbiology ; *beta Carotene/pharmacology/administration &amp; dosage ; Female ; *Dietary Supplements ; beta-Defensins/blood ; Muramidase/blood ; Animal Feed ; Immunoglobulin G/blood ; Maternal Nutritional Physiological Phenomena ; },
abstract = {In poultry, maternal nutritional interventions affect the development and intestinal microbiota of embryos. β-carotene possesses immune-boosting and gut microbiota-regulating properties. We examined the influences of supplementing hen diets with β-carotene on offspring growth, development, and immunity to determine whether maternal β-carotene benefits offspring health. Our findings showed that β-carotene increased serum IgG, lysozyme, and beta-defensins in hens, subsequently elevated these parameters in the serum of their offspring, and promoted their growth and development. In offspring, there were significant positive correlations between body weights and intestinal development indices with serum lysozyme and beta-defensin levels. The augmentation of vertical transfer of lysozyme and beta-defensins may be linked to the increased expression of these genes in the maternal jejunum. The number of shared taxa between the magnum and offspring gut is higher than that between the maternal gut and offspring. Among the taxa, were increased in the maternal magnum and gut microbiome, only the Caloramator abundance was significantly elevated in the guts of 21-day-old offspring. In conclusion, maternal β-carotene inclusion improves offspring growth and development, potentially through enhancing maternal intestinal immunity and thereby promoting immune-mediated maternal effects. The vertical transfer of maternal microbes to offspring exhibits selectivity in chicken.},
}
@article {pmid40449951,
year = {2025},
author = {Huang, C and Rosolowsky, E and Nour, MA and Butalia, S and Ho, J and Mayengbam, S and Wang, W and Pyke, S and Virtanen, H and Reimer, RA},
title = {Prebiotic supplementation in patients with type 1 diabetes: study protocol for a randomised controlled trial in Canada.},
journal = {BMJ open},
volume = {15},
number = {5},
pages = {e102486},
doi = {10.1136/bmjopen-2025-102486},
pmid = {40449951},
issn = {2044-6055},
mesh = {Humans ; *Diabetes Mellitus, Type 1/blood ; *Prebiotics/administration &amp; dosage ; Randomized Controlled Trials as Topic ; Child ; Blood Glucose/metabolism ; Gastrointestinal Microbiome ; Canada ; Pilot Projects ; Hypoglycemia/prevention &amp; control ; Female ; Dietary Supplements ; Male ; Dysbiosis ; Double-Blind Method ; Adolescent ; },
abstract = {INTRODUCTION: Type 1 diabetes (T1D) mellitus is caused by autoimmune destruction of insulin-producing beta-cells, requiring exogenous insulin to sustain life. Achieving near normal blood glucose levels with insulin, a primary goal of diabetes management, carries a significant risk of hypoglycaemia. There is compelling evidence that an abnormal gut microbiota or dysbiosis can increase intestinal permeability (IP) and contribute to dysglycaemia seen in T1D. Given that prebiotic fibre can mitigate dysbiosis, reduce IP and improve glycaemic control, we hypothesise that microbial changes induced by prebiotics contribute to gut and endocrine adaptations that reduce glucose fluctuations, including less hypoglycaemia. In a pilot study, we showed that in children who had T1D for at least 1 year, a 3-month course of prebiotic fibre significantly reduced the frequency of hypoglycaemia. The prebiotic group had an increase in Bifidobacterium with a moderate improvement in IP. Importantly, the prebiotic group maintained their serum C peptide level (marker of residual beta cell function) while the placebo group saw a drop. Given that preserving endogenous beta cell function in patients with T1D, particularly in the first year of diagnosis, reduces hypoglycaemia and glycaemic variability, we propose to examine the effect of prebiotic supplementation in patients with T1D.<br><br>METHODS AND ANALYSIS: This is a multicentre, randomised, double-blind, placebo-controlled study. Individuals (n=144) with T1D will be randomised 1:1 for 6 months to prebiotic (oligofructose-enriched inulin) or placebo (isocaloric maltodextrin). Participants will have three in-person study visits at baseline, 3 months and 6 months. The primary outcome, frequency of hypoglycaemia, will be determined from continuous glucose monitor (CGM) reports and patient blood glucose logs. Secondary outcomes will include glycaemic variability, time-in-range, glycated haemoglobin, stimulated C peptide, IP, serum inflammatory markers, quality of life and fear of hypoglycaemia ratings, as well as gut microbiome and metabolomics analysis. At 9 months, participant CGM data will be used to assess frequency of hypoglycaemia and glycaemic variability at 3 months postintervention.<br><br>ETHICS AND DISSEMINATION: The study received ethical approval from the University of Calgary Conjoint Health Research Ethics Board (REB21-0852). The University of Alberta subsite was granted ethical approval under the province of Alberta's research ethics reciprocity agreement as a participating site (REB21-0852; pSite00000066). The University of Saskatchewan subsite was granted ethical approval by the Biomedical Research Ethics Board (#4149). Trial findings will be disseminated through peer-reviewed publications and conference presentations.<br><br>TRIAL REGISTRATION NUMBER: clinicaltrials.gov NCT04963777.},
}
@article {pmid40449791,
year = {2025},
author = {Bellanti, JA},
title = {Selected IEIs Associated with Severe Atopic Phenotypes: Implications for the Practicing Allergist.},
journal = {Annals of allergy, asthma &amp; immunology : official publication of the American College of Allergy, Asthma, &amp; Immunology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.anai.2025.05.024},
pmid = {40449791},
issn = {1534-4436},
abstract = {BACKGROUND: Food allergies and inborn errors of immunity (IEIs) were once viewed as distinct disorders-hypersensitivity versus infection susceptibility. However, IEIs are now recognized to include immune dysregulation, with autoimmunity, autoinflammation, lymphoproliferation, and severe atopy. Understanding the overlap between food allergies and IEIs is critical, as allergic inflammation often complicates immune deficiencies.<br><br>OBJECTIVE: To examine the shared immunologic mechanisms linking food allergies and IEIs, with a focus on immune dysregulation, barrier defects, microbial dysbiosis, and impaired regulatory T cell (Treg) function.<br><br>METHODS: A comprehensive literature review was conducted using PubMed applying search terms including food allergy, primary immunodeficiency, inborn errors of immunity (IEIs), Treg cells, immune dysregulation, autoimmunity, autoinflammation, epithelial barrier dysfunction, and microbiome. Particular focus was placed on identifying studies describing monogenic IEIs characterized by severe allergic phenotypes and elevated IgE levels. Articles were selected based on relevance to the themes of the review, quality of study design, and their contribution to advancing understanding in the field. Priority was given to original research articles, systematic reviews, meta-analyses, and key historical studies.<br><br>RESULTS: Allergic symptoms, including food allergy and atopic dermatitis, frequently present early in IEIs and may precede infection susceptibility. Common features include Treg dysfunction, cytokine signaling defects, epithelial barrier compromise, and microbiome alterations. Recognition of these pathways has enhanced diagnosis and led to targeted therapies such as biologics and gene therapy.<br><br>CONCLUSION: Regulatory T cells are central to maintaining immune tolerance across allergic, autoimmune, and immunodeficient states. Advances in understanding dysregulated immunity and barrier defects are driving personalized treatment strategies for patients with both food allergy and IEIs.},
}
@article {pmid40449763,
year = {2025},
author = {Liu, W and Chen, S and Yang, J and Chen, Y and Yang, Q and Lu, L and Li, J and Yang, T and Zhang, G and Hu, J},
title = {Characterization of blood and urine microbiome temporal variability in patients with acute myeloid leukemia.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {107734},
doi = {10.1016/j.micpath.2025.107734},
pmid = {40449763},
issn = {1096-1208},
abstract = {BACKGROUND: Investigating the microbiota of blood and urine from acute myeloid leukemia (AML) patients is essential to unravel the complex role of microbiota in systemic host-microbe interactions and implications.<br><br>METHODS: We conducted a longitudinal observational study to characterize the temporal dynamics of blood and urine microbiota in 27 AML patients, utilizing metagenomic analysis pipeline for microbial identification to identify disease-associated microbial signatures.<br><br>RESULTS: The composition of blood and urine microbiota of AML was dominated by Proteobacteria phylum in blood, Firmicutes phylum in urine. The species and diversity of blood and urine microbiota did not have difference between AML patients and healthy controls. Restitution of alpha and beta diversity of blood microbiota and urine microbiota to resemble that of healthy controls occurred after cessation of treatment. Temporal variation of urine microbiome was higher than blood after treatment which was closely related to pathogenic bacteria and beneficial bacteria measured by coefficient of variation (CV) of alpha diversity. The temporal variability of urine microbiota was significantly correlated with platelet and exposure of levofloxacin. The variation of microbiome of AML patients with infection was found that the relative abundance of Burkholderia significantly enriched in blood and urine which had high accuracy and sensitivity. The correlation between blood microbiota and serum amino acid metabolites was similar to that between gut microbiota and serum metabolites.<br><br>CONCLUSION: This study represents the first comprehensive investigation to quantify the longitudinal variability of blood and urine microbiota in AML patients, revealing distinct patterns compared to gut microbiota and associations with adverse clinical outcomes. Our findings highlight the potential of leveraging stabilizing taxa as a target for microbiome restoration.},
}
@article {pmid40449488,
year = {2025},
author = {Brown, EM and Temple, ER and Jeanfavre, S and Avila-Pacheco, J and Taylor, N and Liu, K and Nguyen, PNU and Mohamed, AMT and Ung, P and Walker, RA and Graham, DB and Clish, CB and Xavier, RJ},
title = {Bacteroides sphingolipids promote anti-inflammatory responses through the mevalonate pathway.},
journal = {Cell host &amp; microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2025.05.007},
pmid = {40449488},
issn = {1934-6069},
abstract = {Sphingolipids derived from Bacteroides species are associated with changes in host inflammation and metabolic syndrome; however, the signaling mechanisms within host cells are unknown. We utilize outer membrane vesicles (OMVs) from wild-type and sphingolipid-deficient Bacteroides strains to understand how these lipids modulate host inflammation. Characterization of the lipidome of B. thetaiotaomicron OMVs revealed enrichment of dihydroceramide phosphoethanolamine (CerPE). OMVs deliver bacterial sphingolipids into host dendritic and epithelial cells, where a subset of lipids, including CerPE, stably persist. Similarly, B. thetaiotaomicron colonization results in sphingolipid persistence in murine tissues and host lipidome alterations that are not observed with the sphingolipid-deficient strain. OMVs induce a potent, sphingolipid-dependent interleukin-10 (IL-10) anti-inflammatory response in dendritic cells, which depends on mevalonate pathway activation. Adding a CerPE fraction to sphingolipid-deficient OMVs rescued IL-10 secretion, similarly dependent on mevalonate pathway activation. These data highlight the essential roles of sphingolipids in stimulating anti-inflammatory responses mediated by mevalonate pathway induction.},
}
@article {pmid40449445,
year = {2025},
author = {Zheng, Z and Gustavsson, DJI and Zheng, D and Holmin, F and Falås, P and Wilén, BM and Modin, O and Persson, F},
title = {Genome-centric metagenomics reveals the effect of organic carbon source on one-stage partial denitrification-anammox in biofilm reactors.},
journal = {Journal of environmental management},
volume = {388},
number = {},
pages = {125972},
doi = {10.1016/j.jenvman.2025.125972},
pmid = {40449445},
issn = {1095-8630},
abstract = {Nitrogen removal from wastewater with anammox saves energy and resources. Partial denitrification-anammox (PDA) is a promising process alternative for municipal wastewater treatment, given that the understanding about how to control the microbiome and its activity reach sufficient level. Here, two moving bed biofilm reactors were fed with either acetate or propionate to study the role of organic carbon type for microbiome composition and nitrogen turnover during development of PDA. With acetate, 87 % of the removed nitrogen was converted via anammox during stable operation at a rate of 0.52 g N/(m[2]·d). With propionate, the anammox contribution was considerably lower (41 %), as was the rate of nitrogen removal (0.27 g N/(m[2]·d)). The microbiome composition in the acetate- and propionate-fed reactors was however similar, with an enrichment of metagenome assembled genomes (MAGs) having genes for nitrate reduction (narG, napA). A large fraction of these MAGs had the potential to accumulate nitrite since they lacked genes for nitrite reduction (nirS, nirK, nrfA). Genes for acetate utilization were common among these MAGs, but the necessary genes for propionate conversion were rare, suggesting that the genetic make-up of the individual denitrifiers had major influence on the nitrogen turnover. One anammox MAG (Ca. Brocadia sapporoensis), harboring genes for organic carbon utilization, prevailed in the PDA reactors. Another three anammox MAGs (Ca. B. fulgida, Ca. B. pituitae and a potentially new species within Ca. Brocadia), lacking genes for organic carbon utilization, decreased in abundance in the reactors, indicating the importance of metabolic versatility for anammox bacteria in PDA.},
}
@article {pmid40449316,
year = {2025},
author = {Tarnawska, P and Burkowska-But, A and Brzezińska, MS and Drążkowska, A and Osińska, A and Walczak, M},
title = {Unveiling the hidden microbiome: a microbiological exploration of untouched burial crypts in Krakow, Poland.},
journal = {Systematic and applied microbiology},
volume = {48},
number = {4},
pages = {126618},
doi = {10.1016/j.syapm.2025.126618},
pmid = {40449316},
issn = {1618-0984},
abstract = {Cultural heritage objects provide valuable historical information, but can also harbour biological threats. Still, little is said about the potential risks that may await unaware researchers, conservators, and archaeologists. Our work discusses the study results from the crypts in Krakow, which were opened for the first time. The human and coffin remains were examined. The number of actinomycetes, other mesophilic bacteria, bacterial spores, and xerophilic and non-xerophilic fungi was determined. In general, a low number of microbes was observed. However, scanning electron microscope (SEM) images showed many bacterial conglomerates and confirmed that microbial activity affected the fibres covering cadavers in the crypts. The most abundant were mesophilic bacteria, followed by bacterial spores and actinomycetes. They reached up to 10[7] CFU/g in fabric remains, 5.2 × 10[6] CFU/g in burial remains, and 1.6 × 10[6] CFU/g found under the coffin, and above 7.5 × 10[5] CFU/g for xerophilic and non-xerophilic fungi. NGS (Next-Generation Sequencing) results suggested that the low presence of microorganisms may be due to the dominance of unculturable or long-growing bacteria belonging to Mycobacterium, such as M. coloregonium, M. arupense, and M. pinnipedii. Moreover, other obligatory/non-obligatory pathogens, Bacteroides fragilis, Clostridium botulinum, Coxiella burnetii, Clostridium tetani, Corynebacterium diphtheriae, Enterobacter cloacae, Escherichia coli, Legionella pneumophila, Mycobacterium leprae, Rhodococcus equi, and Staphylococcus aureus have been recorded in examined samples, with the dominance in bone samples. Results indicate the risk of dangerous pathogens present in historical objects, the impact on health may be severe, and the need to use personal protective equipment and proper measures to control the physical conditions of crypts.},
}
@article {pmid40449217,
year = {2025},
author = {Zhou, Z and Tian, J and Si, Q and Tay, YJ and Han, M and Jiang, Q and Wang, L},
title = {Unraveling the stress response: How low temperature and nanoparticles impact the chinese mitten crab (Eriocheir sinensis).},
journal = {Journal of hazardous materials},
volume = {494},
number = {},
pages = {138775},
doi = {10.1016/j.jhazmat.2025.138775},
pmid = {40449217},
issn = {1873-3336},
abstract = {The Chinese mitten crab (Eriocheir sinensis) is a freshwater crustacean of considerable economic significance. To elucidate its physiological regulatory mechanisms under environmental stressors, we examined responses to low temperature (10 °C), ambient temperature (25 °C), and polystyrene nanoparticles (PS-NPs; 0, 1, and 10 mg/L) over a 28-day period. Exposure to these stressors led to a marked increase in glutathione peroxidase (GSH-Px) and lysozyme (LZM) activity, alongside a notable suppression of superoxide dismutase (SOD). Integrative microbiome, metabolome and transcriptome analyses revealed distinct shifts in microbial composition and metabolite profiles, including elevated levels of citric acid, L-isoleucine (L-allo-Ile), and trans-cinnamic acid (t-CA). Functional enrichment of differentially expressed metabolites and microbial taxa implicated pathways involved in oxidative defense, immune regulation, and PI3K-Akt-FoxO signaling. Functional enrichment analyses of differentially expressed metabolites (DEMs) and microbial taxa pointed to coordinated disruptions in redox homeostasis, cellular defense mechanisms, and host-microbe interactions. Collectively, our findings demonstrate that prolonged exposure to low temperatures and PS-NPs imposes considerable physiological burden on E. sinensis, manifested as metabolic dysregulation, oxidative damage, and impaired immune competence. This study provides a comprehensive molecular framework for understanding how E. sinensis responds to multifactorial environmental stressors, offering valuable insights for ecological risk assessment and resilience-oriented aquaculture practices.},
}
@article {pmid40449136,
year = {2025},
author = {Alizadeh, M and Fletcher, C and Oladokun, S and Mallick, AI and Abdelaziz, K and St-Denis, M and Raj, S and Blake, K and Sharif, S},
title = {Treatment of chickens with probiotics under conditions conducive to necrotic enteritis development.},
journal = {Research in veterinary science},
volume = {192},
number = {},
pages = {105711},
doi = {10.1016/j.rvsc.2025.105711},
pmid = {40449136},
issn = {1532-2661},
abstract = {Necrotic enteritis (NE) poses a significant challenge to the global broiler industry, particularly with the increasing restrictions on using antibiotic growth promoters. Probiotics have emerged as a promising alternative for effective disease control. This study evaluated the efficacy of a probiotic cocktail consisting of Lactobacillus crispatus, Ligilactobacillus johnsonii, Limosilactobacillus reuteri, and 2 strains of Ligilactobacillus salivarius, under experimental conditions conducive to NE. Chickens were divided into two groups based on stocking density: high stocking density (30 birds/m[2]) and normal stocking density (15 birds/m[2]). Within each group, one subgroup received 10[8] colony-forming units (CFUs) of lactobacilli on days 1, 7, 14, and 20 of age, while the other received phosphate-buffered saline. Body weight and lesion scores were recorded on days 21 and 24, respectively. Tissues from the intestine were collected for analysis of immunoregulatory genes and lymphocyte population. Cecal contents were collected for microbiome analysis. Probiotic treatment improved body weight gain compared to non-treated controls and reduced gut lesion scoring in the birds raised under high stocking density. Probiotic treatment increased the frequency of Bu-1[+] B cells and CD3[+]CD4[+] T cells in the cecal tonsils and enhanced the relative expression of antimicrobial peptides (zonula occludens and occludin) in the ileum. However, it decreased the expression of heat shock proteins, interleukin (IL)-18, IL-1β, and interferon (IFN)-γ. Probiotics also enhanced alpha diversity and the abundance of Christensenellaceae_R-7 group, Angelakisella, and Clostridia_vadinBB60 group compared to the high stocking density control group. These findings underscore the potential of probiotics to mitigate NE in broiler chickens, particularly under conditions of high stocking density.},
}
@article {pmid40449103,
year = {2025},
author = {Chen, L and Zhang, Z and Deng, W and Jiang, G and Xie, D and Cao, A},
title = {Bile acids enhance fat metabolism and skeletal muscle development in Zhijiang duck by modulating gut microbiota.},
journal = {Poultry science},
volume = {104},
number = {8},
pages = {105319},
doi = {10.1016/j.psj.2025.105319},
pmid = {40449103},
issn = {1525-3171},
abstract = {To optimize livestock production of integrated farms, dietary crude fat levels are often increased, making efficient fat utilization crucial. Bile acids are known to improve fat utilization, but their impact on growth performance and breast muscle development in Zhijiang ducks remains unclear. In this study, a total of 360 twenty-day-old Zhijiang ducks with similar body weights were divided into three groups: the control group (CN) received a basal diet; the high-fat group (FA) received the basal diet plus 1.25 % rapeseed oil; and the high-fat plus bile acids compound (BA) group (FB) received the FA diet supplemented with 250 mg/kg BA for 30 days. Results indicated that the addition of rapeseed oil and BA significantly increased (P < 0.05) average daily gain (ADG) and reduced (P < 0.05) feed conversion ratio (FCR). Slaughter data showed that BA significantly enhanced (P < 0.05) breast muscle weight and percentage while decreasing (P < 0.05) abdominal fat weight. Additionally, BA increased (P < 0.05) the cross-sectional area of breast muscle fibers, total bile acid content, and levels of insulin-like growth factors 1/2 (IGF1/2). Transcriptomic analysis further revealed that BA significantly upregulated (P < 0.05) the levels of PPARα, CPT1α, NR1H4, and CETP in breast muscle. 16S rRNA analysis showed a significant increase (P < 0.05) in the relative abundances of genera Enorma, [Eubacterium nodatum group], Rikenellaceae RC9 gut group, and SP3-e08. Additionally, the Spearman correlation suggested a positive correlation between the genera Olsenella, SP3-e08, Enorma, Rikenellaceae_RC9_gut_group, and [Eubacterium_nodatum_group] with PPARα, CETP, NR1H4, and CPT1α. In contrast, the genera Christensenellaceae_R_7_group and Sutterella exhibited negative correlations with PPARα. These findings provide new insights into the role of BA in promoting growth performance and skeletal muscle development in Zhijiang ducks fed a high-fat diet, with this effect potentially linked to changes in the gut microbiota.},
}
@article {pmid40449069,
year = {2025},
author = {Getz, LJ and Patel, PH and Maxwell, KL},
title = {A solution to the postantibiotic era: phages as precision medicine.},
journal = {Current opinion in microbiology},
volume = {86},
number = {},
pages = {102613},
doi = {10.1016/j.mib.2025.102613},
pmid = {40449069},
issn = {1879-0364},
abstract = {Antibiotic-resistant bacterial infections pose a significant global health challenge. Phage therapy provides a promising alternative to antibiotics that enables the specific targeting of pathogenic bacteria while preserving the healthy microbiome. Recent advances in genetic engineering, synthetic biology, and artificial intelligence have rekindled interest in phage therapy, as they move phages into the realm of precision medicine. Engineered phages can be customized to have a broader host range, encode counter-defenses that overcome bacterial immune systems, or express other proteins that modulate the bacterial host to their advantage. Innovations in artificial intelligence and machine learning promise to speed up the identification of optimal phage candidates and create tailored cocktails for individualized therapies - advances that will transform phage therapy and provide a solution to the antibiotic resistance crisis.},
}
@article {pmid40449064,
year = {2025},
author = {Zhu, X and Jia, M and Zhou, W and Zhou, P and Du, Y and Yang, H and Wang, G and Bai, Y and Wang, N},
title = {Biochar loaded with nicotine-degrading bacteria works synergistically with native microorganisms to efficiently degrade nicotine.},
journal = {Environment international},
volume = {201},
number = {},
pages = {109550},
doi = {10.1016/j.envint.2025.109550},
pmid = {40449064},
issn = {1873-6750},
abstract = {Nicotine, a potential environmental pollutant that has raised increasing concerns, accumulates to significant levels in soils under long-term tobacco monoculture, posing substantial risks to both local ecosystems and human health. Addressing this challenge, the screening and utilization of nicotine-degrading bacteria have emerged as a central remediation strategy. In this study, we isolated nicotine-degrading bacteria from tobacco-cultivated soils and subsequently immobilized them onto biochar to optimize degradation efficiency. A systematic investigation was conducted to examine the synergistic effects and underlying degradation mechanisms of the biochar-bacteria complex. Notably, we successfully isolated Paenarthrobacter ureafaciens N21 (N21), a bacterial strain capable of degrading nicotine through the pyridine pathway. When immobilized on biochar (BN21), the composite maintained robust degradation capabilities in both culture media and soil environments. Compared with free N21, BN21 demonstrated a 1.4 times enhancement in nicotine degradation efficiency and significantly improved colonization capacity by the degrading bacteria (P < 0.0001). Stability assessment tests further confirmed BN21's consistent degradation performance under diverse environmental conditions. Integrated microbiomic and metabolomic analyses revealed that BN21 induced significant alterations in soil microbial community structure and metabolic profiles, while enhancing the soil's resistance to repeated nicotine disturbances. Importantly, BN21 facilitated synergistic interactions between nicotine-degrading bacteria and indigenous microorganisms, collectively mediating nicotine decomposition through coordinated pyridine and pyrrolidine pathways. The novel discovery of bacteria-loaded biochar synergistically enhancing nicotine removal highlights the potential of biochar-microbe composites for targeted pollutant elimination. This approach shows promising prospects for future applications in ecological remediation of various organic contaminants, providing innovative perspectives for developing microbiome-based green remediation strategies.},
}
@article {pmid40448919,
year = {2025},
author = {Wang, R and Wang, J and Tang, D and Li, B and Huang, J and Lin, X and Li, Y and Xu, W and Gao, W and Wang, J and Zhu, H},
title = {Effects of probiotic treatment on the intestinal microbial community of Haliotis diversicolor.},
journal = {AMB Express},
volume = {15},
number = {1},
pages = {87},
pmid = {40448919},
issn = {2191-0855},
support = {2022ZDZX4029//the grants from Guangdong Province university key field special grant/ ; },
abstract = {Probiotic treatment is an effective method for enhancing growth performance and improving intestinal flora in aquaculture species. This study examined the effects of three candidate-probiotics (Bacillus, photosynthetic bacteria, and Lactobacillus) on the rate of weight gain and the intestinal flora of abalone juveniles. Haliotis diversicolor was fed a probiotic-supplemented diet for 30 days. The abalones fed with Lactobacillus showed a more significant weight gain rate than those in the Bacillus, photosynthetic bacteria, and control groups. Through 16S rRNA high-throughput sequencing, 12,490 amplicon sequence variants (ASVs) were obtained from the abalone intestinal tract microbiome. After a short feeding period (5 days), the Bacillus and photosynthetic bacteria-treated groups showed an increased abundance of Proteobacteria in the abalone digestive tract. In the Lactobacillus-treated group, the quantity of Proteobacteria decreased, and the abundance of Bacteroidota increased. After 30 days of feeding, the abundance of Proteobacteria and Bacteroidetes at the phylum level was more significant in the Bacillus-treated group and photosynthetic bacteria-treated group than in the controls. The Lactobacillus-treated group showed an increase in the quantity of Proteobacteria and Chloroflexi. The dominant flora of the three probiotic treated groups changed slightly with respect to the control group. After a short period of feeding (5 days), the abundance of Rhodobacteraceae (at the genus level) in the abalone digestive tract increased in the Bacillus- and photosynthetic bacteria-treated groups, whereas in the Lactobacillus-treated group, Rhodobacteraceae decreased, and Maribacter increased in abundance. After 30 days of feeding, Bacteroidetes and Ruegeria were higher in the Bacillus-treated group than in the control group. Marinirhabdus and Bacteroidetes increased in the photosynthetic bacteria-treated group, and Roseivivax and Ruegeria increased in the Lactobacillus-treated group. The three probiotic-treated groups had higher microbial diversity than the control group. Therefore, our findings confirmed that adding Bacillus, photosynthetic bacteria, and Lactobacillus to the abalone diet increased abalones' weight gain rate and altered their intestinal microbiome composition.},
}
@article {pmid40448869,
year = {2025},
author = {Dash, HR and Al-Snan, NR},
title = {DNA forensics at forty: the way forward.},
journal = {International journal of legal medicine},
volume = {},
number = {},
pages = {},
pmid = {40448869},
issn = {1437-1596},
abstract = {Forensic DNA analysis has transformed criminal investigations since its inception in 1985. Over four decades, this field has evolved through various phases-from the early stages of exploration to today's highly sophisticated methodologies. Key advancements such as the development of rapid DNA analysis techniques, microchip-based systems, and next-generation sequencing have improved the speed, reliability, and utility of DNA forensics. However, despite these technological advances, the field still faces considerable challenges, particularly with increasing case backlogs, limited population-specific databases, and the difficulties associated with analyzing degraded or challenging samples like bones and touch DNA. Emerging technologies such as single-cell genomic analysis, lineage markers, proteomics, and human microbiome analysis offer promising solutions to these challenges. Furthermore, the integration of artificial intelligence (AI) and machine learning (ML) in forensic workflows is enhancing the ability to analyze complex DNA samples efficiently, paving the way for faster and more accurate results. As forensic DNA analysis enters its next phase, the focus will be on expanding databases, refining quality control and assurance protocols, and standardizing training for forensic professionals worldwide. The journey of forensic DNA analysis over the past 40 years demonstrates a field in continuous development. Although significant progress has been made, there remain opportunities for further innovation, particularly in overcoming the current limitations and addressing ethical and legal concerns. By doing so, forensic DNA analysis will continue to play a pivotal role in the future of criminal justice.},
}
@article {pmid40448590,
year = {2025},
author = {Salman, U and Dabdoub, SM and Reyes, A and Sidahmed, A and Weber-Gasperoni, K and Brown, R and Evans, IA and Taylor, E and Mangalam, A and Kanner, L and Curtis, V and Ganesan, SM},
title = {Dysbiotic Microbiome-Metabolome Axis in Childhood Obesity and Metabolic Syndrome.},
journal = {Journal of dental research},
volume = {},
number = {},
pages = {220345251336129},
doi = {10.1177/00220345251336129},
pmid = {40448590},
issn = {1544-0591},
abstract = {The prevalence of childhood metabolic syndrome (MetS) and obesity is rising, with emerging evidence suggesting these conditions negatively affect oral health. However, the underlying molecular determinants are unclear. This study investigated the oral microbiome, inflammatory markers, and metabolites in children with obesity and MetS to explore the interrelationships between systemic disease and oral health. We recruited 76 periodontally healthy, caries-free individuals aged 10 to 17 y into 3 groups: MetS (29), metabolically healthy obesity (MHO) (30), and normal-weight healthy (NWH) controls (17). Unstimulated saliva was collected. Bacterial DNA was isolated, V3-V4 regions amplified, and 16S sequencing performed on the Illumina MiSeq platform. Sequences were annotated against the HOMD database. Multiplex assays quantified adipokines and cytokines, with significance determined by Tukey honestly significant difference. Gas chromatography/mass spectrometry identified metabolite peaks that were annotated against the Small Molecule Pathway Database, with enrichment analysis determining significance. Integrated multiomics analysis was performed using multiblock sparse partial least squares regression discriminant analysis. The MHO and MetS groups demonstrated lower abundances of Streptococcus, Actinomyces, and Schaalia and higher levels of Aggregatibacter, Campylobacter, Alloprevotella, Prevotella, Leptotrichia, and Porphyromonas compared with NWH, despite similar clinical oral status in all cohorts. MetS and MHO also had increased leptin, tumor necrosis factor-α, interleukin (IL)-1β, and IL-15 and decreased adiponectin levels versus NWH. Disease-associated metabolites, including glutamate, cholesterol, isoleucine, tyrosine, phenylalanine, serine, and indoleacetic acid, were significantly enriched in the MetS and MHO groups. Integrated multiomic analysis identified key correlations in the saliva of subjects with metabolic health or disease. Decreases in health-associated species and increases in proinflammatory cytokines and disease-associated metabolites in the saliva of MetS and obese adolescents with clinical oral health indicate an "at-risk" environment, potentially explaining their elevated risk for oral diseases. Increased salivary leptin and decreased adiponectin levels highlight the potential of saliva as a noninvasive biomarker source for childhood MetS.},
}
@article {pmid40448586,
year = {2025},
author = {Jones, LM and El Aidy, S},
title = {Electroactive ecosystem insights from corrosion microbiomes inform gut microbiome modulation.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf112},
pmid = {40448586},
issn = {1751-7370},
abstract = {Electroactive microorganisms influence environmental and host-associated ecosystems through their ability to mediate extracellular electron transfer. This review explores parallels between EAM-driven microbiologically influenced corrosion systems and the human gut microbiome. In corrosion, EAMs contribute to biofilm formation, redox cycling, and material degradation through mechanisms such as direct electron transfer and syntrophic interactions. Similarly, gut-associated EAMs regulate redox balance, drive short-chain fatty acid production, and shape host-microbe interactions. Despite differing contexts, both systems share traits like anoxic niches, biofilm formation, and metabolic adaptability. Insights from well-characterized corrosion microbiomes offer valuable frameworks to understand microbial resilience, electron transfer strategies, and interspecies cooperation in the gut. Bridging knowledge between these systems can inform microbiome engineering approaches aimed at promoting gut health, highlighting the need for further functional metagenomics and exploration of archaeal contributions to biofilm stability and redox modulation.},
}
@article {pmid40448582,
year = {2025},
author = {Hall, LA and Scott, KD and Webster, N and Kerkhof, LJ and Häggblom, MM},
title = {Dehalogenating Desulfoluna spp. are Ubiquitous in Host-Specific Sponge Microbiomes of the Great Barrier Reef.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf113},
pmid = {40448582},
issn = {1751-7370},
abstract = {Marine sponge holobionts are important contributors to numerous biogeochemical cycles, including the natural organohalogen cycle. Sponges produce diverse brominated secondary metabolites, which select for a population of anaerobic debrominating bacteria within the sponge body. Sponge microbiomes can be host-specific, but the selection and host-specificity of debrominating bacteria are unknown currently. In this study, we used nanopore long-read sequencing of nearly full-length ribosomal RNA operons to evaluate host-specificity of the Great Barrier Reef sponge microbiomes at the strain level and to determine if host specificity extends to sponge-associated dehalogenating bacteria. Reductive debromination activity was observed in anaerobic enrichment cultures established from all Great Barrier Reef sponges. Even though other bacterial symbionts of interest, including Nitrospira spp. and Ca. Synechococcus spp. demonstrated strong host-specificity, Desulfoluna spp., a key sponge-associated dehalogenating bacterium showed no evidence of host-specificity. This suggests different modes of transmission and/or retention of different members of the sponge microbiome residing within the same host species. These findings expand our understanding of how sponge microbiomes are assembled and the relationship between the host and individual bacterial strains.},
}
@article {pmid40448308,
year = {2025},
author = {Gu, BH and Jung, HY and Rim, CY and Kim, TY and Lee, SJ and Choi, DY and Park, HK and Kim, M},
title = {Comparative Colonisation Ability of Human Faecal Microbiome Transplantation Strategies in Murine Models.},
journal = {Microbial biotechnology},
volume = {18},
number = {6},
pages = {e70173},
pmid = {40448308},
issn = {1751-7915},
support = {2024-ER2113-00//the Korea National Institute of Health (KNIH) research project/ ; 20019505//the Ministry of Trade, Industry &amp; Energy (MOTIE, Korea)/ ; },
mesh = {Animals ; *Fecal Microbiota Transplantation/methods ; Humans ; Mice ; *Gastrointestinal Microbiome ; *Feces/microbiology ; Disease Models, Animal ; *Bacteria/classification/growth &amp; development/isolation &amp; purification/genetics ; Dysbiosis/therapy/microbiology ; Male ; Models, Animal ; },
abstract = {The gut microbiome plays a crucial role in maintaining intestinal homeostasis and influencing immune-mediated diseases. Human faecal microbiota transplantation (FMT) is often employed in murine models to investigate the role of human microbes in disease regulation, but methods for effective colonisation require refinement. This study aimed to assess the colonisation efficiency of human microbiota in a murine model using FMT with human faeces, focusing particularly on the impact of gut microbiota depletion via polyethylene glycol (PEG) and comparing oral-gastric gavage with enema administration routes. Our findings revealed that PEG-induced depletion enhanced human microbiome colonisation in mice. Oral-gastric gavage prolonged colonisation, while enema administration facilitated quicker resolution of dysbiosis, both inducing selective human microbial colonisation in a time-dependent manner. Notably, genera such as Bacteroides, Blautia, Medicaternibacter and Bifidobacteria were successfully colonised, whereas Roseburia, Anaerostipes, Anaerobutyricum and Faecalibacterium failed to establish in the murine gut post-FMT. These findings highlight the challenges of replicating human gut microbiota in murine models and underscore the importance of selecting appropriate FMT methods based on desired outcomes. This study provides valuable insights into the colonisation dynamics of human microbiota in mice, contributing to the development of more effective FMT strategies for disease treatment.},
}
@article {pmid40448221,
year = {2025},
author = {Fan, KC and Lin, CC and Chiu, YL and Koh, SH and Liu, YC and Chuang, YF},
title = {Compositional and functional gut microbiota alterations in mild cognitive impairment: links to Alzheimer's disease pathology.},
journal = {Alzheimer's research &amp; therapy},
volume = {17},
number = {1},
pages = {122},
pmid = {40448221},
issn = {1758-9193},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Cognitive Dysfunction/microbiology/pathology/metabolism ; *Alzheimer Disease/microbiology/pathology/metabolism ; Male ; Female ; Aged ; Feces/microbiology ; Biomarkers ; Brain/pathology/metabolism ; Aged, 80 and over ; Dysbiosis ; tau Proteins ; Middle Aged ; },
abstract = {BACKGROUND: Emerging evidence highlights the bidirectional communication between the gut microbiota and the brain, suggesting a potential role for gut dysbiosis in Alzheimer's disease (AD) pathology and cognitive decline. Existing literature on gut microbiota lacks species-level insights. This study investigates gut microbiota alterations in mild cognitive impairment (MCI), focusing on their association with comprehensive AD biomarkers, including amyloid burden, tau pathology, neurodegeneration, and cognitive performance.<br><br>METHODS: We analyzed fecal samples from 119 individuals with MCI and 320 cognitively normal controls enrolled in the Taiwan Precision Medicine Initiative on Cognitive Impairment and Dementia cohort. Shotgun metagenomic sequencing was conducted with taxonomic profiling using MetaPhlAn4. Amyloid burden and plasma pTau181 were quantified via PET imaging and Simoa assays, respectively, while APOE genotyping was performed using TaqMan assays. Microbial diversity, differential abundance analysis, and correlation mapping with neuropsychological and neuroimaging measures were conducted to identify gut microbiota species signatures associated with MCI and AD biomarkers.<br><br>RESULTS: We identified 59 key microbial species linked to MCI and AD biomarkers. Notably, species within the same genera, such as Bacteroides and Ruminococcus, showed opposing effects, while Akkermansia muciniphila correlated with reduced amyloid burden, suggesting a protective role. Functional profiling revealed microbial pathways contributing to energy metabolism and neuroinflammation, mediating the relationship between gut microbes and brain health. Co-occurrence network analyses demonstrated complex microbial interactions, indicating that the collective influence of gut microbiota on neurodegeneration.<br><br>CONCLUSIONS: Our findings challenge genus-level microbiome analyses, revealing species-specific modulators of AD pathology. This study highlights gut microbial activity as a potential therapeutic target to mitigate cognitive decline and neurodegeneration.},
}
@article {pmid40448072,
year = {2025},
author = {Iniesta, M and Vasconcelos, V and Laciar, F and Matesanz, P and Sanz, M and Herrera, D},
title = {Impact of toothpaste use on the subgingival microbiome: a pilot randomized clinical trial.},
journal = {BMC oral health},
volume = {25},
number = {1},
pages = {854},
pmid = {40448072},
issn = {1472-6831},
mesh = {Humans ; *Toothpastes/pharmacology/therapeutic use ; *Microbiota/drug effects ; Pilot Projects ; Female ; *Gingivitis/microbiology ; Male ; Adult ; Cetylpyridinium/pharmacology/therapeutic use ; Toothbrushing ; *Gingiva/microbiology ; Middle Aged ; Phosphates/pharmacology ; Fluorides/pharmacology ; },
abstract = {BACKGROUND: The subgingival microbiome plays a key role in the gingivitis development, but the impact of toothbrushing with toothpaste on the subgingival microbial composition is not well understood. Therefore, this study aimed to evaluate the microbiological safety and subgingival impact of a toothpaste containing CPC and cymenol, compared to a fluoride-based toothpaste, and assessed overall subgingival microbiome changes after 6 weeks of routine toothbrushing in patients with gingival inflammation.<br><br>METHODS: A 6-week randomized clinical trial was conducted in patients with gingival inflammation allocated to the use of either a toothpaste with cetylpyridinium chloride and cymenol or a toothpaste with sodium monofluorophosphate. Subgingival samples were collected at baseline and after 6&#xa0;weeks and processed using high-throughput sequencing technology (Miseq&#xae;). Diversity metrics were calculated and the microbiome composition was analyzed using PERMANOVA, ANOSIM and PERMDISP.<br><br>RESULTS: A total of 116 samples from 60 patients were analyzed. No significant changes in diversity were observed in either group after 6&#xa0;weeks. Among taxa with&#x2009;>&#x2009;1% abundance, the toothpaste with cetylpyridinium chloride and cymenol exhibited a higher reduction in Aggregatibacter (p&#x2009;=&#x2009;0.023) and a significant decrease in Fusobacterium nucleatum (p&#x2009;=&#x2009;0.030), while the toothpaste with sodium monofluorophosphate showed a significant increase in the phylum Firmicutes (p&#x2009;=&#x2009;0.033). The relative abundance of Porphyromonas gingivalis, Prevotella intermedia and Tannerella forsythia were not affected by either toothpaste (p&#x2009;>&#x2009;0.05).<br><br>CONCLUSIONS: The daily use of a CPC/cymenol toothpaste was microbiologically safe, with no negative effects on the composition of the subgingival microbiome in patients with gingival inflammation, when compared to a fluoride-based toothpaste. The overall composition of the subgingival microbiome was not significantly affected by the daily use of either toothpaste after 6&#xa0;weeks. In both groups, the observed changes affected mainly the low-abundance taxa.<br><br>TRIAL REGISTRATION: Registration Number: ISRCTN17497809; Registration Date: 12/07/2023 (ISRCTN.org).},
}
@article {pmid40448029,
year = {2025},
author = {Jiang, X and Liu, Q and Xu, D and Pang, H and Shi, Y},
title = {Integrated microbiome and metabolome analysis reveals a novel interplay between gut microbiota and metabolites in differentiated thyroid carcinoma.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {346},
pmid = {40448029},
issn = {1471-2180},
support = {CBYI202105//China Baoyuan Research Fund Project/ ; Q21076//Sichuan Provincial Medical Youth Innovation Research Project/ ; CNNC2021137//Young Talent Program of China National Nuclear Corporation/ ; 2021JDRC0170//Sichuan Science and Technology Innovation and Entrepreneurship Seedling Project/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Thyroid Neoplasms/microbiology/metabolism/pathology ; Male ; *Metabolome ; Feces/microbiology ; Female ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Adult ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Aged ; Chromatography, Liquid ; },
abstract = {BACKGROUND: Differentiated Thyroid carcinoma (DTC) is the most prevalent endocrine malignancy. The identification of novel biomarkers for thyroid carcinoma is essential for enhancing our understanding of the molecular mechanisms underlying DTC development. Notably, gut microorganisms and their metabolites play a role in the development of DTC, although their influence is modulated by the host's genetic background and environmental factors. Our study aimed to identify and classify gut microbiota and metabolites associated with DTC.<br><br>METHODS: 90 patients with a confirmed diagnosis of DTC and 33 healthy volunteers donated stool samples for our analysis. To examine the gut microbiota, we utilized 16&#xa0;S rRNA gene sequencing, a technique that allows for the identification and classification of microorganisms. Additionally, we employed liquid chromatography-mass spectrometry (LC-MS) to investigate the alterations in metabolites present in thyroid carcinoma patients compared to healthy individuals.<br><br>RESULTS: The Venn diagram visualized the distribution of bacterial species, with 926 species shared by both groups and 12,225 species unique to DTC patients. Notably, the gut microbiota of DTC patients exhibited higher species richness and diversity compared to healthy individuals. LDA Effect Size (LEfSe) analysis identified Faecalibacterium and Prevotella_9 as more abundant in healthy individuals, while Oscillospiraceae, Subdoligranulum, and Actinobacteriota were significantly more prevalent in DTC patients. We successfully characterized 3255 metabolites in both groups, which were primarily associated with biosynthesis of plant secondary metabolites, neomycin, kanamycin, and gentamicin biosynthesis, bile secretion, and steroid hormone biosynthesis. Among these metabolites, 550 were differentially expressed, with 402 metabolites being highly expressed in DTC patients. Six metabolites exhibiting an area under the curve (AUC) value exceeding 0.87 were identified as potential clinical diagnostic markers for DTC. Furthermore, Spearman's rank correlations were utilized to explore the potential functional relationships between the 10 distinctive microbial species and the top 10 differential metabolites.<br><br>CONCLUSIONS: The gut microbiota and its associated metabolites may play a crucial role in the development of DTC. The identification of altered metabolites and microbiota in DTC patients suggests their potential as diagnostic markers and therapeutic targets. This offers new insights into the molecular pathogenesis of DTC, providing opportunities for early diagnosis and improved treatment strategies.<br><br>CLINICAL TRIAL NUMBER: Not applicable.},
}
@article {pmid40447995,
year = {2025},
author = {Shen, S and Feng, H and Wang, C and Yang, Y and Chen, Z and Wang, X and Li, J},
title = {Association between the dietary index of gut microbiota and abnormal bowel symptoms in U.S. adults: a cross-sectional study based on NHANES 2007-2010.},
journal = {BMC gastroenterology},
volume = {25},
number = {1},
pages = {419},
pmid = {40447995},
issn = {1471-230X},
support = {GSW2021046//Suzhou Municipal Health Commission/ ; GSW2021046//Suzhou Municipal Health Commission/ ; GSW2021046//Suzhou Municipal Health Commission/ ; GSW2021046//Suzhou Municipal Health Commission/ ; GSW2021046//Suzhou Municipal Health Commission/ ; GSW2021046//Suzhou Municipal Health Commission/ ; GSW2021046//Suzhou Municipal Health Commission/ ; BK20211085//Natural Science Foundation of Jiangsu Province/ ; BK20211085//Natural Science Foundation of Jiangsu Province/ ; BK20211085//Natural Science Foundation of Jiangsu Province/ ; BK20211085//Natural Science Foundation of Jiangsu Province/ ; BK20211085//Natural Science Foundation of Jiangsu Province/ ; BK20211085//Natural Science Foundation of Jiangsu Province/ ; BK20211085//Natural Science Foundation of Jiangsu Province/ ; SS2019073//Suzhou Municipal Science and Technology Bureau/ ; SS2019073//Suzhou Municipal Science and Technology Bureau/ ; SS2019073//Suzhou Municipal Science and Technology Bureau/ ; SS2019073//Suzhou Municipal Science and Technology Bureau/ ; SS2019073//Suzhou Municipal Science and Technology Bureau/ ; SS2019073//Suzhou Municipal Science and Technology Bureau/ ; SS2019073//Suzhou Municipal Science and Technology Bureau/ ; },
mesh = {Humans ; *Constipation/epidemiology/microbiology ; Cross-Sectional Studies ; Male ; Female ; *Gastrointestinal Microbiome ; Adult ; Middle Aged ; Nutrition Surveys ; *Diarrhea/epidemiology/microbiology ; United States/epidemiology ; *Diet ; Aged ; Young Adult ; Chronic Disease ; },
abstract = {BACKGROUND: The Dietary Index of Gut Microbiota (DI-GM) is a newly developed measure for assessing diet quality in relation to the diversity of the gut microbiome. However, whether it is associated with the risk of chronic constipation and chronic diarrhea remains unclear.<br><br>METHODS: We analyzed data from 7,943 U.S. adults aged 20 years and older who participated in the 2007-2010 National Health and Nutrition Examination Survey (NHANES). Weighted logistic regression, subgroup analysis, and restricted cubic spline (RCS) models were used to assess the association between the DI-GM and abnormal bowel symptoms.<br><br>RESULTS: A higher DI-GM score was significantly associated with a reduced risk of abnormal bowel symptoms. For each 1-point increase in the DI-GM, the risk of constipation decreased by 12.4% (OR&#x2009;=&#x2009;0.876, 95% CI&#x2009;=&#x2009;0.806-0.951, p&#x2009;=&#x2009;0.002), and the risk of diarrhea decreased by 14.1% (OR&#x2009;=&#x2009;0.859, 95% CI&#x2009;=&#x2009;0.789-0.936, p&#x2009;<&#x2009;0.001). Compared with the lowest DI-GM quartile, the highest quartile showed a markedly lower risk of both constipation (OR&#x2009;=&#x2009;0.487, 95% CI&#x2009;=&#x2009;0.340-0.696, p&#x2009;<&#x2009;0.001) and diarrhea (OR&#x2009;=&#x2009;0.480, 95% CI&#x2009;=&#x2009;0.338-0.682, p&#x2009;<&#x2009;0.001). RCS analysis indicated a significant linear association between the DI-GM and the risks of both constipation (nonlinear p&#x2009;=&#x2009;0.686) and diarrhea (nonlinear p&#x2009;=&#x2009;0.136).<br><br>CONCLUSIONS: The DI-GM was negatively associated with the prevalence of abnormal bowel symptoms. Further longitudinal studies are warranted to confirm these findings and to inform dietary strategies for gut health.},
}
@article {pmid40447921,
year = {2025},
author = {Xin, T and Pan, Q and Li, J and Zhang, J and Lin, L and Choi, K and Cai, W and Lu, S and Zhang, J},
title = {Fungal Infections in Transplant Recipients Pre- and Post-coronavirus Disease 2019: Results from a Single-Center Retrospective Cohort Study.},
journal = {Mycopathologia},
volume = {190},
number = {3},
pages = {47},
pmid = {40447921},
issn = {1573-0832},
support = {2024A1515013091//Basic and Applied Basic Research Foundation of Guangdong Province/ ; },
mesh = {Humans ; *COVID-19/complications/epidemiology ; Retrospective Studies ; Female ; Male ; *Transplant Recipients/statistics &amp; numerical data ; Middle Aged ; Adult ; *Mycoses/epidemiology/drug therapy/microbiology ; Incidence ; Aged ; SARS-CoV-2 ; Antifungal Agents/therapeutic use ; Young Adult ; },
abstract = {OBJECTIVES: To investigate the incidence, subtypes, and pathogens of fungal infections in transplant recipients pre- and post-coronavirus disease 2019 (COVID-19) and their prognosis.<br><br>METHODS: Data from transplant recipients with fungal infections treated at our hospital between January 2005 and April 2024 were collected. Pre- and post-COVID-19 data were compared.<br><br>RESULTS: Among 3,505 transplant recipients, 203 had fungal infections, mostly in hematopoietic stem cell recipients (178 cases, 8.4%). The pre-COVID-19 incidence of fungal infections was 5.0%, with a median time from transplantation to infection of 96.5&#xa0;days. The post-COVID-19 incidence was 6.3%, with a median time of 92.5&#xa0;days. Before the COVID-19 outbreak, invasive fungal infections were predominant, with Candida as the outbreak, Candida, Aspergillus, Pneumocystis jirovecii, and mixed infections became more common. In addition to the oral cavity and lungs, infection sites following the COVID-19 outbreak also included the skin, blood, and intestinal tract. Twenty-six patients were treated with monotherapy, 14 of whom were treated with voriconazole. Voriconazole, sulfamethoxazole, and caspofungin are typically used in combination or sequentially for treatment. At 180&#xa0;days, 1.4% of transplant recipients were aggravated before the outbreak of COVID-19, with a mortality rate of 8.2%. The proportion of exacerbations after the outbreak was 3.1%, with a mortality rate of 6.9%.<br><br>CONCLUSIONS: Post-COVID-19, transplant recipients exhibited increased fungal infection incidence, broader pathogen diversity, and more frequent exacerbations. However, this was not accompanied by an increase in mortality, likely reflect both enhanced clinical surveillance and SARS-CoV-2-specific biological effects, such as immune dysregulation, endothelial damage and microbiome alterations.},
}
@article {pmid40348017,
year = {2025},
author = {Dong, TS and Mayer, E},
title = {Interorgan and Transcellular Communication in Metabolic Disease: Insights from Recent CMGH Studies.},
journal = {Cellular and molecular gastroenterology and hepatology},
volume = {},
number = {},
pages = {101530},
doi = {10.1016/j.jcmgh.2025.101530},
pmid = {40348017},
issn = {2352-345X},
abstract = {The emergence of interorgan and transcellular signaling as a defining hallmark of metabolic disease has catalyzed a paradigm shift in gastroenterology and hepatology. Increasingly, the gut, liver, adipose tissue, immune system, and the nervous system are being understood as nodes in an integrated metabolic network rather than isolated organs. The gut microbiome and its metabolites, enteroendocrine signaling, bile acid regulation, and epithelial barrier functions now occupy center stage in dissecting the pathophysiology not only of gastroenterologic conditions, such as obesity, metabolically associated steatotic liver disease, and cirrhosis, but also of several disorders making up the chronic noncontagious disease epidemic. This paradigm shift is being driven by advances in molecular biology, systems biology, and computational modeling, which have enabled a holistic understanding of how communication between organs orchestrates metabolic homeostasis.[1] Key to this understanding is the realization that local perturbations in 1 organ, such as gut microbial dysbiosis, can have systemic repercussions that affect distant organs, such as the liver or brain.[2][,][3] This has redefined how researchers conceptualize disease progression and therapeutic interventions. Rather than focusing on a single tissue, there is increasing interest in identifying molecular messengers that mediate crosstalk between organ systems, such as microbial metabolites, enteroendocrine peptides, bile acids, and cytokines. In this review, we highlight 4 recent and impactful studies published in Cellular and Molecular Gastroenterology and Hepatology that exemplify these advances. Each study offers a unique window into the mechanisms by which gut-derived signals influence host metabolism and disease states. Together, they deepen the understanding of the complex dialogue between organs and open new avenues for therapeutic exploration. We conclude by discussing the implications of these findings and outlining emerging questions and future directions for the field.},
}
@article {pmid40447887,
year = {2025},
author = {Ono, A and Hayes, CN and Miura, R and Kawaoka, T and Tsuge, M and Oka, S},
title = {Noninvasive prediction of the clinical benefit of immunotherapy in hepatocellular carcinoma.},
journal = {Journal of gastroenterology},
volume = {},
number = {},
pages = {},
pmid = {40447887},
issn = {1435-5922},
abstract = {Long-term survival following a diagnosis of hepatocellular carcinoma (HCC) is greatly diminished when transplantation and surgical resection are ruled out. Fortunately, the advent of immune checkpoint inhibitors (ICIs) has revolutionized the treatment of advanced unresectable HCC (uHCC), prolonging median survival by over a year. T lymphocytes normally eliminate neoplastic cells, but some tumors suppress this response by binding to immune checkpoint receptors. Blocking this interaction via ICIs restores immune-mediated targeting of cancer cells. While ICI-based combination immunotherapy is currently recommended as the first-line systemic therapy for uHCC, the objective radiological response rate remains limited to 20-30%, as not all tumors exploit this mechanism. Consequently, strategies are being explored to modulate the immune microenvironment into a "hot" environment more responsive to ICIs by combining local therapies such as transarterial chemoembolization, ablation, and radiation therapy. Therapeutic options have also expanded beyond ICIs, emphasizing the importance of selecting the most appropriate treatment. Therefore, the development of biomarkers capable of predicting the efficacy of immunotherapy is a priority. Direct evaluation of immune cell infiltration through biopsy is currently the most effective method but involves issues such as invasiveness and susceptibility to sampling bias. In this review, we aim to highlight promising non-invasive biomarkers and scoring systems that have the potential to improve treatment outcomes, including blood-based biomarkers such as lymphocyte ratios, cytokines, C-reactive protein, and alpha-fetoprotein; imaging biomarkers such as MRI, ultrasound, and contrast-enhanced CT; and other clinical indicators such as sarcopenia, grip strength, and diversity of the gut microbiome.},
}
@article {pmid40447846,
year = {2025},
author = {Blaskovich, MAT and Cooper, MA},
title = {Antibiotics re-booted-time to kick back against drug resistance.},
journal = {npj antimicrobials and resistance},
volume = {3},
number = {1},
pages = {47},
pmid = {40447846},
issn = {2731-8745},
abstract = {After decades of neglect and a decline in antibiotic research and development, we are now finally witnessing the advent of new funding programs dedicated to new therapies. In addition to traditional new chemical entities that directly kill or arrest the growth of bacteria, alternative approaches are being identified and advanced towards proof-of-concept trials in the clinic. We briefly review the current pipeline of conventional new antibiotics and highlight in more depth promising alternatives, including potentiators of antibiotic action, bacteriophage, lysins and microbiome modulation. More innovative approaches, such as adaptive and innate immune modulators, CRISPR-Cas and diagnostic guided 'theranostics' are discussed and contrasted. Such exploratory therapies may require the development of alternative regulatory and clinical development pathways, but represent a potential circuit breaker from the current 'arms race' between bacteria and traditional antibiotics.},
}
@article {pmid40447636,
year = {2025},
author = {Krajewski, K},
title = {Heavy metals, noradrenaline/adrenaline ratio, and microbiome-associated hormone precursor metabolites: biomarkers for social behaviour, ADHD symptoms, and executive function in children.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {19006},
pmid = {40447636},
issn = {2045-2322},
mesh = {Humans ; *Attention Deficit Disorder with Hyperactivity/urine/metabolism ; Child ; Male ; Female ; *Metals, Heavy/urine ; Biomarkers/urine ; *Norepinephrine/urine ; *Executive Function ; *Epinephrine/urine ; *Gastrointestinal Microbiome ; *Social Behavior ; },
abstract = {The gut microbiome significantly influences physical and mental health, including the synthesis and metabolism of hormones and the detoxification of heavy metals, which are linked to behavioural disorders. This study investigated the associations of these biological factors with the behaviour of primary school children, specifically examining the effects of heavy metals, catecholamines, and microbiome-associated metabolites of dopamine, noradrenaline, adrenaline, and thyroxine precursors. Urine samples from 87 unselected primary school children were analysed to assess heavy metal load (arsenic, cadmium, lead, mercury), noradrenaline/adrenaline ratio, and microbiome-associated metabolites of phenylalanine, tyrosine and L-dopa (3-phenylpropionic acid, p-OH-phenylacetic acid, 4-hydroxybenzoic acid, 3,4-dihydroxyphenylpropionic acid). Three months later, executive functions, ADHD symptoms (inattention, hyperactivity and impulsivity), and social behaviour were evaluated via parent and teacher questionnaires. In a path model, heavy metal load, microbiome-associated metabolites, and the noradrenaline/adrenaline ratio measured in urine accounted for 32% of social behaviours. Microbiome-associated metabolites predicted 11% of the variance in executive functions and 17% in ADHD symptoms. Executive functions shared 55% of the variance with ADHD symptoms and 17% with social behaviours. Children with the lowest social behaviours had a sixfold increase in the odds of high heavy metal loads and a 3.4-fold increase in the odds of elevated microbiome-associated metabolites. Similarly, children with the most compromised executive functions had a threefold increase in the odds of such high metabolite levels. Overall, the results indicate that children's social behaviours are influenced by heavy metal accumulation, catecholamine balance, and the microbiome-associated metabolism of amino acids, that are crucial for producing stress and thyroid hormones.},
}
@article {pmid40447628,
year = {2025},
author = {Liu, J and Zhang, Y and Li, X and Hou, Z and Wang, B and Chen, L and Chen, M},
title = {Stratified dietary inflammatory potential identifies oral and gut microbiota differences associated with cognitive function in older adults.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {18988},
pmid = {40447628},
issn = {2045-2322},
support = {2023Y9283//Joint Funds for the innovation of science and Technology, Fujian province/ ; 2023CXA004//Medical Innovation Project of Fujian Province/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; Aged ; Male ; Female ; *Cognition/physiology ; Middle Aged ; *Inflammation/microbiology ; *Diet/adverse effects ; RNA, Ribosomal, 16S/genetics ; *Mouth/microbiology ; Aged, 80 and over ; },
abstract = {Diet is a crucial factor that shapes the composition of the microbiota throughout the life cycle. Systemic chronic inflammation and microbial imbalance may play a key role in the pathogenesis of cognitive disorders. Inflammatory diets can influence the host microbiome and inflammatory state. This study investigated the impact of the inflammatory potential of the diet on the diversity and composition of the oral-gut microbiome, as well as on cognitive performance, in older adults over 60 years of age. The Energy-adjusted Dietary Inflammatory Index (E-DII) and 16S rRNA sequencing were used to analyze dietary inflammatory properties and oral-gut microorganisms in 54 patients. The results showed that significant differences in the diversity of oral microbiota among different E-DII groups was detected (p < 0.05), whereas gut microbiota diversity didn't exhibit variations. In the anti-inflammatory diet group, the class Saccharimonadia, the order Corynebacteriaceae, the genera TM7x, Eubacterium_yurii_group, and Centipeda were more abundant in oral microbiomes, and lower abundance of Holdemanella and Haemophilus was observed in the gut microbiomes. Specific oral and gut genera were associated with MMSE, MoCA, AVLT-LR, BNT, and VFT scores (p < 0.05). These results provide insights into anti-inflammatory diets were associated with an increased abundance of beneficial microbes, and a specific oral and gut microbial composition was associated with cognition.},
}
@article {pmid40447622,
year = {2025},
author = {Sayavedra, L and Yasir, M and Goldson, A and Brion, A and Le Gall, G and Moreno-Gonzalez, M and Altera, A and Paxhia, MD and Warren, M and Savva, GM and Turner, AK and Beraza, N and Narbad, A},
title = {Bacterial microcompartments and energy metabolism drive gut colonization by Bilophila wadsworthia.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {5049},
pmid = {40447622},
issn = {2041-1723},
support = {BB/Z514445/10//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; Food Microbiome &amp; Health ISP BB/X011054/1 and its constituent project BBS/E/QU/230001//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; Food Microbiome &amp; Health ISP BB/X011054/1 and its constituent project BBS/E/QU/230001//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; Food Microbiome &amp; Health ISP BB/X011054/1 and its constituent project BBS/E/QU/230001//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; Food Microbiome &amp; Health ISP BB/X011054/1 and its constituent project BBS/E/QU/230001//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; Food Microbiome &amp; Health ISP BB/X011054/1 and its constituent project BBS/E/QU/230001//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; Food Microbiome &amp; Health ISP BB/X011054/1 and its constituent project BBS/E/QU/230001//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; Food Microbiome &amp; Health ISP BB/X011054/1 and its constituent project BBS/E/QU/230001//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; Food Microbiome &amp; Health ISP BB/X011054/1 and its constituent project BBS/E/QU/230001//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; Food Microbiome &amp; Health ISP BB/X011054/1 and its constituent project BBS/E/QU/230001//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; Food Microbiome &amp; Health ISP BB/X011054/1 and its constituent project BBS/E/QU/230001//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; Food Microbiome &amp; Health ISP BB/X011054/1 and its constituent project BBS/E/QU/230001//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; Food Microbiome &amp; Health ISP BB/X011054/1 and its constituent project BBS/E/QU/230001//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; Food Microbiome &amp; Health ISP BB/X011054/1 and its constituent project BBS/E/QU/230001//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; },
mesh = {Animals ; *Energy Metabolism ; Male ; *Gastrointestinal Microbiome/genetics/physiology ; Mice ; Diet, High-Fat/adverse effects ; *Bilophila/genetics/metabolism/growth &amp; development ; Mice, Inbred C57BL ; Ethanol/metabolism ; Taurine/metabolism ; },
abstract = {High-fat diets reshape gut microbiota composition and promote the expansion of Bilophila wadsworthia, a sulfidogenic bacterium linked to inflammation and gut barrier dysfunction. The genetic basis for its colonisation and physiological effects remain poorly understood. Here, we show that B. wadsworthia colonises the gut of germ-free male mice fed a high-fat diet by relying on genes involved in microcompartment formation and anaerobic energy metabolism. Using genome-wide transposon mutagenesis, metatranscriptomics and metabolomics, we identify 34 genes essential for gut colonisation, including two clusters encoding a bacterial microcompartment (BMC), and a NADH dehydrogenase (hdrABC-flxABCD) complex. These systems enable B. wadsworthia to metabolise taurine and isethionate, producing H2S, acetate, and ethanol. We further demonstrate that B. wadsworthia can produce and consume ethanol depending on the available electron donors. While B. wadsworthia reached higher abundance and H2S production in the absence of the simplified microbiota, its co-colonisation with the defined microbial consortium exacerbated host effects, including increased gut permeability, slightly elevated liver ethanol concentrations, and hepatic macrophage infiltration. Our findings reveal how microbial interactions and metabolic flexibility -including using alternative energy sources such as formate- rather than H2S alone, shape B. wadsworthia's impact on host physiology, with implications for understanding diet-driven microbiome-host interactions.},
}
@article {pmid40447393,
year = {2025},
author = {Zuo, J and Chen, J and Wang, J},
title = {Reassessing the role of the gut microbiome in bladder cancer: A review of methodological approaches and future research directions.},
journal = {Urologic oncology},
volume = {43},
number = {7},
pages = {436-437},
doi = {10.1016/j.urolonc.2024.12.268},
pmid = {40447393},
issn = {1873-2496},
}
@article {pmid40447275,
year = {2025},
author = {Odom, AR and Anderson, J and Gill, CJ and Pieciak, R and Ismail, A and MacLeod, WB and Johnson, WE and Lapidot, R},
title = {Longitudinal Analysis of Nasopharyngeal Microbial Risk Markers for Fatal Acute Febrile Illness in a Zambian Birth Cohort.},
journal = {The Journal of infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/infdis/jiaf292},
pmid = {40447275},
issn = {1537-6613},
abstract = {INTRODUCTION: Fatal acute febrile illness (fAFI) is a known predecessor of many infant mortality events in low-resource settings, yet early risk markers for this condition remain poorly understood. Nasopharyngeal (NP) microbiome patterns may influence the severity of these infections.<br><br>METHODS: We analyzed longitudinal changes in the NP microbiota of Zambian infants with fAFI onset compared to healthy controls, aiming to identify microbial indicators associated with severe illness outcomes. We conducted a pooled analysis of a longitudinal nested case-control study comprised of 26 samples from 9 infants who developed fAFI compared with 69 samples from 10 healthy infants. Infants underwent nasopharyngeal sampling from 1 week through 14 weeks of age at 2-2.5-week intervals. We performed 16S rRNA gene amplicon sequencing on all infant nasopharyngeal (NP) samples and characterized NP microbiome maturation among infants with febrile acute febrile illness (fAFI(+)) and healthy controls (fAFI(-)).<br><br>RESULTS: Beta diversity measures of fAFI(-) infants were markedly higher than those of fAFI(+) infants. The fAFI(+) infant NP microbiome was marked by lower abundances of Dolosigranulum, Haemophilus, Streptococcus, and Corynebacterium, with higher relative presence of Pseudomonas.<br><br>CONCLUSIONS: Our findings suggest that specific microbial community patterns and early NP microbiome dysbiosis may be associated with increased illness risk. These findings can motivate further studies to inform foundational markers for fAFI in infants, contributing to precision pediatric care.},
}
@article {pmid40447159,
year = {2025},
author = {Jeong, SH and Vasavada, SP and Lashner, B and Werneburg, GT},
title = {Fecal microbiota transplant is associated with resolution of recurrent urinary tract infection.},
journal = {Urology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.urology.2025.05.052},
pmid = {40447159},
issn = {1527-9995},
abstract = {OBJECTIVE: To investigate the association of fecal microbiota transplant (FMT) therapy, an effective treatment for recurrent C. difficile colitis, with resolution of recurrent UTI (rUTI).<br><br>METHODS: A prospectively accrued database of patients who underwent FMT for recurrent Clostridoides difficile colitis was retrospectively reviewed for individuals with rUTI in the two years prior to FMT. Recurrent UTI status (defined as two UTI episodes in six months or three UTI episodes in one year) and UTI frequency in the two years prior to the FMT were compared to those in the two year follow up period after FMT using the two-tailed Wilcoxin matched pairs signed rank test. A p-value <0.05 was considered statistically significant.<br><br>RESULTS: Of 11 patients who had rUTI in the two years preceding FMT, no patient had rUTI over the follow up period following FMT (p=0.001). The average number of UTIs in the two years prior to FMT was 3.7 (range 2-6), and the average number of UTIs in the follow up period was 0.27 (range 0-1) (p=0.001). The Kaplan-Meier estimate, the median time to UTI recurrence, was 19.6 months (95% CI: 15.2 - 23.9). There was no marked difference in antibiotic susceptibility profiles before and after FMT.<br><br>CONCLUSIONS: FMT was associated with resolution of rUTI and reduction in UTI frequency in this cohort. The results of this study support the hypothesis that modulation of the gut microbiome may reduce rUTI risk, and support a clinical trial to further assess the safety and efficacy of FMT for rUTI.},
}
@article {pmid40447085,
year = {2025},
author = {Maughan, L and Koolman, L and Macori, G and Killian, C and Fanning, S and Whyte, P and Bolton, D},
title = {Characterization of bacterial and fungal populations in retail kefirs in Ireland.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2025-26587},
pmid = {40447085},
issn = {1525-3198},
abstract = {Kefir is an increasingly popular dairy- or sugar-based fermented food product. The aim of our study was to investigate the bacterial and fungal communities in 28 retail kefirs including 21 milk kefirs, including 3 thick kefir yogurt and 4 water kefir products. Full-length amplicon nanopore sequencing of both 16S rRNA (for bacteria) and intergenic spacer (for fungi) was undertaken. The diversity within and between groups was analyzed (α and β diversity) and linear discriminant analysis effect size analysis was undertaken to identify biomarkers that differentially characterize the microbial communities associated with different kefir types. The pH, lactic acid concentration, total viable counts (TVC), lactic acid bacteria (LAB), total coliform counts (TCC), and yeast counts were also investigated. The main bacterial genera (and species) were Lactococcus (cremoris) and Streptococcus (thermophilus), and other bacteria such as Lactobacillus (delbrueckii) and Lentilactobacillus (kefiri) were also detected. The fungal populations were mainly composed of Brettanomyces (anomalus), Zygotorulaspora (florentina) and Kazachstania (unispora), but with many different fungal genera/species detected. The pH ranged from 3.1 to 4.7 with a mean of 4.2 ± 0.07 and the lactic acid content ranged from 0.1 to 9 g/L with a mean of 5.6 ± 0.53. In milk kefirs the TVC, LAB, TCC, and yeast counts ranged from 3.1 to 9.1, 3.4 to 9.0, not detected (ND) to 1.6 and ND to 6.5 log10 cfu/mL or cfu/g, respectively. The corresponding counts in water kefirs were 4.1 to 7.3 (TVC), 4.1 to 7.0 (LAB), ND to 1.1 (TCC), and 3.9 to 7.0 (yeast) log10 cfu/mL or cfu/g, respectively. It was concluded that although the 28 retail kefirs analyzed had a rich diversity of bacteria and fungi the bacteriome was dominated by bacteria belonging to the Lactococcus and Streptococcus genera and the main bacterial species were Lactococcus cremoris, Streptococcus thermophiles, Streptococcus suis, Lactobacillus delbrueckii, and Streptococcus sp. HSISS1. The fungal microbiome was dominated by Zygotorulaspora and the most abundant fungal species included Zygotorulaspora florentina, Brettanomyces anomalus, and Kazachstania unispora. To the best of our knowledge, this is the first study in Ireland to use full-length nanopore sequencing to characterize both bacterial and fungal communities in retail kefirs.},
}
@article {pmid40446899,
year = {2025},
author = {Fang, P and Ye, S and Luo, Z and Guo, R and Jiang, Y and Liu, L and Li, S and Xiao, F},
title = {Nanoplastics under the charge effect: Unveiling the potential threats to amphibian (Rana nigromaculata) growth, intestinal damage, and microbial ecology.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {126566},
doi = {10.1016/j.envpol.2025.126566},
pmid = {40446899},
issn = {1873-6424},
abstract = {Nanoplastics (NPs) are a contaminant that may be found in charged forms in the environment, capable of accumulating in aquatic organisms and affecting their health. This study compared the effects of positively charged NPs (PS-NH2, 30nm) and negatively charged NPs (PS-COOH, 30nm) at 6 and 60 mg/L on the growth and development of black-spotted frog tadpoles (Rana nigromaculata), as well as on intestinal damage, and microbial ecology. The results indicated that exposure to both types of NPs significantly reduced the survival rate of tadpoles, while significantly increasing their body weight and body length (p <0.05). Compared to PS-COOH, exposure to PS-NH2 resulted in more adverse intestinal tissue damage and induced more severe intestinal oxidative stress. Furthermore, exposure to PS-NH2 significantly reduced the abundance and diversity of the microbiome associated with gut function and nutrient absorption, indirectly leading to more severe intestinal damage and growth changes. In addition, functional prediction and gene transcription analysis showed that exposure to charged PS-NPs caused changes in genes associated with glycolysis and lipid metabolism, indicating that the glucose-lipid metabolism of tadpoles is impacted. This study demonstrated the growth differences and intestinal toxicity of NPs exposure in tadpoles, explores the potential connections between gut microbiota and glucose-lipid metabolism, and provides new perspectives on the health risks of NPs in amphibians.},
}
@article {pmid40446807,
year = {2025},
author = {Ding, X and Ting, NL and Wong, CC and Huang, P and Jiang, L and Liu, C and Lin, Y and Li, S and Liu, Y and Xie, M and Liu, W and Yuan, K and Wang, L and Zhang, X and Ding, Y and Li, Q and Sun, Y and Miao, Y and Ma, L and Gao, X and Li, W and Wu, WKK and Sung, JJY and Wong, SH and Yu, J},
title = {Bacteroides fragilis promotes chemoresistance in colorectal cancer, and its elimination by phage VA7 restores chemosensitivity.},
journal = {Cell host &amp; microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2025.05.004},
pmid = {40446807},
issn = {1934-6069},
abstract = {Chemoresistance is a main cause of colorectal cancer (CRC) treatment failure. We identified that Bacteroides fragilis is enriched in patients with CRC resistant to chemotherapy in two independent cohorts, and its abundance is associated with poor survival. Consistently, administration of B. fragilis to CRC xenografts and Apc[Min/+]- and AOM/DSS-induced CRC mice all significantly attenuated the antitumor efficacy of 5-FU and OXA. Mechanistically, B. fragilis colonized colon tumors and mediated its effect via its surface protein SusD/RagB binding to the Notch1 receptor in CRC cells, leading to activation of the Notch1 signaling pathway and the induction of epithelial-to-mesenchymal transition (EMT)/stemness to suppress chemotherapy-induced apoptosis. Either deletion of SusD/RagB or blockade of Notch1 signaling abrogated B. fragilis-mediated chemoresistance. Finally, B. fragilis-targeting phage VA7 selectively suppressed B. fragilis and restored chemosensitivity in preclinical CRC mouse models. Our findings have offered insights into the potential of precise gut microbiota manipulation for the clinical management of CRC.},
}
@article {pmid40446806,
year = {2025},
author = {Li, J and Liu, H and Wang, J and Macdonald, CA and Singh, P and Cong, VT and Klein, M and Delgado-Baquerizo, M and Singh, BK},
title = {Drought-induced plant microbiome and metabolic enrichments improve drought resistance.},
journal = {Cell host &amp; microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2025.05.002},
pmid = {40446806},
issn = {1934-6069},
abstract = {Plant-microbiome interactions are crucial in maintaining plant health and productivity under stress; however, little is known about these interactions under drought. Here, using wheat as a model, we combine genomics and culture-dependent methods to investigate the interactions between the soil, root, and rhizosphere microbiomes with rhizosphere metabolomes and plant phenotypes. We find that drought conditions promote microbial colonization in plant microbiomes, enriching Streptomyces coeruleorubidus and Leifsonia shinshuensis, while also increasing 4-oxoproline levels in the rhizosphere, potentially attracting S. coeruleorubidus. Consistently, genes facilitating microbial responses to drought, including the N-terminal acetyltransferase rimJ, are enriched, while S. coeruleorubidus and L. shinshuensis reintroduction promotes host drought resistance. Drought-legacy-effect experiments further support these benefits, with increased plant biomass and yield in the subsequent growth cycle under drought. Collectively, this study informs how drought-induced microbial and metabolite enrichments improve plant adaptation to abiotic stresses, potentially informing development of bio-based tools to mitigate drought effects. VIDEO ABSTRACT.},
}
@article {pmid40446645,
year = {2025},
author = {Toporcerová, S and Badovská, Z and Kriváková, E and Mikulová, V and Mareková, M and Altmäe, S and Rabajdová, M},
title = {Embryo secretome in predicting embryo quality and IVF treatment outcome.},
journal = {Reproductive biomedicine online},
volume = {51},
number = {1},
pages = {104825},
doi = {10.1016/j.rbmo.2025.104825},
pmid = {40446645},
issn = {1472-6491},
abstract = {In IVF treatment, accurate prediction of embryo quality and successful embryo implantation are critical challenges. Recent research has highlighted the importance of the embryo secretome, the collection of molecules secreted by the embryo into the culture medium, in assessing embryo quality as a non-invasive preimplantation testing platform. The secretome plays a role in many essential processes, from gamete maturation to embryonic development. Molecules such as cell-free DNA, mitochondrial DNA and small non-coding RNA, including microRNA and PIWI-interacting RNA, together with the proteome, metabolome, microbiome and extracellular vesicles, have emerged as important players in predicting IVF outcomes. These molecules, present in the culture medium, have shown correlations with embryo viability, ploidy and implantation potential. Nevertheless, extensive validation in larger cohorts and an assessment of the applicability of the identified biomarkers in clinical settings is warranted. This article summarizes the molecular markers analysed in spent embryo culture medium and their potential for assessing embryo quality and predicting success in IVF outcomes.},
}
@article {pmid40446472,
year = {2025},
author = {Chen, L and Ahmad, M and Li, J and Li, J and Yang, Z and Hu, C},
title = {Gut microbiota manipulation to mitigate the toxicities of environmental pollutants.},
journal = {Aquatic toxicology (Amsterdam, Netherlands)},
volume = {285},
number = {},
pages = {107425},
doi = {10.1016/j.aquatox.2025.107425},
pmid = {40446472},
issn = {1879-1514},
abstract = {The gut microbiome, commonly termed as a "super organ", plays a crucial role in the modulation of various biological functions associated with metabolism, endocrinology, immunology, and neurology. However, gut microbiome is extremely susceptible to the risks of environmental pollutants, which will drive gut microbial community to dysbiosis. Simultaneously, restoring healthy gut microbiome can protect the hosts from the health hazards of pollutants. It is increasingly verified that probiotics, prebiotics, and fecal microbiota transplantation (FMT) are efficacious measures to manipulate and remediate gut microecosystem. Among various probiotic strains, lactic acid bacteria are the most extensively applied in toxicity mitigation, which is characterized by shaping gut microbiota structure and metabolism, increasing gut epithelial barrier integrity, promoting fecal elimination of pollutants, suppressing inflammation symptoms, and then improving host systemic physiology. Prebiotics are dietary fibers that cannot be digested by the host, but can be fermented by specific gut bacteria to produce short chain fatty acids, which are identified as the key effect molecules in the manifestation of prebiotic toxicity mitigation actions. In addition, by transplanting the entire community of healthy gut microbiota, FMT also shows effective performances in counteracting the adverse effects of environmental pollutants and recovering host animal health. Intriguingly, FMT from young donors is even found to inhibit the toxic disturbances in healthy aging progression. Based on current evidence, this review summarized the findings about using probiotics, prebiotics, and FMT to manipulate gut microbiota and alleviate the health impairment of environmental pollutants. Key mechanistic insights into the interactive behaviors were underlined. Furthermore, the challenges and future directions in harnessing gut microbiota manipulation as a novel therapeutic approach to mitigate pollutant-induced toxicities were postulated. This review is expected to advocate comprehensive scientific research and literally favor the application of health intervention strategies.},
}
@article {pmid40446444,
year = {2025},
author = {Eveleens Maarse, BC and Hofstede, AD and Jansen, MAA and Moerland, M},
title = {A systematic review of pharmaceutical targets in the mucosal immune system for treatment of non-intestinal auto-immune diseases.},
journal = {Biomedicine &amp; pharmacotherapy = Biomedecine &amp; pharmacotherapie},
volume = {188},
number = {},
pages = {118205},
doi = {10.1016/j.biopha.2025.118205},
pmid = {40446444},
issn = {1950-6007},
abstract = {The mucosal immune system entails the immune cells located in the body's mucosal surfaces and their mediators. Its function is to balance immune responses to pathogens and tolerance to harmless antigens. Treatment of autoimmune diseases is complicated by adverse events caused by suppression of systemic immunity by immunosuppressive medication. Targeting the mucosal immune system specifically in treating autoimmune diseases could circumvent systemic immune suppression and thereby reduce infection risk. This systematic review aims to provide an overview of pharmaceutical targets in the mucosal immune system, as a starting point in the search for new treatments for extra-intestinal auto-immune diseases. Preclinical and clinical studies were included and categorized into eight target categories: 'immune cells', 'signal transduction', 'inflammatory mediators', 'antibodies', 'microbiome', 'tolerance and mucosal vaccination', 'intestinal barrier' and 'other'. Studies investigating the most promising targets, namely mucosal-associated invariant T cells (MAIT cells) and tolerance induction by mucosal vaccination, are described in more detail. MAIT cells have been shown to play a role in the pathophysiology of various auto-immune diseases, particularly in multiple sclerosis (MS). Although the role of these cells has not yet been established fully, mouse studies show that the antagonism of MAIT cells has the potential to be used in the treatment of auto-immune diseases. Mucosal vaccination has demonstrable effects on the immune system, but treatment regimens and antigens must be improved to demonstrate clinical effects more extensively. This systematic review was registered in PROSPERO under number CRD42023421093.},
}
@article {pmid40446379,
year = {2025},
author = {Jiang, G and Ruan, Z and Yin, Y and Hu, C and Tian, L and Lu, JN and Wang, S and Tang, YT and Qiu, R and Chao, Y},
title = {Keystone species in microbial communities: From discovery to soil heavy metal-remediation.},
journal = {Journal of hazardous materials},
volume = {494},
number = {},
pages = {138753},
doi = {10.1016/j.jhazmat.2025.138753},
pmid = {40446379},
issn = {1873-3336},
abstract = {Keystone species have significant impacts on community structure and function regardless of their abundance in space and time, whether individually or collectively. They play a unique and crucial role, and their removal can lead to substantial changes in the microbiome. It is one of the necessary processes to explore key microbial functions and interactions by studying keystone species. The term "keystone species" has been proposed and developed for nearly 60 years, but in microbiology, it is often used interchangeably with similar terms, which hinders the integration and advancement of research. Here, we review similar terms for keystone species in the microbial field and suggest using "keystone species" instead of "keystone taxa". We also summarize and analyze identification approaches for keystone species, highlighting the advantages and disadvantages of each while providing recommendations for selecting appropriate approaches in the environmental field. Based on the serious soil environment problem, this review also takes the research in the field of heavy metal-contaminated soils as case studies, and summarizes and analyzes the research situation of keystone species. Finally, we discuss the current limitations in research on keystone species, offering insights into their future development and application in the microbial field, particularly in remediation for heavy metal-contaminated soils. This review aims to summarize existing research on microbial keystone species and connect the findings to the field of environmental remediation, providing a reference for developing more effective remediation strategies and enhancing our understanding of ecosystem health.},
}
@article {pmid40446358,
year = {2025},
author = {Porcari, S and Ng, SC and Zitvogel, L and Sokol, H and Weersma, RK and Elinav, E and Gasbarrini, A and Cammarota, G and Tilg, H and Ianiro, G},
title = {The microbiome for clinicians.},
journal = {Cell},
volume = {188},
number = {11},
pages = {2836-2844},
doi = {10.1016/j.cell.2025.04.016},
pmid = {40446358},
issn = {1097-4172},
mesh = {Humans ; *Microbiota ; Clinical Trials as Topic ; },
abstract = {Despite promising evidence in diagnostics and therapeutics, microbiome research is not yet implemented into clinical medicine. Several initiatives, including the standardization of microbiome research, the refinement of microbiome clinical trial design, and the development of communication between microbiome researchers and clinicians, are crucial to move microbiome science toward clinical practice.},
}
@article {pmid40446105,
year = {2025},
author = {Saxena, V and Datla, A and Pradhan, P and Deheriya, M and Tiwari, N and Shoukath, S},
title = {Impact of smokeless and smoking tobacco on subgingival microbial composition: A comparative study.},
journal = {Przeglad epidemiologiczny},
volume = {79},
number = {1},
pages = {95-103},
doi = {10.32394/pe/203721},
pmid = {40446105},
issn = {0033-2100},
mesh = {Humans ; Female ; Male ; Adult ; *Tobacco, Smokeless/adverse effects ; Cross-Sectional Studies ; India/epidemiology ; Middle Aged ; *Gingiva/microbiology ; *Microbiota ; *Smoking ; },
abstract = {BACKGROUND: Environmental perturbations such as tobacco use causes increased bacterial diversity in the subgingival microbiome. Despite the recognized impact of tobacco on oral health, there is a notable gap in the literature regarding the specific characteristics of the subgingival microbiome among Indian tobacco users.<br><br>OBJECTIVE: This study seeks to provide a comparative analysis of subgingival microbial profile of smokeless tobacco users and smokers with an otherwise healthy periodontal environment.<br><br>MATERIAL AND METHODS: This cross-sectional study at a Tertiary Dental Hospital in India recruited 118 participants: 52 non-tobacco users (Group 1), 36 smokeless tobacco users (Group 2), and 30 smokers (Group 3). Subgingival samples were collected from mesial surfaces of teeth (16, 46) using sterile paper points and analysed via the streak plate method for bacterial profiling. Clinical examinations assessed oral hygiene, gingival, and periodontal health using indices: Bleeding on Probing (BoP), Pocket Depth (PD), and Approximate Plaque Index (API). Categorical variables were analysed using the Chi-square test, and odds ratios were calculated.<br><br>RESULTS: Gender distribution was 76.3% male and 23.7% female (p < 0.05). Group 2 had a significantly higher prevalence of gram-positive cocci (100%) and gram-negative coccobacilli (94.4%) compared to Group 1, with a 12.4 times increased risk for gram-negative coccobacilli (p < 0.05). Group 2 also showed a higher occurrence of Aggregatibacter (88.9%) and a 3.5 times increased risk (p < 0.05). Group 3 exhibited significantly more gram-positive cocci and gram-negative coccobacilli than Group 1, with 3.8 times and 4.7 times increased risks, respectively (p < 0.05). Rothia species were significantly more common in smokers (13.3%) than non-tobacco users (0%) (p < 0.05).<br><br>CONCLUSIONS: Despite the absence of periodontal disease, the elevated presence of Aggregatibacter, Enterococcus, Klebsiella, and Rothia species indicates a shift towards increased bacterial diversity and a higher risk of future periodontitis.},
}
@article {pmid40445957,
year = {2025},
author = {Mhanna, MA and Gauthier, DT and Shollenberger, LM},
title = {Schistosoma mansoni infection causes consistent changes to the fecal bacterial microbiota of mice across and within sites.},
journal = {PloS one},
volume = {20},
number = {5},
pages = {e0324638},
pmid = {40445957},
issn = {1932-6203},
mesh = {Animals ; *Feces/microbiology ; *Schistosomiasis mansoni/microbiology/parasitology ; Mice ; *Schistosoma mansoni ; Female ; *Gastrointestinal Microbiome ; Male ; },
abstract = {Eggs of Schistosoma mansoni are produced by adult female worms in mesenteries of infected hosts. Eggs can cross the intestinal barrier and form granulomas in the tissue or breach and exit the host through fecal excretion. These interactions may affect the host microbiome assemblages. Given the potential for schistosomal alteration of host gut microbiome and subsequent effects on the fecal bacterial composition, it is important to conduct controlled microbiome studies on model animals. While pursuing these studies, it is important to take into account the different conditions in which microbiome studies are conducted and their consequent impacts on variability and reproducibility of results. In particular, we are interested in inter-institutional effects on controlled microbiome studies, in which the study location itself may impact study outcomes. In this work, we report global changes caused by acute and chronic schistosomiasis on the fecal microbiome of mice at two different institutions and three timepoints.},
}
@article {pmid40445867,
year = {2025},
author = {Cai, X and Zhong, L},
title = {Gut microbiome and host interactions in catfish: hybridization structures bacterial communities along catfish intestinal tract.},
journal = {Physiological genomics},
volume = {},
number = {},
pages = {},
doi = {10.1152/physiolgenomics.00058.2025},
pmid = {40445867},
issn = {1531-2267},
support = {CARS-46//China Agriculture Research System of MOF and MARA/ ; },
}
@article {pmid40445430,
year = {2025},
author = {Chen, F and Zhou, Y and Mao, X and Lin, R and Huang, H},
title = {A systematic Mendelian randomized study of the effects of the gut microbiome and immune cells on pancreatic neuroendocrine tumors.},
journal = {Discover oncology},
volume = {16},
number = {1},
pages = {961},
pmid = {40445430},
issn = {2730-6011},
support = {No. 2020J011013//Natural Science Foundation of Fujian Province, China/ ; No. 2023Y9149//Joint Funds for the Innovation of Science and Technology, Fujian province, China/ ; No. 2021-76//Medical Minimally Invasive Center Program of Fujian Province and National Key Clinical Specialty Discipline Construction Program, China/ ; },
abstract = {Pancreatic neuroendocrine tumors (pNETs) are a rare subset of pancreatic cancers often diagnosed late and characterized by complex behaviors. Recent evidence suggests the gut microbiome (GM) significantly influences various diseases by modulating the immune system. This study utilized a Mendelian randomization (MR) approach to investigate the causal relationship between GM and pNETs, using single nucleotide polymorphism data as instrumental variables. Two-sample MR analysis identified significant correlations between GM and immune cell types. The study found eight specific GMs affecting pNETs risk: the family Sutterellaceae (OR: 1.52, 95% CI 1.10-2.10, p = 0.01), the genus Paraprevotella (OR: 1.34, 95% CI 1.05-1.72, p = 0.02), the species Paraprevotella unclassified (OR: 1.40, 95% CI 1.08-1.81, p = 0.01), and the species Ruminococcus torques (OR: 1.45, 95% CI 1.12-1.89, p = 0.01) increased risk, while the class Gammaproteobacteria (OR: 0.75, 95% CI 0.57-0.98, p = 0.04), the family Acidaminococcaceae (OR: 0.70, 95% CI 0.52-0.94, p = 0.02), the species Paraprevotella xylaniphila (OR: 0.72, 95% CI 0.54-0.96, p = 0.03), and the species Bacteroides finegoldii (OR: 0.68, 95% CI 0.51-0.91, p = 0.01) decreased it. Mediation analysis indicated the species Ruminococcus torques mediated the effect of CD25 on CD45RA+ CD4 non-regulatory T cells on pNETs, accounting for 3.6% of the total effect. This study provides evidence suggestive of a potential causal role of specific GM compositions in pNETs progression and their mediation through immune cell signatures. However, mechanistic studies are required to further validate this relationship.},
}
@article {pmid40445204,
year = {2025},
author = {Schaible, GA and Cliff, JB and Crandall, JA and Bougoure, JJ and Mathuri, MN and Sessions, AL and Atwood, J and Hatzenpichler, R},
title = {Comparing Raman and NanoSIMS for heavy water labeling of single cells.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0165924},
doi = {10.1128/spectrum.01659-24},
pmid = {40445204},
issn = {2165-0497},
abstract = {Stable isotope probing (SIP) experiments in conjunction with Raman microspectroscopy (Raman) or nano-scale secondary ion mass spectrometry (NanoSIMS) are frequently used to explore single cell metabolic activity in pure cultures as well as complex microbiomes. Despite the increasing popularity of these techniques, the comparability of isotope incorporation measurements using both Raman and NanoSIMS directly on the same cell remains largely unexplored. This knowledge gap creates uncertainty about the consistency of single-cell SIP data obtained independently from each method. Here, we conducted a comparative analysis of 543 Escherichia coli cells grown in M9 minimal medium in the absence or presence of heavy water ([2]H2O) using correlative Raman and NanoSIMS measurements to quantify the results between the two approaches. We demonstrate that Raman and NanoSIMS yield highly comparable measurements of [2]H incorporation, with varying degrees of similarity based on the mass ratios analyzed using NanoSIMS. The [12]C[2]H/[12]C[1]H and [12]C2[2]H/[12]C2[1]H mass ratios provide targeted measurements of C-H bonds but may suffer from biases and background interference, while the [2]H/[1]H ratio captures all hydrogen with lower detection limits, making it suitable for applications requiring comprehensive [2]H quantification. Importantly, despite its higher mass resolution requirements, the use of C2[2]H/C2[1]H may be a viable alternative to the use of C[2]H/C[1]H due to lower background and higher overall count rates. Furthermore, using an empirical approach in determining Raman wavenumber ranges via the second derivative improved the data equivalency of [2]H quantification between Raman and NanoSIMS, highlighting its potential for enhancing cross-technique comparability. These findings provide a robust framework for leveraging both techniques, enabling informed experimental design and data interpretation. By enhancing cross-technique comparability, this work advances SIP methodologies for investigating microbial metabolism and interactions in diverse systems.IMPORTANCEAccurate and reliable measurements of cellular properties are fundamental to understand the function and activity of microbes. This study addresses to what extent Raman microspectroscopy and nano-scale secondary ion mass spectrometry (NanoSIMS) measurements of single cell anabolic activity can be compared. Here, we study the relationship of the incorporation of a stable isotope ([2]H through incorporation of [2]H2O) as determined by the two techniques and calculate a correlation coefficient to support the use of either technique when analyzing cells incubated with [2]H2O. The ability to discern between the comparative strengths and limitations of these techniques is invaluable in refining experimental protocols, enhancing data comparability between studies, data interpretation, and ultimately advancing the quality and reliability of outcomes in microbiome research.},
}
@article {pmid40445192,
year = {2025},
author = {Mullinax, SR and Darby, AM and Gupta, A and Chan, P and Smith, BR and Unckless, RL},
title = {A suite of selective pressures supports the maintenance of alleles of a Drosophila immune peptide.},
journal = {eLife},
volume = {12},
number = {},
pages = {},
doi = {10.7554/eLife.90638},
pmid = {40445192},
issn = {2050-084X},
support = {AI139154/NH/NIH HHS/United States ; 2330095//National Science Foundation/ ; CMADP COBRE P20-GM103638/NH/NIH HHS/United States ; },
mesh = {Animals ; *Alleles ; Female ; Male ; *Drosophila Proteins/genetics/immunology ; *Selection, Genetic ; Providencia/immunology ; *Drosophila/genetics/immunology/microbiology ; Gastrointestinal Microbiome ; *Drosophila melanogaster/genetics/immunology/microbiology ; *Antimicrobial Peptides/genetics/immunology ; },
abstract = {The innate immune system provides hosts with a crucial first line of defense against pathogens. While immune genes are often among the fastest evolving genes in the genome, in Drosophila, antimicrobial peptides (AMPs) are notable exceptions. Instead, AMPs may be under balancing selection, such that over evolutionary timescales, multiple alleles are maintained in populations. In this study, we focus on the Drosophila AMP Diptericin A, which has a segregating amino acid polymorphism associated with differential survival after infection with the Gram-negative bacteria Providencia rettgeri. Diptericin A also helps control opportunistic gut infections by common Drosophila gut microbes, especially those of Lactobacillus plantarum. In addition to genotypic effects on gut immunity, we also see strong sex-specific effects that are most prominent in flies without functional diptericin A. To further characterize differences in microbiomes between different diptericin genotypes, we used 16S metagenomics to look at the microbiome composition. We used both lab-reared and wild-caught flies for our sequencing and looked at overall composition as well as the differential abundance of individual bacterial families. Overall, we find flies that are homozygous for one allele of diptericin A are better equipped to survive a systemic infection from P. rettgeri, but in general have a shorter lifespans after being fed common gut commensals. Our results suggest a possible mechanism for the maintenance of genetic variation of diptericin A through the complex interactions of sex, systemic immunity, and the maintenance of the gut microbiome.},
}
@article {pmid40444979,
year = {2025},
author = {Axelsson-Olsson, D and Gubonin, N and Israelsson, S and Pinhassi, J},
title = {Experimental assessment of interactions between marine bacteria and model protists: from predator-prey relationships to bacterial-mediated lysis.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0092925},
doi = {10.1128/aem.00929-25},
pmid = {40444979},
issn = {1098-5336},
abstract = {Bacteria in aquatic environments are a principal food source for predatory protists. Whereas interactions between bacteria and protists are recognized to determine the pathogenesis and epidemiology of several human pathogens, few studies have systematically characterized the interactions between specific aquatic bacteria and protists beyond the prey-predator relation. We, therefore, surveyed individual co-cultures between 18 different genome-sequenced marine bacteria with known virulence gene repertoires and three model protist species widely used for assessing bacteria-protist interactions. Strikingly, 10, 5, and 3 bacterial isolates were capable of lysing the protists Acanthamoeba polyphaga, Tetrahymena pyriformis, and Euglena gracilis, respectively. A majority of the bacteria were able to grow and/or maintain viable populations in the presence of viable protists. Some bacteria survived longer with viable protists but not heat-killed protists and were observed in protist vacuoles. In this respect, marine bacteria are similar to several protist-dependent human pathogens, including Legionella. Analyses of growth patterns in low-nutrient media showed that co-cultivation with A. polyphaga allowed one bacterial strain to overcome nutritional stress and obtain active growth. Five isolates depended on viable amoebae to grow, notwithstanding nutrient media status. The remarkable capability of these marine bacteria to survive encounters with, and even actively kill, model predatory protists under laboratory conditions suggests that diverse bacterial defense strategies and virulence mechanisms to access nutrients may be important in shaping microbial interactions. If verified with native marine and freshwater populations, the diversity of interactions uncovered here has implications for understanding ecological and evolutionary consequences of population dynamics in bacteria and protists.IMPORTANCEThe microbiome constitutes the base of food webs in aquatic environments. Its composition partly reflects biotic interactions, where bacteria primarily are considered prey of predatory protists. However, studies that focus on one or a few species have shown that some bacteria have abilities to escape grazing and may even be capable of lysing their protist predators. In this study, we substantially extend these findings by systematically investigating interactions among multiple taxa of both bacteria and protists. Our results show that marine bacteria display a wider and more complex range of interactions with their predators than generally recognized-from growth dependency to protist lysis. Given that such interactions play key roles in the pathogenesis and epidemiology of several human pathogens, our findings imply that bacterial virulence traits can contribute to defining the structure and ecology of aquatic microbiomes.},
}
@article {pmid40444969,
year = {2025},
author = {Xie, J and Kim, T and Liu, Z and Panier, H and Bokoliya, S and Xu, M and Zhou, Y},
title = {Young gut microbiota transplantation improves the metabolic health of old mice.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0160124},
doi = {10.1128/msystems.01601-24},
pmid = {40444969},
issn = {2379-5077},
abstract = {UNLABELLED: The gut microbiota evolves over a lifetime and significantly impacts the aging process. Targeting the gut microbiota represents a novel avenue to delay aging and aging-related physical and mental decline. However, the underlying mechanism by which the microbiota modulates the aging process, particularly age-related physical and behavioral changes is not completely understood. We conducted fecal microbiota transplantation (FMT) from young or old male donor mice to the old male recipients. Old recipients with young microbiota had a higher alpha diversity than the old recipients with old microbiota. Compared to FMT with old microbiota, FMT with young microbiota reduced body weight and prevented fat accumulation in the old recipients. FMT with young microbiota also lowered frailty, increased grip strength, and alleviated depression and anxiety-like behavior in the old recipients. Consistent with observed physical changes, untargeted metabolomic analysis of serum and stools revealed that FMT with young microbiota lowered age-related long-chain fatty acid levels and increased amino acid levels in the old recipients. Bulk RNAseq analysis of the amygdala of the brain showed that FMT with young microbiota downregulated inflammatory pathways and upregulated oxidative phosphorylation in the old recipients. Our results demonstrate that FMT with young microbiota has substantial positive influences on age-related body composition, frailty, and psychological behaviors. These effects are associated with changes in host lipid and amino acid metabolism in the periphery and transcriptional regulation of neuroinflammation and energy utilization in the brain.<br><br>IMPORTANCE: The gut microbiome is a key hallmark of aging. Fecal microbiota transplantation (FMT) using young microbiota represents a novel rejuvenation strategy to delay aging. Our study provides compelling evidence that transplanting microbiota from young mice significantly improved grip strength, frailty, and body composition in aged recipient mice. At the molecular level, FMT improved aging-related metabolic markers in the gut and circulation. Additionally, FMT from young microbiota rejuvenated the amygdala of the aged brain by downregulating inflammatory pathways. This study highlights the importance of metabolic reprogramming via young microbiota FMT in improving physical and metabolic health in elderly recipients.},
}
@article {pmid40444942,
year = {2025},
author = {McClure, R and Rivas-Ubach, A and Hixson, KK and Farris, Y and Garcia, M and Danczak, R and Davison, M and Paurus, VL and Jansson, JK},
title = {Multi-omics of a model bacterial consortium deciphers details of chitin decomposition in soil.},
journal = {mBio},
volume = {},
number = {},
pages = {e0040425},
doi = {10.1128/mbio.00404-25},
pmid = {40444942},
issn = {2150-7511},
abstract = {UNLABELLED: Soil microorganisms interact to carry out decomposition of complex organic carbon and nitrogen compounds, such as chitin, but the high diversity and complexity of the soil microbiome and habitat have posed a challenge to elucidating such interactions. Here, we sought to address this challenge by analysis of a model soil consortium (MSC-2) consisting of eight soil bacterial species. Our aim was to elucidate the specific roles of the member species during chitin metabolism. Samples were collected from MSC-2 incubated in chitin-enriched soil over 3 months. Multi-omics was used to understand how the community composition, transcripts, proteins, and chitin decomposition shifted over time. The data clearly and consistently revealed a temporal shift during chitin decomposition with defined contributions by individual species. A Streptomyces genus member (sp001905665) was a key player in early steps of chitin decomposition, with other MSC-2 members being central in carrying out later steps. These results illustrate how multi-omics applied to a defined consortium untangles the interactions between soil microorganisms.<br><br>IMPORTANCE: Although soil microorganisms carry out decomposition of organic matter in soil, the details are unclear due to the complexity of the soil microbiome and the heterogeneity of the soil habitat. Understanding carbon decomposition is of vital importance to determine how the soil carbon cycle functions. This is especially important with regard to understanding the fertility of soils and their ability to support plant growth. To overcome these challenges, we investigated in considerable detail a model soil community during its decomposition of a typical soil organic molecule-chitin. By using a multi-omics approach, we were able to decipher community interactions during chitin breakdown. This information provides a basis for understanding how more complex soil microbial communities interact in nature.},
}
@article {pmid40444793,
year = {2025},
author = {Seo, B and Lim, MY},
title = {Balancing harm and harmony: Evolutionary dynamics between gut microbiota-derived flagellin and TLR5-mediated host immunity and metabolism.},
journal = {Virulence},
volume = {16},
number = {1},
pages = {2512035},
doi = {10.1080/21505594.2025.2512035},
pmid = {40444793},
issn = {2150-5608},
mesh = {*Flagellin/immunology/genetics/metabolism/chemistry ; *Toll-Like Receptor 5/immunology/metabolism ; *Gastrointestinal Microbiome/immunology ; Humans ; Animals ; Immunity, Innate ; Adaptive Immunity ; Host Microbial Interactions/immunology ; Evolution, Molecular ; Bacteria/immunology/genetics ; },
abstract = {The gut microbiota maintains host health and shapes immune responses through intricate host-microbe interactions. Bacterial flagellin, a key microbe-associated molecular pattern, is recognized by Toll-like receptor 5 (TLR5) and NOD-like receptor family caspase activation and recruitment domain-containing 4 inflammasome. This dual recognition maintains the delicate balance between immune tolerance and activation, thereby influencing health and disease outcomes. Therefore, we explored the structural and functional evolution of bacterial flagellin to elucidate its role in innate and adaptive immune responses, along with its impact on metabolic processes, particularly via TLR5. In this review, we highlight the diagnostic and therapeutic potential of flagellin, including its application in vaccine development, cancer immunotherapy, and microbiome-based therapies. We integrated perspectives from structural biology, immunology, and microbiome research to elucidate the co-evolutionary dynamics between gut microbiota-derived flagellin and host immunity. Our interpretations provide a basis for the development of innovative strategies to improve health and disease management.},
}
@article {pmid40444642,
year = {2025},
author = {Unger, K and Agler, MT},
title = {Beyond defense: microbial modifications of plant specialized metabolites alter and expand their ecological functions.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.70254},
pmid = {40444642},
issn = {1469-8137},
support = {//Carl-Zeiss-Stiftung/ ; 458884166//Deutsche Forschungsgemeinschaft/ ; EXC 2051, project number 390713860//Deutsche Forschungsgemeinschaft/ ; },
abstract = {Plant specialized metabolites (PSMs) are compounds that are not involved in primary metabolism but instead confer other roles for the plant host, often related to ecological interactions. In the field of plant-microbe interactions, many PSMs have traditionally been considered for their roles in shaping interactions with pathogens. However, it is increasingly clear that 'defensive' PSMs have broader functions in regulating assembly and functions of plant-associated microbes, a phenomenon that is best studied in the rhizosphere. PSMs, however, are secreted throughout plants to mediate interactions with the environment. In this Tansley insight, we argue that these molecules also play outsize roles in shaping microbial community assembly and functions in the phyllosphere. Additionally, we argue that it is important to consider how microbial activity transforms PSMs, because this may shape how plants interact with the environment. Increased attention to these effects and improved strategies to understand them across scales will lead to insights into how microbial responses to PSMs shape broader plant interactions in the environment.},
}
@article {pmid40444400,
year = {2025},
author = {Burdon, I and Bouras, G and Fenix, K and Yeo, K and Connell, J and Cooksley, C and Barry, E and Vreugde, S and Wormald, PJ and Psaltis, AJ},
title = {Metagenomics or Metataxonomics: Best Practice Methods to Uncover the Sinus Microbiome.},
journal = {International forum of allergy &amp; rhinology},
volume = {},
number = {},
pages = {e23617},
doi = {10.1002/alr.23617},
pmid = {40444400},
issn = {2042-6984},
support = {//Garnett Passe and Rodney Williams Memorial Foundation/ ; APP1196832//National Health and Medical Research Council/ ; },
}
@article {pmid40444264,
year = {2025},
author = {Dalton, KR and Chang, VC and Lee, M and Maki, K and Saint-Maurice, P and Purandare, V and Hua, X and Wan, Y and Dagnall, CL and Jones, K and Hicks, BD and Hutchinson, A and Liao, LM and Gail, MH and Shi, J and Sinha, R and Abnet, CC and London, SJ and Vogtmann, E},
title = {Sleep duration associated with altered oral microbiome diversity and composition in the NIH AARP cohort.},
journal = {Sleep advances : a journal of the Sleep Research Society},
volume = {6},
number = {2},
pages = {zpaf023},
pmid = {40444264},
issn = {2632-5012},
abstract = {STUDY OBJECTIVES: The microbiome is proposed as a contributor to the adverse health impacts from altered sleep. The oral microbiome is a multifaceted microbial community that influences many health functions. However, data on the relationship between sleep and the oral microbiome are limited, and no studies have incorporated lifestyle and environmental exposures.<br><br>METHODS: Within a subset (N=1,139) of the NIH-AARP cohort, we examined the association between self-reported sleep duration and the oral microbiome via 16S rRNA gene amplicon sequencing. Statistical models were adjusted for demographic characteristics. Additional models examined the role of various lifestyle and neighborhood exposures on the sleep-oral microbiome association.<br><br>RESULTS: Compared to participants reporting the recommended 7-8 hours average sleep duration (n=702), those reporting short sleep (6 or fewer hours, n=284) had consistently decreased within-sample oral microbial diversity [e.g. number of observed amplicon sequence variants&#xa0;difference -8.681, p-value=0.009]. Several bacterial genera were more likely to be absent in the short sleep group. We found a higher relative abundance of Streptococcus and Rothia, and lower abundance of Fusobacterium, Atopobium, and Campylobacter in the short compared to the recommended sleep duration group. Results were consistent when controlling for lifestyle and neighborhood factors.<br><br>CONCLUSIONS: Our findings provide evidence for an association of short sleep duration with oral microbial diversity and composition. This suggests that oral bacteria may play a possible mechanistic role related to sleep health. Improved understanding of physiological pathways can aid in the design of interventions that may beneficially improve overall sleep health.},
}
@article {pmid40444051,
year = {2025},
author = {Yang, SF and Chen, XC and Pan, YJ},
title = {Microbiota-derived metabolites in tumorigenesis: mechanistic insights and therapeutic implications.},
journal = {Frontiers in pharmacology},
volume = {16},
number = {},
pages = {1598009},
pmid = {40444051},
issn = {1663-9812},
abstract = {Intestinal microbiota is a complex ecosystem of microorganisms that perform diverse metabolic activities to maintain gastrointestinal homeostasis. These microorganisms provide energy and nutrients for growth and reproduction while producing numerous metabolites including lipopolysaccharides (LPS), Bacteroides fragilis toxin (BFT), bile acids (BAs), polyamines (PAs), and short-chain fatty acids (SCFAs). These metabolites are linked to inflammation and various metabolic diseases, such as obesity, type-2 diabetes, non-alcoholic fatty liver disease, cardiometabolic disease, and malnutrition. In addition, they may contribute to tumorigenesis. Evidence suggests that these microbes can increase the susceptibility to certain cancers and affect treatment responses. In this review, we discuss the current knowledge on how the gut microbiome and its metabolites influence tumorigenesis, highlighting the potential molecular mechanisms and prospects for basic and translational research in this emerging field.},
}
@article {pmid40444006,
year = {2025},
author = {Yuan, H and Zhou, J and Wu, X and Wang, S and Park, S},
title = {Enterotype-stratified gut microbial signatures in MASLD and cirrhosis based on integrated microbiome data.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1568672},
pmid = {40444006},
issn = {1664-302X},
abstract = {INTRODUCTION: Metabolic dysfunction-associated steatotic liver disease (MASLD) is a growing global health challenge, characterized by significant variability in progression and clinical outcomes. While the gut microbiome is increasingly recognized as a key factor in liver disease development, its role in disease progression and associated mechanisms remains unclear. This study systematically investigated the gut microbiota's role in MASLD and liver cirrhosis progression, focusing on individual bacterial strains, microbial community dynamics, and functional characteristics across different enterotypes.<br><br>METHODS: Publicly available next-generation sequencing(NGS) datasets from healthy individuals and patients with MASLD and cirrhosis were analyzed. Enterotype classification was performed using principal component analysis, with advanced bioinformatics tools, including Linear Discriminant Analysis Effect Size (LEfSe), eXtreme Gradient Boosting (XGBoost), and Deep Cross-Fusion Networks for Genome-Scale Identification of Pathogens (DCiPatho), to identify differentially abundant microbes and potential pathogens. Microbial co-occurrence networks and functional predictions via PICRUSt2 revealed distinct patterns across enterotypes.<br><br>RESULTS AND DISCUSSION: The Prevotella-dominated(ET-P) group exhibited a 33% higher cirrhosis rate than the Bacteroides-dominated(ET-B) group. Unique microbial signatures were identified: Escherichia albertii and Veillonella nakazawae were associated with cirrhosis in ET-B, while Prevotella copri was linked to MASLD. In ET-P, Prevotella hominis and Clostridium saudiense were significantly associated with cirrhosis. Functional analysis revealed reduced biosynthesis of fatty acids, proteins, and short-chain fatty acids (SCFAs), coupled with increased lipopolysaccharide(LPS) production and altered secondary bile acid metabolism in MASLD and cirrhosis patients. There were significant microbial and functional differences across enterotypes in MASLD and cirrhosis progression, providing critical insights for developing personalized microbiome-targeted interventions to mitigate liver disease progression.},
}
@article {pmid40444003,
year = {2025},
author = {Guo, Y and Sun, S and Wang, Y and Chen, S and Kou, Z and Yuan, P and Han, W and Yu, X},
title = {Microbial dysbiosis in obstructive sleep apnea: a systematic review and meta-analysis.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1572637},
pmid = {40444003},
issn = {1664-302X},
abstract = {BACKGROUND: The association between the microbiota and obstructive sleep apnea (OSA) remains understudied. In this study, we conducted a comprehensive systematic review and meta-analysis of studies investigating the diversity and relative abundance of microbiota in the gut, respiratory tracts and oral cavity of patients with OSA, aiming to provide an in-depth characterization of the microbial communities associated with OSA.<br><br>METHODS: A comprehensive literature search across PubMed, the Cochrane Library, Web of Science, and Embase databases were conducted to include studies published prior to Dec 2024 that compared the gut, respiratory and oral microbiota between individuals with and without OSA. The findings regarding alpha-diversity, beta-diversity, and relative abundance of microbiota extracted from the included studies were summarized. This meta-analysis was conducted in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines, and the study protocol was registered with PROSPERO (CRD42024525114).<br><br>RESULTS: We identified a total of 753 articles, out of which 27 studies were ultimately included in the systematic review, involving 1,381 patients with OSA and 692 non-OSA populations, including 1,215 OSA patients and 537 non-OSA populations in adults and 166 OSA patients and 155 non-OSA populations in children. The results of alpha diversity revealed a reduction in the Chao1 index (SMD&#x202f;=&#x202f;-0.40, 95% CI&#x202f;=&#x202f;-0.76 to -0.05), Observed species (SMD&#x202f;=&#x202f;-0.50, 95% CI&#x202f;=&#x202f;-0.89 to -0.12) and Shannon index (SMD&#x202f;=&#x202f;-0.27, 95% CI&#x202f;=&#x202f;-0.47 to -0.08) of the gut microbiota in patients with OSA. Beta diversity analysis indicated significant differences in the gut, respiratory and oral microbial community structure between individuals with OSA and those without in more than half of the included studies. Furthermore, in comparison to the non-OSA individuals, the gut environment of patients with OSA exhibited an increased relative abundance of phylum Firmicutes, along with elevated levels of genera Lachnospira; conversely, there was a decreased relative abundance of phylum Bacteroidetes and genus Ruminococcus and Faecalibacterium. Similarly, within the oral environment of OSA patients, there was an elevated relative abundance of phylum Actinobacteria and genera Neisseria, Rothia, and Actinomyces.<br><br>CONCLUSION: Patients with OSA exhibit reduced diversity, changes in bacterial abundance, and altered structure in the microbiota, especially in the gut microbiota. The results of this study provide basic evidence for further exploration of microbiome diagnostic markers and potential intervention strategies for OSA.},
}
@article {pmid40444002,
year = {2025},
author = {Shao, Q and Zhou, S and Li, Y and Jin, L and Fu, X and Liu, T and Wang, J and Du, S and Chen, C},
title = {The effects of a semen cuscutae flavonoids-based antidepressant treatment on microbiome and metabolome in mice.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1558833},
pmid = {40444002},
issn = {1664-302X},
abstract = {BACKGROUND: Depression is a prevalent psychiatric disorder and one of the leading causes of disability worldwide. Previous studies have shown that Semen Cuscutae flavonoids (SCFs) exert antidepressant effects by modulating the microbiota-neuroinflammation axis and ameliorating hippocampal metabolic disturbances. However, the impact of SCFs on gut microbiota and related metabolomics remains largely undefined. Given that the gut microbiota has been proven to play a significant role in the etiology of depression and serves as a promising target for its treatment in humans, this study aims to elucidate the antidepressant effects of SCFs and to investigate how they modulate microbial and metabolic pathways to alleviate depressive symptoms.<br><br>MATERIALS AND METHODS: Chronic unpredictable mild stress (CUMS)-induced mice were used as a depression model. The normal mice and CUMS-induced mice were treated with either vehicle or with SCFs. A range of standardized behavioral assays and physiological indicators were employed to evaluate the antidepressant effects of SCFs. Upon the confirmation of the effectiveness of the SCFs treatment, the composition, richness, and diversity of the fecal microbiota were assessed using 16S rRNA gene sequencing. Additionally, fecal metabolic profiling was analyzed using UHPLC-MS/MS-based metabolomics. Multivariate data analysis was subsequently performed to identify differential metabolites and characterize alterations in fecal metabolites. Furthermore, a correlation analysis between differential metabolites and key microbiota was conducted.<br><br>RESULTS: SCFs significantly ameliorated depressive behaviors and the dysregulated diversity of fecal microbiota induced by CUMS. SCFs enhanced the gut microbiota structure in the CUMS group by increasing the Firmicutes/Bacteroidota ratio, significantly elevating the abundance of Firmicutes, Lactobacillus, Limosilactobacillus, and Actinobacteria while reducing the abundance of Bacteroidota and Bacteroides in CUMS-treated mice. Fecal metabolomics analyses revealed that SCFs could modulate metabolic pathways, including aldosterone synthesis and secretion, arachidonic acid metabolism, and primary bile acid biosynthesis.<br><br>CONCLUSIONS: Mice with depression induced by CUMS exhibited disturbances in both their gut microbiota and fecal metabolism. However, SCFs restored the balance of the microbial community and corrected metabolic disturbances in feces, exerting antidepressant effects through a multifaceted mechanism.},
}
@article {pmid40443994,
year = {2025},
author = {Kidangathazhe, A and Amponsah, T and Maji, A and Adams, S and Chettoor, M and Wang, X and Scaria, J},
title = {Synthetic vs. non-synthetic sweeteners: their differential effects on gut microbiome diversity and function.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1531131},
pmid = {40443994},
issn = {1664-302X},
abstract = {The rising use of artificial sweeteners, favored for their zero-calorie content and superior sweetness, necessitates understanding their impact on the gut microbiome. This study examines the effects of five common artificial sweeteners-Acesulfame K, Rebaudioside A, Saccharin, Sucralose, and Xylitol-on gut microbiome diversity using minibioreactor arrays. Fecal samples from three healthy individuals were used to inoculate bioreactors that were subsequently supplemented with each sweetener. Over 35 days, microbial diversity and network composition were analyzed. Results revealed synthetic sweeteners like Sucralose and Saccharin significantly reduced microbial diversity, while non-synthetic sweeteners, particularly Rebaudioside A and Xylitol, were less disruptive. Acesulfame K increased diversity but disrupted network structure, suggesting potential long-term negative impacts on microbiome resilience. Sucralose enriched pathogenic families such as Enterobacteriaceae, whereas natural sweeteners promoted beneficial taxa like Lachnospiraceae. Random Matrix Theory (RMT) based analysis highlighted distinct microbial interaction patterns, with Acesulfame K causing persistent structural changes. Findings suggest non-synthetic sweeteners may be more favorable for gut health than synthetic ones, emphasizing cautious use, particularly for those with gut health concerns. This study enhances our understanding of artificial sweeteners' effects on the gut microbiome, highlighting the need for further research into their long-term health implications.},
}
@article {pmid40443829,
year = {2025},
author = {Bacaloni, S and Agrawal, DK},
title = {Nutrition, Gut Microbiota, and Epigenetics in the Modulation of Immune Response and Metabolic Health.},
journal = {Cardiology and cardiovascular medicine},
volume = {9},
number = {3},
pages = {111-124},
pmid = {40443829},
issn = {2572-9292},
abstract = {Immune system function is intricately shaped by nutritional status, dietary patterns, and gut microbiota composition. Micronutrients such as vitamins A, C, D, E, B-complex, zinc, selenium, iron, and magnesium are critical for maintaining physical barriers, supporting immune cell proliferation, and regulating inflammation. Macronutrients-including proteins, fats, and carbohydrates-also modulate immune responses through their impact on immune metabolism and the gut-immune axis. Epigenetic mechanisms, including DNA methylation, histone modifications, and microRNA expression, mediate the long-term effects of diet on immune function and tolerance. Diet-induced alterations in gut microbiota further influence immune homeostasis via microbial metabolites like short-chain fatty acids. Imbalanced diets, particularly the Western diet, contribute to immune dysregulation, chronic inflammation, and the development of metabolic disorders such as obesity and type 2 diabetes. While plant-based and Mediterranean dietary patterns have shown anti-inflammatory and immunoregulatory benefits, gaps remain in understanding the long-term epigenetic impacts of these diets. This review integrates current knowledge on how nutrition and the microbiome regulate immunity, highlighting future directions for personalized dietary strategies in preventing chronic immune-related conditions.},
}
@article {pmid40443663,
year = {2025},
author = {Teuscher, JL and Lupatsii, M and Graspeuntner, S and Jonassen, S and Bringewatt, A and Herting, E and Stichtenoth, G and Bossung, V and Rupp, J and Härtel, C and Demmert, M},
title = {Persistent reduction of Bifidobacterium longum in the infant gut microbiome in the first year of age following intrapartum penicillin prophylaxis for maternal GBS colonization.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1540979},
pmid = {40443663},
issn = {1664-3224},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; Female ; Infant ; *Antibiotic Prophylaxis ; *Streptococcal Infections/prevention &amp; control/microbiology/immunology ; Infant, Newborn ; Pregnancy ; *Streptococcus agalactiae/drug effects ; *Bifidobacterium longum ; *Penicillins/therapeutic use/administration &amp; dosage ; Feces/microbiology ; Male ; *Anti-Bacterial Agents/therapeutic use ; Infectious Disease Transmission, Vertical/prevention &amp; control ; RNA, Ribosomal, 16S/genetics ; },
abstract = {INTRODUCTION: Group B Streptococcus is a significant cause of early-onset disease in term newborns, with a global incidence of 0.41/1000 live births. Intrapartum antibiotic prophylaxis (IAP) has reduced EOD incidence by over 80%, but concerns exist about its impact on the neonatal gut microbiome and potential long-term health effects.<br><br>METHODS: This single center study examines the effects of IAP on the fecal infant microbiome in the first year of age and on the T cell phenotype in the first days after birth among 22 infants receiving IAP with penicillin due to maternal GBS colonization and 26 infants not exposed to IAP. The fecal microbiome was analyzed at birth, one month and one year of age through 16S rRNA gene sequencing. Additionally, a T cell phenotyping of peripheral blood was performed between the second and fifth day of age.<br><br>RESULTS: At one month, IAP exposed infants had a significantly lower relative abundance of Bifidobacterium longum in fecal samples, an effect which was sustained at one year. In IAP exposed infants we found a proinflammatory T-helper cell profile, characterized by higher IL-17A, RORgt, and TGF-b expression.<br><br>DISCUSSION: This study proposes a sustained impact of IAP on the neonatal microbiome and T cell repertoire.},
}
@article {pmid40443528,
year = {2025},
author = {Zhang, Y and Zhu, H and Fan, J and Zhao, J and Xia, Y and Zhang, N and Xu, H},
title = {A glutamine metabolism gene signature with prognostic and predictive value for colorectal cancer survival and immunotherapy response.},
journal = {Frontiers in molecular biosciences},
volume = {12},
number = {},
pages = {1599141},
pmid = {40443528},
issn = {2296-889X},
abstract = {BACKGROUND: Colorectal cancer (CRC) remains a major cause of cancer mortality, and dysregulated glutamine metabolism has emerged as a potential therapeutic target. However, the precise role of glutamine in CRC progression and treatment response remains debated.<br><br>METHODS: The authors collected transcriptome and microbiome information, from multiple sources to construct the GLMscore, a prognostic signature in CRC. To comprehensively characterize the biological features of GLMscore groups, the integration of transcriptomic profiling, KEGG pathway enrichment analysis, immune infiltration analysis, tumor immune microenvironment characterization, microbiome analysis, and tissue imaging were applied. Furthermore, CRC patients were stratified into GLMscore high and GLMscore low groups. The robustness of GLMscore was validated in both training and validation cohorts, and the predictive value for immunotherapy response was assessed. Finally, single-cell RNA sequencing (scRNA-seq) analysis was conducted to delineate the differences between GLMscore high and GLMscore low groups.<br><br>RESULTS: High GLMscore was associated with elevated expression of pathways related to tumorigenesis, epithelial-mesenchymal transition (EMT), and angiogenesis. Furthermore, high GLMscore patients exhibited an immunosuppressive TME characterized by increased infiltration of M0 and M2 macrophages, reduced overall immune infiltration (supported by ESTIMATE and TIDE scores), and increased expression of immune exclusion and suppression pathways. Analysis of pathological whole-slide images (WSIs) revealed a lack of intratumoral tertiary lymphoid structures (TLSs) in high GLMscore patients. The GLMscore also predicted resistance to common chemotherapeutic agents (using GDSC data) and, importantly, predicted poor response to immunotherapy in the IMvigor210 cohort. Analysis of 16S rRNA gene sequencing data revealed an enrichment of potentially oncogenic microbiota, including Hungatella and Selenomonas, in high GLMscore group. Single-cell analysis further confirmed the immunosuppressive TME and identified increased cell-cell communication between inflammatory macrophages and tumor cells in high GLMscore group.<br><br>CONCLUSION: The authors innovatively constructed GLMscore, a robust scoring system in quantifying CRC patients, exploring the distinct biological features, tumor immune microenvironment and microbiome ecology, exhibiting high validity in predicting survival prognosis and clinical treatment efficacy.},
}
@article {pmid40443227,
year = {2025},
author = {Green, GBH and Cox-Holmes, AN and Marlow, GH and Potier, ACE and Wang, Y and Zhou, L and Chen, D and Morrow, CD and McFarland, BC},
title = {Human microbiota influence the immune cell composition and gene expression in the tumor environment of a murine model of glioma.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2508432},
doi = {10.1080/19490976.2025.2508432},
pmid = {40443227},
issn = {1949-0984},
mesh = {Animals ; *Glioma/immunology/microbiology/genetics ; Mice ; Humans ; *Gastrointestinal Microbiome/immunology ; Disease Models, Animal ; *Tumor Microenvironment/immunology/genetics ; *Brain Neoplasms/immunology/microbiology/genetics ; Cell Line, Tumor ; Feces/microbiology ; Programmed Cell Death 1 Receptor/antagonists &amp; inhibitors/immunology ; RNA, Ribosomal, 16S/genetics ; Bacteria/classification/genetics/isolation &amp; purification ; Mice, Inbred C57BL ; },
abstract = {BACKGROUND: Immunotherapy has shown success against other cancers but not glioblastoma. Previous data has revealed that microbiota influences anti-PD-1 efficacy. We have previously found that, when using gnotobiotic mice transplanted with human fecal microbiota, the gut microbial composition influenced the response to anti-PD-1 in a mouse model of glioma. However, the role of the human microbiota in influencing the mouse immune cells in the glioma microenvironment and anti-PD-1 response was largely unknown. Using two distinct humanized microbiome (HuM) lines, we used single-cell RNA sequencing (scRNA-seq) to determine how gut microbiota affect immune infiltration and gene expression in a murine glioma model.<br><br>METHODS: 16S rRNA sequencing was performed on fecal samples from HuM1 (H1) and HuM2 (H2) mice. Mice were intracranially injected with murine glioma cells (GL261), and on day 13 treated with one dose of isotype control or anti-PD1. Mice were euthanized on day 14 for analysis of all immune cells in the tumors by scRNA-seq.<br><br>RESULTS: HuM1 and HuM2 mice had different microbial populations, with HuM1 being primarily dominated via Alistipes, and HuM2 being primarily composed of Odoribacter. Sc-RNA-seq of the tumor immune cells revealed 21 clusters with significant differences between H1 and H2 samples with a larger population of M1 type macrophages in H1 samples. Gene expression analysis revealed higher expression of inflammatory markers in the M1 population in H2 mice treated with anti-PD-1.<br><br>CONCLUSIONS: Microbial gut communities influence the presence and gene activation patterns of immune cells in the brain tumors of mice both under control (isotype) and following anti-PD-1 treatment.},
}
@article {pmid40443224,
year = {2025},
author = {Kim, DR and Ko, YM and Lee, D and Kwak, YS},
title = {Root Rot Disease Biocontrol and Microbiome Community Modulation by Streptomyces Strains in Soybean.},
journal = {Journal of microbiology and biotechnology},
volume = {35},
number = {},
pages = {e2502010},
doi = {10.4014/jmb.2502.02010},
pmid = {40443224},
issn = {1738-8872},
mesh = {*Glycine max/microbiology ; *Streptomyces/physiology/isolation &amp; purification/classification ; *Plant Diseases/microbiology/prevention &amp; control ; *Microbiota ; *Plant Roots/microbiology ; Fusarium ; Rhizosphere ; Antibiosis ; Soil Microbiology ; Antifungal Agents/pharmacology ; Biological Control Agents ; },
abstract = {Traditionally, phytopathogenic fungi control strategies rely primarily upon chemical fungicides, but fungicide resistance pathogen strains have appeared in the fields. Therefore, biocontrol approaches highlighted with sustainable agriculture aspects, especially the genus Streptomyces, are known to suppress numerous plant diseases. Streptomyces bacillaris S8 was isolated from turfgrass rhizosphere, and Streptomyces globisporus SP6C4 was obtained from strawberry pollen. Both strains showed excellent antifungal and antibacterial activities and suppressed various plant diseases in vitro. However, beneficial microorganisms are rarely studied and introduced to another effect on microbial communities when incompatible with the host. The present study aims to assess the potential of effective control of plant diseases by both strains in new crops and to assess the impact of endogenous microbiota. Various diseases pose significant concerns in soybean production, leading to substantial grain yield and quality losses. Root rot caused by Fusarium spp. is known to be the most problematic disease in the soybean cropping system. In the results, S. globisporus SP6C4 and S. bacillaris S8 showed antifungal activity against soybean root rot pathogen, but strain S8 had less than SP6C4. The strain SP6C4 played a role as hub-taxa in the early stage, and the strain S8 was a modulator in microbial communities. Our results demonstrate the antifungal activity of S. globisporus SP6C4 and S. bacillaris S8, which can be expected to grow and reduce the disease of soybeans. The S8 and SP6C4 can also modify the plant microbiota which may open a new dimension of crop microbiome research.},
}
@article {pmid40443219,
year = {2025},
author = {Kim, J and Ha, J and Kim, S and Kim, G and Shin, H},
title = {Impact of Ginger on Gut Microbiota Composition and Function in a Bacteroides-Dominant Enterotype.},
journal = {Journal of microbiology and biotechnology},
volume = {35},
number = {},
pages = {e2503032},
doi = {10.4014/jmb.2503.03032},
pmid = {40443219},
issn = {1738-8872},
mesh = {*Zingiber officinale/chemistry ; *Gastrointestinal Microbiome/drug effects ; Humans ; Feces/microbiology ; *Bacteroides/classification/isolation &amp; purification/genetics/drug effects ; Bacteria/classification/genetics/isolation &amp; purification ; Male ; Adult ; RNA, Ribosomal, 16S/genetics ; Proteobacteria/classification/isolation &amp; purification/genetics ; Female ; Plant Extracts/pharmacology ; },
abstract = {Ginger (Zingiber officinale) has been used worldwide for centuries, valued for both its culinary applications and potential therapeutic properties. Its bioactive compounds exhibit antioxidant, anti-inflammatory, and metabolic regulatory effects, providing physiological benefits to the human body. However, its influence on the gut microbiota remains poorly understood. In this study, we investigated the impact of ginger on gut microbiota using an in vitro fecal incubation model. To minimize interindividual variability, we classified participants into enterotypes based on gut microbial composition, focusing on the Bacteroides-dominant enterotype. While ginger treatment did not significantly affect microbial alpha diversity, it induced distinct shifts in bacterial structure, suggesting compositional changes in the microbiota. At the phylum level, taxonomic analysis revealed a lower relative abundance of Bacteroidota and a higher relative abundance of Proteobacteria in the ginger-treated group compared to the control. Consistently, genus-level analysis showed an increased relative abundance of Acinetobacter and Enterobacteriaceae, both belonging to Proteobacteria, in the ginger-treated group. Predicted functional pathway analysis further revealed that ginger treatment enriched pathways related to linoleic acid metabolism, beta-alanine metabolism, geraniol degradation, and tetracycline biosynthesis. These findings suggest that ginger modulates gut microbiota composition, particularly by increasing the abundance of Proteobacteria-associated genera. This enterotype-based study provides a structured framework for evaluating dietary effects and may support the development of personalized dietary strategies targeting gut microbiome modulation.},
}
@article {pmid40442920,
year = {2025},
author = {Ordner, J and Narula, N and Chiriboga, L and Zeck, B and Majd, M and Gupta, K and Gaglia, R and Zhou, F and Moreira, A and Iman, R and Ko, JP and Le, L and Wells, RG and Theise, ND},
title = {Continuity of interstitial spaces within and outside the human lung.},
journal = {Journal of anatomy},
volume = {},
number = {},
pages = {},
doi = {10.1111/joa.14280},
pmid = {40442920},
issn = {1469-7580},
abstract = {There is a body-wide network of interstitial spaces that includes three components: a large-scale fascial network made up of fluid-filled spaces containing collagens and other extracellular matrix components like hyaluronic acid (HA), the peri-vascular/capillary interstitium, and intercellular interstitial spaces. Staining for HA within the colon, skin, and liver has demonstrated spatial continuity of the fascial interstitium across tissue layers and between organs, while continuity of HA staining between perineurial and adventitial sheathes beyond organ boundaries confirmed that they also participate in this body-wide network. We asked whether the pulmonary interstitium comprises a continuous organ-wide network that also connects to the body-wide interstitium via routes along nerves and the vasculature. We studied archival lung lobectomy specimens containing normal tissues inclusive of all lung anatomical units from six females and three males (mean age 53+/- 16.5 years). For comparison, we also studied normal mouse lung. Multiplex immunohistochemical cocktails were used to identify: (1) HA, CD34, and vimentin - highlighting interstitium; (2) HA, CD34, and podoplanin (D2-40) - highlighting relationships between the interstitium, vasculature, and lymphatics. Sizes of extracellular APP were measured. Tissues from nine patients (six females, three males, mean age 53+/- 16.5 years) were studied. HA staining was continuous throughout the five major anatomic compartments of the lung: alveolar walls, subpleural connective tissue, centrilobular peribronchovascular compartment, interlobular septal compartment, and axial peribronchovascular of the hilum, with similar findings in murine lung tissue. Continuity with interstitial spaces of the perineurium and adventitia was confirmed. The distribution of APP corresponded to known routes of lymphatic drainage, superficial and deep. APP within perineurium and perivascular adventitia further demonstrated continuity between intra- and extrapulmonary interstitium. To conclude, all segments of the lung interstitium are connected and are linked along nerves and the vascular tree to a body-wide communication network. These findings have significant implications for understanding lung physiology and pathobiology, suggesting routes of passage for inflammatory cells and mediators, malignant cells, and infectious agents. Interstitial spaces may be important in microbiome signaling within and beyond the lung and may be a component of the lung-brain axis.},
}
@article {pmid40442917,
year = {2025},
author = {Fakruddin, M and Amin, T and Shishir, MA and Jameel, RM and Bari, MM and Shameem, NF and Hossain, A and Jerin, N and Bin Mannan, S and Sultana Jime, J and Bulbul, N},
title = {Early-Life Microbiome and Neurodevelopmental Disorders: A Systematic Review and Meta-Analysis.},
journal = {Current neuropharmacology},
volume = {},
number = {},
pages = {},
doi = {10.2174/011570159X360129250508113618},
pmid = {40442917},
issn = {1875-6190},
abstract = {BACKGROUND AND OBJECTIVES: This systematic review intends to find out how neurodevelopmental disorders, including Attention Deficit Hyperactivity Disorder (ADHD) and Autism Spectrum Disorder (ASD), are influenced by the gut microbiota throughout early childhood. The study looks at the variety and types of microbes that a child is exposed to, the particular microbiome profiles associated with neurodevelopmental outcomes, and the molecular processes that underlie these relationships.<br><br>METHODS: We performed a thorough search of PubMed, Scopus, the WHO Global Health Library (GHL), and ISI Web of Science. After screening 2,744 original studies based on predetermined eligibility criteria, 19 studies were included. Microbial groupings, presence (high/low), and related neurodevelopmental disorders were among the primary areas of data extraction. The methodological quality of the studies was assessed using the Newcastle-Ottawa Quality Assessment Scale (NOS).<br><br>RESULTS: The investigated literature repeatedly showed a strong correlation between dysbiosis of the gut microbiota and neurodevelopmental disorders. Cases of ASD were associated with both a high number of Clostridium species and a low number of Bifidobacterium species. On the other hand, a Low number of E. coli and a high number of the class Clostridia, phylum Firmicute, genus Bifidobacterium, and Akkermansia, as well as the species Listeria monocytogenes, Toxoplasma gondii, Streptococcus mutans, and Mycobacterium tuberculosis have been linked to ADHD. The NOS evaluation showed variation in the quality of the methodology; some studies had high scores, suggesting sound technique, while other studies had lower scores, indicating serious methodological flaws.<br><br>CONCLUSION: The results highlight the potential impact of the gut microbiome throughout early life on neurodevelopmental outcomes, indicating that microbial imbalances may play a role in the onset of disorders like ASD and ADHD. However, to improve the quality of data, larger-scale longitudinal studies would be required.},
}
@article {pmid40442807,
year = {2025},
author = {Deng, J and Dai, S and Liu, S and Tu, L and Cui, J and Hu, X and Qiu, X and Lu, H and Jiang, T and Xu, J},
title = {Clinical study of intelligent tongue diagnosis and oral microbiome for classifying TCM syndromes in MASLD.},
journal = {Chinese medicine},
volume = {20},
number = {1},
pages = {78},
pmid = {40442807},
issn = {1749-8546},
support = {82104738//Innovative Research Group Project of the National Natural Science Foundation of China/ ; 2023M732337//China Postdoctoral Science Foundation/ ; ZYYZDXK-2023069//State Administration of Traditional Chinese Medicine of the People's Republic of China/ ; 20244Y0129//Shanghai Municipal Health Commission/ ; 2022509//Intelligence Community Postdoctoral Research Fellowship Program/ ; },
abstract = {BACKGROUND: This study aimed to analyze the tongue image features and oral microbial markers in different TCM syndromes related to metabolic dysfunction-associated steatotic liver disease (MASLD).<br><br>METHODS: This study involved 34 healthy volunteers and 66 MASLD patients [36 with Dampness-Heat (DH) and 30 with Qi-Deficiency (QD) syndrome]. Oral microbiome analysis was conducted through 16S rRNA sequencing. Tongue image feature extraction used the Uncertainty Augmented Context Attention Network (UACANet), while syndrome classification was performed using five different machine learning methods based on tongue features and oral microbiota.<br><br>RESULTS: Significant differences in tongue color, coating, and oral microbiota were noted between DH band QD syndromes in MASLD patients. DH patients exhibited a red-crimson tongue color with a greasy coating and enriched Streptococcus and Rothia on the tongue. In contrast, QD patients displayed a pale tongue with higher abundances of Neisseria, Fusobacterium, Porphyromonas and Haemophilus. Combining tongue image characteristics with oral microbiota differentiated DH and QD syndromes with an AUC of 0.939 and an accuracy of 85%.<br><br>CONCLUSION: This study suggests that tongue characteristics are related to microbial metabolism, and different MASLD syndromes possess distinct biomarkers, supporting syndrome classification.},
}
@article {pmid40442718,
year = {2025},
author = {Pivrncova, E and Bohm, J and Barton, V and Klanova, J and Borilova Linhartova, P},
title = {Viable bacterial communities in freshly pumped human milk and their changes during cold storage conditions.},
journal = {International breastfeeding journal},
volume = {20},
number = {1},
pages = {44},
pmid = {40442718},
issn = {1746-4358},
support = {LM2023069//Ministerstvo &#x160;kolstv&#xed;, Ml&#xe1;de&#x17e;e a T&#x11b;lov&#xfd;chovy/ ; 857560//Horizon 2020 Framework Programme/ ; },
mesh = {Humans ; *Milk, Human/microbiology ; Female ; *Bacteria/isolation &amp; purification/genetics/classification ; *Food Storage/methods ; Adult ; RNA, Ribosomal, 16S ; *Microbiota ; Freezing ; Refrigeration ; Azides ; Propidium/analogs &amp; derivatives ; },
abstract = {BACKGROUND: Human milk harbors diverse bacterial communities that contribute to infant health. Although pumping and storing milk is a common practice, the viable bacterial composition of pumped milk and the impact of storage practice on these bacteria remains under-explored. This metagenomic observational study aimed to characterize viable bacterial communities in freshly pumped human milk and its changes under different storage conditions.<br><br>METHODS: In 2023, twelve lactating mothers from the CELSPAC: TNG cohort (Czech Republic) provided freshly pumped milk samples. These samples were stored under various conditions (refrigeration for 24&#xa0;h, 48&#xa0;h, or freezing for six weeks) and treated with propidium monoazide (PMA) to selectively identify viable cells. The DNA extracted from individual samples was subsequently analyzed using 16S rRNA amplicon sequencing on the Illumina platform.<br><br>RESULTS: The genera Streptococcus, Staphylococcus, Diaphorobacter, Cutibacterium, and Corynebacterium were the most common viable bacteria in fresh human milk. The median sequencing depth and Shannon index of fresh human milk samples treated with PMA (+&#x2009;PMA) were significantly lower than in untreated (-PMA) samples (p&#x2009;<&#x2009;0.05 for all), which was true also for each time point. Also, significant changes in these parameters were observed between fresh human milk samples and their paired frozen samples (p&#x2009;<&#x2009;0.05), while no differences were found between fresh human milk samples and those refrigerated for up to 48&#xa0;h (p&#x2009;>&#x2009;0.05). Of specific genera, only&#x2009;+&#x2009;PMA frozen human milk samples showed a significant decrease in the central log-ratio transformed relative abundances of the genera Diaphorobacter and Cutibacterium (p&#x2009;<&#x2009;0.05) in comparison to&#x2009;+&#x2009;PMA fresh human milk samples.<br><br>CONCLUSIONS: The study demonstrated that the bacterial profiles significantly differed between human milk samples treated with PMA, which represent only viable bacteria, and those untreated. While storage at 4&#xa0;&#xb0;C for up to 48&#xa0;h did not significantly alter the overall diversity and composition of viable bacteria in human milk, freezing notably affected both the viability and relative abundances of some bacterial genera.},
}
@article {pmid40442715,
year = {2025},
author = {Millar, CL and Wolfe, A and Baldyga, K and Dufour, AB and Lipsitz, LA},
title = {Berries and Steps: a protocol of a randomized, placebo-controlled pilot study testing freeze-dried blueberry powder in sedentary older adults with mild depressive symptoms.},
journal = {Nutrition journal},
volume = {24},
number = {1},
pages = {87},
pmid = {40442715},
issn = {1475-2891},
support = {P30AG048785//NIA and Boston Roybal Center/ ; P30AG048785//NIA and Boston Roybal Center/ ; P30AG048785//NIA and Boston Roybal Center/ ; 2022-09412//USDA NIFA/ ; 2022-09412//USDA NIFA/ ; 2022-09412//USDA NIFA/ ; },
mesh = {Humans ; *Blueberry Plants/chemistry ; Pilot Projects ; Aged ; *Sedentary Behavior ; Freeze Drying ; Male ; Female ; Double-Blind Method ; *Fruit/chemistry ; *Depression/diet therapy ; Dietary Supplements ; Powders ; Anthocyanins/administration &amp; dosage ; Dietary Fiber/administration &amp; dosage ; Inflammation ; Motivation ; Middle Aged ; },
abstract = {BACKGROUND: Older adults spend the majority of their day engaging in sedentary behavior, which increases risk of mortality by 22%. Despite the well-established health benefits of physical activity, a large portion of older adults remain sedentary. Recent evidence suggests that inflammation contributes to lack of motivation, which is a critical barrier to overcoming sedentary behavior in older adults. Given that inflammation is highly modifiable by diet, an anti-inflammatory dietary strategy may be a viable way to improve inflammation-driven lack of motivation and ultimately increase physical activity in sedentary older adults. However, interventions targeting such a pathway are scarce. We propose a study intervention protocol, which aims to determine the feasibility and preliminary efficacy of daily supplementation of freeze-dried blueberries. Supplementation with blueberries provides 2 anti-inflammatory nutrients (fiber and anthocyanins) to theoretically reduce inflammation-driven lack of motivation and thereby enhance physical activity in older adults with sedentary behavior and mild depressive symptoms.<br><br>METHODS: The current study is planned as&#xa0;a single-site, randomized, double-blind, parallel pilot study in 40 older adults with sedentary behavior and mild depressive symptoms. Individuals with depressive symptoms often lack motivation and have increased levels of inflammatory cytokines, representing an ideal population for an anti-inflammatory dietary intervention to improve motivation. Participants will be randomized to consume either 48&#xa0;g of freeze-dried blueberry powder (~&#x2009;600&#xa0;mg of anthocyanins and&#x2009;~&#x2009;8&#xa0;g of fiber) or a nutritionally matched placebo powder (without any known amounts of anthocyanins and fiber) each day for a total of 12&#xa0;weeks.<br><br>DISCUSSION: Identification of a dietary intervention to target the inflammatory pathways may offer a novel and feasible approach to increase motivation and engagement of physical activity in older adults. If feasible and effective, such a strategy would help avoid the plethora of health consequences associated with sedentary behavior and physical inactivity.<br><br>TRIAL REGISTRATION: The current study is approved by the Advarra IRB (#Pro00064749) and registered at Clinicaltrials.gov (Identifier: NCT05735587).},
}
@article {pmid40442493,
year = {2025},
author = {Madhan Kumar, S and Natarajan, S and Ks, S and Sundarajan, SK and Natarajan, P and Arockiam, AS},
title = {Dentures and the oral microbiome: Unraveling the hidden impact on edentulous and partially edentulous patients - a systematic review and meta-analysis.},
journal = {Evidence-based dentistry},
volume = {},
number = {},
pages = {},
pmid = {40442493},
issn = {1476-5446},
abstract = {OBJECTIVE: This systematic review and meta-analysis evaluate the impact of edentulism and denture use on the oral microbiome, focusing on microbial diversity, colonization and biofilm formation in completely and partially edentulous patients.<br><br>METHODS: A comprehensive search was conducted across five databases (PubMed-Medline, Scopus, Embase, Lilacs, and Google Scholar) until June 1, 2024. Randomized and non-randomized clinical trials, observational studies, and cohort studies were included. Data extraction and risk of bias assessment followed PRISMA guidelines. Meta-analysis was performed using STATA and R software with a random effects maximum likelihood model. Microbial co-occurrence networks, heatmaps, and longitudinal trends were analyzed, with heterogeneity assessed using Higgin's I&#xb2; (substantial heterogeneity defined as I&#xb2; > 50%).<br><br>RESULTS: Thirty-two studies met the inclusion criteria. The oral microbiome in edentulous patients differed significantly from dentate individuals, influenced by denture materials, design, and time. Veillonella abundance in acrylic complete dentures was 13.63% (95% CI&#x2009;=&#x2009;-0.04, 27.29), I&#xb2;&#x2009;=&#x2009;90.98%, compared to 49.10% (95% CI&#x2009;=&#x2009;-29.62, 115.81), I&#xb2;&#x2009;=&#x2009;99.47% in dentate patients. Candida albicans increased over time in acrylic dentures, from 63.13% (95% CI&#x2009;=&#x2009;48.93, 77.33), I&#xb2;&#x2009;=&#x2009;99.84% after insertion to 344.72 CFU/ml&#x2009;&#xd7;&#x2009;10&#xb2; (95% CI&#x2009;=&#x2009;139.19, 550.24), I&#xb2;&#x2009;=&#x2009;98.30% at nine months. Streptococcus mutans in CAD/CAM dentures increased from 45.54 CFU/ml&#x2009;&#xd7;&#x2009;10&#xb2; (95% CI&#x2009;=&#x2009;33.82, 57.25), I&#xb2;&#x2009;=&#x2009;87.26% at three months to 125.22 CFU/ml&#x2009;&#xd7;&#x2009;10&#xb2; (95% CI&#x2009;=&#x2009;38.25, 212.18), I&#xb2;&#x2009;=&#x2009;97.89% at nine months. Co-occurrence networks revealed strong Candida albicans-Streptococcus mutans synergy, while Fusobacterium nucleatum showed antagonistic interactions. Heatmaps demonstrated microbial dysbiosis in denture stomatitis cases, with increased Porphyromonas gingivalis and Candida albicans and reduced commensals. Longitudinal analyses highlighted the progressive dominance of opportunistic pathogens, emphasizing the need for early and consistent hygiene interventions.<br><br>CONCLUSION: Denture wearers exhibit distinct microbial communities influenced by biofilm formation, denture materials, and hygiene practices. Findings highlight the importance of antimicrobial denture materials and effective cleaning protocols in managing microbial colonization. Given high heterogeneity, standardized methodologies are essential for future research. Frequent professional cleaning and individualized hygiene strategies are necessary to prevent denture-associated infections and maintain oral health.},
}
@article {pmid40442386,
year = {2025},
author = {O'Riordan, KJ and Aburto, MR and Nagpal, J and Clarke, G and Cryan, JF},
title = {Microbiome: A Key Regulator of Body-Brain Interactions.},
journal = {Advances in experimental medicine and biology},
volume = {1477},
number = {},
pages = {139-203},
pmid = {40442386},
issn = {0065-2598},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Brain/physiology/microbiology ; Animals ; *Brain-Gut Axis/physiology ; },
abstract = {The gut microbiota, consisting of trillions of microorganisms, plays a critical role in regulating host physiology, including metabolism, immune responses, and brain function. This chapter examines the microbiota-gut-brain axis, a multifaceted bidirectional communication system connecting gut microbial activity with central nervous system processes through immune pathways, metabolic byproducts, and neural circuits like the vagus nerve. The evolution of the gut microbiota throughout an individual's life-from early developmental influences like birth mode and antibiotic use to changes associated with aging and neurodegenerative conditions-highlights its dynamic nature. The chapter reviews experimental approaches and microbiome-based interventions to demonstrate the influence of gut microbiota on neurological conditions such as autism spectrum disorder, anxiety, and Alzheimer's disease. Finally, it emphasises the importance of advancing microbiome-targeted therapies, integrating emerging technologies, and clinical trials to develop personalised strategies for enhancing brain health through gut microbiome modulation.},
}
@article {pmid40442236,
year = {2025},
author = {Jeng, TM and Hsieh, YC and Chang, PY and Li, YL and Tang, SC and Jeng, JS and Hu, CJ and Chiou, HY},
title = {Association between post-stroke cognitive impairment and gut microbiota in patients with ischemic stroke.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {18849},
pmid = {40442236},
issn = {2045-2322},
support = {NSTC107-2314-B-038-070-MY3//National Science and Technology Council/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; Male ; Female ; Middle Aged ; *Cognitive Dysfunction/microbiology/etiology ; *Ischemic Stroke/complications/microbiology ; Aged ; Cross-Sectional Studies ; Biomarkers ; Inflammation ; *Stroke/complications/microbiology ; },
abstract = {More than half of stroke survivors have post-stroke cognitive impairment (PSCI). The role of gut microbiota, which can communicate with the brain through the gut-brain axis and affect inflammation, has been receiving increased attention. This cross-sectional study aimed to investigate the association of PSCI, gut microbiota, and inflammatory markers. Patients with first ischemic stroke and complete 3-month and 1-year follow-up data were included and divided into PSCI and non-PSCI groups according to the Montreal Cognitive Assessment (MoCA) score at the above time points. PSCI was defined as having a MoCA less than 23 at either 3 months or 1 year, or a decrease of more than 2 points at both time points. Gut microbiota was assessed by 16 S rRNA gene sequencing and Next Generation Sequencing analysis. The inflammatory markers included interleukins (ILs), eotaxin, G-CSF, TNF-α, IFNγ, sCD40L, and MCP-1. There were 95 ischemic stroke patients (mean age, 60.5 ± 12.1 years; male, 68.4%), including 30 with PSCI and 65 with non-PSCI. In gut microbiota analysis, the PSCI group had a higher abundance of Bacteroidaceae and Clostridiaceae, and the non-PSCI group had a higher abundance of Prevotellaceae, Ruminococcaceae, Oscillibacter, and Faecalibacterium. Ruminococcaceae family under the Oscillospirales order remains significantly different in the two groups in logistic regression model adjusting confounding variables (p = 0.044). In an analysis of inflammatory markers, the plasma levels of eotaxin (p = 0.041) and IL-12p40 (p = 0.031) were significantly higher in the PSCI group than those in the non-PSCI group, and the plasma level of eotaxin was significantly positively correlated with the amount of Clostridiaceae (rho = 0.389, p = 0.045). The study found that PSCI was associated with certain gut microbiota, and these gut microbiotas correlated with the pro-inflammatory marker eotaxin. This suggests that gut microbiota might play a role in the development of cognitive impairment after ischemic stroke.},
}
@article {pmid40442154,
year = {2025},
author = {Seong, HJ and Park, YM and Kim, BS and Yoo, HJ and Kim, T and Yoon, SM and Kim, JH and Lee, SY and Lee, YK and Lee, DW and Nam, MH and Hong, SJ},
title = {Integrated multi-omics reveals different host crosstalk of atopic dermatitis-enriched Bifidobacterium longum Strains.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {91},
pmid = {40442154},
issn = {2055-5008},
mesh = {Humans ; *Dermatitis, Atopic/microbiology ; *Gastrointestinal Microbiome ; Infant ; *Bifidobacterium longum/genetics/isolation &amp; purification/classification/metabolism ; Female ; Male ; Metabolomics ; Metagenomics/methods ; Feces/microbiology ; *Host Microbial Interactions ; Clostridium/genetics/isolation &amp; purification ; Transcriptome ; Multiomics ; },
abstract = {The infant gut microbiome is essential for long-term health and is linked to atopic dermatitis (AD), although the underlying mechanisms are not fully understood. This study investigated gut microbiome-host interactions in 31 infants with AD and 29 healthy controls using multi-omics approaches, including metagenomic, host transcriptomic, and metabolomic analyses. Microbial diversity was significantly altered in AD, with Bifidobacterium longum and Clostridium innocuum associated with these changes. At the strain-level, only B. longum differed significantly between groups, with pangenome analyses identifying genetic variations potentially affecting amino acid and lipid metabolites. Notably, B. longum subclade I, which was more prevalent in healthy controls, correlated with host transcriptomic pathways involved in phosphatidylinositol 3-kinase-AKT signaling and neuroactive ligand-receptor pathways, as well as specific metabolites, including tetrahydrocortisol and ornithine. These findings highlight the role of B. longum strain-level variation in infants, offering new insights into microbiome-host interactions related to AD.},
}
@article {pmid40442038,
year = {2025},
author = {Turjeman, S and Koren, O},
title = {Bridging the bench-to-bedside divide in microbiome research.},
journal = {Clinical and translational medicine},
volume = {15},
number = {5},
pages = {e70358},
doi = {10.1002/ctm2.70358},
pmid = {40442038},
issn = {2001-1326},
support = {ERC-2020-COG no. 101001355//HORIZON EUROPE European Research Council/ ; 1527/21//Israel Science Foundation/ ; },
}
@article {pmid40441709,
year = {2025},
author = {Dang, T and Fuji, Y and Kumaishi, K and Usui, E and Kobori, S and Sato, T and Narukawa, M and Toda, Y and Sakurai, K and Yamasaki, Y and Tsujimoto, H and Hirai, MY and Ichihashi, Y and Iwata, H},
title = {I-SVVS: integrative stochastic variational variable selection to explore joint patterns of multi-omics microbiome data.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {3},
pages = {},
doi = {10.1093/bib/bbaf132},
pmid = {40441709},
issn = {1477-4054},
support = {JP21J21850//JSPS KAKENHI/ ; JPMJCR1602//JST-CREST Program/ ; JPMJMI120C7//JST-Mirai Program/ ; JPMJAN23D1//JST ALCA-Next Program/ ; },
mesh = {*Microbiota ; Mice ; Animals ; Humans ; Stochastic Processes ; Bayes Theorem ; Glycine max/microbiology ; *Metabolomics/methods ; Algorithms ; *Computational Biology/methods ; Metabolome ; Cluster Analysis ; Multiomics ; },
abstract = {High-dimensional multi-omics microbiome data play an important role in elucidating microbial community interactions with their hosts and environment in critical diseases and ecological changes. Although Bayesian clustering methods have recently been used for the integrated analysis of multi-omics data, no method designed to analyze multi-omics microbiome data has been proposed. In this study, we propose a novel framework called integrative stochastic variational variable selection (I-SVVS), which is an extension of stochastic variational variable selection for high-dimensional microbiome data. The I-SVVS approach addresses a specific Bayesian mixture model for each type of omics data, such as an infinite Dirichlet multinomial mixture model for microbiome data and an infinite Gaussian mixture model for metabolomic data. This approach is expected to reduce the computational time of the clustering process and improve the accuracy of the clustering results. Additionally, I-SVVS identifies a critical set of representative variables in multi-omics microbiome data. Three datasets from soybean, mice, and humans (each set integrated microbiome and metabolome) were used to demonstrate the potential of I-SVVS. The results indicate that I-SVVS achieved improved accuracy and faster computation compared to existing methods across all test datasets. It effectively identified key microbiome species and metabolites characterizing each cluster. For instance, the computational analysis of the soybean dataset, including 377 samples with 16 943 microbiome species and 265 metabolome features, was completed in 2.18 hours using I-SVVS, compared to 2.35 days with Clusternomics and 1.12 days with iClusterPlus. The software for this analysis, written in Python, is freely available at https://github.com/tungtokyo1108/I-SVVS.},
}
@article {pmid40441385,
year = {2025},
author = {Wirkus, J and Ead, AS and Krga, I and Wang, Y and Pontifex, MG and Muller, M and Vauzour, D and Matsukuma, KE and Zhang, G and Mackenzie, GG},
title = {Normalizing body weight with a dietary strategy mitigates obesity-accelerated pancreatic carcinogenesis in mice.},
journal = {The Journal of nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tjnut.2025.05.039},
pmid = {40441385},
issn = {1541-6100},
abstract = {BACKGROUND: Obesity is a modifiable risk factor for pancreatic cancer, but the impact of dietary changes leading to weight loss in pancreatic carcinogenesis remains unknown.<br><br>OBJECTIVE: To determine the effects of weight normalization via dietary switch on pancreatic carcinogenesis and associated mechanisms.<br><br>METHODS: Five-week-old male and female LSL-Kras[G12D/+]; p48[Cre/+] (KC) mice (8-12/diet group/sex) were fed a high-fat, diet-induced obesity diet (DIO; 60% kcal from fat) or a low-fat, control diet (CD; 11% kcal from fat) for 21 weeks. A subset of mice was fed the DIO for 8 weeks, then switched to CD for 13 additional weeks (DIO&#x2192;CD). Cancer incidence was evaluated by histology. Lipidomics and RNAseq followed by bioinformatic analysis identified potential mechanisms. The gut microbiome was characterized using 16s rRNA amplicon sequencing. Data were analyzed using one-way analysis of variance.<br><br>RESULTS: After 21 weeks, DIO-fed mice had 1.7-fold higher body weight gain, and 60% increase (p<0.05 DIO vs. CD) in pancreatic acinar-to-ductal metaplasia, compared to the other 2 groups. None of the 21 mice fed a CD developed cancer, while 2 out of 21 DIO-fed male mice did. Switching from a DIO to a CD normalized body weight and composition to CD levels, slowed acinar-to-ductal metaplasia and prevented cancer incidence, with no mice developing cancer. Mechanistically, DIO affected gene expression related to cellular metabolism, pancreatic secretions, immune function, and cell-signaling, while CD and DIO&#x2192;CD had similar global gene expression. Moreover, DIO increased epoxy metabolites of linoleic acid, which were mitigated by the dietary switch. Finally, compared to a CD, DIO altered the gut microbiome and switching from a DIO to a CD restored the gut microbiome profile to resemble that of CD-fed mice.<br><br>CONCLUSIONS: Body weight normalization slowed obesity-accelerated pancreatic carcinogenesis, in part, by affecting inflammatory and cell signaling pathways, reducing epoxy metabolites, and modulating the gut microbiome.},
}
@article {pmid40441298,
year = {2025},
author = {Piché, ME and Poirier, P and Wong, JA},
title = {Impact of metabolic surgery on cardiovascular disease outcomes.},
journal = {The Canadian journal of cardiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cjca.2025.05.013},
pmid = {40441298},
issn = {1916-7075},
abstract = {Obesity is strongly associated with a range of cardiovascular conditions, including coronary artery disease, heart failure, atrial fibrillation, and stroke. Metabolic surgery has emerged as one of the most effective interventions for individuals with severe obesity, not only by promoting substantial and durable weight loss but also by improving cardiovascular risk factors and outcomes. Cardiovascular benefits may also be mediated via weight independent mechanisms involving insulin sensitivity, gastrointestinal hormones, bile acid dynamics, and gut microbiome. Long-term cohort studies have documented that metabolic surgery is associated with a reduction in all-cause mortality and major adverse cardiovascular events in this population. This narrative review examines the role of metabolic surgery in the prevention and management of cardiovascular disease associated with severe obesity. It provides an overview of the most common metabolic surgery procedures, including sleeve gastrectomy, Roux-en-Y gastric bypass and biliopancreatic diversion with duodenal switch as well as newer procedures like single-anastomosis duodenal switch. This review also evaluates the impact of these interventions on key cardiovascular risk factors such as type 2 diabetes, hypertension, dyslipidemia, and obstructive sleep apnea, as well as their effects on cardiac structure and function. Metabolic surgery is associated with reductions in all-cause mortality and cardiovascular events, including myocardial infarction and heart failure, especially in individuals with obesity and pre-existing cardiovascular disease. The current evidence supporting the link between metabolic surgery and cardiovascular outcomes is reviewed. Notably, randomized trials specifically focusing on cardiovascular outcomes after metabolic surgery are lacking highlighting an important knowledge gap and their crucial need. Addressing this gap is essential for guiding future clinical practice and optimizing patient care.},
}
@article {pmid40441277,
year = {2025},
author = {Chapron, L and Meistertzheim, AL and Ghiglione, JF and Peru, E and Galand, PE and Lartaud, F},
title = {Beyond plastisphere transfer, deep corals are subject to dysbiosis when exposed to plastics.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {126554},
doi = {10.1016/j.envpol.2025.126554},
pmid = {40441277},
issn = {1873-6424},
abstract = {Plastic pollution has been identified as a major threat to marine life and ecosystems, but their biological impacts are still largely unknown. Coral reefs, which are one of the most biodiverse ecosystems on earth that provide essential ecological and economical services, are now recognized to be impacted by plastic pollution from the surface to the deep. Here, we investigated the impact of colonized macro- and microplastics on the microbiome of the most emblematic cold-water coral, Lophelia pertusa. Studies at the associated bacterial level help better understand the early biological pathways that may lead to coral physiological alterations. Both macro- and microplastics induced early (7 days) microbial shifts for L. pertusa polyps, with specific exacerbated effects between plastic sizes observed after 47 days. In the case of stressed corals, we observed an increase of opportunistic and/or pathogenic bacteria that may be induced by different processes whether corals are exposed to macro- (barrier effect) or microplastics (ingestion). Our results however confirm that very few specific bacteria can be directly transferred from plastisphere to coral microbiome. We suggest that shift in coral microbiome was due to general dysbiosis from stress, and poorly from a transfer of microorganisms from the plastisphere. Considering the widespray distribution of macroplastics in the ocean that are continuously fragmented into microplastics, our conclusions suggest that plastics could seriously endangered the cold-water coral reefs.},
}
@article {pmid40441229,
year = {2025},
author = {Wei, F and Zhao, M and Sun, X and Ma, H and Yin, H and Shen, X},
title = {Causal associations between gut microbiota and rheumatoid arthritis: A two-sample Mendelian randomization study.},
journal = {Medicine},
volume = {104},
number = {22},
pages = {e42596},
doi = {10.1097/MD.0000000000042596},
pmid = {40441229},
issn = {1536-5964},
mesh = {*Arthritis, Rheumatoid/microbiology/genetics ; *Gastrointestinal Microbiome/genetics ; Humans ; Mendelian Randomization Analysis ; Genome-Wide Association Study ; },
abstract = {The gut microbiota has been implicated in the development of rheumatoid arthritis (RA), but whether these associations reflect causal relationships remains unclear. We conducted a two-sample Mendelian randomization analysis to investigate the potential causal effects of gut microbial taxa on RA risk. Summary-level data from the MiBioGen consortium (n = 13,266) and a large RA genome-wide association study (n = 97,173) were used. Multiple Mendelian randomization methods and sensitivity analyses were applied to ensure robustness. Four microbial taxa showed nominal associations with RA. Increased abundance of Catenibacterium, Desulfovibrio, and Ruminiclostridium 6 was associated with a higher risk of RA, while Lachnospiraceae (UCG008) appeared to have a protective effect. Although these associations did not meet Bonferroni-corrected significance, results were consistent across analytical methods with no evidence of pleiotropy or heterogeneity. This study provides genetic evidence supporting a potential causal link between specific gut microbes and RA risk. The findings highlight host immune modulation as a possible pathway connecting the gut microbiome to RA and identify candidate taxa for future mechanistic and therapeutic research.},
}
@article {pmid40441205,
year = {2025},
author = {Zhou, J and Xu, Y and Wang, H and Wang, K and Chen, C},
title = {Investigating the causal links among gut microbiome features, inflammation-related proteins, and diverticular disease: Insights from a mediation Mendelian randomization study.},
journal = {Medicine},
volume = {104},
number = {22},
pages = {e42676},
doi = {10.1097/MD.0000000000042676},
pmid = {40441205},
issn = {1536-5964},
support = {No. JDY2023018//Jiangsu University Medical Education Collaborative Innovation Fund Project/ ; No. Z2021010//Medical Research Project of Jiangsu Health Commission/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Mendelian Randomization Analysis ; *Diverticular Diseases/microbiology/genetics ; *Inflammation/genetics ; Genome-Wide Association Study ; Mediation Analysis ; },
abstract = {The pathophysiological mechanisms underlying diverticular disease (DD) remain incompletely understood, and there is considerable debate regarding the roles of gut microbiome features and inflammation-related proteins in the development of the disease. In this study, we employed mediation Mendelian randomization (MR) analysis to investigate the causal relationships among these 3 factors. In this study, we conducted a MR analysis on the genome-wide association studies data of 412 gut microbiome features (207 microbial taxa and 205 pathways), 91 inflammation-related proteins, and DD. We employed the inverse-variance weighted (IVW) method as our primary screening approach, followed by a mediation MR analysis to explore potential causal relationships among these 3 aspects. Our findings were further reinforced by comprehensive heterogeneity analyses, horizontal pleiotropy testing, outlier detection, and "leave-one-out" sensitivity analysis. Through our screening process, we identified potential causal relationships between DD and 18 gut microbiome features, as well as 6 inflammation-related proteins. These include s_Oscillibacter_unclassified (IVW odds ratio (OR): 1.139; 95% confidence interval (CI): 1.044-1.241, P = .003), g_Bilophila (IVW OR: 1.107, 95% CI: 1.016-1.206, P = .020), T-cell surface glycoprotein CD5 levels (IVW OR: 1.065, 95% CI: 1.011-1.123, P = .019), and inosine 5'-phosphate biosynthesis I (IVW OR: 0.882, 95% CI: 0.800-0.973, P = .012), etc. In the mediation MR analysis, we found that the genetic predictors of g_Bilophila and inosine 5'-phosphate biosynthesis I could explain 23.956% and 24.630% of the variation in T-cell surface glycoprotein CD5 levels, respectively. This study detailed analysis of the links between gut microbiome features, inflammation-related proteins, and DD offers key insights into DD pathogenesis and prevention.},
}
@article {pmid40441146,
year = {2025},
author = {Yang, Y and Duan, Y and Lang, S and Fondevila, MF and Schöler, D and Harberts, A and Cabré, N and Chen, S and Shao, Y and Vervier, K and Miyamoto, Y and Zhang, X and Chu, H and Yang, L and Tan, C and Eckmann, L and Bosques-Padilla, F and Verna, EC and Abraldes, JG and Brown, RS and Vargas, V and Altamirano, J and Caballería, J and Shawcross, DL and Louvet, A and Lucey, MR and Mathurin, P and Garcia-Tsao, G and Bataller, R and Stärkel, P and Lawley, TD and Schnabl, B},
title = {Targeted inhibition of pathobiont virulence factor mitigates alcohol-associated liver disease.},
journal = {Cell host &amp; microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2025.05.003},
pmid = {40441146},
issn = {1934-6069},
abstract = {Alcohol-associated liver disease poses a global health burden with high mortality. Imbalances in the gut microbiota are important for disease progression. Using metagenomic sequencing of fecal samples from a multicenter, international cohort of patients with alcohol-associated hepatitis, we found that the presence of virulence factor KpsM, encoded in the genome of Escherichia coli (E. coli), correlated with patient mortality. Functional studies using gnotobiotic mouse models and genetic manipulation of bacteria demonstrated that kpsM-positive E. coli exacerbate ethanol-induced liver disease. The kpsM gene mediates the translocation of capsular polysaccharides to the cell surface. This enables kpsM-positive E. coli to evade phagocytosis by the scavenger receptor Marco on Kupffer cells in the liver, leading to bacterial spread. Importantly, inhibiting kpsM-dependent capsules with the small molecule 2-(4-phenylphenyl)benzo[g]quinoline-4-carboxylic acid (C7) attenuated ethanol-induced liver disease in mice. We show that precision targeting of the virulence factor KpsM is a promising approach to improve outcomes of patients with alcohol-associated hepatitis.},
}
@article {pmid40441086,
year = {2025},
author = {Sharma, P and Das, S and Rituraj, R and Bhagyashree, B},
title = {Understanding oncobiosis in ovarian cancer: Emerging concepts in tumor progression.},
journal = {Pathology, research and practice},
volume = {271},
number = {},
pages = {156026},
doi = {10.1016/j.prp.2025.156026},
pmid = {40441086},
issn = {1618-0631},
abstract = {Ovarian cancer is a leading cause of gynecologic cancer mortality and has recently been linked to microbial dysbiosis or oncobiosis. Tumorigenesis is a highly complex process, and recent research has revealed numerous new mechanisms showing how tumors interact with their surrounding microenvironment. The inclusion of microbiome studies has significantly advanced this field revealing the important role microbes play, not only in maintaining normal physiological functions of the human body but also in influencing oncogenic pathways. This expanding knowledge is deepening our understanding of tumor pathophysiology and is helping to create new diagnostic, prognostic, therapeutic and preventive strategies for specific cancers. This review explores the role of the microbiome in ovarian carcinogenesis, focusing on its interaction with the tumor microenvironment (TME) and its influence on inflammation, immune regulation and metabolic signaling. This review studied dysbiosis in several anatomical compartments such as the gut, oral cavity, lower and upper genital tracts and ovarian tissues, in relation to ovarian oncobiosis. Emerging clinical implications of these studies include the use of microbial profiles as diagnostic or prognostic biomarkers. Therapeutic strategies such as fecal microbiota transplantation and probiotics are also discussed for their ability to restore microbial balance and enhance treatment efficacy. This review highlights the importance of continued research to explore causal relationships between the microbiome and tumorigenesis, positioning microbiome studies as promising tools in ovarian cancer management and improving patient care.},
}
@article {pmid40440906,
year = {2025},
author = {Zhan, Z and Zhang, J and Huang, W and Huang, J},
title = {Transcriptomic strategy provides molecular insights into the growth and ginsenosides accumulation of Panax ginseng.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {143},
number = {},
pages = {156834},
doi = {10.1016/j.phymed.2025.156834},
pmid = {40440906},
issn = {1618-095X},
abstract = {BACKGROUND: Panax ginseng C. A. Meyer, a well-known phytomedicine has been widely used in traditional medicine for centuries. However, its quality and yield are heavily influenced by environmental conditions and cultivation years. For example, ginsenosides as the primary active component of ginseng, the concentration increased with the age of the roots and unevenly distributed across different tissues. Recently, transcriptomic technologies have provided powerful tools for revealing the relationship between gene expression and ginsenoside accumulation during ginseng growth, and researches in this field is continuously expanding, influencing the quality and sustainability of ginseng cultivation.<br><br>PURPOSE: Investigating the relationship between ginseng growth and the accumulation of active components may provide new insights for improving ginseng performance and medicinal value. This requires a systematic review and in-depth discussion of relevant research.<br><br>STUDY DESIGN AND METHODS: This article reviews the application of transcriptomic strategies in studying the molecular mechanisms of ginseng growth and ginsenoside accumulation. A literature search and analysis were conducted using keywords such as "Panax ginseng" and "transcriptomics/transcriptome," along with terms including "ginsenoside biosynthesis," "microbe/microorganism," "RNA-seq," "cultivation years," "rhizosphere," and "stress."<br><br>RESULT: Our study focuses on the transcriptome strategy provides molecular insights into the growth and ginsenosides accumulation of Panax ginseng, we summarized and discussed the dynamic changes in gene expression across cultivation years, specific-tissue, environmental stress, and imbalance of rhizosphere microbes during the ginseng growth and ginsenosides accumulation process. In addition, we also highlight future directions.<br><br>CONCLUSION: The cultivation years, specific-tissue, environmental stress, and rhizosphere microbiome imbalance of Panax ginseng are indirectly or directly involved in plant health, biomass production, and the synthesis of ginsenosides. Harnessing these factors to improve the quality and yield of ginseng holds great promise.},
}
@article {pmid40440849,
year = {2025},
author = {Ramadoss, R and Nishad, AK and Moovarkumudalvan, B and Shomar, B},
title = {Bacterial composition of dust deposited in Qatar: A seasonal study.},
journal = {The Science of the total environment},
volume = {985},
number = {},
pages = {179766},
doi = {10.1016/j.scitotenv.2025.179766},
pmid = {40440849},
issn = {1879-1026},
abstract = {Dust storms in the Middle East threaten public health by deteriorating air quality and transporting microorganisms over vast distances. This study analyzes seasonal variations in dust-borne bacterial diversity on photovoltaic (PV) panels using 16S rRNA gene sequencing and bioinformatics to assess community composition and metabolic potential. Our findings suggest that seasonal ecological factors have potential effects on the composition of the airborne bacterial community. In Qatar, the high atmospheric CO2 levels associated with hydrocarbon refining had promoted the growth of hydrocarbon-degrading bacteria belonging to the phyla Campilobacterota, Proteobacteria, and Bacteroidota. High temperatures and photothermal reactions of summer conditions have favored sulfur-metabolizing bacteria. Conversely, milder temperatures, increased humidity, reduced wind speed, and a decline in summer-favoring bacteria had contributed to the increased abundance of the phyla Patescibacteria, Firmicutes, and Actinobacteriota during other seasons. This study had also identified dust borne pathogenic bacteria associated with human and plant diseases, highlighting the need for environmental surveillance to monitor microbial diversity and its shifts driven by ecological factors. This knowledge is crucial for public health, environmental protection, sustainable farming and advancing our understanding of microbial ecology.},
}
@article {pmid40440748,
year = {2025},
author = {Cimmino, F and Silvestri, C and Trinchese, G and Petrella, L and Cavaliere, G and Fogliano, C and Piscitelli, F and Cristino, L and Avallone, B and Banni, S and Sihag, J and Di Marzo, V and Mollica, MP},
title = {Anti-obesity effects of Oleoylethanolamide: Modulation of mitochondrial bioenergetics, endocannabinoidome and gut microbiome.},
journal = {Biomedicine &amp; pharmacotherapy = Biomedecine &amp; pharmacotherapie},
volume = {188},
number = {},
pages = {118201},
doi = {10.1016/j.biopha.2025.118201},
pmid = {40440748},
issn = {1950-6007},
abstract = {The endocannabinoidome (eCBome) and gut microbiome play key roles in metabolism and obesity, and oleoylethanolamide (OEA), a lipid mediator within the eCBome, is known to reduce food intake and promote fat oxidation. This study investigated the effects of OEA administration on mice with diet-induced obesity, focusing on hepatic inflammation and mitochondrial function, the endocannabinoidome (eCBome), and the gut microbiome. Mice fed standard (STD) or high-fat (HFD) diets for 18 weeks were treated with either vehicle or OEA. Metabolic, inflammatory, oxidative stress and mitochondrial parameters were assessed, along with intestinal and hepatic levels of eCBome lipids and fecal microbiota and short chain fatty acid composition. In HFD-fed mice, OEA decreased body weight, food intake, and serum and liver inflammatory markers, limiting hepatic and body fat accumulation. OEA improved liver mitochondrial oxidative capacity, lipid metabolism and oxidative stress. It reduced intestinal levels of the endocannabinoid 2-arachidonoylglycerol. Effects on microbiota composition were mostly found in the STD-fed group. However, OEA increased the relative abundance of Akkermansia muciniphila more strongly in HFD-fed mice. These findings suggest that OEA may help counteract obesity-related metabolic dysfunction and inflammation, and gut microbiota unbalance, thus representing a promising candidate for future therapeutic strategies.},
}
@article {pmid40440482,
year = {2025},
author = {Zhao, L},
title = {Guild-Level Response of the Gut Microbiome to Nutritional Signals: Advancing Precision Nutrition for Metabolic Health.},
journal = {Annual review of nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1146/annurev-nutr-122424-022254},
pmid = {40440482},
issn = {1545-4312},
abstract = {The gut microbiome functions as a hidden organ, providing essential ecosystem services to sustain human health. By identifying stably connected bacteria, we reveal two competing guilds (TCG) as the resilient core of the microbiome: the health-promoting foundation guild (FG) and the proinflammatory pathobiont guild (PG). FG members produce short-chain fatty acids (SCFAs), enhancing gut barrier integrity and systemic resilience, while PG members disrupt metabolism through endotoxins, indoles, and hydrogen sulfide. Together, the FG and PG mediate ∼85% of ecological interactions in a dynamic, seesaw-like relationship. As evolved nutrient sensors for coping with feast-famine cycles, these guilds align host metabolism with dietary patterns. Fiber-rich diets bolster FG activity, maintaining microbial balance and metabolic health, whereas fiber-deficient diets in modern-day society favor chronic PG dominance, driving inflammation and disease. Synthesizing clinical and experimental evidence, this review positions the TCG model as a transformative framework for precision nutrition, guiding strategies to restore microbial balance and address metabolic disorders.},
}
@article {pmid40439988,
year = {2025},
author = {Davidson, IM and Nikbakht, E and Haupt, LM and Dunn, PJ},
title = {Toward accurate vaginal microbiome profiling: protocol, bioinformatics, and core microbiota characterisation.},
journal = {Journal of assisted reproduction and genetics},
volume = {},
number = {},
pages = {},
pmid = {40439988},
issn = {1573-7330},
abstract = {PURPOSE: Rising demand for assisted reproductive technologies (ART) with limited improvements in success rates has driven interest in the impact of the vaginal microbiome on fertility outcomes. In order to fully examine the relationship between the vaginal microbiome and fertility outcomes, methodologies and technological developments must be standardised and benchmarked to provide the most accurate assessment of microbial population representation.<br><br>METHODS: This study sought to investigate the utility of 16S sequencing and bioinformatic approaches using nanopore sequencing to characterize core vaginal microbiota in a healthy Australian cohort of reproductive-age women.<br><br>RESULTS: Optimisation and comparison of different PCR strategies for whole 16S amplification was undertaken, along with the generation of bioinformatic analysis strategies. Initial qPCR identified the 27F-YM (MIX) primer as the most sensitive for C. trachomatis. However, nanopore sequencing revealed no detectable C. trachomatis across all six samples. Among the bioinformatic tools, Porechop with NanoCLUST most accurately identified microbial presence. Community state type (CST) I-characterised by Lactobacillus crispatus dominance-was identified as the most common CST (66%), aligning with patterns of a healthy vaginal microbiome.<br><br>CONCLUSION: The findings highlight a Lactobacillus-rich microbiome as the most common among healthy females; however, further refinement-potentially through a metagenomics approach-is recommended to address 16S rRNA primer limitations to enable improved accuracy of microbial detection for the vaginal microbiome.},
}
@article {pmid40439987,
year = {2025},
author = {Wang, X and Sun, C and Yang, X and Xu, G and Pei, L and Tang, L and Xu, S and Xie, C},
title = {Exploring the potential mechanism of tofacitinib therapy for ankylosing spondylitis through gut microbiome and plasma metabolomics.},
journal = {Clinical rheumatology},
volume = {},
number = {},
pages = {},
pmid = {40439987},
issn = {1434-9949},
abstract = {OBJECTIVE: To explore the role of gut microbiota and plasma metabolites in the therapeutic mechanism of tofacitinib in ankylosing spondylitis (AS).<br><br>METHOD: Ten AS patients and ten matched healthy controls (HC) were enrolled in this study. 16S rRNA sequencing and LC-MS profiling was conducted to investigate the gut microbiota and plasma metabolite before and after tofacitinib therapy. An AS mouse model was established to validate the effect of tofacitinib in vivo via H&amp;E staining, western blot, and ELISA.<br><br>RESULTS: Tofacitinib improved clinical symptoms in AS patients. Microbiota analysis revealed Microbiota analysis revealed reduced &#x3b1;-diversity (ACE, Chao1) and altered community structure in AS patients compared to HC, which partially normalized post-treatment. LEfSe identified 84 taxa biomarkers; Barnesiella, Coprobacter, Lachnospira, and Lactobacillus tended to return to normal after tofacitinib treatment. Plasma metabolomics uncovered 3 key metabolies, including choline metabolism, glycerophospholipid metabolism, and phenylalanine metabolism. Spearman analysis revealed that the gut microbiota were closely related to the changes in differential plasma metabolites. Combinated tofacitinib and trichostatin therapy attenuated inflammation, restored metabolism caused by AS in mice in vivo.<br><br>CONCLUSION: AS patients suffer from dysbiosis of gut microbiota, and the mechanism of tofacitinib treatment of AS may be related to the modulation of gut microbiota and alteration of plasma metabolites. Key Points &#x2022; Tofacitinib improves clinical symptoms in patients with AS. &#x2022; Tofacitinib regulates gut microbiota in AS patients. &#x2022; Tofacitinib regulates plasma metabolites in patients with AS. &#x2022; Tofacitinib regulates the choline metabolism.},
}
@article {pmid40439700,
year = {2025},
author = {Zaghloul, HAH and Xiao, Z and Tang, J and Xiao, T and Gao, J and Hu, J and Huang, GH},
title = {An aegerolysin-like protein from Heliothis virescens ascovirus 3h (HvAV-3h) shows immune suppression and antibacterial activity.},
journal = {The Journal of general virology},
volume = {106},
number = {5},
pages = {},
doi = {10.1099/jgv.0.002107},
pmid = {40439700},
issn = {1465-2099},
mesh = {Animals ; *Ascoviridae/genetics/immunology ; *Viral Proteins/genetics/immunology/metabolism ; *Moths/virology/immunology ; *Anti-Bacterial Agents/pharmacology ; Immunity, Innate ; Larva/virology ; Host-Pathogen Interactions ; Virus Replication ; Fungal Proteins ; Hemolysin Proteins ; },
abstract = {Aegerolysins are lipid-binding proteins associated with multiple functions, including membrane pore-formation, insecticidal toxicity and defence against predators. Whilst distributed over the kingdoms of the Tree of Life, ascoviruses are the only representative viruses that encode an aegerolysin-like protein. Ascoviruses are entomopathogenic and possess a large dsDNA genome. The present study aimed to functionally characterize the aegerolysin-like protein of Heliothis virescens ascovirus 3h (HvAV-3h), encoded by ORF85, and to explore its potential roles in the interaction between the ascovirus and its host. Our results demonstrate the importance of this species-specific protein to HvAV-3h replication in host cells. In vivo, silencing of this gene for 12-72 h significantly increased the expression of some innate immunity-associated genes, including Toll (114-fold), IMD (44.7-fold) and Hopscotch (22.9-fold). In parallel, we detected significant gradual increases in MyD88 and Relish and decreases in PIAS. Moreover, histopathological analyses of infected larval tissues indicated reduced tissue damage after 72 h of ORF85 gene silencing. The prokaryotic expression of the HvAV-3h aegerolysin, followed by feeding to third-instar Spodoptera exigua larvae for 24 or 48 h led to significant reductions in larval weight. Moreover, the in vitro treatment demonstrated a bactericidal action against Lysinibacillus xylanilyticus, a bacterial resident of some insect guts. Overall, our findings suggest that the protein encoded by ORF85 is associated with the pathogenicity of HvAV-3h and its ability to replicate in host cells. Additionally, aegerolysin may inhibit or kill specific bacterial species in the host microbiome during infection, potentially modulating the host immune response.},
}
@article {pmid40439571,
year = {2025},
author = {Hadjigeorgiou, AG and Harkos, C and Mishra, AK and Morad, G and Johnson, SB and Ajami, NJ and Wargo, JA and Munn, LL and Stylianopoulos, T and Jain, RK},
title = {Mathematical Modeling and Association Analysis Deciphers the Impact of the Gut Microbiome on Cancer Immunotherapy.},
journal = {Cancer research},
volume = {},
number = {},
pages = {},
doi = {10.1158/0008-5472.CAN-24-2232},
pmid = {40439571},
issn = {1538-7445},
abstract = {The gut microbiome has emerged as a key regulator of response to cancer immunotherapy. However, a better understanding of the underlying mechanisms by which the microbiome influences immunotherapy is needed to identify strategies to optimize outcomes. To this end, we developed a mathematical model to obtain insights into the effect of the microbiome on the immune system and immunotherapy response. This model was based on i) gut microbiome data derived from preclinical studies, ii) mathematical modeling of the antitumor immune response, iii) association analysis of microbiome profiles with model-predicted immune profiles, and iv) statistical models that correlate model parameters with the microbiome. The model was used to investigate the complexity of murine and human studies on microbiome modulation. Comparison of model predictions with experimental observation of tumor response in the training and test datasets supported the hypothesis that two model parameters, the activation and killing rate constants of immune cells, are the most influential in tumor progression and are potentially affected by microbiome composition. Evaluation of the associations between the gut microbiome and immune profile indicated that the components and structure of the gut microbiome affect the activation and killing rate of adaptive and innate immune cells. Overall, this study contributes to a deeper understanding of microbiome-cancer interactions and offers a framework for understanding how microbiome interactions influence cancer treatment outcomes.},
}
@article {pmid40439440,
year = {2025},
author = {Su, X and Li, X and He, X and Zhou, S and Lyu, A and Cai, Z},
title = {A biotin-free diet attenuates the incidence of collagen-induced arthritis and alleviates microbial dysbiosis.},
journal = {Food &amp; function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5fo01457c},
pmid = {40439440},
issn = {2042-650X},
abstract = {Emerging evidence has shown that the gut microbiota and its products are important triggers in the pathogenesis of rheumatoid arthritis (RA). Biotin is a diet- and microbiome-dependent metabolite and an immune regulator; however, the role of biotin in RA remains unknown. In this study, we observed abnormal fecal biotin excretion in RA patients, which correlated with microbial alterations. Specifically, biotin content was inversely associated with gut microbial genera enriched in healthy controls, including Roseburia and Dorea. Meanwhile, it positively correlated with Oscillospira, which was highly enriched in RA individuals. Moreover, collagen-induced arthritis (CIA) mice fed a biotin-free diet had attenuated arthritis incidence with depressed differentiation of splenic CD3[+] T cells and restored microbial diversities. The biotin-free diet also increased bone mass and protected against inflammation-induced bone loss in CIA mice. Additionally, the biotin-free diet reshaped the host metabolic phenotype of amino acids and microbial composition. Notably, biotin deficiency ameliorated the augmentation of Oscillospira in CIA mice. Collectively, our results suggested a potential link between biotin deficiency, gut microbiota dysbiosis and CIA progression.},
}
@article {pmid40439420,
year = {2025},
author = {Park, J and Kohn, E and Schenk, S and Davis, KM and Clark, JS and Parfrey, LW},
title = {An experimental test of the influence of microbial manipulation on sugar kelp (Saccharina latissima) supports the core influences host function hypothesis.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0030125},
doi = {10.1128/aem.00301-25},
pmid = {40439420},
issn = {1098-5336},
abstract = {UNLABELLED: Kelp are valued for a wide range of commercial products and their role in kelp forest ecosystems, making kelp cultivation a rapidly expanding economic sector. Microbes associated with kelp and other macroalgae play a critical role in processes such as nutrient exchange, chemical signaling, and defense against pathogens. Thus, manipulating the microbiome to enhance macroalgal growth and resilience is a promising yet underexplored approach for sustainable kelp cultivation. The core microbiome hypothesis suggests that the bacteria that are consistently found on a host (the core microbes) are likely to have a disproportionate impact on host biology, making them an attractive target for microbiome manipulation. In this study, we surveyed wild Saccharina latissima and their surrounding environment to identify core bacterial taxa, compared them to cultivated kelp, and experimentally tested how cultured bacterial isolates affect kelp development. We found that core bacteria are nearly absent in cultivated juvenile sporophytes in nurseries, but eventually colonize them after outplanting to ocean farm sites. Bacterial inoculants had both positive and negative effects on kelp development. Notably, the strength of association of a bacterial genus with kelp in the wild positively correlated with its impact on gametophyte settlement and sporophyte development in kelp co-culture experiments, aligning with predictions from the core microbiome influences host function hypothesis. These findings affirm the feasibility of using microbial manipulations to improve current kelp aquaculture practices and provide a framework for developing these techniques.<br><br>IMPORTANCE: Microorganisms consistently associated with hosts are widely thought to be more likely to impact host biology and health. However, this intuitive concept has not been experimentally evaluated. This study formalizes this concept as the Core Microbiome Influences Host Function hypothesis and experimentally tests this hypothesis in sugar kelp (Saccharina). The distribution of bacteria on wild kelp and core microbes was first identified by compiling a broad dataset of the kelp microbiome sampled across space and time. Bacterial cultures were isolated from the surface of sugar kelp and individually grown in laboratory co-culture with sugar kelp spores to assess the ability of bacterial isolates to influence kelp growth and development. In support of the core influences host function hypothesis, isolates belonging to bacterial genera that are more strongly associated with wild sugar kelp are more likely to influence development in laboratory experiments.},
}
@article {pmid40439402,
year = {2025},
author = {Gill, DS and Ram, S and Rice, PA},
title = {Biologic drug development for treatment and prevention of sexually transmitted infections.},
journal = {Clinical microbiology reviews},
volume = {},
number = {},
pages = {e0010724},
doi = {10.1128/cmr.00107-24},
pmid = {40439402},
issn = {1098-6618},
abstract = {SUMMARYSexually transmitted infections (STIs) represent a significant global health burden, with over one million new infections occurring daily. In some instances, the prevalence of antibiotic-resistant pathogens is rising, which exacerbates the challenge. STIs cause severe complications, including infertility, ectopic pregnancies, pre-term births, and heightened risks of HIV acquisition. These outcomes underscore the need for innovative therapeutic and prophylactic strategies. In this review, we provide a comprehensive analysis of the current state of biologic drug development targeting key STIs, focusing on Chlamydia trachomatis, Neisseria gonorrhoeae, herpes simplex virus type 2 (HSV-2), and Treponema pallidum. We examine the complexity of host-pathogen interactions that inform biologic drug design, such as multiple mechanisms of infection, immune evasion strategies, and pathogenic latency. We also explore the role of mucosal immunity, highlighting advances in resident memory T cells and cytokine-driven responses that guide therapeutic targeting, concentrating on Chlamydia trachomatis and Neisseria gonorrhoeae, where recent advances in vaccine development appear promising. We conduct a comprehensive survey of platforms, including vaccines, and explore modalities such as monoclonal antibodies and protein therapeutics. Additionally, we examine emerging technologies like nucleic acid-based therapies, microbiome modulation, and phage-based interventions, highlighting their potential against challenging pathogens like HSV-2 and Treponema pallidum. By examining these established and emerging approaches, this review prioritizes critical opportunities for innovation in biologic therapeutics, addressing unmet needs in STI management. It advocates for integrated strategies leveraging antigenic conservation, host immunity modulation, and novel delivery platforms to achieve durable prophylaxis and effective treatment for high-burden infections globally.},
}
@article {pmid40439232,
year = {2025},
author = {McGivern, BB and Ellenbogen, JB and Hoyt, DW and Bouranis, JA and Stemple, BP and Daly, RA and Bosman, SH and Sullivan, MB and Hagerman, AE and Chanton, JP and Tfaily, MM and Wrighton, KC},
title = {Polyphenol rewiring of the microbiome reduces methane emissions.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf108},
pmid = {40439232},
issn = {1751-7370},
abstract = {Methane mitigation is regarded as a critical strategy to combat the scale of global warming. Currently, about 40% of methane emissions originate from microbial sources, which is causing strategies to suppress methanogens-either through direct toxic effects or by diverting their substrates and energy-to gain traction. Problematically, current microbial methane mitigation knowledge lacks detailed microbiome-centered insights, limiting translation across conditions and ecosystems. Here we utilize genome-resolved metatranscriptomes and metabolomes to assess the impact of a proposed methane inhibitor, catechin, on greenhouse gas emissions for high-methane-emitting peatlands. In microcosms, catechin drastically reduced methane emissions by 72-84% compared to controls. Longitudinal sampling allowed for reconstruction of a catechin degradation pathway involving Actinomycetota and Clostridium, which break down catechin into smaller phenolic compounds within the first 21 days, followed by degradation of phenolic compounds by Pseudomonas_E from days 21 to 35. These genomes co-expressed hydrogen-uptake genes, suggesting hydrogenases may act as a hydrogen sink during catechin degradation and consequently reduce hydrogen availability to methanogens. In support of this idea, there was decreased gene expression by hydrogenotrophic and hydrogen-dependent methylotrophic methanogens under catechin treatment. There was also reduced gene expression from genomes inferred to be functioning syntrophically with hydrogen-utilizing methanogens. We propose that catechin metabolic redirection effectively starves hydrogen-utilizing methanogens, offering a potent avenue for curbing methane emissions across diverse environments including ruminants, landfills, and constructed or managed wetlands.},
}
@article {pmid40439217,
year = {2025},
author = {Ma, H and Dong, Z and Zhang, X and Li, N and Liu, C and Zhou, X and He, J and Ma, J and Zhang, S and Kan, H and Liu, S},
title = {Microbial Dysbiosis in the Lung and Gut in Response to Inhalable Particulate Matters in Pneumoconiosis Patients and Animals.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c00798},
pmid = {40439217},
issn = {1520-5851},
abstract = {Pneumoconiosis is a progressive and life-threatening fibrotic lung disorder caused by the prolonged deposition of inhaled particulate matters (PMs); thus far, no cure is available. Emerging evidence has suggested that the resulting disordered respiratory microbiome is caused by disturbed lung architecture and homeostasis responding to inhalable PMs. Lung microbiome dysbiosis also contributes to injury to the lung and distant organs, such as the intestine, through the lung-gut axis. Current studies on the microbiome-disease interplay are still in their infancy, and sufficient understanding of microbial heterogeneity in pathological processes is lacking. Here we investigated the microbiome in the lung and gut of patients with pneumoconiosis in comparison to healthy individuals. Our findings indicated reciprocal causation between lung injuries and microbial dysbiosis under particle exposure; pulmonary Streptococcus and Stenotrophomonas, along with intestinal Ligilactobacillus and Blautia, may represent key microbial communities influencing pneumoconiosis progression. We defined close microbiota crosstalk between the lung and gut, as evidenced by their interaction networks, implying considerable effects on the gut microenvironment through either direct microbial translocation or other mechanisms such as inflammation-driven alterations. Animal experiments further corroborated the findings in humans. Collectively, our results highlight the potential involvement of the lung-gut axis microbial dysbiosis in pneumoconiosis pathogenesis and open a new avenue to develop microbiome-targeted diagnosis and treatment strategies.},
}
@article {pmid40439157,
year = {2025},
author = {Wang, Z and Cheng, X and Xu, Y and Wang, Z and Ma, L and Li, C and Jiang, S and Li, Y and Guo, S and Du, W},
title = {Unveiling Neonatal Pneumonia Microbiome by High-Throughput Sequencing and Droplet Culturomics.},
journal = {Genomics, proteomics &amp; bioinformatics},
volume = {},
number = {},
pages = {},
doi = {10.1093/gpbjnl/qzaf047},
pmid = {40439157},
issn = {2210-3244},
abstract = {Neonatal pneumonia is a leading cause of infant mortality worldwide; however, a lack of microbial profiling, especially of low-abundance species, makes accurate diagnosis challenging. Traditional methods can fail to capture the complexity of the neonatal respiratory microbiota, thereby obscuring its role in disease progression. We describe a novel approach that combines high-throughput sequencing with droplet-based microfluidic cultivation to investigate microbiome shifts in neonates with pneumonia. Using 16S ribosomal RNA (rRNA) gene sequencing of 71 pneumonia cases and 49 controls, we identified 1009 genera, including 930 low-abundance taxa, which showed significant compositional differences between groups. Linear Discriminant Analysis Effect Size analysis identified key pneumonia-associated genera, such as Streptococcus, Rothia, and Corynebacterium. Droplet-based cultivation recovered 299 strains from 94 taxa, including rare species and ESKAPE pathogens, thereby supporting targeted antimicrobial management. Host-pathogen interaction assays showed that Rothia and Corynebacterium induced inflammation in lung epithelial cells, likely via dysregulation of the PI3K-Akt pathway. Integrating these marker taxa with clinical factors, such as gestational age and delivery type, offers the potential for precise diagnosis and treatment. The recovery of diverse species can support the construction of a biobank of neonatal respiratory microbiota to advance mechanistic studies and therapeutic strategies.},
}
@article {pmid40439013,
year = {2025},
author = {Alsergani, M and Zaini, RH and Al Kholaif, N and Al Admawi, M and Savo, MT and Cozac, DA and Tansella, D and Aladani, BA and Di Michele, S and Pergola, V},
title = {Infective endocarditis and oral health: a long-known threat, still a challenge.},
journal = {Monaldi archives for chest disease = Archivio Monaldi per le malattie del torace},
volume = {},
number = {},
pages = {},
doi = {10.4081/monaldi.2025.3497},
pmid = {40439013},
issn = {2532-5264},
abstract = {Infective endocarditis (IE) remains a life-threatening condition associated with high morbidity and mortality, often influenced by the complex interplay between systemic and oral health. The increasing recognition of oral health as a risk modifier has led to greater focus on the oral microbiome, dental procedures, and periodontal disease as potential contributors to bacteremia and IE. This review critically examines the relationship between oral health and IE, exploring pathophysiological mechanisms, risk factors, and the evolving epidemiology of the disease. The discussion includes diagnostic challenges, particularly in culture-negative cases, and the emerging role of advanced imaging and molecular diagnostics in improving early detection. A central focus is placed on preventive strategies, highlighting the debate surrounding antibiotic prophylaxis (AP) in high-risk individuals and the potential role of periodontal therapy in reducing systemic inflammation and transient bacteremia. The review also addresses the growing concern of antimicrobial resistance and the necessity of balancing AP recommendations with antimicrobial stewardship. Additionally, this review identifies critical research gaps, including the need for longitudinal studies on the impact of oral health interventions on IE incidence and the importance of interdisciplinary collaboration between dental and medical professionals in optimizing patient care. By synthesizing current guidelines and emerging evidence, this review underscores the necessity of an integrated, multidisciplinary approach to mitigate the burden of IE and establish oral health as a key pillar of infection prevention.},
}
@article {pmid40438840,
year = {2025},
author = {Saleem, MM and Masood, S and Rahmatullah, MM and Ayesha Imdad, I and Mohammed Aslam Sange, A and Nasr, D},
title = {Gut Microbiota Dysbiosis and Its Role in the Development of Irritable Bowel Syndrome.},
journal = {Cureus},
volume = {17},
number = {4},
pages = {e83084},
pmid = {40438840},
issn = {2168-8184},
abstract = {The gut microbiota refers to the diverse community of symbiotic and pathogenic microorganisms inhabiting the host digestive tract. This microbiome plays a vital role in maintaining the integrity of the digestive system. Irritable bowel syndrome (IBS) is a functional gastrointestinal disorder (FGID) characterized by chronic abdominal pain and altered bowel habits. Although the pathophysiology of IBS remains unclear, recent studies suggest that the disruption of the gut microbiota (dysbiosis) may play a significant role. This study aims to examine the role of the gut microbiota in the development of IBS, analyze factors influencing the gut microbiome, and explore the potential for microbiota-targeted therapies. Relevant literature published from 2014 until 2024 was sourced from Google Scholar, PubMed, and Scopus using the keywords "microbiome", "irritable bowel syndrome", "dysbiosis", "faecal transplantation", and "probiotics". This review revealed consistent evidence of gut microbiota dysbiosis in individuals with IBS, characterized by altered microbial diversity, composition, and metabolic function. Contributing factors included a reduced abundance of beneficial commensals, overgrowth of potentially pathogenic species, and disrupted host-microbiota interactions. This dysbiosis was also frequently associated with symptom severity and specific IBS subtypes. Emerging evidence further highlights the role of diet, stress, and genetic factors in modulating gut microbiota and influencing IBS development. The growing body of research supports a strong link between dysbiosis and the pathogenesis and symptomatology of IBS. Understanding the microbial underpinnings of IBS opens avenues for potential diagnostic biomarkers and innovative therapeutic interventions aimed at restoring a balanced gut microbiota. However, further research is needed to elucidate the underlying mechanisms and translate these insights into effective clinical strategies for the management of IBS. This review underscores the significance of gut microbiota in IBS and its potential as a target for future therapeutic interventions.},
}
@article {pmid40438776,
year = {2025},
author = {Lomelí-Valdez, R and Orozco-Covarrubias, L and Sáez-de-Ocariz, M},
title = {Skin and systemic infections in children with atopic dermatitis: review of the current evidence.},
journal = {Frontiers in pediatrics},
volume = {13},
number = {},
pages = {1513969},
pmid = {40438776},
issn = {2296-2360},
abstract = {Atopic dermatitis is a chronic, pruritic inflammatory skin disorder that affects approximately 2%-42% of children worldwide. Its course is frequently complicated by secondary bacterial, viral, and fungal infections, which can exacerbate disease severity and hinder treatment outcomes. These infections are thought to arise due to a disrupted skin barrier, reduced antimicrobial peptide production, alterations in the skin microbiome, and Th2-dominant inflammatory response. Identifying the most prevalent and pathogenic microorganisms in patients with AD is critical for early diagnosis, effective management, and prevention of complications. This review provides an updated synthesis of current knowledge on the infectious agents implicated in AD pathogenesis, summarizing recent findings on the epidemiology, microbial interactions, and immune mechanisms involved. Furthermore, it provides an overview of the latest therapeutic strategies for managing AD and its associated infections. By integrating recent insights into pathogenesis and treatment, this study offers a comprehensive perspective on the evolving landscape of AD management in children.},
}
@article {pmid40438731,
year = {2025},
author = {Gyriki, D and Nikolaidis, CG and Bezirtzoglou, E and Voidarou, C and Stavropoulou, E and Tsigalou, C},
title = {The gut microbiota and aging: interactions, implications, and interventions.},
journal = {Frontiers in aging},
volume = {6},
number = {},
pages = {1452917},
pmid = {40438731},
issn = {2673-6217},
abstract = {The human microbiota, a complex ecosystem of microorganisms inhabiting various body sites, particularly the gut, plays a crucial role in maintaining health and influencing disease susceptibility. Dysbiosis, characterized by alterations in microbial composition and diversity, has been implicated in numerous diseases, including those associated with aging. This review examines the complex relationship between gut microbiota and aging, highlighting the age-associated gut microbiota alterations, the factors contributing to these changes, the links between microbiota and age-related diseases, and the potential of interventions targeting the microbiome to extend lifespan and improve health outcomes in the elderly. Further research is needed to unravel the intricate mechanisms underlying the interplay between the microbiome and aging, paving the way for innovative strategies to promote healthy aging.},
}
@article {pmid40438491,
year = {2025},
author = {Pongsupasamit, P and Thonusin, C and Luewan, S and Chattipakorn, N and Chattipakorn, SC},
title = {Beyond hormones: 3PM approach to vaginal microbiota dynamics in postmenopausal women.},
journal = {The EPMA journal},
volume = {16},
number = {2},
pages = {299-350},
pmid = {40438491},
issn = {1878-5077},
abstract = {Menopause marks a critical transition characterized by ceased ovarian function and declining estrogen levels, affecting multiple systems with vasomotor symptoms and genitourinary syndrome of menopause (GSM). Recent evidence shows vaginal microbiota undergoes significant alterations during menopause, influencing GSM severity. This comprehensive review examined vaginal microbiota dynamics in postmenopausal women through Predictive, Preventive, and Personalized Medicine (3PM/PPPM), revealing characteristic shifts-increased alpha diversity, reduced Lactobacillus dominance, and transitions toward non-Lactobacillus species-that serve as potential predictive biomarkers for the menopausal state, premature ovarian insufficiency, and GSM symptoms. The analysis evaluated microbiota-based risk stratification strategies for vaginal dysbiosis and demonstrated the effectiveness of both hormonal interventions (systemic/local estrogen, tibolone, ospemifene) and non-hormonal alternatives (probiotics, energy-based devices, pessary) in normalizing microbiota composition and improving vaginal health. The application of PPPM/3PM transformed menopausal healthcare from reactive to proactive precision-based care by establishing microbiota-based biomarkers that predict health risks, enable early targeted interventions tailored to specific microbiota profiles, and guide personalized treatment approaches based on individual microbial compositions. While this paradigm shift significantly advances gynecological medicine, research gaps remain in validating baseline microbiota signatures as predictive biomarkers and establishing standardized screening protocols. Further studies are needed to validate interventions such as probiotics and prebiotics, optimizing strain selection for personalized, evidence-based preventive and therapeutic strategies. Developing standardized yet personalized protocols to restore a balanced vaginal microbiome could help alleviate menopause-related symptoms. Advancing microbiota-based personalized therapeutic approaches is crucial to enhancing the quality of life for postmenopausal women through targeted and individualized vaginal health management.},
}
@article {pmid40438350,
year = {2025},
author = {Peng, H and Fu, J},
title = {Unveiling horizontal gene transfer in the gut microbiome: bioinformatic strategies and challenges in metagenomics analysis.},
journal = {National science review},
volume = {12},
number = {6},
pages = {nwaf128},
pmid = {40438350},
issn = {2053-714X},
}
@article {pmid40438348,
year = {2025},
author = {Cao, J and Zhang, Y and Zhang, W and Zhang, F and Wang, J},
title = {Deep-learning of Nanopore sequences reveals the 6mA distribution and dynamics in human gut microbiome.},
journal = {National science review},
volume = {12},
number = {6},
pages = {nwaf120},
pmid = {40438348},
issn = {2053-714X},
}
@article {pmid40438215,
year = {2025},
author = {Hanna, A and Abbas, H and Yassine, F and AlBush, A and Bilen, M},
title = {Systematic review of gut microbiota composition, metabolic alterations, and the effects of treatments on PCOS and gut microbiota across human and animal studies.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1549499},
pmid = {40438215},
issn = {1664-302X},
abstract = {INTRODUCTION: Polycystic ovary syndrome (PCOS) is an endocrine disorder affecting around 12% of women globally, associated with infertility and various comorbidities. Emerging evidence suggests a crucial role of gut microbiota in PCOS pathophysiology, prompting research to investigate alterations in gut microbial composition in patients with PCOS.<br><br>METHODS: This systematic review aims to analyze human and animal studies that compare gut microbiota composition, gut-derived metabolites, and treatment interventions in PCOS patients versus healthy controls. A comprehensive literature search was conducted using PubMed, Scopus, and Web of Science, yielding studies examining gut microbiota, metabolomic shifts, and treatment responses in PCOS models and human populations.<br><br>RESULTS: Our analysis revealed decreases in alpha diversity in PCOS patients, with more pronounced changes in beta diversity in animal models. Specific bacterial taxa, such as Bacteroides vulgatus, Escherichia-Shigella and Lactobacillus, showed implication in PCOS pathogenesis, suggesting potential microbial markers. Furthermore, discrepancies between human and animal studies show the need for humanized mouse models to bridge this gap. Interventions like probiotics and fecal microbiota transplantation (FMT) showed varying levels of efficacy, with FMT emerging as a more promising but invasive option, offering live bacteriotherapy as a potential therapeutic alternative. Alterations in gut-derived metabolites, including short-chain fatty acids and bile acids, highlighted the multifaceted nature of PCOS, with implications extending to metabolic, hormonal, and gut-brain axis disruptions.<br><br>DISCUSSION: In conclusion, PCOS exhibits complex interactions between gut microbiota and metabolic pathways, necessitating further research with standardized methods and larger sample sizes to elucidate the microbiome's role in PCOS.},
}
@article {pmid40438213,
year = {2025},
author = {Ignatyeva, O and Daniel, V and Zelenova, E and Cherdakli, A and Bolashova, E and Matkava, L and Shegurova, A and Volkov, M and Zagainova, A and Kashtanova, D and Ivanov, M and Bembeeva, B and Zubkov, V and Gordeev, A and Priputnevich, T and Yudin, V and Makarov, V and Keskinov, A and Kraevoy, S and Yudin, S and Skvortsova, V},
title = {The "crossover effect" of COVID-19 in pregnancy on the infant microbiome.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1569279},
pmid = {40438213},
issn = {1664-302X},
abstract = {BACKGROUND: The COVID-19 pandemic has had a significant impact on public health. However, the impact of COVID-19 infection during pregnancy on the microbiome of the mother and her newborn child still remains poorly understood.<br><br>METHODS: This study involved 94 mother-child pairs whose mothers had COVID-19 during pregnancy and 44 newborns as a control group recruited in 2018. Stool samples were collected from women before delivery and from infants at 5-7 days after birth and used for 16S rRNA sequencing.<br><br>RESULTS: We found that the microbiomes of infants exposed in utero to COVID-19 showed decreased microbial diversity and richness. Moreover, we observed a higher inter-sample variability between infant samples in the case group, which might suggest destabilization of their microbiomes. Neither alpha- nor beta-diversity metrics differed significantly between the groups depending on the trimester when the mother contracted COVID-19. Thus, the timing of prenatal COVID-19 exposure had no effect on the infant gut microbiome.<br><br>CONCLUSION: COVID-19 during pregnancy can significantly compromise the establishment of the infant gut microbiome presumably by disrupting the mother's microbiome.},
}
@article {pmid40438189,
year = {2025},
author = {Temmermans, J and Legein, M and Checchia, I and Felis, GE and Smets, W and Karise, R and Lebeer, S},
title = {Agricultural practices and pollinators modulate the anthosphere microbiome.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf026},
pmid = {40438189},
issn = {2730-6151},
abstract = {The flower microbiome is pivotal in plant health, influencing reproductive success, fruit quality, and pathogen vulnerability. However, the impact of intensified agricultural practices on these microbial communities remains to be understood. This study examines how specific agricultural practices influence the bacterial composition of the strawberry anthosphere, focusing on cultivation intensification. Intensified systems were defined by practices such as indoor glasshouse substrate-based cultivation, increased use of plant protection products, larger cultivation areas, and reliance on managed pollinators. Using citizen science and V4 16S rRNA gene sequencing, we found that flowers in these more intensively managed systems had lower bacterial diversity, more variable microbiomes, and loss of core taxa such as Sphingomonas and Pseudomonas. To determine if pollinators could help mitigate these effects, we conducted exclusion experiments. In a tunnel system, we observed that foraging pollinators facilitated the dispersal of specific bacteria, such as Staphylococcus and Pseudomonas, and increased flower bacterial richness. However, in an open field, foraging pollinators had no significant impact. Our findings highlight the significant impact of cultivation intensification on the anthosphere microbiome and suggest that pollinators may play a role in restoring microbiome diversity. This research fills a critical gap in understanding how agricultural practices shape plant microbiomes and underscores the potential for microbe-based strategies to improve plant health in intensively managed systems.},
}
@article {pmid40438118,
year = {2025},
author = {Diallo, D and Sun, S and Somboro, AM and Baya, B and Koné, A and Diarra, B and Nantoumé, M and Koloma, I and Diakite, M and Holl, J and Maiga, AI and Seydi, M and Theron, G and Hou, L and Fodor, A and Maiga, M},
title = {Metabolic and immune consequences of antibiotic related microbiome alterations during first-line tuberculosis treatment in Bamako, Mali.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1561459},
pmid = {40438118},
issn = {1664-3224},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/immunology ; Male ; Female ; Adult ; Mali ; *Dysbiosis/chemically induced/immunology ; Middle Aged ; *Tuberculosis/drug therapy/microbiology/immunology/metabolism ; Cytokines/blood ; Longitudinal Studies ; *Antitubercular Agents/therapeutic use/adverse effects ; Young Adult ; Metabolomics ; },
abstract = {BACKGROUND: Individuals with a history of tuberculosis (TB) treatment are at a higher risk of experiencing a recurrent episode of the disease. Previous cross-sectional studies identified a connection between dysbiosis (alterations) in the gut microbiota composition and the administration of first-line TB antibiotics. However, these studies have not successfully elucidated this dysbiosis's resulting metabolic and immune consequences.<br><br>METHODS: In a longitudinal assessment, we studied the antituberculosis drug-related changes in the gut microbiota's composition and the resulting functional consequences. Sputum for TB culture, peripheral blood for metabolomics and cytokines analysis, and stool for shotgun metagenomics were collected from TB participants at Month-0, Month-2, Month-6 of treatment, and 9 Months after treatment (Month-15). Healthy controls were sampled at Month-0 and Month-6.<br><br>FINDINGS: We found notable differences in gut microbiota between individuals with TB and healthy controls. While gut microbiota tended to resemble healthy controls at the end of TB treatment, significant differences for many taxa persisted up to Month-15. Concurrently, disturbances in plasma metabolites, including tryptophan, tricarboxylic acids, and cytokine levels were observed. Certain fatty acids associated with inflammation pathways negatively correlated with the abundance of several taxa.<br><br>CONCLUSION: We observed alterations in the gut microbiota composition and function during treatment and at Month-15. Numerous changes in bacterial taxa abundances and inflammation-linked metabolites did not reverse at Month-15. This study suggests potential influences of anti-TB drugs and the gut microbiome on the disease outcome, response to treatment, and resistance to future TB infections.},
}
@article {pmid40438084,
year = {2025},
author = {Intini, R and Balsells, S and Bagan, L and Fortuna, G and Sroussi, H and Bagan, J},
title = {Comparative analysis of oral microbiome in saliva samples of oral leukoplakia, proliferative leukoplakia and oral squamous cell carcinoma.},
journal = {Frontiers in oral health},
volume = {6},
number = {},
pages = {1600090},
pmid = {40438084},
issn = {2673-4842},
abstract = {BACKGROUND: Oral potentially malignant disorders (OPMDs), including conventional leukoplakia (OL) and proliferative verrucous leukoplakia (PVL), have distinct risks of progression to oral squamous cell carcinoma (OSCC). A role of the oral microbiome in this transformation is increasingly recognized, but its contribution remains unclear.<br><br>OBJECTIVE: This study aimed to analyze and compare the oral microbiota in patients with OL, PVL, and OSCC using 16S rRNA gene sequencing of saliva samples to identify microbial signatures associated with disease progression and to uncover potential biomarkers that would justify an aggressive treatment of OPMDs.<br><br>METHODS: Sixty-six subjects with OPMDs were enrolled, comprising OL (n&#x2009;=&#x2009;10), PVL (n&#x2009;=&#x2009;28), and OSCC (n&#x2009;=&#x2009;28). Saliva samples were collected, and DNA was extracted. The V3-V4 regions of the 16S rRNA gene were sequenced using the Illumina MiSeq platform. Bioinformatic analyses, including diversity assessments and taxonomic classification with the SILVA v138 database, were performed using QIIME2. Alpha diversity was evaluated with Chao1, Shannon, and Simpson indices, while beta diversity was assessed using Bray-Curtis and Jaccard distances.<br><br>RESULTS: PVL exhibited the highest species richness, followed by OL, with OSCC showing the lowest diversity. While alpha diversity differences among the groups were not statistically significant (p&#x2009;>&#x2009;0.05), beta diversity revealed distinct microbial community structures between OL and both PVL and OSCC (p&#x2009;<&#x2009;0.05), but not between PVL and OSCC. At the phylum level, Firmicutes predominated across all groups, with significantly higher Actinobacteriota levels in OL (p&#x2009;=&#x2009;0.002).<br><br>CONCLUSION: Distinct microbial patterns differentiate OL from PVL and OSCC, with OL being different from PVL and OSCC, suggesting progressive microbial dysbiosis in malignant transformation. These findings support the potential of oral microbiome profiling as a non-invasive diagnostic and prognostic tool in oral oncology and highlight the need for longitudinal studies to establish causal relationships.},
}
@article {pmid40437865,
year = {2025},
author = {},
title = {Correction to "Effects of a ketogenic and low-fat diet on the human metabolome, microbiome, and foodome in adults at risk for Alzheimer's disease".},
journal = {Alzheimer's &amp; dementia : the journal of the Alzheimer's Association},
volume = {21},
number = {5},
pages = {e14281},
doi = {10.1002/alz.14281},
pmid = {40437865},
issn = {1552-5279},
}
@article {pmid40437630,
year = {2025},
author = {Almarmouri, C and El-Gamal, MI and Haider, M and Hamad, M and Qumar, S and Sebastian, M and Ghemrawi, R and Muhammad, JS and Burucoa, C and Khoder, G},
title = {Anti-urease therapy: a targeted approach to mitigating antibiotic resistance in Helicobacter pylori while preserving the gut microflora.},
journal = {Gut pathogens},
volume = {17},
number = {1},
pages = {37},
pmid = {40437630},
issn = {1757-4749},
support = {2201110266//University of Sharjah/ ; 24011102102//University of Sharjah/ ; },
abstract = {The global rise in antibiotic resistance has posed significant challenges to the effective management of Helicobacter pylori (H. pylori), a gastric pathogen linked to chronic gastritis, peptic ulcers, and gastric cancer. Conventional antibiotic therapies, while effective, face significant challenges, such as increasing antibiotic resistance, high recurrence rates, and adverse effects such as gut microflora dysbiosis. These limitations have driven the exploration of alternative antibiotic-free therapies, including the use of plant-based compounds, probiotics, nanoparticles, phage therapy, antimicrobial peptides, and H. pylori vaccines. Among these, urease-targeted therapy has shown particular promise. Urease enables the survival and colonization of H. pylori by neutralizing stomach acidity. Targeting this urease without disrupting beneficial gut microflora offers a selective mechanism to impair H. pylori, due to the absence of this enzyme in most of the human gut microbiome. In this review, we highlight advancements and limitations in the field of antibiotic-free therapies, with a particular focus on anti-urease strategies. We explore the structural and functional characteristics of urease, its role in H. pylori pathogenesis, and its potential as a therapeutic target. For the first time, we provide a comprehensive analysis of natural, semisynthetic, and synthetic anti-urease compounds, emphasizing their mechanisms of action, efficacy, and safety profiles. Advances in silico, in vitro, and in vivo studies have identified several promising anti-urease compounds with high specificity and minimal toxicity. By focusing on urease inhibition as a targeted strategy, this review underscores its potential to overcome antibiotic resistance while minimizing gut dysbiosis and improving the outcomes of H. pylori infection treatment.},
}
@article {pmid40437450,
year = {2025},
author = {Yang, S and Zhang, S and Cao, Q and Zhu, G and Liu, J and Li, G and Zhu, M},
title = {Association between oral microbial diversity (only bacteria) and diabetes in U.S. adults: analysis of NHANES 2009-2012 data.},
journal = {BMC oral health},
volume = {25},
number = {1},
pages = {837},
pmid = {40437450},
issn = {1472-6831},
support = {JSYGY-3-2024-123//Jiangsu Hospital Association's Hospital Management Innovation Research Program/ ; KX-24-C039//Wuxi Association for Science and Technology's Key Soft Science Project/ ; T202325//Wuxi Municipal Health Commission's Science and Technology Achievements and Appropriate Technology Promotion Project/ ; },
mesh = {Humans ; Male ; Cross-Sectional Studies ; Female ; United States/epidemiology ; *Diabetes Mellitus/microbiology/epidemiology ; Adult ; Middle Aged ; *Mouth/microbiology ; Nutrition Surveys ; Microbiota ; Body Mass Index ; RNA, Ribosomal, 16S ; },
abstract = {OBJECTIVE: Studies on the relationship between oral microbial diversity and diabetes were limited. This study analyzed the oral microbial composition and diversity using NHANES data to explore its potential role in diabetes pathogenesis; Methods: A cross-sectional design was employed, utilizing NHANES data (2009-2012), including oral microbiota samples and diabetes-related indicators. Oral samples were collected via mouthwash and analyzed using 16 S rRNA gene sequencing. The Shannon-Wiener Index represented microbial diversity (Only bacteria). Multivariate logistic regression, restricted cubic splines, and subgroup analyses were employed to evaluate associations.<br><br>RESULTS: A significant association was found between oral microbial diversity and diabetes. According to the completely adjusted model, a one-unit increment in the Shannon-Wiener Index was associated with a 12.1% increase in the likelihood of developing diabetes (OR&#x2009;=&#x2009;1.121, 95%CI: 1.120&#x2009;~&#x2009;1.122). Subgroup analyses showed divergent findings. In subgroups with lower body weight and BMI, increased microbial diversity correlated with a decreased likelihood of developing diabetes (OR&#x2009;=&#x2009;0.68 (0.68-0.68)); Conclusions: Oral microbial diversity exhibits a complex relationship with diabetes risk. The increase and subsequent decrease of oral microbiota diversity in relation to diabetes risk. This suggests that certain specific microbes or interactions between microbes may influence the development of diabetes. However, due to the many limitations of this study, it cannot prove the causal relationship between oral microbial richness and diabetes. Further longitudinal and mechanistic studies are essential to elucidate the causal links and dynamic alterations between the oral microbiome and the progression of diabetes.},
}
@article {pmid40437375,
year = {2025},
author = {Qin, S and Yang, Z and Lei, J and Xie, Q and Jiang, L and Fan, Y and Luo, Y and Wei, K and Luo, W and Yu, B},
title = {Comparative efficacy of preventive vs. therapeutic resveratrol in modulating gut microbiota and alleviating inflammation in DSS-induced colitis.},
journal = {BMC immunology},
volume = {26},
number = {1},
pages = {42},
doi = {10.1186/s12865-025-00718-3},
pmid = {40437375},
issn = {1471-2172},
support = {No. 2023GXNSFAA026166//Natural Science Foundation of Guangxi Zhuang Autonomous Region/ ; No. 2024GXNSFAA010132//Natural Science Foundation of Guangxi Zhuang Autonomous Region/ ; GXZYA20230264//Guangxi Zhuang Autonomous Region Administration of Traditional Chinese Medicine/ ; No. 82260109//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Resveratrol/therapeutic use/pharmacology ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Colitis/chemically induced/drug therapy/microbiology/prevention &amp; control/immunology ; Dextran Sulfate ; Disease Models, Animal ; Mice, Inbred C57BL ; Cytokines/metabolism ; Inflammation/drug therapy ; Toll-Like Receptor 4/metabolism ; Macrophages/immunology ; Male ; Intestinal Mucosa/drug effects/pathology ; Humans ; *Anti-Inflammatory Agents/pharmacology/therapeutic use ; NF-kappa B/metabolism ; },
abstract = {BACKGROUND: Inflammatory bowel disease (IBD) management remains challenging due to limited preventive strategies and the low bioavailability of therapeutic agents like resveratrol (RSV). While RSV exhibits anti-inflammatory properties, its preventive potential via gut microbiome modulation remains unexplored.<br><br>METHODS: A murine colitis model was established using 2.5% DSS, with mice randomized into control (CON), DSS, therapeutic RSV treatment (RSV), and preventive RSV treatment (PRE) groups. Clinical outcomes, intestinal barrier integrity, inflammatory cytokines, macrophage polarization, TLR4/NF-&#x3ba;B signaling, and gut microbiota (16S rRNA sequencing) were systematically evaluated.<br><br>RESULTS: Preventive RSV (PRE) outperformed therapeutic RSV across all metrics. PRE attenuated colitis severity by 51.4% (weight loss, P&#x2009;<&#x2009;0.001 vs. RSV) and restored mucosal architecture (P&#x2009;=&#x2009;0.048 vs. DSS). Mechanistically, PRE normalized barrier function via transcriptional (ZO-1: 56.7% of CON; Occludin: 14-fold induction vs. DSS) and protein-level recovery (ZO-1: 96.5% of CON, P&#x2009;=&#x2009;0.02), suppressed pro-inflammatory cytokines (TNF-&#x3b1;: 80.8%; IL-6: 69.9%; IL-18: >96%, P&#x2009;<&#x2009;0.001 vs. DSS), and promoted M2 macrophage polarization (CD206: 1.7-fold vs. CON, P&#x2009;=&#x2009;0.02) through TLR4/NF-&#x3ba;B inhibition (53% TLR4 reduction vs. 15% with RSV, P&#x2009;<&#x2009;0.001). Despite comparable &#x3b1;-diversity between RSV and PRE, PRE uniquely enriched barrier-protective taxa (Lactococcus, Muribaculum) and restored microbial amino acid biosynthesis. Crucially, PRE's efficacy despite low systemic bioavailability implicated microbiome-mediated "luminal priming" as its primary mechanism.<br><br>CONCLUSIONS: This study redefines preventive RSV as a microbial ecosystem engineer that preemptively fortifies the gut against inflammation via microbiome-immune-metabolic crosstalk. By prioritizing ecological prevention over symptom suppression, our findings offer a transformative "food as medicine" strategy for IBD, highlighting RSV's potential as a chronotherapeutic agent to reshape clinical paradigms.},
}
@article {pmid40437354,
year = {2025},
author = {Mekadim, C and Mrazek, J and Fliegerová, KO and Sechovcová, H and Mahayri, TM and Jarošíková, R and Husáková, J and Wosková, V and Tůma, P and Polák, J and Sojáková, D and Němcová, A and Dubský, M and Fejfarová, V},
title = {The effect of the administration form of antibiotic therapy on the gut microbiome in patients with infected diabetic foot ulcers - DFIATIM trial.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {339},
pmid = {40437354},
issn = {1471-2180},
support = {LX22NPO5104//the European Union- Next Generation EU/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Diabetic Foot/drug therapy/microbiology ; *Anti-Bacterial Agents/administration &amp; dosage/therapeutic use ; Male ; Middle Aged ; Female ; Aged ; Feces/microbiology ; Bacteria/classification/genetics/drug effects/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Dysbiosis/microbiology ; Ceftazidime/administration &amp; dosage/therapeutic use ; Amoxicillin-Potassium Clavulanate Combination/administration &amp; dosage ; },
abstract = {BACKGROUND: Diabetic foot infections (DFIs) contribute to the global disability burden. Beta-lactams are the most commonly used antibiotics for treating DFIs. However, the use of antibiotics may lead to disruption of the healthy balance of the gut microbiota, causing dysbiosis.<br><br>METHODS: Patients with infected diabetic foot ulcers (iDFUs) were treated with two kinds of beta-lactams (amoxicillin/clavulanic acid or ceftazidime) according to microbial sensitivity of causative agents via bolus or continuous administration modes. Changes in the gut microbiome of patients were analyzed. Diabetic patients without iDFUs were used as a control group. 16&#xa0;S ribosomal RNA gene amplicon sequencing was performed on stool samples collected from participants.<br><br>RESULTS: Alpha diversity and beta diversity of gut microbiota of treated patients did not show significant differences between bolus and continuous modes. However, significant differences were observed between gut microbiota diversity of treated patients and control group. PCoA plots showed individualized responses of the patient's gut microbiota to antibiotics at different times using both administration forms associated with the pre-treatment state of microbiota composition. Enterococcus, Sellimonas, and Lachnoclostridium were the common bacterial markers differentially abundant in the gut microbiota of antibiotic-treated patients with iDFUs while Roseburia, Dorea, and Monoglobus were mainly abundant in the gut microbiota of patients without iDFUs. Predicted pathways like "Transporters", "ABC transporters" and "Phosphotranspherase system (PTS)" were upregulated in the gut microbiome of patients treated with bolus regime which may lead to increased intestinal barrier permeability.<br><br>CONCLUSION: The present study reported alterations in gut microbiota composition and functionality and provided the bacterial markers as well as potential metabolic signatures associated with each administration mode in patients with iDFUs, which may be used as a reference set for future studies of the effect of antibiotics administration on the gut microbiome of patients with iDFUs. This study shed light on the importance of understanding the effect of antibiotic administration form on gut microbiome in patients with iDFUs.<br><br>TRIAL REGISTRATION: The DFIATIM Clinical Trial (Full title: "Rationalisation of ATB therapy in diabetic foot infection and its impact on the intestinal microbiota") is submitted to the European Union Clinical Trials Database under the EudraCT Number: 2019-001997-27. The date of registration is July 17th, 2020.},
}
@article {pmid40437350,
year = {2025},
author = {Benning, S and Mahmoud, FM and Espindola-Hernandez, P and Liu, B and Pritsch, K and Radl, V and Winkler, JB and Winkelmann, T and Beerhues, L and Schloter, M},
title = {Inoculation of apple plantlets with Rhodococcus pseudokoreensis R79[T] enhances diversity and modulates the structure of bacterial rhizosphere communities in soil affected by apple replant disease.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {715},
pmid = {40437350},
issn = {1471-2229},
mesh = {*Malus/microbiology ; *Rhizosphere ; *Soil Microbiology ; *Rhodococcus/physiology ; RNA, Ribosomal, 16S/genetics ; Plant Roots/microbiology ; *Plant Diseases/microbiology ; Biodiversity ; },
abstract = {BACKGROUND: Apple replant disease (ARD) represents a dysbiotic rhizosphere condition potentially driven by root exudates including phytoalexins at the root-soil interface. A promising mitigation strategy could be the application of bioinoculants that reduce these compounds and foster a diverse microbiome. This study investigated the effects of Rhodococcus pseudokoreensis R79[T], a strain with benzoate-degrading capabilities and genetic potential to degrade biphenyls, on the rhizosphere microbiome of apple plantlets grown in ARD-affected soil in a greenhouse experiment.<br><br>RESULTS: We applied R79[T] at 10&#x2076; to 10&#x2079; CFU/ml, assessing its impact on bacterial 16S rRNA diversity and abundance, as well as the abundance of biphenyl dioxygenase (bphd) genes. Eight weeks post-inoculation reads of strain R79[T] persisted in the rhizosphere, particularly at higher inoculation levels. Inoculation enhanced bacterial diversity and bphd gene abundance, with significant shifts in community composition. Key responders included members of Gaiellales, which increased, and Streptomyces, which decreased. Co-occurrence network analysis revealed that inoculation promoted positive interactions, more homogeneous connectivity, and a higher degree of connections. Effects on bacterial community structure varied significantly with inoculation concentration.<br><br>CONCLUSIONS: The fact that R79[T] enhanced rhizosphere bacterial diversity and modulated community composition in ARD-affected soil highlights the potential of R79[T] to reshape microbial interactions. Further research is needed to elucidate the mechanisms underlying these effects, including studies on in situ degradation of phytoalexins and inoculation of R79[T] alongside bacteria for plant growth promotion (PGP) in synthetic communities for elevated efficiency against ARD.},
}
@article {pmid40437096,
year = {2025},
author = {Yoshida, TM and Nguyen, M and Zhang, L and Lu, BY and Zhu, B and Murray, KN and Mineur, YS and Zhang, C and Xu, D and Lin, E and Luchsinger, J and Bhatta, S and Waizman, DA and Coden, ME and Ma, Y and Israni-Winger, K and Russo, A and Wang, H and Song, W and Al Souz, J and Zhao, H and Craft, JE and Picciotto, MR and Grutzendler, J and Distasio, M and Palm, NW and Hafler, DA and Wang, A},
title = {The subfornical organ is a nucleus for gut-derived T cells that regulate behaviour.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {40437096},
issn = {1476-4687},
abstract = {Specialized immune cells that reside in tissues orchestrate diverse biological functions by communicating with parenchymal cells[1]. The contribution of the innate immune compartment in the meninges and the central nervous system (CNS) is well-characterized; however, whether cells of the adaptive immune system reside in the brain and are involved in maintaining homeostasis is unclear[2-4]. Here we show that the subfornical organ (SFO) of the brain is a nucleus for parenchymal αβ T cells in the steady-state brain in both mice and humans. Using unbiased transcriptomics, we show that these extravascular T cells in the brain are distinct from meningeal T cells: they secrete IFNγ robustly and express tissue-residence proteins such as CXCR6, which are required for their retention in the brain and for normal adaptive behaviour. These T cells are primed in the periphery by the microbiome, and traffic from the white adipose and gastrointestinal tissues to the brain. Once established, their numbers can be modulated by alterations to either the gut microbiota or the composition of adipose tissue. In summary, we find that CD4 T cells reside in the brain at steady state and are anatomically concentrated in the SFO in mice and humans; that they are transcriptionally and functionally distinct from meningeal T cells; and that they secrete IFNγ to maintain CNS homeostasis through homeostatic fat-brain and gut-brain axes.},
}
@article {pmid40437008,
year = {2025},
author = {Zhu, Y and Wang, J and Zhang, X and Cidan, Y and Wang, H and Pubu, P and Ali, M and Li, K and Basang, W},
title = {Traditional Chinese herbal formulas modulate inflammatory mediators, antioxidant enzyme levels, and ruminal microbiota composition in postpartum female Yaks.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {18610},
pmid = {40437008},
issn = {2045-2322},
mesh = {Animals ; Female ; Cattle ; *Rumen/microbiology/drug effects ; Postpartum Period/drug effects ; *Antioxidants/metabolism ; *Drugs, Chinese Herbal/pharmacology ; *Gastrointestinal Microbiome/drug effects ; *Inflammation Mediators/metabolism ; Animal Feed ; Bacteria/genetics/classification ; },
abstract = {Traditional Chinese Medicine (TCM) is an emerging area due to increased antimicrobial resistance (AMR). The objective of this research was to explore the antioxidant, and anti-inflammatory potential of three traditional Chinese herbal formulas (TCHFs), along with variations in rumen bacteria. In this study, forty postpartum (80 ± 15) female yaks after the calves had weaned (PWFs) were divided into three experimental groups, which were offered basal feed with 5% (95% basal diet) TCHF1 (DE group), 5% TCHF2 (DF group) and 5% TCHF3 (DG group), and fourth, control group (DH group), fed only a basal diet for 30 days. Following blood and rumen fluid samples on the 15th and 30th day, ELISA testing was performed to check antioxidant enzyme levels and inflammatory mediators. The results indicated that TCHF2 significantly upregulated the interleukin-10 (IL-10) (p < 0.05). Additionally, 16 S rRNA sequencing results showed that TCHF2 significantly enhanced Firmicutes to Bacteroidetes ratio (F/B) at the phylum level. On day 15th, phylum Actinobacteria, SR1, Cyanobacteria, and Armatimonadetes were found to be significantly (p < 0.05) different, while, at the genus level, Butyrivibrio, CF231, YRC22, Moraxella, Clostridium, etc. were significantly different (p < 0.05). On day 30, phylum SR1, Armatimonadetes, Chlorobi, and genus Coprococcus, Oscillospira, Selenomonas, L7A_E11, Clostridium, etc. were found to be significantly different (p < 0.05). This study concluded that TCHF2 is the most effective one among all.},
}
@article {pmid40436959,
year = {2025},
author = {Nath, S and Zilm, P and Jamieson, L and Santiago, PHR and Ketagoda, DHK and Weyrich, L},
title = {The influence of diet, saliva, and dental history on the oral microbiome in healthy, caries-free Australian adults.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {18755},
pmid = {40436959},
issn = {2045-2322},
support = {2019/GNT1187737//NHMRC Ideas Grant/ ; },
mesh = {Humans ; *Saliva/microbiology ; Adult ; Middle Aged ; Male ; Female ; *Microbiota ; Aged ; *Dental Caries/microbiology ; Young Adult ; Adolescent ; Cross-Sectional Studies ; Australia ; *Diet ; Aged, 80 and over ; RNA, Ribosomal, 16S/genetics ; *Mouth/microbiology ; Hydrogen-Ion Concentration ; },
abstract = {Oral microbiome transplantation (OMT) has the potential to serve as a therapeutic approach for managing dental caries; however, it is essential to identify suitable donors. The aim of this study was to analyse the relationship between dietary (i.e., energy, water, carbohydrate and sugar intake), saliva quality (i.e., saliva flow rate and salivary pH), and clinical factors (i.e., past caries experience and fluoride exposure) on the oral microbiome composition of potential OMT donors. For this cross-sectional study, a comprehensive dental examination was conducted for 93 healthy, caries-free adults (aged 18-85 years) without systemic or oral disease. All participants completed questionnaires on food frequency and socio-economic, lifestyle, and behavioural factors. Supragingival plaque samples were collected, and bacterial 16S rRNA genes were amplified, sequenced, and assigned to bacterial taxa. Stimulated saliva samples were collected for salivary flow rate and pH measurements. Constrained partial ordination analysis revealed that dietary factors, such as carbohydrate and sugar intake, had strong directional influences on microbial composition, while salivary factors like flow rate and pH showed opposing effects. Correlation analysis linked high sugar intake and reduced salivary pH to increased Streptococcus abundance. Differential abundance analysis identified significantly higher abundance of Streptococcus species among low water and high carbohydrate and sugar consumers. In mediation analysis, sugar consumption was directly and indirectly linked to reduced salivary pH, with Streptococcus showing a significant negative mediation effect (mean: -0.198; 95% CI: -0.387 to -0.010). High carbohydrate and sugar intake significantly influenced alpha diversity metrics (p < 0.05). Beta diversity permutational multivariate ANOVA revealed that covariates explained 11.45-12.52% of microbial variation (p < 0.05). This study emphasises that OMT donors with diverse oral microbiomes, low sugar and carbohydrate intake, and reduced levels of acidogenic taxa, such as Streptococcus, which significantly mediate salivary pH reduction, may be preferred for caries prevention.},
}
@article {pmid40436954,
year = {2025},
author = {Rahimi-Rizi, M and Norouzi, H and Sohrabi, M and Dashtipoor, S and Omidi Nasab, M and Boustie, J},
title = {Elevational microhabitats influence some endolichenic traits of Umbilicaria aprina, an alpine lichen species.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {18602},
pmid = {40436954},
issn = {2045-2322},
mesh = {*Lichens/metabolism/microbiology/physiology ; *Altitude ; Microbiota ; *Ecosystem ; Metabolomics/methods ; Metabolome ; },
abstract = {Understanding the dynamics of lichen-environment interactions, particularly in terms of elemental composition, microbial, and metabolic profiles, is crucial for elucidating the adaptive strategies of lichens. Here we aimed to investigate the impact of elevational microhabitats on the elemental compositions, microbial profiles, and metabolic profiles of different colonies of Umbilicaria aprina along an elevational gradient. Ionomics showed variations in elemental compositions of colonies at different elevations with distinct patterns of accumulation for specific elements. Untargeted metabolomics revealed metabolic alterations in different colonies of U. aprina across elevations, suggesting a potential role of lichen secondary metabolites in responding to environmental changes. Culture-based analysis of microbiome also showed variations in the microbial profiles of colonies with changes in elevation, confirming the influence of elevational microhabitats on lichen-associated microbial communities. We further examined possible correlations between the relative intensity of different metabolites and the other two endolichenic traits (i.e., elemental composition and microbial profile). Although no consistent correlative patterns emerged, some metabolite-specific correlations were observed. Overall, our study shows that certain endolichenic traits undergo variations even within a restricted alpine range, corresponding to minor changes in environmental conditions.},
}
@article {pmid40436643,
year = {2025},
author = {Li, J and Wu, Y and Yang, Y and Chen, L and He, C and Zhou, S and Huang, S and Zhang, X and Wang, Y and Gui, Q and Lu, H and Zhang, Q and Yang, Y},
title = {Metagenomics reveals an increased proportion of an Escherichia coli-dominated enterotype in elderly Chinese people.},
journal = {Journal of Zhejiang University. Science. B},
volume = {26},
number = {5},
pages = {477-492},
doi = {10.1631/jzus.B2400341},
pmid = {40436643},
issn = {1862-1783},
support = {82101665, 82271588, 82200665 and 82100795//the National Natural Science Foundation of China/ ; LY22H030009//the Zhejiang Provincial Natural Science Foundation of China/ ; 2023ZL480//the Zhejiang Provincial Science and Technology Program of Traditional Chinese Medicine/ ; 2023RC153//the Medical and Health Research Project of Zhejiang Province/ ; },
mesh = {Aged ; Aged, 80 and over ; Female ; Humans ; Male ; Middle Aged ; Bacteroides ; China ; Diabetes Mellitus, Type 2/microbiology ; *Escherichia coli/genetics/isolation &amp; purification/classification ; *Gastrointestinal Microbiome/genetics ; *Metagenomics ; East Asian People ; },
abstract = {Gut microbial communities are likely remodeled in tandem with accumulated physiological decline during aging, yet there is limited understanding of gut microbiome variation in advanced age. Here, we performed a metagenomics-based enterotype analysis in a geographically homogeneous cohort of 367 enrolled Chinese individuals between the ages of 60 and 94 years, with the goal of characterizing the gut microbiome of elderly individuals and identifying factors linked to enterotype variations. In addition to two adult-like enterotypes dominated by Bacteroides (ET-Bacteroides) and Prevotella (ET-Prevotella), we identified a novel enterotype dominated by Escherichia (ET-Escherichia), whose prevalence increased in advanced age. Our data demonstrated that age explained more of the variance in the gut microbiome than previously identified factors such as type 2 diabetes mellitus (T2DM) or diet. We characterized the distinct taxonomic and functional profiles of ET-Escherichia, and found the strongest cohesion and highest robustness of the microbial co-occurrence network in this enterotype, as well as the lowest species diversity. In addition, we carried out a series of correlation analyses and co-abundance network analyses, which showed that several factors were likely linked to the overabundance of Escherichia members, including advanced age, vegetable intake, and fruit intake. Overall, our data revealed an enterotype variation characterized by Escherichia enrichment in the elderly population. Considering the different age distribution of each enterotype, these findings provide new insights into the changes that occur in the gut microbiome with age and highlight the importance of microbiome-based stratification of elderly individuals.},
}
@article {pmid40436366,
year = {2025},
author = {DiK, B and Hatipoglu, D and Kahraman, O and Parlak, TM and Inanc, ZS and Celik, M and Damar, S},
title = {Liraglutide as a Novel Therapeutic for Overweight in Canines: A Clinical Study.},
journal = {Veterinary journal (London, England : 1997)},
volume = {},
number = {},
pages = {106376},
doi = {10.1016/j.tvjl.2025.106376},
pmid = {40436366},
issn = {1532-2971},
abstract = {BACKGROUND: The overweight/obesity in dogs is defined as a condition of abnormal fat accumulation or, beyond that, a multifactorial condition involving excessive fat accumulation along with different factors (insufficient physical activity, genetics (breed), metabolism, the microbiome, etc.). Preclinical obesity conditions increases the risk of progressing to clinical obesity and developing obesity-associated diseases such as type 2 diabetes, cardiovascular disease, certain cancers, and mental disorders.<br><br>OBJECTIVES: This study aimed to determine the weight-loss effects of liraglutide in dogs that do not engage in sufficient exercise, are fed table scraps, and develop obesity owing to aging.<br><br>ANIMALS: In this study, 21 senior Golden Retriever dogs were divided into three equal groups.<br><br>METHODS: Group 1 was considered healthy and consisted of dogs within the range of ideal body live weight and body condition scores, and fed dry commercial dog food at the amount of their daily metabolizable energy requirements. Group 2 included seven senior dogs with obesity fed commercial dry food adjusted for their daily metabolizable energy requirements. Group 3 comprised seven senior dogs with obesity fed commercial dry food adjusted for their daily energy requirements and concurrently treated with subcutaneous liraglutide at a dose of 1.2mg/dog. The trial lasted for 40 days.<br><br>RESULTS: Liraglutide treatment resulted in a decrease in body condition score (BCS) and body weight by day 40, although the reduction in body weight (13.27%) did not reach statistical significance. Liraglutide significantly lowered cholesterol and triglyceride levels, and appetite tests revealed a marked suppression of food intake over consecutive days in treated dogs.<br><br>Liraglutide treatment may offer a viable option for treating obesity in dogs, and could potentially be used as a new anti-obesity drug in canines. Future long-term and detailed trials of liraglutide in dogs with obesity could facilitate its effective use in the field.},
}
@article {pmid40436194,
year = {2025},
author = {Chang, VC and Purandare, V and Li, S and Andreotti, G and Hua, X and Wan, Y and Dagnall, CL and Jones, K and Hicks, BD and Hutchinson, A and Yano, Y and Dalton, KR and Lee, M and Parks, CG and London, SJ and Sandler, DP and Gail, MH and Shi, J and Hofmann, JN and Sinha, R and Abnet, CC and Vogtmann, E and Beane Freeman, LE},
title = {Animal farming and the oral microbiome in the Agricultural Health Study.},
journal = {Environmental research},
volume = {},
number = {},
pages = {121964},
doi = {10.1016/j.envres.2025.121964},
pmid = {40436194},
issn = {1096-0953},
abstract = {BACKGROUND: Raising farm animals imparts various exposures that may shape the human microbiome. The oral microbiome has been increasingly implicated in disease development. Animal farming has also been associated with certain chronic diseases such as cancer; however, underlying biological mechanisms are unclear. We investigated associations between raising farm animals and the oral microbiome in the Agricultural Health Study.<br><br>METHODS: This analysis included 1,245 participants (865 farmers and 380 spouses) who provided oral wash specimens and information on types and numbers of specific animals raised on their farms within 2 years before sample collection. The oral microbiome was measured by sequencing the V4 region of the 16S ribosomal RNA gene. We evaluated associations of farm animal exposures with alpha and beta diversity metrics (within- and between-sample diversity, respectively), as well as presence and relative abundance of specific bacterial genera. All analyses adjusted for potential confounders (e.g., age, sex, smoking, alcohol consumption).<br><br>RESULTS: Overall, 63% of participants raised farm animals, most commonly cattle (46%) and hogs (20%). Those who raised a large number of hogs (&#x2265;2,000 vs. no hogs) had higher alpha diversity. Conversely, raising sheep/goats and raising larger numbers of poultry were associated with lower alpha diversity. Beta diversity was not significantly different between participants with and without any farm animals. Participants raising any farm animals had higher relative abundance of Porphyromonas and lower relative abundances of Prevotella and Ruminococcaceae UCG-014. Several genera were more likely to be absent with specific animal exposures (e.g., Capnocytophaga for cattle and sheep/goats; Corynebacterium, Dialister, Stomatobaculum, and Solobacterium for sheep/goats and poultry).<br><br>CONCLUSIONS: This was the largest study of farm animal exposures and the human microbiome to date. Findings suggest that raising specific farm animals may influence the oral microbiome, supporting the need to further investigate the potential role of animal farming in disease etiology.},
}
@article {pmid40435940,
year = {2025},
author = {Wang, J and Tan, Q and Ni, M and Chen, F and Yang, J and Wang, G and Zhao, X and Zhang, X and Zhang, S},
title = {High-Fat Diet-Induced Gut Microbiota Disruption Promotes Colorectal Cancer Lymphatic Metastasis via Propionate/GPR41 Signaling.},
journal = {Digestion},
volume = {},
number = {},
pages = {1-27},
doi = {10.1159/000545843},
pmid = {40435940},
issn = {1421-9867},
abstract = {OBJECTIVE: High-fat diets (HFD) are known to affect the gut microbiome structure and potentially promote the development and metastasis of colorectal cancer (CRC). This study aims to elucidate the molecular mechanisms through which gut microbiome dysbiosis, mediated by the propionate/GPR41 signaling pathway, promotes lymphangiogenesis and lymph node (LN) metastasis in CRC, providing new insights for CRC treatment.<br><br>METHODS: Microbial diversity and composition in rectal cancer were compared between CRC patients and healthy controls using 16s rRNA sequencing. Key genes related to short-chain fatty acid metabolism, HFD, and gut microbiota were identified. In vitro assays assessed CRC cell proliferation, migration, invasion, and lymphangiogenesis. A CRC mouse model on an HFD was used to measure fecal propionate levels and analyze GPR41 expression in tumors. In vivo fluorescence imaging was employed to track cancer cell migration and lymph node metastasis.<br><br>RESULTS: HFD-induced microbial dysbiosis led to a significant reduction in SCFA-producing bacteria and an increase in pro-inflammatory species. This dysbiosis contributed to the suppression of propionate's protective effects. Propionate inhibited CRC cell proliferation, migration, and invasion under HFD conditions by activating the GPR41 pathway. Silencing GPR41 reversed these inhibitory effects, highlighting the key role of GPR41 in mediating propionate's anti-tumor effects. In vivo experiments further confirmed that propionate suppressed HFD-enhanced CRC lymphatic metastasis through the GPR41 signaling pathway, linking microbial dysbiosis with the modulation of cancer progression.<br><br>CONCLUSION: This study reveals that HFD promotes CRC lymphangiogenesis and LN metastasis through gut microbiota dysbiosis and suppression of the propionate-activated GPR41 signaling pathway. These findings highlight the therapeutic potential of targeting the propionate/GPR41 axis , offering a promising strategy for developing novel anticancer therapies.},
}
@article {pmid40435904,
year = {2025},
author = {Liu, Z and Yan, K and Li, J and Zhang, C and Xu, D and Wang, Y and Xie, X and Li, H and Qie, J and Li, J and Dong, X and Dong, L and Cui, H},
title = {Acute appendicitis in children: Two microbial states associated with clinical indicators and severity.},
journal = {Diagnostic microbiology and infectious disease},
volume = {113},
number = {2},
pages = {116925},
doi = {10.1016/j.diagmicrobio.2025.116925},
pmid = {40435904},
issn = {1879-0070},
abstract = {BACKGROUND: Acute appendicitis (AA) is one of the most common abdominal emergencies worldwide. It is associated with dysbiosis and is usually classified clinically as either simple appendicitis (SA) or complicated appendicitis (CA) . The etiology and pathogenesis of AA remain incompletely understood.<br><br>METHODS: A total of 74 pediatric intra-abdominal pus samples from appendectomy cases (aged 3-15) were collected for AA at Tianjin Children's Hospital (Feb 2022-Sep 2023). The samples were categorised into two groups based on pathological findings: SA (n = 27) and CA (n = 47). Metagenomic profiling was employed to characterized the microbial composition and function in both groups. Additionally, clinical parameters associated with the microbiota were analysed.<br><br>RESULTS: The SA group exhibited higher levels of Burkholderia, Mycobacterium, and Klebsiella, while the CA group demonstrated higher levels of Porphyromonas, Bacteroides, Fusobacterium, Prevotella, and Tannerella. Additionaly, there were significant differences in clinical parameters, including C-reactive protein (CRP), procalcitonin (PCT), fibrinogen, sodium, potassium, phosphorus, complement C3, and chloride, between two groups. Furthermore, functional profiling revealed alterations in microbial metabolism and antibiotic resistance, highlighting the complex interplay between microbial communities and host inflammatory responses in appendicitis.<br><br>CONCLUSIONS: This study identifies unique microbial and serum biomarkers and their correlates in varying severities of acute appendicitis, highlighting the role of the microbiome in the aetiology of acute appendicitis.},
}
@article {pmid40435837,
year = {2025},
author = {Torre, V and Marchese, E and Willison, E and Monaco, M and Bozzo, M and De Negri Atanasio, G and Taddeucci, A and Trebesova, H and Rispo, F and Rosenwasser, N and Turrini, F and Olivero, G and Candiani, S and Grasselli, E and Marchese, A and Alcaro, S and Boggia, R and Romeo, I and Grilli, M and Di Pilato, V and Costa, G and Pittaluga, A},
title = {Presynaptic release-regulating α2 receptors and Urolithins: A bridge between systemic EA administration and central health properties.},
journal = {Biomedicine &amp; pharmacotherapy = Biomedecine &amp; pharmacotherapie},
volume = {188},
number = {},
pages = {118187},
doi = {10.1016/j.biopha.2025.118187},
pmid = {40435837},
issn = {1950-6007},
abstract = {Ellagic acid (EA) is a natural compound exerting beneficial effects in mammals, including central neuroprotection. Among the central targets, the noradrenergic pathway has been proposed as a suitable candidate and, in this view, we recently proposed the presynaptic α2 autoreceptors as possible sites of action of this natural polyphenol. Although attractive, our hypothesis is questioned by the unfavourable pharmacokinetic profile of EA, which limits its access to the central nervous system, making impossible its interaction with these receptors. To substantiating the correlation linking EA treatment and the central noradrenergic pathway, we have now extended the study to Urolithins. These are the principal EA metabolites, which are brought in for EA central effects because of their high systemic bioavailability. To address the point, we employed a multidisciplinary approach, which included computational, "in vitro" and "in vivo" studies. The results from "computational" and "in vitro" experiments revealed that Urolithin A (UroA), but not Urolithin B (UroB) or C (UroC), binds to and activates α2 receptor subtypes. Furthermore, the "in vivo" prolonged administration of formulated microdispersion of EA (EAm) in mice led to a marked desensitization of cortical and hippocampal α2 autoreceptors, also reducing their density. Notably, central effects were associated to a significant changes in gut microbiome composition, towards a metabotype that would preferentially produce UroA. Based on these observations, we propose UroA as one of the systemic "effectors" of the EAm-induced central noradrenergic adaptation, confirming the role of noradrenaline in mediating the EA-mediated health effects.},
}
@article {pmid40435624,
year = {2025},
author = {Soufi, L and Kampouris, ID and Lüneberg, K and Heyde, BJ and Pulami, D and Glaeser, SP and Siebe, C and Siemens, J and Smalla, K and Grohmann, E and Gallego, S},
title = {Wastewater-borne pollutants influenced antibiotic resistance genes and mobile genetic elements in the soil without affecting the bacterial community composition in a changing wastewater irrigation system.},
journal = {Journal of hazardous materials},
volume = {494},
number = {},
pages = {138680},
doi = {10.1016/j.jhazmat.2025.138680},
pmid = {40435624},
issn = {1873-3336},
abstract = {Over decades, untreated wastewater from México City was used to irrigate crops in the Mezquital Valley. With the construction of a wastewater treatment plant (WWTP), irrigation was replaced by WWTP effluent. To investigate how this shift affects the abundance, diversity, and dissemination of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) in the short term, we conducted a soil microcosm experiment over 4 weeks. Soils from the Mezquital Valley with a long history of irrigation with untreated wastewater were irrigated with WWTP influent or effluent, both spiked with or without antibiotics and disinfectants. The spiking of irrigation water increased water-extractable soil concentrations of sulfamethoxazole. ARG and MGE abundances were affected by the spiking, whereas soil type and water quality had no effect. Contrarily, the soil microbiome was only determined by the soil type and the duration of incubation. Among the most abundant soil amplicon sequence variants (ASVs), one affiliated to Pseudomonas was affected by the spiking. Two ASVs affiliated to Methylotenera detected among the most abundant in wastewater and soil increased in relative abundance in soil after wastewater irrigation, indicating that they were likely introduced with the irrigation water or benefited from it. Most isolates from WWTP influent or effluent belonged to Proteobacterial genera. These findings highlight the importance of water pollution on the dissemination and spread of ARGs.},
}
@article {pmid40435194,
year = {2025},
author = {Ito, A and Shoji, H and Arai, H and Kakiuchi, S and Sato, K and Jinno, S and Takahashi, N and Masumoto, K and Yoda, H and Shimizu, T},
title = {Feeding infant formula with low sn-2 palmitate causes changes in newborn's intestinal environments through an increase in fecal soaped palmitic acid.},
journal = {PloS one},
volume = {20},
number = {5},
pages = {e0324256},
pmid = {40435194},
issn = {1932-6203},
mesh = {Humans ; *Infant Formula/chemistry ; *Feces/chemistry ; *Palmitic Acid/analysis/metabolism ; Infant, Newborn ; Male ; Female ; *Gastrointestinal Microbiome/drug effects ; Infant ; Bifidobacterium/growth &amp; development ; *Palmitates/analysis ; *Intestines/microbiology ; },
abstract = {BACKGROUND/OBJECTIVES: Soaped palmitic acid (PA) has been reported to be excreted in stool after feeding infant formulas containing low sn-2 palmitate levels, which corresponds to high sn-1 or -3 palmitate levels. While an in vitro study showed that soaped PA inhibits the Bifidobacteria growth, few clinical studies have evaluated effects of soaped PA on intestinal environments of infants. In this study, we aimed to evaluate associations between increased fecal soaped PA levels and inhibition of growth of the intestinal microbiome using clinical data, and to evaluate changes in the intestinal environment with formula-feeding.<br><br>METHODS: This study was conducted as a secondary analysis to our observational study of Japanese 1-month-old infants (n&#x2009;=&#x2009;172). Infant formulas were classified into high sn-2 formula (&#x2265; 50%) and low sn-2 formula (< 50%) according to the sn-2 binding ratio of PA. Multiple regression analyses and path analysis were performed as statistical analyses.<br><br>RESULTS: In the multiple regression analysis, the occupancy of Bifidobacteria was negatively correlated with the fecal soaped PA levels (&#x3b2;&#x2009;= -0.15, 95% confidence interval&#x2009;= -0.28-&#x2009;-&#x2009;0.02). A path analysis suggested that low sn-2 formula feeding led to increased fecal soaped PA levels, decreased Bifidobacteria occupancy, and finally increased fecal pH.<br><br>CONCLUSIONS: Our clinical data showed significant associations between higher fecal soaped PA levels and lower Bifidobacteria occupancy in the newborn gut, which agreed well with the report of the in vitro study. Our study also suggests that feeding infant formula with low sn-2 palmitate causes changes in the intestinal environment through an increase in fecal soaped palmitic acids.},
}
@article {pmid40435188,
year = {2025},
author = {Eladham, MW and Sharif-Askari, NS and Sekar, P and Mdkhana, B and Selvakumar, B and Al-Sheakly, BKS and Sharif-Askari, FS and Hachim, I and Halwani, R},
title = {The role of gut leakage and immune cell miss-homing on gut dysbiosis-induced lung inflammation in a DSS mice model.},
journal = {PloS one},
volume = {20},
number = {5},
pages = {e0324230},
pmid = {40435188},
issn = {1932-6203},
mesh = {Animals ; *Dysbiosis/immunology/complications/microbiology/chemically induced ; Mice ; Disease Models, Animal ; *Pneumonia/immunology/pathology/etiology/microbiology ; *Gastrointestinal Microbiome/immunology ; Dextran Sulfate/toxicity ; Mice, Inbred C57BL ; Lung/pathology/immunology ; Colitis/chemically induced/immunology/microbiology/pathology ; Male ; },
abstract = {BACKGROUND: Inflammatory Bowel Disease (IBD), encompassing Crohn's disease and ulcerative colitis, affects millions globally, with extraintestinal manifestations (EIMs) occurring in 25-40% of patients. Among these, respiratory complications are of particular concern, yet the immunologic and physiologic mechanisms underlying gut-lung interactions remain poorly understood. The gut-lung axis (GLA) describes bi-directional communication between the gut and lungs, where microbial dysbiosis in the gut can drive lung inflammation and immune dysregulation.<br><br>METHODS: Mice were treated with 4% DSS for 7 days to induce colitis. Gut permeability, tight junction protein expression, lung inflammation, immune cell trafficking, and microbial translocation were assessed through histology, qPCR, flow cytometry, and GFP-tagged fecal microbiome experiments.<br><br>RESULTS: DSS treatment led to significant disruption of the gut barrier, with upregulation of gut leakage markers and downregulation of tight junction proteins. Lung inflammation was characterized by elevated IL-17, neutrophil infiltration, and airway hyperresponsiveness. Flow cytometry revealed mis-homing of gut-primed immune cells (&#x3b1;4&#x3b2;7+ and CCR9&#x2009;+&#x2009;CD4+) to the lungs and tracking bacteria via GFP- tagged fecal microbiome confirmed microbial translocation from the gut to the lungs which may contribute to lung inflammation.<br><br>CONCLUSION: Disrupted gut integrity facilitates microbial translocation and immune cell mis-homing, contributing to lung inflammation. These results provide new insights into how gut dysbiosis influences respiratory inflammation.},
}
@article {pmid40434948,
year = {2025},
author = {Brock, MT and Nozue, K and Kliebenstein, DJ and Ewers, BE and Mackay, DS and Maignien, L and Wang, DR and Weinig, C and Maloof, JN},
title = {Characterization of transcriptional and metabolic responses to a complex plant growth-promoting soil inoculum.},
journal = {Plant biology (Stuttgart, Germany)},
volume = {},
number = {},
pages = {},
doi = {10.1111/plb.70034},
pmid = {40434948},
issn = {1438-8677},
support = {CA-D-PLB-2795-H//National Institute of Food and Agriculture/ ; 1444571//National Science Foundation/ ; 1547796//National Science Foundation/ ; },
abstract = {Soil microbes can have large impacts on plant growth and physiology. However, how these impacts manifest at the transcriptional and metabolite level is not well understood, especially responses to complex mixtures of soil microbes. Here we characterize the transcriptional and metabolomic response of Brassica rapa to a complex, naturally occurring soil inoculum that promotes shoot growth. Brassica rapa plants were treated with mock or growth-promoting soil inocula and monitored for growth. Root and shoot tissues were harvested for RNA-seq and metabolite analysis. Gene co-expression analysis and penalized regression were used to test for gene co-expression modules and metabolites that influence growth. We identify gene co-expression modules that both respond to microbial treatment and are associated with leaf growth. Gene ontology and custom category analysis of these modules revealed root modules that are enriched for mineral nutrition (especially nitrogen, phosphorus, and sulfur) and leaf modules enriched for photosynthetic and cellular processes. The metabolite data show an association of leaf length with nucleotide and amino acid levels, consistent with gene ontology terms observed in the leaf and perhaps reflecting the overall impact of growth-promoting microbes on key nitrogen-associated metabolic processes. Overall, this work provides an in-depth characterization of the molecular responses of plants to plant growth-promoting microbes.},
}
@article {pmid40434915,
year = {2025},
author = {Kuntz, TM and Liu, L and Wang, K and Everett, C and Eliassen, AH and Willett, WC and Sinha, R and Chan, AT and Rimm, EB and Garrett, WS and Segata, N and Piccinno, G and Huttenhower, C and Morgan, X and Song, M},
title = {Comparing the metagenomic performance of stools collected from custom cards and 95% ethanol in epidemiologic studies.},
journal = {Cancer epidemiology, biomarkers &amp; prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology},
volume = {},
number = {},
pages = {},
doi = {10.1158/1055-9965.EPI-25-0157},
pmid = {40434915},
issn = {1538-7755},
abstract = {Background Stool cards have been used for microbiome assessment in epidemiological studies. Methods We compared shotgun metagenomic sequencing from 32 participants who self-collected stool samples from the same bowel movement using a custom stool card vs. a collection tube with 95% ethanol fixative in the Nurses' Health Study II. We evaluated the agreement between methods at both the whole-community and individual species levels. To contextualize the comparison for disease association studies, we assessed the performance of the two collection methods for differentiating colorectal cancer-associated taxa. Results Overall, metagenomes from cards and 95% ethanol were highly correlated within individuals. No difference was found in alpha diversity and only ~1% of variation in beta diversity was explained by the collection method. At the species level, while the relative abundances were highly correlated between card and ethanol sample pairs (Spearman rho = 0.96), 10 (out of 239) species showed a differential abundance in paired samples, including overrepresentation of Escherichia coli and underrepresentation of three Streptococcus species in cards compared with ethanol. Among a set of 99 colorectal cancer-associated species, 4 showed differential abundances between collection methods; however, this number was consistent with what would be expected by chance. Conclusions Metagenomic sequencing using stool samples self-collected using stool cards or 95% ethanol yielded largely consistent results, although differential abundances were observed for a small number of individual species. Impact Stool cards can be a cost-effective alternative to collect stool samples for metagenomic sequencing in epidemiologic studies but warrant additional considerations for data analysis.},
}
@article {pmid40434833,
year = {2025},
author = {Müller, L and Steiger, S and Körner, M},
title = {Surviving in the fast lane: No increased mortality, but faster growth for pathogen-exposed larvae of a family living beetle.},
journal = {Journal of evolutionary biology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jeb/voaf068},
pmid = {40434833},
issn = {1420-9101},
abstract = {Animal taxa exhibiting post-hatching care can be found throughout the animal kingdom. During this period, parents aggregate with their offspring and allow them to invest their resources into growth and development as parents take over energy consuming tasks. For instance, studies show that food provisioning and social immunity by parents can alleviate the costs of an offspring's immune response to pathogen exposure. However, this issue has rarely been explored in offspring of species showing plasticity in their dependency on parental care. Here, we raise the question of how offspring are affected by pathogen exposure if they have access to social immunity through a caring parent. Parents of Nicrophorus vespilloides, a species exhibiting facultative post-hatching care, control the carcass microbiome by coating it with their antimicrobial exudates, stopping further decay and protecting their offspring from potential pathogens. We exposed N. vespilloides offspring to a generalist entomopathogenic fungus, Beauveria bassiana, while manipulating presence or absence of post-hatching parental care. We monitored offspring performance parameters throughout their development and found, curiously, larvae showed an increase in mean weight and growth rate after being exposed to the pathogen, while their survival and adult immunity were unaffected. These effects of pathogen exposure occurred regardless of parental care. Simultaneously, our results indicate that females invest fewer resources into their offspring if they have been exposed to the pathogen. Overall, we show that offspring of facultative subsocial species may not respond differently to pathogen exposure depending on their parents' aid. Additionally, our results indicate that offspring of facultatively subsocial species may adjust their growth rate in response to pathogen exposure in the nest.},
}
@article {pmid40434822,
year = {2025},
author = {Berelson, MFG and Heavens, D and Nicholson, P and Clark, MD and Leggett, RM},
title = {From air to insight: the evolution of airborne DNA sequencing technologies.},
journal = {Microbiology (Reading, England)},
volume = {171},
number = {5},
pages = {},
doi = {10.1099/mic.0.001564},
pmid = {40434822},
issn = {1465-2080},
mesh = {*High-Throughput Nucleotide Sequencing/methods ; *Air Microbiology ; *Sequence Analysis, DNA/methods ; *DNA, Environmental/genetics/analysis/isolation &amp; purification ; Humans ; Environmental Monitoring/methods ; Computational Biology/methods ; Biodiversity ; },
abstract = {Historically, the analysis of airborne biological organisms relied on microscopy and culture-based techniques. However, technological advances such as PCR and next-generation sequencing now provide researchers with the ability to gather vast amounts of data on airborne environmental DNA (eDNA). Studies typically involve capturing airborne biological material, followed by nucleic acid extraction, library preparation, sequencing and taxonomic identification to characterize the eDNA at a given location. These methods have diverse applications, including pathogen detection in agriculture and human health, air quality monitoring, bioterrorism detection and biodiversity monitoring. A variety of methods are used for airborne eDNA analysis, as no single pipeline meets all needs. This review outlines current methods for sampling, extraction, sequencing and bioinformatic analysis, highlighting how different approaches can influence the resulting data and their suitability for specific use cases. It also explores current applications of airborne eDNA sampling and identifies research gaps in the field.},
}
@article {pmid40434804,
year = {2025},
author = {Kohl, KD},
title = {Through the microbial looking glass: our shifting understanding of the holobiont and microbes as mediators of organismal biology.},
journal = {Integrative and comparative biology},
volume = {},
number = {},
pages = {},
doi = {10.1093/icb/icaf059},
pmid = {40434804},
issn = {1557-7023},
abstract = {Our understanding and appreciation for the role of microbial symbioses in the evolution and speciation of macro-organisms has fluctuated over time. Even in contemporary times our collective understanding of the microbiome has shifted from an adaptationist focus on beneficial interactions, to better incorporate ecological, stochastic, and neutral interactions. From the 1900s to today, the holobiont concept has repeatedly been proposed as a guiding hypothesis and principle. However, it has also received continuous dispute and critique, often regarding the universality of processes, fidelity of partnerships, and lack of explicit delineation of holobionts from individual units. Modern interpretation of the holobiont is meant to be an extension of multilevel selection theory, and natural selection need not always act at this collective level. The solution may be for scientists to remove conceptual mind blocks and consider a hazy, flexible, and dynamic definition of the holobiont. Such a frame of mind will be similar to the lack of clarity generally surrounding the biological species concept - a muddled yet unifying concept. Viewing the world through the "microbial looking glass" of the holobiont will offer a more accurate understanding of biological systems and will facilitate research progress.},
}
@article {pmid40434797,
year = {2025},
author = {Zhao, Z and Gao, H and Yang, Y and Deng, Y and Ju, F},
title = {Fungi as a Critical Component of Lake Microbiota in Response to Cyanobacterial Harmful Algal Blooms.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c09164},
pmid = {40434797},
issn = {1520-5851},
abstract = {Cyanobacterial Harmful Algal Blooms (CyanoHABs) pose a growing threat to lake ecosystems. While microbial communities constitute the resilient power of lake ecosystems to CyanoHAB disturbances, the role of fungi remains underexplored. Here, the dynamics of size-fractionated fungal and associated bacterial communities were tracked across the peak and decline stages of a CyanoHAB event in shallow subtropical Lake Taihu. The results revealed that the composition of fungal and bacterial communities in separated size fractions varied between bloom stages, with enrichment patterns likely influenced by their reliance on algal-derived nutrients. Null model-based analysis revealed a shift in fungal community assembly, from dominance by dispersal limitation (44%) and drift (30%) at the peak stage to increased homogeneous selection (44%) at the early decline stage, whereas bacterial communities remained predominantly shaped by stochastic processes, highlighting their distinct responses to cyanobacterial biomass decomposition. Comparative topological analysis of microbial co-occurrence networks showed strengthened cross-kingdom fungi-bacteria interactions as the bloom declined, especially within decomposing cyanobacterial colonies, facilitating nutrient cycling and accelerating cyanobacterial biomass removal. These findings led to a conceptual model proposing fungi as critical members of the freshwater microbiome in eutrophic lakes, driving biogeochemical cycling and potentially contributing to the resilience of the lake ecosystem against CyanoHABs.},
}
@article {pmid40434783,
year = {2025},
author = {Collard, M and Grbic, N and Mumber, H and Wyant, WA and Shen, L and Alani, RM},
title = {Gut Microbiome in Adult and Pediatric Patients With Hidradenitis Suppurativa.},
journal = {JAMA dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1001/jamadermatol.2025.1318},
pmid = {40434783},
issn = {2168-6084},
}
@article {pmid40434575,
year = {2025},
author = {Kumar, A and Kumar, V and Pramanik, J and Rustagi, S and Prajapati, B and Jebreen, A and Pande, R},
title = {Lactiplantibacillus Plantarum as a Complementary Approach for Diabetes Treatment and Management.},
journal = {Current nutrition reports},
volume = {14},
number = {1},
pages = {72},
pmid = {40434575},
issn = {2161-3311},
mesh = {*Probiotics/therapeutic use ; Humans ; Gastrointestinal Microbiome ; Animals ; *Lactobacillus plantarum ; *Diabetes Mellitus/therapy/microbiology ; Blood Glucose/metabolism ; Dysbiosis ; Insulin Resistance ; },
abstract = {PURPOSE OF REVIEW: This review explores the impact of Lactiplantibacillus plantarum on diabetes management and discusses the potential mechanism.<br><br>RECENT FINDINGS: Recent studies have highlighted that gut dysbiosis has emerged as a key factor in the development of diabetes. In this context, probiotics, specifically Lactiplantibacillus plantarum, offer potential benefits in modulating gut microbiota and improving metabolic health. Several studies have demonstrated the positive impact of L. plantarum on glycemic control, insulin sensitivity, and inflammatory markers in diabetic animal models. The potential mechanisms of action of L. plantarum in diabetes management include inhibiting enzymes involved in glucose metabolism, modulating inflammatory responses, improving insulin sensitivity, restoring gut microbiota, and producing short-chain fatty acids.<br><br>SUMMARY: The article concludes that L. plantarum is a promising candidate for managing glucose hemostasis, thus offering a potential alternative or adjunct to conventional approaches. However, further clinical studies are necessary to understand the exact mechanism and long-term effects of L. plantarum in humans.},
}
@article {pmid40434533,
year = {2025},
author = {Phillips, R},
title = {Diet, Mitochondrial Dysfunction, Vascular Endothelial Damage, and the Microbiome: Drivers of Ocular Degenerative and Inflammatory Diseases.},
journal = {Ophthalmology and therapy},
volume = {},
number = {},
pages = {},
pmid = {40434533},
issn = {2193-8245},
abstract = {There is abundant evidence in medical literature that Western diet and lifestyle drive the cellular and metabolic processes which underlie chronic non-communicable diseases. However, non-pharmaceutical interventions, which focus on nutrition, the microbiome and lifestyle, to prevent non-communicable diseases are not part of mainstream treatment, for a variety of reasons. Lack of progress in stemming the rise in chronic non-communicable diseases can be attributed to the current 'downstream' medical paradigm which is focused on treating disease and symptoms, rather than preventing disease via an 'upstream' approach, which looks at cause and process. Metabolic abnormalities and obesity have previously been noted as correlated with common chronic ophthalmic conditions such as age related macular degeneration (AMD), glaucoma, ocular inflammation, diabetic retinopathy and retinal vascular occlusive disease. These are ocular manifestations of an underlying common cause. The aim of this paper, using an ophthalmic context, is to provide an overview of the cellular pathophysiological mechanisms that underlie chronic non-communicable diseases, including ophthalmic diseases, and to draw the links between diet and lifestyle, the microbiome and chronic non-communicable diseases.},
}
@article {pmid40434505,
year = {2025},
author = {Gupta, MK and Srivastava, R},
title = {Gut Microbiome Interventions: From Dysbiosis to Next-Generation Probiotics (NGPs) for Disease Management.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {40434505},
issn = {1867-1314},
abstract = {The gut microbiome, sometimes referred to as the "second brain," the "lost organ," the "identification card of the individual," and the "fingerprint of the host," possesses diverse traits and functions that influence health. The impact of gut commensal bacteria on health, as opposed to environmental pathogenic factors, has generated increasing interest in recent years, culminating in a substantial body of study. Research indicates that dysbiosis of the intestinal microbiota is commonly observed in chronic inflammatory diseases, including colitis, obesity/metabolic syndrome, diabetes mellitus, liver infections, allergic conditions, cardiovascular diseases, COVID-19, cancers, and neurodegenerative disorders. The International Scientific Association for Probiotics and Prebiotics has recently refined the theory of complementary and synergistic synbiotics. In recent years, the field of microbiome research has been significantly advanced by technological developments such as massive culturomics, gnotobiotics, metabolomics, parallel DNA sequencing, and RNA sequencing. This review article examined the potential next generation probiotics (NGPs) and explored some of them, Faecalibacterium prausnitzii, Bacteroides thetaiotaomicron, Akkermansia muciniphila, Parabacteroides goldsteinii, Bacteroides fragilis, Eubacterium hallii, Roseburia intestinalis, Christensenella minuta, Prevotella copri, and Oscillospira guilliermondii. In addition to these useful probiotic strains, psychobiotics, members of the families of Lactobacilli, Streptococci, Bifidobacteria, Escherichia, and Enterococci, have extended applicability in the use for neurodevelopmental and neurodegenerative disorders. The article also reviewed current trends and limitations in NGPs to enhance our comprehensive understanding of key concepts associated with the consumption of probiotics and proposed necessary initiatives for researchers to engage in collaborative translational research as future therapeutic solutions.},
}
@article {pmid40434504,
year = {2025},
author = {Anvarbatcha, R and Kunnathodi, F and Arafat, AA and Azmi, S and Mustafa, M and Ahmad, I and Alotaibi, HF},
title = {Harnessing Probiotics: Exploring the Role of the Gut Microbiome in Combating Obesity.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {40434504},
issn = {1867-1314},
abstract = {Obesity has become a global health crisis driven by genetic, environmental, and lifestyle factors, often linked to gut microbiome imbalances. Probiotics, particularly Lactobacillus and Bifidobacterium strains, have shown promise in clinical trials by promoting weight loss, improving lipid profiles, and addressing gut dysbiosis associated with obesity. This review surveys the literature on the microbiome and obesity, emphasizing the clinical relevance of probiotics in treatment strategies. Our comprehensive PubMed search highlights the mechanisms through which probiotics influence metabolic health, including their effects on inflammation and appetite regulation. We also explore promising future research directions and the potential for integrating probiotics into clinical practice. While results are encouraging, the evidence is limited by strain variability, small sample sizes, short trial durations, and individual differences in microbiota composition. More extensive, long-term studies with standardized methods are crucial to confirm the effectiveness of probiotics as viable anti-obesity treatments.},
}
@article {pmid40434363,
year = {2025},
author = {Luévano, JM and Liu, J and Stappenbeck, T},
title = {The Enteric Microbiome in Early Onset Colorectal Cancer: A Comprehensive Review of its role as a Biomarker of Disease.},
journal = {Clinical and translational gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.14309/ctg.0000000000000864},
pmid = {40434363},
issn = {2155-384X},
abstract = {Early onset colorectal cancer (EoCRC), a distinct entity from late onset colorectal cancer (LoCRC), continues to increase in incidence. Known risk factors for LoCRC have been explored to explain this trend, but do not account for it completely. The gastrointestinal microbiome has been associated with LoCRC and additional risk factors of disease, however it is only now being investigated in the context of EoCRC. A better understanding of the microbiome's function in EoCRC could elucidate its role in the increasing incidence of EoCRC. This article reviews the state of literature related to studies specifically isolating microbiome related changes in EoCRC compared to LoCRC and age matched controls. Several studies reviewed in this article highlight the varied results of overall diversity and specific bacteria that are influenced by EoCRC, and the utility of these unique changes to predict for EoCRC. Although the microbiome can be useful in understanding EoCRC, to better predict for disease the microbiome must be studied in more diverse populations, and with deeper, more functional characterization in a manner that allows for transference of findings amongst future studies. These studies indicate that the enteric microbiome holds significant potential as a biomarker for disease but has yet to fully meet an understanding necessary for direct clinical utilization.},
}
@article {pmid40434156,
year = {2025},
author = {Wang, X and Li, F and Sun, Y and Meng, F and Song, Y and Su, X},
title = {Microbial dysbiosis and its diagnostic potential in androgenetic alopecia: insights from multi-kingdom sequencing and machine learning.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0054825},
doi = {10.1128/msystems.00548-25},
pmid = {40434156},
issn = {2379-5077},
abstract = {Androgenetic alopecia (AGA), the most common form of hair loss, has been linked to dysbiosis of the scalp microbiome. In this study, we collected microbiome samples from the frontal baldness and occipital regions of patients with varying stages of AGA and conducted a comprehensive analysis of bacterial and fungal communities using 16S rRNA and ITS1 sequencing. Our results revealed that although the scalp microbiome dynamics in healthy subjects correlated strongly with chronological age, this trend was disrupted in AGA patients due to severe microbial imbalances, emphasizing the significant impact of AGA on the scalp microecology. Notably, microbial dysbiosis was not confined to the localized areas of hair loss but extended across the entire scalp. Moreover, the degree of dysbiosis was consistent with the severity of AGA. Leveraging multi-kingdom microbial features and machine learning, we developed a microbial index of scalp health (MiSCH), which effectively detects AGA and stratifies its severity. More importantly, MiSCH was able to identify high-risk individuals, those with significantly disrupted microbiome structures but no overt AGA phenotypic characteristics, thereby offering opportunities for early diagnosis, risk assessment, and personalized treatment of AGA.IMPORTANCEBy analyzing the bacteria and fungi on the scalp, this study shows how androgenetic alopecia (AGA) disrupts the balance of microbes not just in the hair loss areas, but across the entire scalp. Thus, we introduce the microbial index of scalp health (MiSCH), which leverages microbiome data for the early detection and severity prediction of AGA. This method is especially valuable for identifying people at risk of developing more severe hair loss, even before visible symptoms appear. By combining microbiome analysis with machine learning, this research offers a potential breakthrough for early diagnosis and personalized treatments, changing how we approach hair loss and offering new hope for managing the condition more effectively.},
}
@article {pmid40434114,
year = {2025},
author = {Degregori, S and Manus, MB and Qu, EB and Mendall, CP and Baker, JS and Hopper, LM and Amato, KR and Lieberman, TD},
title = {The microbiome of the human facial skin is unique compared to that of other hominids.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0008125},
doi = {10.1128/msystems.00081-25},
pmid = {40434114},
issn = {2379-5077},
abstract = {The human facial skin microbiome is remarkably similar across all people sampled to date, dominated by facultative anaerobe Cutibacterium. The origin of this genus is unknown, with no close relatives currently described from samples of primate skin. This apparent human-specific bacterial taxon could reflect the unique nature of human skin, which is significantly more oily than that of our closest primate relatives. However, previous studies have not sampled the facial skin microbiome of our closest primates. Here, we profiled the skin microbiome of zoo-housed chimpanzees (Pan troglodytes) and gorillas (Gorilla gorilla gorilla), alongside their human care staff, using both 16S and shotgun sequencing. We showed that facial skin microbiomes differ significantly across host species, with humans having the lowest diversity and the most unique community among the three species. We were unable to find a close relative of Cutibacterium on either chimpanzee or gorilla facial skin, consistent with human specificity. Hominid skin microbiome functional profiles were more functionally similar compared to their taxonomic profiles. However, we still found notable functional differences, including lower proportions of fatty acid biosynthesis in humans, consistent with microbes' reliance on host-derived lipids. Our study highlights the uniqueness of the human facial skin microbiome and supports a horizontal acquisition of its dominant resident from a yet unknown source.IMPORTANCEUnderstanding how and why human skin bacteria differ from our closest animal relatives provides crucial insights into human evolution and health. While we have known that human facial skin hosts distinct bacteria-particularly Cutibacterium acnes-we did not know if these bacteria and their associated genes were also present on the faces of our closest relatives, chimpanzees and gorillas. Our study shows that human facial skin hosts markedly different bacteria than other primates, with C. acnes being uniquely abundant on human faces. This finding suggests that this key bacterial species may have adapted specifically to human skin, which produces more oils than other primates.},
}
@article {pmid40434104,
year = {2025},
author = {Putri, DS and Shepherd, FK and Sanders, AE and Roach, SN and Jay, S and Pierson, MJ and Wieking, G and Anderson, JL and Meyerholz, DK and Schacker, TW and Langlois, RA},
title = {Naturally transmitted mouse viruses highlight the heterogeneity of virus transmission dynamics in the dirty mouse model.},
journal = {Journal of virology},
volume = {},
number = {},
pages = {e0018725},
doi = {10.1128/jvi.00187-25},
pmid = {40434104},
issn = {1098-5514},
abstract = {UNLABELLED: Specific-pathogen-free (SPF) mice are widely used in biomedical research to model human infections. However, these animals do not always accurately recapitulate human immune responses. This is due, in part, to their lack of infection history. A growing number of studies show that the host microbiome influences the development, progression, and responses of many diseases. To date, the majority of research on the microbiome has focused on the bacterial populations and less on the eukaryotic virome of the host. Here, we characterize a transmission model where SPF mice are exposed to natural mouse pathogens at physiologic doses and routes. We found that pet store mice acquired from different sources have distinct viromes and infection histories. We also found significant heterogeneity in the kinetics of the transmission of natural mouse viruses. A common virus found in our model was murine Kobuvirus. Surprisingly, murine Kobuvirus infection was found in the glandular stomach epithelia and not intestinal epithelia like other enteric picornaviruses. Together, these data characterize the heterogeneity of the dirty mouse cohousing system and provide a foundation for studying the biology of natural mouse viruses.<br><br>IMPORTANCE: Increasing evidence supports microbial exposure as a critical factor in shaping responses to immune challenges such as infections and vaccinations. However, many experimental models introducing microbial exposure into laboratory animals have confounding factors that may impact phenotypes and are not well characterized. Here, we characterized the pet store reservoir virome diversity, prior infection history, and transmission kinetics. We found significant heterogeneity across these features of the pet store cohousing model. Moreover, we leveraged this model to investigate the tropism of two less characterized viruses-murine Kobuvirus and murine astrovirus 2-in a natural transmission setting. These findings highlight the importance of characterizing the virome of pet store reservoirs to better mimic microbial exposure in humans.},
}
@article {pmid40434093,
year = {2025},
author = {Koldaş, SS and Sezerman, OU and Timuçin, E},
title = {Exploring the role of microbiome in cystic fibrosis clinical outcomes through a mediation analysis.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0019625},
doi = {10.1128/msystems.00196-25},
pmid = {40434093},
issn = {2379-5077},
abstract = {UNLABELLED: Human microbiome plays a crucial role in host health and disease by mediating the impact of environmental factors on clinical outcomes. Mediation analysis is a valuable tool for dissecting these complex relationships. However, existing approaches are primarily designed for cross-sectional studies. Modern clinical research increasingly utilizes long follow-up periods, leading to complex data structures, particularly in metagenomic studies. To address this limitation, we introduce a novel mediation framework based on structural equation modeling that leverages linear mixed-effects models using penalized quasi-likelihood estimation with a debiased lasso. We applied this framework to a 16S rRNA sputum microbiome data set collected from patients with cystic fibrosis over 10 years to investigate the mediating role of the microbiome in the relationship between clinical states, disease aggressiveness phenotypes, and lung function. We identified richness as a key mediator of lung function. Specifically, Streptococcus was found to be significantly associated with mediating the decline in lung function on treatment compared to exacerbation, while Gemella was associated with the decline in lung function on recovery. This approach offers a powerful new tool for understanding the complex interplay between microbiome and clinical outcomes in longitudinal studies, facilitating targeted microbiome-based interventions.<br><br>IMPORTANCE: Understanding the mechanisms by which the microbiome influences clinical outcomes is paramount for realizing the full potential of microbiome-based medicine, including diagnostics and therapeutics. Identifying specific microbial mediators not only reveals potential targets for novel therapies and drug repurposing but also offers a more precise approach to patient stratification and personalized interventions. While traditional mediation analyses are ill-equipped to address the complexities of longitudinal metagenomic data, our framework directly addresses this gap, enabling robust investigation of these increasingly common study designs. By applying this framework to a decade-long cystic fibrosis study, we have begun to unravel the intricate relationships between the sputum microbiome and lung function decline across different clinical states, yielding insights that were previously unknown.},
}
@article {pmid40434086,
year = {2025},
author = {Nieves-Morales, R and Paez-Diaz, JA and Rodriguez-Carrio, SM and Melendez Martinez, G and Rivera-Lopez, EO and Rodríguez-Ramos, J and García-Arrarás, JE and Rios-Velazquez, C},
title = {Intestinal microbiome profile of the brown rock sea cucumber (Holothuria glaberrima) using ITS and 16S rDNA amplicons from direct mechanical, enzymatic, and chemical metagenomic extraction.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0029325},
doi = {10.1128/mra.00293-25},
pmid = {40434086},
issn = {2576-098X},
abstract = {Using direct mechanical, enzymatic, and chemical extraction methods, the intestinal microbiome of the marine invertebrate Holothuria glaberrima was obtained. ITS and 16S rDNA regions were sequenced to enrich and investigate the prokaryotic and fungal diversity profiles from different anatomical regions within the sea cucumber's intestinal biology.},
}
@article {pmid40433987,
year = {2025},
author = {Zhou, Z and Yang, M and Fang, H and Zhang, B and Ma, Y and Li, Y and Liu, Y and Cheng, Z and Zhao, Y and Si, Z and Zhu, H and Chen, P},
title = {Tailoring a Functional Synthetic Microbial Community Alleviates Fusobacterium nucleatum-infected Colorectal Cancer via Ecological Control.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e14232},
doi = {10.1002/advs.202414232},
pmid = {40433987},
issn = {2198-3844},
support = {24ZDFA001//Gansu Provincial Science and Technology Major Project/ ; 2024-8-27//Lanzhou Municipal Science and Technology Program/ ; 2024-8-30//Lanzhou Municipal Science and Technology Program/ ; 2024-4-2//Lanzhou Municipal Science and Technology Program/ ; 20250260006//College Students' Innovation and Entrepreneurship Program of Lanzhou University, China/ ; 20250260016//College Students' Innovation and Entrepreneurship Program of Lanzhou University, China/ ; 20250260020//College Students' Innovation and Entrepreneurship Program of Lanzhou University, China/ ; },
abstract = {Polymorphic microbiomes play important roles in colorectal cancer (CRC) occurrence and development. In particular, Fusobacterium nucleatum (F. nucleatum) is prevalent in patients with CRC, and eliminating it is beneficial for treatment. Here, multiple metagenomic sequencing cohorts are combined with multiomics to analyze the microbiome and related functional alterations. Furthermore, local human metagenome and metabolomics are used to discover commensal consortia. A synthetic microbial community (SynCom) is then designed by metabolic network reconstruction, and its performance is validated using coculture experiments and an AOM-DSS induced mouse CRC model. The sequencing result shows that F. nucleatum is more abundant in both the feces and tumor tissues of CRC patients. It causes alterations through various pathways, including microbial dysbiosis, lipid metabolism, amino acid metabolism, and bile acid metabolism disorders. The designed SynCom contains seven species with low competition interrelationship. Furthermore, the SynCom successfully inhibits F. nucleatum growth in vitro and achieves colonization in vivo. Additionally, it promotes F. nucleatum decolonization, and enhances tryptophan metabolism and secondary bile acid conversion, leading to reduced lipid accumulation, decreased inflammatory reaction, and enhanced tumor inhibition effect. Overall, the bottom-up designed SynCom is a controllable and promising approach for treating F. nucleatum-positive CRC.},
}
@article {pmid40433907,
year = {2025},
author = {Niu, Y and Zhao, X and Li, Y and Ma, X and Yang, W and Ma, J and Li, W and Yuan, W},
title = {Neutrophil-Mimicking Nanomedicine Eliminates Tumor Intracellular Bacteria and Enhances Chemotherapy on Liver Metastasis of Colorectal Cancer.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e04188},
doi = {10.1002/advs.202504188},
pmid = {40433907},
issn = {2198-3844},
support = {2023YFA1506503//National Key Research and Development Program of China/ ; 22378429//National Natural Science Foundation of China/ ; 51937011//National Natural Science Foundation of China/ ; 2023-I2M-QJ-016//CAMS Innovation Fund for Medical Sciences/ ; 2021-I2M-1-066//CAMS Innovation Fund for Medical Sciences/ ; 20220484168//Beijing Nova Program/ ; 202201020363//Science and Technology Projects in Guangzhou/ ; 2021B1515420004//Guangdong Basic and Applied Basic Research Foundation/ ; LC2021A06//China Cancer Foundation Beijing Hope Marathon Special Fund/ ; },
abstract = {Fusobacterium nucleatum (Fn) enrichment has been identified in colorectal cancer and its liver metastases. In this study, we found that Fn predominantly accumulated within colorectal cancer cells, correlating with colorectal cancer liver metastasis. Clinically, the administration of high doses of antibiotics and chemotherapeutic agents can disrupt the balance of the host microbiota. To address this clinical challenge, metronidazole (MTI) and oxaliplatin (OXA) are encapsulated within poly (lactic-co-glycolic acid) (PLGA) nanoparticles. Neutrophil membrane vesicles are extracted from murine bone marrow and coated with these nanoparticles (NM@PLGA-MTI-OXA), creating neutrophil-mimetic nanoparticles with dual targeting capabilities for antibacterial and anticancer purposes. The neutrophil membrane coating, compared with free drugs, is found to enhance nanoparticle uptake by tumor cells, facilitating intracellular bacterial elimination and tumor cell death. Further experiments reveal that NM@PLGA-MTI-OXA reverses the Fn-induced epithelial-mesenchymal transition (EMT) in tumor cells during metastasis and remodels the immunosuppressive microenvironment, suppressing colorectal cancer and liver metastasis development while minimizing broad-spectrum damage to the commensal microbiota.},
}
@article {pmid40433668,
year = {2025},
author = {von Ameln Lovison, O and Zempulski Volpato, FC and Weber, LG and Barth, AL and Simon Coitinho, A and Martins, AF},
title = {Unveiling the role of the upper respiratory tract microbiome in susceptibility and severity to COVID-19.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1531084},
pmid = {40433668},
issn = {2235-2988},
mesh = {Humans ; *COVID-19/microbiology/pathology/virology ; Cross-Sectional Studies ; Disease Susceptibility ; *Microbiota ; SARS-CoV-2 ; Female ; Male ; Severity of Illness Index ; Middle Aged ; *Respiratory System/microbiology ; Metagenomics ; Bacteria/classification/genetics/isolation &amp; purification ; Adult ; Biomarkers ; Aged ; },
abstract = {It is argued that commensal bacteria in the upper respiratory tract (URT) protect against pathogen colonization and infection, including respiratory viruses. Given that the microbiome can mediate immune modulation, a link between the URT microbiome (URTM) and COVID-19 susceptibility and severity is expected. This 16S metagenomics cross-sectional study assessed URTM composition, metabolic prediction, and association with laboratory biomarkers in non-COVID-19 pneumonia (NO-CoV), moderate (M-CoV), severe (S-CoV) COVID-19 patients, as well as COVID-19-negative, asymptomatic (NC) patients. The S-CoV group exhibited reduced URTM diversity, primarily due to a decreased abundance of eubiotic taxa. Some of these taxa (e.g., Haemophilus sp., Neisseria sp.) were also associated with inflammatory biomarkers. Multiple metabolic pathways (e.g., short-chain fatty acids, vitamin B12) linked to immune response, antiviral activity, and host susceptibility showed decreased abundance in S-CoV. These pathways could suggest potential alternatives for the therapeutic arsenal against COVID-19, providing reassurance about the progress in understanding and treating this disease.},
}
@article {pmid40433663,
year = {2025},
author = {Guo, Y and Xiao, Y and Zhang, C and Wang, Y and Cao, G and Tse, KY and Han, Z and Li, F and Zhi, Y},
title = {The intratumoral microbiota heterogenicity is related to the prognosis and tumorigenesis of cervical cancer.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1574511},
pmid = {40433663},
issn = {2235-2988},
mesh = {*Uterine Cervical Neoplasms/microbiology/pathology/genetics ; Humans ; Female ; *Microbiota ; Prognosis ; RNA, Ribosomal, 16S/genetics ; Fibrinogen/metabolism/genetics ; *Carcinogenesis ; Bacteria/classification/genetics/isolation &amp; purification ; Cell Line, Tumor ; *Carcinoma, Squamous Cell/microbiology/pathology ; Tumor Microenvironment ; Middle Aged ; Pseudomonas/genetics/isolation &amp; purification ; },
abstract = {BACKGROUND: The intratumoral microbe-host interaction plays crucial role in the development of cancer. The microbiome can influence cancer development by modulating inflammation, immune responses and metabolic pathways. Therefore, we aim to delineate the landscape and role of intratumoral microbiota in cervical cancer (CC).<br><br>METHODS: The presence of bacterial community in CC tissues was confirmed by fluorescence in situ hybridization (FISH). Then 16s rRNA and RNA-Seq were used to characterize the composition of intratumoral microbiota. Combined with cervical squamous cell carcinoma (CESC) data from the Tumor Cancer Genome Atlas (TCGA), the clinical signatures of intratumoral microbiota and DEGs were further analyzed. Finally, the effect of the up-regulated Fibrinogen beta chain (FGB) expressed fragment peptide on the biological behavior of cancer was verified in vitro.<br><br>RESULTS: We found the composition heterogeneity of bacteria in CC tumors. Pseudomonas was most highly enriched in CC tissues and grouped according to the relative abundance level. The clinical characteristics of patients with relatively high abundance of Pseudomonas had the higher levels of fibrinogen and lower levels of white blood cell (WBC) and albumin (ALB) expression. Combining transcriptome data from the two our collective CC and TCGA-CESC cohorts, we found that Pseudomonas abundance was significantly associated with fibrinogen beta peptide expression and worse overall survival in CC patients. In vitro experiment revealed that Pseudomonas could promote the proliferation and migration of cervical cancer cells through overexpression of FGB.<br><br>CONCLUSIONS: We characterized the composition of the intratumoral microbiota in CC tissues and identified the most significantly differentially abundant bacteria between cancerous and non-cancerous tissues. Our findings provide novel insights into the relationship between intratumoral Pseudomonas and the tumorigenesis of CC. A deeper understanding of the tumor microenvironment and its associated microbiota may reveal new potential therapeutic targets and improve clinical outcomes.},
}
@article {pmid40433658,
year = {2025},
author = {Śmiga, M and Olczak, T},
title = {HmuY proteins of the Porphyromonas genus show diversity in heme-binding properties.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1560779},
pmid = {40433658},
issn = {2235-2988},
mesh = {*Heme/metabolism ; *Bacterial Proteins/metabolism/genetics/chemistry ; Humans ; *Porphyromonas gingivalis/metabolism/genetics ; Protein Binding ; *Porphyromonas/metabolism/genetics ; Computational Biology ; Phylogeny ; Iron/metabolism ; Protoporphyrins/metabolism ; Binding Sites ; },
abstract = {INTRODUCTION: Bacteria of the Porphyromonas genus, belonging to the Bacteroidota phylum, colonize various host niches in health and disease. As heme auxotrophs, they rely on heme uptake for iron and protoporphyrin IX. A key heme acquisition system in Porphyromonas gingivalis is the Hmu system, where the hemophore-like HmuY[Pg] protein plays a major role. HmuY[Pg] coordinates heme-iron using two histidines, whereas other known HmuY proteins produced by other Bacteroidota members prefer a pair of histidine-methionine or two methionines. Some of them bind heme via the protoporphyrin ring without heme-iron coordination, similar to the P. gingivalis HusA protein.<br><br>METHODS: This study used bioinformatics, spectroscopic, and electrophoretic methods to compare the genomic organization of the Hmu system and the structural and functional properties of HmuY proteins within the Porphyromonas genus.<br><br>RESULTS AND DISCUSSION: We revealed variations in the heme-binding properties of proteins belonging to the HmuY family and susceptibility to modifications in their heme-binding pockets. These findings suggest that HmuY proteins may have undergone evolutionary adaptations to enhance bacterial survival in the human microbiome, contributing to dysbiosis and disease development. These evolutionary changes may explain the superior heme-binding ability of P. gingivalis HmuY[Pg] compared to HmuY homologs produced by other Porphyromonas species.},
}
@article {pmid40433629,
year = {2025},
author = {Staton, DV and Tang, J and Barbisan, M and Nussbaum, J and Baker, JL},
title = {The effect of Beta vulgaris on an in vitro oral microbiome of electronic cigarette users.},
journal = {Journal of oral microbiology},
volume = {17},
number = {1},
pages = {2509669},
pmid = {40433629},
issn = {2000-2297},
abstract = {BACKGROUND: Although touted as a safer alternative to cigarette smoking, electronic cigarette usage has been increasingly linked to a myriad of health issues and appears to impact the oral microbiome. Meanwhile, nitrate supplementation has shown promise as a prebiotic that induces positive effects on the oral microbiome.<br><br>METHODS: In this pilot study, the impact of nitrate supplementation as a countermeasure to e-cigarette usage was explored using in vitro growth and 16S rRNA analysis of microcosms derived from e-cigarette users and nonusers and supplementation with nitrate-rich beetroot juice extract.<br><br>RESULTS: The impacts of e-cigarette usage and beetroot supplementation were somewhat limited, with beetroot juice extract supplementation having a significant impact on diversity according to some, but not all, diversity metrics examined. The saliva of the e-cigarette users was depleted in nitrate-reducing Neisseria spp. In terms of differentially abundant individual taxa, the addition of beetroot juice extract to the saliva-derived microcosms had a larger impact on the communities derived from the e-cigarette users compared to that of the nonusers.<br><br>CONCLUSIONS: Overall, this limited pilot study suggests that beetroot juice extract supplementation may impact the microbiota of e-cigarette users and adds to contemporary research paving the way for more in-depth studies examining the role of nitrate-rich supplements as prebiotics to promote oral health.},
}
@article {pmid40433157,
year = {2025},
author = {Li, W and Zhao, C and Tao, Q and Zhang, W and Wang, H and Han, G and Yan, Z},
title = {Study on the changes in the microbiome before and after seed embryo after-ripening of Fritillaria cirrhosa.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1544052},
pmid = {40433157},
issn = {1664-462X},
abstract = {INTRODUCTION: Microorganisms play an important role in the embryonic development of plant seeds; however, there are no existing reports on the microbial communities associated with Fritillaria cirrhosa before and after embryo after-ripening.<br><br>METHODS: In this study, the microbial communities of Fritillaria cirrhosa seeds before and after after-ripening were analyzed using the Illumina MiSeq platform, targeting the V4-V5 region of the bacterial 16S rRNA gene and the ITS1 and ITS2 regions of fungal ribosomal RNA.<br><br>RESULTS: The results showed that bacterial communities were more susceptible to environmental stress and exhibited greater fluctuations compared to fungal communities, as reflected in higher diversity and significant changes in the relative abundance of dominant genera and species. After embryo after-ripening, the dominant fungal genera were Botrytis (SBAR, 29.35%), Tetracladium (SBAR, 15.86%), Ilyonectria (SBAR, 15.35%), and Mrakia (SBAR, 13.14%), while the dominant bacterial genera were Pseudomonas (SBAR, 26.69%) and Stenotrophomonas (SBAR, 16.30%).Prediction results suggested that the bacterial communities with sharply increased relative abundance after embryo after-ripening may interact with seeds through various pathways, including carbohydrate metabolism, absorption and utilization of nitrogen (N), sulfur (S), phosphorus (P), and iron (Fe), as well as secretion of antibiotics, vitamins, cytokinins, and amino acids. Functional validation revealed that most culturable fungi with sharply increased relative abundance had cellulase-degrading abilities, while most of the bacterial isolates were capable of absorbing and utilizing C, N, S, P, and Fe elements. Microbial co-occurrence network analysis indicated that the microbiome after embryo after-ripening formed an unstable, expansive, and rapidly changing network.<br><br>DISCUSSION: In summary, this study revealed the overall dynamics of the microbiome in Fritillaria cirrhosa seeds after embryo after-ripening and identified key microbial taxa exhibiting sharp shifts in relative abundance. This work provides a foundational understanding of the microbial succession associated with seed embryo after-ripening in Fritillaria cirrhosa, which may support seed after-ripening and germination, and enhance seed stress resistance.},
}
@article {pmid40432969,
year = {2025},
author = {Wang, JQ and Yu, T and Qiu, HY and Ji, SW and Xu, ZQ and Cui, QC and Li, HF and Liang, WF and Feng, S and Fu, CT and Gao, X and Han, ZZ and Tian, WN and Li, JX and Xue, SJ},
title = {Differential impact of spotted fever group rickettsia and anaplasmosis on tick microbial ecology: evidence from multi-species comparative microbiome analysis.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1589263},
pmid = {40432969},
issn = {1664-302X},
abstract = {Tick-borne diseases (TBDs) pose a significant public health challenge, as their incidence is increasing due to the effects of climate change and ecological shifts. The interplay between tick-borne pathogens and the host microbiome is an emerging area of research that may elucidate the mechanisms underlying disease susceptibility and severity. To investigate the diversity of microbial communities in ticks infected with vertebrate pathogens, we analyzed the microbiomes of 142 tick specimens. The presence of Rickettsia and Anaplasma pathogens in individual samples was detected through PCR. Our study aimed to elucidate the composition and variation of microbial communities associated with three tick species, which are known vectors for various pathogens affecting both wildlife and humans. We employed high-throughput sequencing techniques to characterize the microbial diversity and conducted statistical analyses to assess the correlation between the presence of specific pathogens and the overall microbial community structure. Pathogen screening revealed an overall positivity rate of 51.9% for Anaplasma and 44.6% for spotted fever group rickettsia (SFGR). Among the three tick species (Dermacentor silvarum, Haemaphysalis concinna, and Haemaphysalis japonica) analyzed, D. silvarum (the predominant species) exhibited the highest pathogen prevalence. The results indicate significant variation in microbial diversity between tick samples, with the presence of Anaplasma and SFGR associated with distinct changes in the microbial community composition. These findings underscore the complex interactions between ticks and their microbial inhabitants, enriching our understanding of tick-borne diseases.},
}
@article {pmid40432964,
year = {2025},
author = {Ghose, SL and Eisen, JA},
title = {Skin microbiomes of frogs vary among body regions, revealing differences that reflect known patterns of chytrid infection.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1579231},
pmid = {40432964},
issn = {1664-302X},
abstract = {INTRODUCTION: The amphibian skin microbiome is an important line of defense against pathogens including the deadly chytrid fungus, Batrachochytrium dendrobatidis (Bd). Bd is known to preferentially infect ventral skin surfaces and feet of host amphibians, often leaving dorsal surfaces like the back uninfected. Within-individual variation in infection distribution across the skin, therefore, may relate to differences in microbiomes among skin regions. However, microbiome heterogeneity within amphibian individuals remains poorly characterized.<br><br>METHODS: We utilized 16S rRNA gene amplicon sequencing to compare microbiomes of 10 body regions from nine captive Rana sierrae individuals and their tank environments. These individuals were naive to Bd, allowing us to assess whether microbiomes differed among body regions prior to any impacts that may be caused by infection.<br><br>RESULTS: We found that frog skin and tank environments harbored distinct microbial communities. On frog skin, the bacterial families Burkholderiaceae (phylum Proteobacteria) and Rubritaleaceae (phylum Verrucomicrobia) were dominant, driven in large part by relative abundances of undescribed members of these families that were significantly higher on frogs than in their environment. Within individuals, we detected differences between microbiomes of body regions where Bd infection would be expected compared to regions that infrequently experience infection. Notably, putative Bd-inhibitory relative abundance was significantly higher on body regions where Bd infection is often localized.<br><br>DISCUSSION: These findings suggest that microbiomes in certain skin regions may be predisposed for interactions with Bd. Further, our results highlight the importance of considering intraindividual heterogeneities, which could provide insights relevant to predicting localized interactions with pathogens.},
}
@article {pmid40432815,
year = {2025},
author = {van Duuren, IC and Smits, HH and Duijts, L and Penders, J and Tramper-Stranders, GA},
title = {PROTEA study: a protocol for a randomised controlled trial evaluating the efficacy, immune effects and cost-effectiveness of oral bacterial lysate therapy to protect moderate-late preterm infants from respiratory tract infections and wheezing.},
journal = {ERJ open research},
volume = {11},
number = {3},
pages = {},
pmid = {40432815},
issn = {2312-0541},
abstract = {Infants, children and adults born moderate-late preterm (after 30-36 weeks of pregnancy) are at increased risk of respiratory infections, wheezing and lower lung function leading to increased medication use and hospitalisation. Risk factors frequently present in this population are, at least in part, associated with (lack of) exposure to microbes and subsequent perturbations in microbiome and immune system development. This manuscript presents the protocol of the double-blinded randomised placebo-controlled PROTEA trial, which will demonstrate whether treatment with immunomodulatory bacterial lysates (OM-85) can reduce lower respiratory tract infections and wheeze in the first year of life. The follow-up PROTEA-2 trial will identify possible carry-over effects of OM-85 treatment and investigate the clinical effect of continued treatment in the second year of life. Infants included are otherwise healthy infants born after 30-36 weeks of gestation, excluding those small for gestational age (<3rd percentile). They are recruited shortly after birth in 22 medical centres in the Netherlands. Participants will take OM-85 or placebo starting from 6-10 weeks of life till age 1 year (PROTEA study) or 2 years (PROTEA-2 study) and are closely monitored regarding respiratory health through e-applications. Biological samples, lung function measurements and detailed information on covariates will be collected at ages 2, 6, 12 and 24 months. Biological samples will aid in estimating the impact of bacterial lysate administration on immune cell composition, activation and maturation, vaccination responses, and microbiome diversity and maturation. Participant recruitment started in March 2022.},
}
@article {pmid40432814,
year = {2025},
author = {Smith, DJF and Teng, NMY and Denneny, EK and Mehta, P and Stanel, SC and Blaikley, JF and Chambers, RC and Chaudhuri, N and Garfield, B and Garner, JL and George, PM and Ghai, P and Kon, OM and Li, Y and Man, WD and Porter, JC and Quinn, V and Rivera-Ortega, P and Ross, C and Segal, LN and Walker, SA and Wu, BG and Lloyd, CM and Stewart, I and Jenkins, RG and Molyneaux, PL},
title = {The respiratory microbiome in patients with post-COVID-19 residual lung abnormalities resembles that of healthy individuals and is distinct from idiopathic pulmonary fibrosis.},
journal = {ERJ open research},
volume = {11},
number = {3},
pages = {},
pmid = {40432814},
issn = {2312-0541},
abstract = {INTRODUCTION: Up to 11% of patients are left with residual lung abnormalities following COVID-19 infection. It is unclear whether these changes resolve over time or progress to fibrosis. The airway microbiome is altered in interstitial lung disease, potentially contributing to pathogenesis and disease progression. We hypothesised that the airway microbiome in patients with post-COVID-19 residual lung abnormalities may be altered.<br><br>METHODS: The POST COVID-19 interstitial lung DiseasE (POSTCODE) study recruited subjects with post-COVID-19 residual lung abnormalities for bronchoscopy. 16S ribosomal RNA gene amplicon sequencing was performed on DNA extracted from bronchoalveolar lavage fluid and compared with that from patients with idiopathic pulmonary fibrosis, fibrotic hypersensitivity pneumonitis and control subjects.<br><br>RESULTS: 28 subjects with post-COVID-19 residual lung abnormalities were recruited an average of 11&#x2005;months after infection. No significant associations were found between the lower airway microbiome or bacterial burden and disease severity or trajectory. There was no difference in bacterial burden between post-COVID-19 patients and interstitial lung disease or control subjects. Furthermore, no differences in microbial composition were observed between these patients and those with fibrotic hypersensitivity pneumonitis or controls. However, compared with idiopathic pulmonary fibrosis, there was an increased abundance of Streptococcus and higher &#x3b1;-diversity in subjects with post-COVID-19 residual lung abnormalities.<br><br>CONCLUSIONS: The microbiome and bacterial burden in the lower airways of subjects with post-COVID-19 residual lung abnormalities do not differ from those of controls. The microbiome differs from idiopathic pulmonary fibrosis. This, and the absence of associations between microbial features and disease severity or clinical outcomes, suggests that the microbiome is unlikely to contribute to residual lung abnormalities in patients recovering from COVID-19 infection.},
}
@article {pmid40432552,
year = {2025},
author = {Schenk, S and Wardrop, CG and Parfrey, LW},
title = {Abiotic stress destabilizes the bacterial community of sugar kelp, Saccharina latissima (Phaeophyceae).},
journal = {Journal of phycology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jpy.70033},
pmid = {40432552},
issn = {1529-8817},
support = {//Canadian Network for Research and Innovation in Machining Technology, Natural Sciences and Engineering Research Council of Canada/ ; //University of British Columbia/ ; //Tula Foundation/ ; },
abstract = {As climate change progresses, the intensity and variability of freshwater outflow into the ocean are predicted to increase. The resulting increase in low-salinity events, paired with other abiotic stressors (including increasing temperatures), will be a source of stress for the kelp Saccharina latissima (Saccharina hereafter) and potentially Saccharina-associated bacteria. Bacteria influence host health and can facilitate or hinder host survival and acclimation to stressful abiotic conditions. Therefore, understanding how bacterial communities change under abiotic stress is critical for understanding how abiotic stress will affect kelp physiology. We investigated the effect of abiotic stress on Saccharina and associated bacteria by surveying the bacterial community associated with Saccharina across naturally occurring salinity and temperature gradients, coupled with salinity manipulation experiments. Overall, Saccharina harbored a stable core bacterial community, which decreased in relative abundance under abiotic stress. In the field, both salinity and temperature shaped the bacterial community, with temperature having higher explanatory power most of the time. In the lab, we confirmed that the patterns observed in the field could be replicated by manipulating salinity alone. Decreased relative abundance of core bacteria and increased community dissimilarity in low-salinity in the lab suggest that low-salinity alone can induce a stress response, detectable in the bacterial community of Saccharina.},
}
@article {pmid40432377,
year = {2025},
author = {Gubert, C and Kong, G and Shadani, S and Connell, S and Masson, BA and van de Garde, N and Narayana, VK and Renoir, T and Hannan, AJ},
title = {Prebiotics Rescue Gut Microbiome Dysregulation and Enhance Cognitive and Gastrointestinal Function in a Mouse Model of Schizophrenia.},
journal = {Schizophrenia bulletin},
volume = {},
number = {},
pages = {},
doi = {10.1093/schbul/sbaf056},
pmid = {40432377},
issn = {1745-1701},
support = {//Bethlehem Griffiths Research Foundation (BGRF) Grant/ ; //National Health and Medical Research Council (NHMRC) Principal Research Fellowship and Ideas Grant/ ; //EU-JPND Grant/ ; //DHB Foundation/ ; //Equity Trustees/ ; //Flicker of Hope Foundation/ ; //NHMRC Project Grants/ ; //NHMRC Dementia Fellowship/ ; },
abstract = {BACKGROUND AND HYPOTHESIS: Schizophrenia is a devastating psychiatric disorder characterized by positive (eg, hallucinations) and negative (eg, reduced motivation) symptoms, and cognitive deficits. Chronic gastrointestinal tract issues exist as comorbid symptoms of schizophrenia. Recent findings indicate the involvement of the microorganisms that inhabit the gut, the microbiota (and the broader microbiome which also includes microbial genomes, etc.) in schizophrenia pathogenesis. In the present study, we hypothesized that chronic administration with prebiotics fructooligosaccharide and galactooligosaccharide (FOS and GOS; a combination used clinically for other disorders) would restore gut microbiome composition of the metabotropic glutamate receptor 5 (mGlu5) knockout (KO) mouse model of schizophrenia, which we previously demonstrated to exhibit gut dysbiosis.<br><br>STUDY DESIGN: We assessed the impact of prebiotics on gut microbiome composition and function, as well as the gastrointestinal function and schizophrenia-like phenotype of mGlu5 KO mice and wild-type littermates. We administered a combination of the prebiotics FOS and GOS, vs vehicle control administration, in both the mouse model of schizophrenia and wild-type littermates.<br><br>STUDY RESULTS: The present study firstly corroborated the altered gut microbiome composition in the mGlu5 KO mouse model of schizophrenia. Importantly, we have revealed an altered microbial metabolic profile. We have also shown that the prebiotics we administered were not only able to rescue these gut microbiome changes but also had additional beneficial effects including cognitive enhancement and improved gastrointestinal function.<br><br>CONCLUSION: These preclinical findings indicate that prebiotics, such as the combination of FOS and GOS used in the present study, may have therapeutic potential in schizophrenia as an add-on intervention with an exceptional safety profile.},
}
@article {pmid40432236,
year = {2025},
author = {Ashman, TL},
title = {Uncovering the reciprocal effects of plant polyploidy and the microbiome: implications for understanding of polyploid success.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.70226},
pmid = {40432236},
issn = {1469-8137},
support = {2027604//Division of Environmental Biology/ ; },
abstract = {Polyploidy plays a major role in diversification and speciation of almost all plants. Separately, the microbiome is recognized for its ubiquitous role in plant functioning. Despite the importance of both processes, we lack a synthetic picture of their reciprocal relationship. I forge this missing linkage by presenting the ways in which plant polyploidy can shape the microbiome and how the microbiome in turn can affect polyploid phenotype and fitness. I illustrate these interactions by drawing on the small, but compelling, set of comparisons of the plant-microbial community interaction with taxa representing different stages of the polyploid continuum and thereby shed light on how the advantages of polyploidy may be influenced by microbes. I use findings from a range of studies to build the case for plant-microbiome reciprocal interactions in both key pathways for polyploid persistence: overcoming their minority cytotype disadvantage and increasing competitive ability and/or niche shifts relative to diploids. I put forward how the microbiome likely plays a role in polyploid stress tolerance, abiotic niche breadth, range limits and coexistence. I conclude by identifying the research needed to test these hypotheses and how doing so could transform our understanding of polyploidy as a driver of plant ecology and evolution.},
}
@article {pmid40432173,
year = {2025},
author = {Zhang, W and Cheng, Y and Shao, L and Li, Z and Sarwar, R and Wei, Q and Liu, B and Huang, K and Liang, Y and Tan, X},
title = {The Glycosylation Status of Small Molecules Impacts Different Aspects of Plant Immunity.},
journal = {Physiologia plantarum},
volume = {177},
number = {3},
pages = {e70292},
doi = {10.1111/ppl.70292},
pmid = {40432173},
issn = {1399-3054},
support = {31600993//National Natural Science Foundation of China/ ; 21JDG073//Jiangsu University/ ; 5501330014//Advanced Talent Foundation from Jiangsu University/ ; },
mesh = {Glycosylation ; *Plant Immunity/physiology ; Glycosyltransferases/metabolism ; Glycoside Hydrolases/metabolism ; *Plants/immunology/metabolism ; Plant Proteins/metabolism ; },
abstract = {Plants, as sessile organisms, are constantly exposed to biotic stresses and have evolved intricate defense mechanisms to survive. Small molecules, including hormones, novel signaling compounds, and secondary metabolites, play pivotal roles in plant immunity. UDP-glycosyltransferases (UGTs) and family 1 glycoside hydrolases (GH1 β-glycosidases) are key enzymes that regulate the glycosylation and deglycosylation of these small molecules. Through the addition or removal of sugar moieties, these enzymes modulate the biological properties and functions of defense-related hormones, signaling compounds, and secondary metabolites. Extensive research has elucidated the substrates of UGTs and GH1 β-glycosidases and their roles in regulating the glycosylation status of small molecules, which is critical for various layers of plant immunity. This review explores the contributions of UGTs and GH1 β-glycosidases in: (1) the primary defense layer, including physical barriers and chemical defenses; (2) modifying small signaling molecules to enhance disease resistance; and (3) mediating interactions between the root microbiome and plant immune responses. Understanding the dynamic regulation of glycosylation in plant immunity is essential for advancing our knowledge of plant defense mechanisms.},
}
@article {pmid40432163,
year = {2025},
author = {Bolhofner, KL and Sweat, KG and Buss, K and Mata Salinas, J and Marshall, PA},
title = {The forensic footprint: Elemental and microbial evidence in relocated remains.},
journal = {Journal of forensic sciences},
volume = {},
number = {},
pages = {},
doi = {10.1111/1556-4029.70092},
pmid = {40432163},
issn = {1556-4029},
support = {N/A//Barrett, The Honors College, Arizona State University/ ; },
abstract = {Here, we investigate the microbial and elemental signatures left behind at the sites of relocated remains, providing insights into postmortem processes that can assist forensic investigations of clandestine burials and relocated remains. We allowed two 90.7 kg (200lbs) clothed porcine models to decompose in open, varied environments in Arizona for a period of 25 days prior to the removal of the remains to secondary burial locations. After a period of 9 months, we collected soil samples from both the primary and secondary sites, as well as from control sites nearby. Our findings support the prevailing suggestion that microbial communities associated with decomposing remains exhibit distinct signatures, here dominated by Gammaproteobacteria and Clostridium, and demonstrate for the first time that these signatures remain detectable at a primary site for an extended period after a short decomposition period and relocation of remains to a secondary site. Additionally, elemental analyses identified significant differences in soil composition, particularly in macronutrients such as phosphorus and sulfur, between control and both primary and secondary deposition sites. These findings suggest that the traces left behind by decomposing remains can serve as forensic markers for an extended period after relocation. Our results highlight the potential of combining microbial and elemental analyses to enhance the understanding of decomposition and inform investigative strategies in forensic contexts. This research underscores the importance of microbial signatures in forensic science and calls for further exploration of their broader applicability in various burial environments.},
}
@article {pmid40431635,
year = {2025},
author = {Rodrigues, GVP and Santos, JPN and Ferreira, LYM and Conceição, LBA and Porto, JAM and Aguiar, ERGR},
title = {Theobroma cacao Virome: Exploring Public RNA-Seq Data for Viral Discovery and Surveillance.},
journal = {Viruses},
volume = {17},
number = {5},
pages = {},
doi = {10.3390/v17050624},
pmid = {40431635},
issn = {1999-4915},
support = {Financial Code 001//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior (CAPES)/ ; //Conselho Nacional de Pesquisa Cient&#xed;fica (CNPq)/ ; },
mesh = {*Cacao/virology ; *Virome/genetics ; Plant Diseases/virology ; RNA-Seq ; Computational Biology/methods ; Phylogeny ; *Plant Viruses/genetics/classification/isolation &amp; purification ; Genome, Viral ; Badnavirus/genetics/isolation &amp; purification/classification ; Microbiota ; },
abstract = {Cocoa (Theobroma cacao L.) is a major agricultural commodity, essential for the global chocolate industry and the livelihoods of millions of farmers. However, viral diseases pose a significant threat to cocoa production, with Badnavirus species causing severe losses in Africa. Despite its economic importance, the overall virome of T. cacao remains poorly characterized, limiting our understanding of viral diversity and potential disease interactions. This study aims to assess the cocoa-associated virome by analyzing 109 publicly available RNA-seq libraries from nine BioProjects, covering diverse conditions and geographic regions. We implemented a comprehensive bioinformatics pipeline integrating multiple viral sequence enrichment steps, a hybrid assembly strategy using different assemblers, and sequence similarity searches against NCBI non-redundant databases. Our approach identified ten putative novel viruses associated with the cocoa microbiome and a novel Badnavirus species. These findings provide new insights into the viral landscape of T. cacao, characterizing the diversity of cacao-associated viruses and their potential ecological roles. Expanding the catalog of viruses associated with cocoa plants not only enhances our understanding of plant-virus-microbiome interactions but also contributes to the development of more effective disease surveillance and management strategies, ultimately supporting sustainable cocoa production.},
}
@article {pmid40431577,
year = {2025},
author = {Jia, J and Bao, P and Yu, Q and Li, N and Ren, H and Chen, Q and Yan, P},
title = {Lactobacillus Re-Engineers Gut Microbiota to Overcome E. coli Colonization Resistance in Mice.},
journal = {Veterinary sciences},
volume = {12},
number = {5},
pages = {},
doi = {10.3390/vetsci12050484},
pmid = {40431577},
issn = {2306-7381},
support = {KCXF20201221173205015//the Shenzhen Science and Technology Program/ ; TCYC-TP2023//Xinjiang Tianchi introduction of talent research Program/ ; },
abstract = {The intestinal health and functionality of animals play pivotal roles in nutrient digestion and absorption, as well as in maintaining defense against pathogenic invasions. These biological processes are modulated by various determinants, including husbandry conditions, dietary composition, and gut microbial ecology. The excessive use of anthropogenic antibiotics may disrupt intestinal microbiota composition, potentially leading to dysbiosis that directly compromises host homeostasis. While Lactobacillus species are recognized for their immunomodulatory properties, their precise mechanisms in regulating host anti-inflammatory gene expression and influencing mucosal layer maturation, particularly regarding E. coli colonization resistance, require further elucidation. To investigate the regulatory mechanisms of Lactobacillus in relation to intestinal architecture and function during E. coli infection, we established a colonic infection model using Bal b/c mice, conducting systematic analyses of intestinal morphology, inflammatory mediator profiles, and microbial community dynamics. Our results demonstrate that Lactobacillus supplementation (Pediococcus acidilactici) effectively mitigated E. coli O78-induced enteritis, with co-administration during infection facilitating the restoration of physiological parameters, including body mass, intestinal histoarchitecture, and microbial metabolic functions. Microbiome profiling revealed that the Lactobacillus intervention significantly elevated Lactococcus abundance while reducing Weissella populations (p < 0.05), concurrently enhancing metabolic pathways related to nutrient assimilation and environmental signal processing (including translation mechanisms, ribosomal biogenesis, amino acid transport metabolism, and energy transduction systems; p < 0.05). Mechanistically, Lactobacillus administration attenuated E. coli-induced intestinal pathology through multiple pathways: downregulating pro-inflammatory cytokine expression (IL-1β, IL-1α, and TNF-α), upregulating epithelial junctional complexes (Occludin, Claudin-1, and ZO-1), and stimulating mucin biosynthesis (MUC1 and MUC2; p < 0.05). These modifications collectively enhanced mucosal barrier integrity and promoted epithelial maturation. This investigation advances our comprehension of microbiota-host crosstalk during enteropathogenic infections under probiotic intervention, offering valuable insights for developing novel nutritional strategies and microbial management protocols in animal husbandry.},
}
@article {pmid40431533,
year = {2025},
author = {Du, H and Xu, J and Zhang, H and Li, J and Wang, F and Li, H and Han, S and Gala, J and Wang, J},
title = {Parity-Associated Differences in the Antioxidants and Fecal Microbiota of Bactrian Camels.},
journal = {Veterinary sciences},
volume = {12},
number = {5},
pages = {},
doi = {10.3390/vetsci12050440},
pmid = {40431533},
issn = {2306-7381},
support = {No. 2021MS03028//Inner Mongolian Natural Science Foundation of China/ ; No. 202114//Doctorate Job Project by the Bayannur Science and Technology Bureau/ ; },
abstract = {Camels survive in deserts through unique, adapted metabolic and immunological processes that are normally lethal to other species. Antioxidants and the gastrointestinal microbiota play major roles in redox homeostasis, yet they remain unexplored in camels to date. The objectives of this study were to characterize the dynamics of milk antioxidants, serum antioxidants, and the fecal microbiome of lactating Bactrian camels with different parities. In total, 30 lactating camels were selected and categorized into the following 3 groups: 10 were assigned to the first parity group (P_1), 10 were classified into the third parity group (P_3), and 10 belonged to the fifth parity group (P_5). The antioxidant parameters of the lactating camels were determined in milk and serum. The fecal microbial community of lactating camels was assessed using 16S rRNA amplicon sequencing, and the resulting library was sequenced on an Illumina NovaSeq platform. The amount of total antioxidant capacity (T-AOC) and antioxidant activity for polypepetides (DPPH) in the third parity was the highest among the groups both in the camel milk and its serum. In the case of hydroxyl radical (OH) and SOD, the amounts were 9.62 U/mL (SEM = 0.4950) and 13.64 U/mL (SEM = 0.5144), respectively, for P_1 in the serum, which were extremely significantly greater than those of the other groups. The Shannon index was significantly different between the P_1 group and either the P_3 or P_5 group. Additionally, Simpson's diversity index significantly differed between the P_1 group and the P_5 group. Furthermore, the number of OH in camels is positively associated with the metabolic pathway of non-oxidative pentose phosphate pathway and ANAGLYCOLYSIS-PWY. In conclusion, this study revealed that different parities were associated with distinct levels of antioxidant parameters and fecal microbial ecologies in lactating Bactrian camels, where parity affects metabolic and microbial health. Understanding these dynamics in camels could optimize their nutritional management, enhancing their welfare in challenging environments.},
}
@article {pmid40431516,
year = {2025},
author = {Várhidi, Z and Jurkovich, V and Sátorhelyi, P and Erdélyi, B and Palócz, O and Csikó, G},
title = {Identification of Naturally Occurring Inhabitants of Vaginal Microbiota in Cows and Determination of Their Antibiotic Sensitivity.},
journal = {Veterinary sciences},
volume = {12},
number = {5},
pages = {},
doi = {10.3390/vetsci12050423},
pmid = {40431516},
issn = {2306-7381},
support = {2020-1.1.2-PIACI-KFI-2020-00002//National Research, Development and Innovation Office/ ; },
abstract = {The vaginal microbiota plays a crucial role in bovine reproductive health in the periparturient period. This study aimed to characterize the naturally occurring bacterial species in the vaginal microbiome of healthy Holstein Frisian cows and evaluate their antibiotic sensitivity. Vaginal samples were collected from 44 healthy cows on three dairy farms. A total of 54 bacterial species were detected, with Gram-positive bacteria comprising 87% of the isolates. The most prevalent genera were Bacillus, Streptococcus, and Staphylococcus. Antibiotic susceptibility tests indicated that some isolates carried resistance genes, but most remained sensitive to commonly used antibiotics. The average vaginal mucosa pH was 7.2. These findings provide valuable insights into the diversity of vaginal microbiota of healthy dairy cows. Understanding the bacterial composition and antibiotic susceptibility can support reproductive health management and prudent use of antibiotics in dairy herds.},
}
@article {pmid40431489,
year = {2025},
author = {Ren, J and Ren, S and Yang, H and Ji, P},
title = {Effects of Phytogenic Feed Additive on Production Performance, Slaughtering Performance, Meat Quality, and Intestinal Flora of White-Feathered Broilers.},
journal = {Veterinary sciences},
volume = {12},
number = {5},
pages = {},
doi = {10.3390/vetsci12050396},
pmid = {40431489},
issn = {2306-7381},
support = {2021-RC-57//The Lanzhou talent innovation and entrepreneurship project/ ; Gaufx-02Y05//A university-level Fuxi talent project/ ; },
abstract = {This study systematically evaluates the effects of dietary supplementation with phytogenic feed additive (0.2%, 0.4%, and 0.8%) on white-feathered broilers (n = 88) through a 42-day controlled trial with the weight of approximately 50 g. The experimental design incorporates a triplicate-group-replicated protocol with daily feed intake monitoring, culminating in comprehensive assessments of the growth performance, slaughter traits, meat quality, and cecal microbiome dynamics. The results demonstrated that the 0.8% supplementation significantly enhanced average daily weight gain (p < 0.05), optimized meat characteristics (elevated the redness of meat, reduced pH; p < 0.05), and restructured cecal microbiota by enriching Deinococcus-Thermus, Bacteroidetes, Actinobacteria, and Cyanobacteria (p < 0.05). Based on microbiota-based functional prediction analyses (COG/KEGG/MetaCyc), phytogenic feed additive significantly activated lipid metabolism pathways in broilers. The immunomodulatory correlations between Deinococcus/Thermus/Cyanobacteria and immune indicators suggested their potential immune-enhancing effects mediated through host immune regulation. The findings established the 0.8% phytogenic feed additive as a multifunctional phytogenic additive that synchronously improves zootechnical performance, meat quality, and microbiome homeostasis, offering a scientifically validated strategy for antibiotic-free precision nutrition in sustainable poultry production.},
}
@article {pmid40431453,
year = {2025},
author = {Barber, TM and Kabisch, S and Pfeiffer, AFH and Weickert, MO},
title = {The Gut Microbiome as a Key Determinant of the Heritability of Body Mass Index.},
journal = {Nutrients},
volume = {17},
number = {10},
pages = {},
doi = {10.3390/nu17101713},
pmid = {40431453},
issn = {2072-6643},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics/physiology ; *Body Mass Index ; *Obesity/genetics/microbiology ; Female ; Diet ; },
abstract = {The pathogenesis of obesity is complex and incompletely understood, with an underlying interplay between our genetic architecture and obesogenic environment. The public understanding of the development of obesity is shrouded in myths with widespread societal misconceptions. Body Mass Index (BMI) is a highly heritable trait. However, despite reports from recent genome-wide association studies, only a small proportion of the overall heritability of BMI is known to be lurking within the human genome. Other non-genetic heritable traits may contribute to BMI. The gut microbiome is an excellent candidate, implicating complex interlinks with hypothalamic control of appetite and metabolism via entero-endocrine, autonomic, and neuro-humeral pathways. The neonatal gut microbiome derived from the mother via transgenerational transmission (vaginal delivery and breastfeeding) tends to have a permanence within the gut. Conversely, non-maternally derived gut microbiota manifest mutability that responds to changes in lifestyle and diet. We should all strive to optimize our lifestyles and ensure a diet that is replete with varied and unprocessed plant-based foods to establish and nurture a healthy gut microbiome. Women of reproductive age should optimize their gut microbiome, particularly pre-conception, ante- and postnatally to enable the establishment of a healthy neonatal gut microbiome in their offspring. Finally, we should redouble our efforts to educate the populace on the pathogenesis of obesity, and the role of heritable (but modifiable) factors such as the gut microbiome. Such renewed understanding and insights would help to promote the widespread adoption of healthy lifestyles and diets, and facilitate a transition from our current dispassionate and stigmatized societal approach towards people living with obesity towards one that is epitomized by understanding, support, and compassion.},
}
@article {pmid40431425,
year = {2025},
author = {Andreou, E and Papaneophytou, C},
title = {Boosting Immunity Through Nutrition and Gut Health: A Narrative Review on Managing Allergies and Multimorbidity.},
journal = {Nutrients},
volume = {17},
number = {10},
pages = {},
doi = {10.3390/nu17101685},
pmid = {40431425},
issn = {2072-6643},
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; *Hypersensitivity/immunology/diet therapy ; *Multimorbidity ; *Nutritional Status ; Diet, Mediterranean ; Precision Medicine ; Diet ; *Immunity ; },
abstract = {The increasing global burden of allergic diseases and multimorbidity underscores the urgent need for innovative strategies to strengthen immune health. This review explores the complex relationships among nutrition, gut microbiota, immune regulation, allergic diseases, and multimorbidity. It highlights how targeted nutritional and microbial interventions may influence disease outcomes. Dietary components and microbial metabolites dynamically modulated immune function, highlighting the critical role of the gut-immune-metabolism axis in disease pathogenesis and management. Personalized nutrition, guided by advances in diagnostics such as component-resolved diagnostics, basophil activation tests, and epigenetic biomarkers, allows for precise dietary interventions tailored to individual allergy phenotypes and multimorbidity profiles. The Mediterranean diet, breastfeeding, and microbiota-targeted therapies have emerged as effective strategies to enhance immune resilience, reduce inflammation, and manage allergic reactions. Technological advancements, including artificial intelligence-driven dietary assessments, wearable devices, and mobile applications, have further revolutionized personalized dietary management, enabling real-time, precise nutritional monitoring and intervention. Despite these advances, challenges in implementing personalized nutrition persist, including variability in dietary patterns, cultural and socioeconomic factors, and accessibility concerns. Future research should focus on long-term interventional and longitudinal studies to validate precision nutrition strategies and enhance clinical applicability. This integrative approach, combining nutrition, microbiome science, technology, and personalized healthcare, holds substantial promises for sustainable disease prevention and enhanced immune resilience across diverse populations.},
}
@article {pmid40431390,
year = {2025},
author = {Wang, X},
title = {Unveiling the Gut Microbiota: How Dietary Habits Shape Health Through Microbiome Modulation.},
journal = {Nutrients},
volume = {17},
number = {10},
pages = {},
doi = {10.3390/nu17101650},
pmid = {40431390},
issn = {2072-6643},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Feeding Behavior ; *Diet ; },
abstract = {This Editorial provides an overview of the Special Issue "Dietary Habit, Gut Microbiome, and Human Health" which was recently published in Nutrients [...].},
}
@article {pmid40431365,
year = {2025},
author = {Kreimeyer, H and Sydor, S and Buchholz, L and Toskal, C and Özcürümez, M and Schnabl, B and Syn, WK and Sowa, JP and Manka, P and Canbay, A},
title = {Non-Alcoholic Beer Influences Glucose and Lipid Metabolism and Changes Body Composition in Healthy, Young, Male Adults.},
journal = {Nutrients},
volume = {17},
number = {10},
pages = {},
doi = {10.3390/nu17101625},
pmid = {40431365},
issn = {2072-6643},
support = {IF-026N-22//Innovation-FORUM Ruhr-University Bochum/ ; 031L0257F//Federal Ministry of Education and Research/ ; P30 DK120515/NH/NIH HHS/United States ; },
mesh = {Humans ; Male ; *Beer ; *Body Composition/drug effects ; *Lipid Metabolism/drug effects ; Young Adult ; Adult ; *Blood Glucose/metabolism ; Gastrointestinal Microbiome/drug effects ; Liver ; Insulin/blood ; Triglycerides/blood ; Biomarkers/blood ; Single-Blind Method ; },
abstract = {Background and Aims: Non-alcoholic beers (NABs) are gaining popularity as alternatives to alcoholic beverages, yet their metabolic and health effects compared to no consumption of these drinks remain unclear. Material and Methods: The investigator-blinded, single-center, randomized study compares the effects on the metabolism, health, and gut microbiome of the daily consumption of different NABs-pilsener, mixed beer, and wheat beer-on glucose and fat metabolism, body composition, and liver function in 44 healthy young men. The participants consumed 660 mL of one of these beers or water daily for 4 weeks. We measured indicators of glucose and lipid metabolism, liver enzymes, body composition, and the composition of the gut microbiota. Results: The findings revealed that mixed beer increased fasting glucose and triglycerides, and wheat beer increased insulin, C-peptide, and triglycerides. The intake of pilsener and water decreased cholesterol and LDL levels without significantly affecting glucose metabolism. Biomarkers of liver damage such as M30 lowered in water and pilsener, while ALT and AST lowered in mixed beer. The pattern of the gut microbiota also changed, as pilsener lowered Firmicutes and increased Actinobacteria. Conclusions: In summary, consumption of NABs, especially mixed and wheat beers, exerts an unfavorable metabolic impact on glucose and fat, while pilsener and water are more favorable from a metabolic perspective. We concluded that the metabolic alterations seen are probably due to the caloric and sugar content in NABs, rather than polyphenols. The chronic effects of NABs on health should be evaluated in future studies.},
}
@article {pmid40431325,
year = {2025},
author = {Bhattacharya, SS and Yadav, B and Jandarov, R and Jetter, WA and Yadav, JS},
title = {Oral Microbiota Dysbiosis in Firefighters and the Potential Contributing Environmental and Lifestyle Factors Based on a Case-Control Study.},
journal = {Microorganisms},
volume = {13},
number = {5},
pages = {},
doi = {10.3390/microorganisms13051154},
pmid = {40431325},
issn = {2076-2607},
support = {#T42OH008432//This research study was supported in part by the National Institute for Occupa-tional Safety and Health (NIOSH) through the Pilot Research Project Program of the University of Cincinnati Education and Research Center/ ; },
abstract = {Epidemiological studies show firefighters have increased risks of cancer, diabetes, and cardiovascular disease. To explore links between occupational/environmental exposures and dysbiosis-associated health risks, this case-control study compared oral microbiota of age-matched firefighters (n = 13) and non-firefighters (n = 13) using next-generation sequencing. Firefighters exhibited significantly reduced overall microbial diversity (p ≤ 0.05) and compositional shifts. Firmicutes increased from 53.5% to 68.5%, and Bacteroidetes from 9.5% to 14.1%, while Proteobacteria decreased from 24.6% to 8.3%, and Fusobacteria from 3.3% to 1.1%. This resulted in a higher Firmicutes to Bacteroidetes ratio (5.63 vs. 4.89 in controls), indicating a pro-inflammatory oral microenvironment. At the family level, Streptococcaceae (45.1% to 60.3%) and Prevotellaceae (6.2% to 10.0%) increased, whereas Neisseriaceae (17.7% to 4.9%) and Fusobacteriaceae (2.1% to 0.8%) decreased. The genus Streptococcus dominated firefighters' microbiota, rising from 45.1% to 60.3%. Diversity indices confirmed reduced microbial evenness and richness in firefighters. Metadata analysis linked frequent fire exposures to perturbations in Comamonadaceae and Carnobacteriaceae (p ≤ 0.05). Barbecue consumption, a source of polycyclic aromatic hydrocarbons, correlated with elevated Spirochaetaceae and Peptostreptococcaceae. This first report on oral dysbiosis in firefighters reveals significant alterations in microbiota abundance, diversity, and evenness, implying potential health risks for this group.},
}
@article {pmid40431264,
year = {2025},
author = {Silva, V and Brito, I and Alexandre, A},
title = {The Vineyard Microbiome: How Climate and the Main Edaphic Factors Shape Microbial Communities.},
journal = {Microorganisms},
volume = {13},
number = {5},
pages = {},
doi = {10.3390/microorganisms13051092},
pmid = {40431264},
issn = {2076-2607},
support = {Project UIDB/05183 and PhD fellowship UI/BD/153513/2022//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e Tecnologia/ ; },
abstract = {The soil microbiome is a complex system that encompasses millions of microbes including archaea, bacteria, fungi, protozoa and viruses. The role of abiotic factors is crucial in shaping the distribution patterns of microorganisms, its abundance and also the interactions between species, from local to the global level. In the particular case of the vineyard, the microbial communities have a potential impact in both the grapevine development and health and, later on, in the grape production and quality. The present review focuses on how the composition of soil microbial communities is influenced by climate and several edaphic factors, such as soil moisture, soil nutrients and soil pH. It also discusses the role of microorganisms and their metabolic activity on the fermentation process, influencing the sensorial characterisation of the wine and suggesting the definition of a microbial terroir.},
}
@article {pmid40431261,
year = {2025},
author = {Mendes Silva Cruz, A and Cardoso, JF and Pinheiro, KC and Ferreira, JA and Barbagelata, LS and Silva, SP and Chagas Junior, WD and Lobo, PS and Teixeira, DM and André Junior, W and Ordenes Silva, I and Santos, MC and Soares Farias, LS and Sousa, MS and Neto Tavares, F},
title = {Impact of SARS-CoV-2 P.1 Variant Infection on the Nasopharyngeal Commensal Bacterial Microbiome of Individuals from the Brazilian Amazon.},
journal = {Microorganisms},
volume = {13},
number = {5},
pages = {},
doi = {10.3390/microorganisms13051088},
pmid = {40431261},
issn = {2076-2607},
support = {4648 MPT/IEC/FADESP//Public Ministry of Labor through the Research Support and Development Foudation/ ; 159996/2021-0//National Council for Scientific and Technological Development/ ; NU2GGH002174/CC/CDC HHS/United States ; NU2GGH002174//Funda&#xe7;&#xe3;o Oswaldo Cruz/ ; },
abstract = {It is important to understand which bacterial taxa are most abundant during SARS-CoV-2 infection and to promote mitigation strategies for conditions subsequent to infection. Nasopharyngeal swab samples were collected from patients infected with SARS-CoV-2 and their family contacts (uninfected and asymptomatic) during the outbreak of the P.1 variant of SARS-CoV-2 in Parintins, Amazonas-Brazil, in March 2021. The samples were investigated by a shotgun sequencing metagenomic approach using the NextSeq 500 Illumina® system. The samples were stratified according to the presence or absence of SARS-CoV-2, household group, sex, and age. Of the total of 63 individuals, 37 (58.73%) were positive for SARS-CoV-2 and 26 (41.27%) were negative for SARS-CoV-2 and other respiratory viruses (FLU, AdV, HBoV, HCoV, HMPV, RSV, PIV, HRV). The alpha diversity indexes Chao1, species observed, Simpson, and Inv Simpson demonstrated a significant difference (p < 0.05) in both the diversity of observed species and the abundance of some taxa between positive and negative individuals. We also observed an abundance of opportunists such as Klebsiella pneumoniae, Staphylococcus spp, and Shigella sonnei, previously associated with the severity of COVID-19. Our results suggest that SARS-CoV-2 infection causes changes in the microenvironment of the nasopharyngeal region, allowing greater proliferation of opportunistic bacteria and decreased abundance of commensal bacteria.},
}
@article {pmid40431257,
year = {2025},
author = {Origüela, V and Lopez-Zaplana, A},
title = {Gut Microbiota: An Immersion in Dysbiosis, Associated Pathologies, and Probiotics.},
journal = {Microorganisms},
volume = {13},
number = {5},
pages = {},
doi = {10.3390/microorganisms13051084},
pmid = {40431257},
issn = {2076-2607},
abstract = {The importance of the microbiome, particularly the gut microbiota and its implications for health, is well established. However, an increasing number of studies further strengthen the link between an imbalanced gut microbiota and a greater predisposition to different diseases. The gut microbiota constitutes a fundamental ecosystem for maintaining human health. Its alteration, known as dysbiosis, is associated with a wide range of conditions, including intestinal, metabolic, immunological, or neurological pathologies, among others. In recent years, there has been a substantial increase in knowledge about probiotics-bacterial species that enhance health or address various diseases-with numerous studies reporting their benefits in preventing or improving these conditions. This review aims to analyze the most common pathologies resulting from an imbalance in the gut microbiota, as well as detail the most important and known gut probiotics, their functions, and mechanisms of action in relation to these conditions.},
}
@article {pmid40431255,
year = {2025},
author = {Mendes, E and Umana, ERP and Di Pace Soares Penna, D and de Oliveira, FA and Lemos, LN and Ribeiro, WR and Casaro, MB and Lazarini, M and Oliveira, VM and Ferreira, CM},
title = {Probiotic Administration Contributes to the Improvement in Intestinal Dysregulation Induced by Allergic Contact Dermatitis.},
journal = {Microorganisms},
volume = {13},
number = {5},
pages = {},
doi = {10.3390/microorganisms13051082},
pmid = {40431255},
issn = {2076-2607},
support = {2021/06751-4//S&#xe3;o Paulo Research Foundation/ ; },
abstract = {Recent studies have emphasized the impact of gut microbiota on skin health, but the reverse, how skin diseases affect gut homeostasis, has received less attention. Allergic contact dermatitis (ACD), a common skin disorder affecting one in four people worldwide, can be accompanied by intestinal disturbances. To explore this, we used an experimental model of ACD to investigate the intestinal changes induced by the disease. Parameters assessed included intestinal microbiota, short-chain fatty acids (SCFAs), gene expression related to intestinal permeability, inflammatory cytokines, and mucus production. To evaluate potential therapeutic interventions, the probiotic Bifidobacterium longum strain BB536 was administered via gavage, starting 10 days before dermatitis induction and continuing until the last day of disease induction. ACD caused alterations in the composition of intestinal microbiota compared to naïve mice but did not affect SCFA production. The probiotic altered microbiota composition and increased acetate production in dermatitis-induced mice. ACD decreased the gene expression of TjP1, ATHO1, and MUC2, while probiotic treatment restored TjP1 and ATHO1 to normal levels. The cytokine IL-6 increased in the ACD group compared to naïve mice, whereas IL-10 decreased; probiotic treatment also restored these levels. Intestinal mucus production, affected by ACD, was partially restored by probiotic treatment. The findings suggest that probiotics could be a therapeutic strategy to prevent intestinal issues caused by skin diseases.},
}
@article {pmid40431238,
year = {2025},
author = {D'Urso, F and Paladini, F and Miraglia, A and D'Amuri, A and Chieppa, M and Pollini, M and Broccolo, F},
title = {Translating Patent Innovation into Clinical Practice: Two Decades of Therapeutic Advancements in Dysbiosis Management.},
journal = {Microorganisms},
volume = {13},
number = {5},
pages = {},
doi = {10.3390/microorganisms13051064},
pmid = {40431238},
issn = {2076-2607},
abstract = {Dysbiosis, characterized by a microbial imbalance, particularly within the gut microbiota, has emerged as a significant health concern linked to various diseases. This study analyzed 8097 patent documents from The Lens database (2005-2024) to examine global innovation trends in dysbiosis management. The patent filings showed exponential growth, peaking at 1222 documents in 2022, with the United States leading in publications (4361 documents). The analysis revealed three primary innovation clusters: bacterial-based therapeutics (44.8% of patents), specific therapeutic applications (27.6%), and diagnostic methods (15.9%). The disease associations predominantly included inflammatory conditions, infections, and cancer. The patent classifications highlighted a significant focus on probiotic development and microbiota modulation. The surge in patent activity since 2014 correlates with advances in DNA sequencing technology and the growing recognition of dysbiosis's role in human health. This analysis provides valuable insights into the evolving landscape of microbiome therapeutics and future directions for dysbiosis management.},
}
@article {pmid40431230,
year = {2025},
author = {An, J and Kwon, H and Kim, YJ and Moon, BI},
title = {Microbiome-Induced Microenvironmental Changes Before and After Breast Cancer Treatment.},
journal = {Microorganisms},
volume = {13},
number = {5},
pages = {},
doi = {10.3390/microorganisms13051057},
pmid = {40431230},
issn = {2076-2607},
support = {(RS-2021-NR058775), (RS-2022-NR067387),//National Research Foundation of Korea (NRF) grants funded by the Korean government (MSIT)/ ; (RS-2023-00262969)//the Ministry of Health and Welfare/ ; (202201770001)//the Korean Association for Women Surgeons/ ; },
abstract = {Breast cancer treatment, including surgery, chemotherapy, radiotherapy, and endocrine therapy, can affect the microbiome and microenvironment of the human body. The present study examined how the microbiome changes before and after treatment in patients with breast cancer and explored variations in the expression of putative proteins linked to these shifts. Forty-five patients enrolled in this study, and blood samples were collected and sequenced to analyze microbiome composition. Using these sequences, we estimated and compared the putative protein expression levels. In addition, complete blood count results were analyzed to evaluate treatment-induced alterations. The findings indicate that treatment leads to microbiome modifications associated with changes in the human microenvironment. Moreover, key putative proteins involved in these processes were identified. This study provides valuable insights into how breast cancer treatment affects the microbiome and helps elucidate the potential role of microbial protein expression in patient outcomes.},
}
@article {pmid40431226,
year = {2025},
author = {Laivacuma, S and Oblate, O and Derovs, A},
title = {Gut Microbiota and the Gut-Liver Axis in Liver Disease: From Chronic Viral Hepatitis to Cirrhosis, Hepatocellular Carcinoma, and Microbiome-Based Therapies.},
journal = {Microorganisms},
volume = {13},
number = {5},
pages = {},
doi = {10.3390/microorganisms13051053},
pmid = {40431226},
issn = {2076-2607},
abstract = {Chronic viral hepatitis B and C remain major global health challenges, contributing significantly to liver-related morbidity and mortality. Despite antiviral therapies and vaccines for HBV, progression to cirrhosis and hepatocellular carcinoma remains common. For HCV, the lack of a vaccine and high chronicity rates further complicate outcomes. Recent evidence highlights gut-liver axis dysfunction and microbiota dysbiosis in disease progression, immune dysregulation, and fibrosis. Notably, alterations in microbiota composition, including reduced commensal bacteria such as Bifidobacteria and Lactobacilli and an increase in putatively harmful Enterobacteriaceae and Veillonellaceae, have been observed in HBV/HCV infections and cirrhosis. While antiviral therapies do not directly target the gut microbiota, they can contribute to partial restoration of microbial balance by reducing hepatic inflammation and improving gut-liver axis integrity. Nonetheless, post-treatment patients remain at elevated risk of HCC due to persistent epigenetic and immune-mediated changes. Emerging interventions, including probiotic strains, prebiotics, and symbiotics, demonstrate potential in enhancing gut health, alleviating inflammation, and enhancing the quality of life for liver disease patients. Moreover, the gut microbiota is gaining increasing recognition as a potential non-invasive biomarker for early disease detection and monitoring. Ultimately, modulating the gut microbiota could become an integral component of future strategies for managing chronic liver diseases and preventing their complications.},
}
@article {pmid40431225,
year = {2025},
author = {Wang, M and Zhang, L and Liu, Z and Guo, A and Yang, G and Yu, T},
title = {Host-Microbiota Interactions in the Pathogenesis of Porcine Fetal Mummification.},
journal = {Microorganisms},
volume = {13},
number = {5},
pages = {},
doi = {10.3390/microorganisms13051052},
pmid = {40431225},
issn = {2076-2607},
support = {2021YFD1301200//the Shaanxi Livestock and Poultry Breeding Double-chain Fusion Key Project/ ; 2022GD-TSLD-46//the Shaanxi Livestock and Poultry Breeding Double-chain Fusion Key Project/ ; },
abstract = {The number of mummies (MUM) in pigs is a major factor affecting sow reproductive performance. Reducing the incidence of MUM can effectively improve sow utilization efficiency. However, the complex mechanisms by which the host genome, gut microbiome, and metabolome interact to influence sow MUM remain unclear. Based on the current research landscape, this study systematically reveals the regulatory mechanisms of the host genome-gut microbiome-metabolome interaction network on sow MUM. By conducting a multi-omics analysis on the intestinal contents of Yorkshire sows during late gestation across different parities, we constructed a dynamic atlas of the gut microbiota and identified 385 core microbial taxa. Through multi-model MWAS and meta-analysis, we screened six key microbial taxa significantly associated with MUM, including Bacteroidales_RF16_group, Prevotellaceae_Ga6A1_group, Comamonas, Paraprevotella, Dorea, and Gallicola. An mGWAS analysis further identified Bacteroidales_RF16_group as regulated by host genetics, as well as candidate genes such as EGF, ENPEP, and CASP6, and important SNP loci such as rs345237235 and rs3475666995. The study found that the abundance of Proteobacteria in the sow's gut increased progressively from the first parity, providing a theoretical basis for pathogen suppression mechanisms. By integrating fecal metabolomics data, we constructed a four-dimensional regulatory network of host gene-gut microbiota-metabolite-host phenotype. This study innovatively combines quantitative genetics with multi-omics approaches, not only providing a theoretical foundation for understanding host-microbiota interaction mechanisms but also offering critical scientific guidance for reducing sow MUM incidence and improving reproductive efficiency.},
}
@article {pmid40431221,
year = {2025},
author = {Nadeem-Tariq, A and Kazemeini, S and Michelberger, M and Fang, C and Maitra, S and Nelson, K},
title = {The Role of Gut Microbiota in Orthopedic Surgery: A Systematic Review.},
journal = {Microorganisms},
volume = {13},
number = {5},
pages = {},
doi = {10.3390/microorganisms13051048},
pmid = {40431221},
issn = {2076-2607},
abstract = {The human gut microbiome represents a complex ecosystem comprising numerous microorganisms critical to basic physiological processes. The gut microbiome's composition and functionality influence surgical outcomes following orthopedic procedures. The purpose of this study was to evaluate the gut microbiota on critical aspects of orthopedic surgical outcomes. A comprehensive literature search was conducted via PubMed, the Cumulative Index for Nursing and Allied Health Literature (CINAHL), Google Scholar, Cochrane Library, Medline, and Web of Science. A total of 18 research articles of the 599 retrieved results were included in this study. Significant correlations were identified between microbial composition and surgical outcomes, including infection rates, inflammatory responses, and postoperative complications. Bacterial genera like Alistipes and Helicobacter increased postoperative cognitive dysfunction (POCD) risk, while short-chain fatty acid (SCFA)-producing bacteria showed negative correlations with inflammatory markers. Probiotic interventions reduced POCD incidence from 16.4% to 5.1% and modulated inflammatory responses. Additionally, bacterial composition was associated with critical surgical parameters such as bone healing, infection rate, and recovery trajectory. Inflammation, healing processes, and recovery trajectories are influenced by microbial composition in surgical settings. Targeted interventions, such as probiotics, show promise in reducing surgical risks and improving patient recovery.},
}
@article {pmid40431220,
year = {2025},
author = {Goldiș, A and Dragomir, R and Mercioni, MA and Goldiș, C and Sirca, D and Enătescu, I and Olariu, L and Belei, O},
title = {Personalized Microbiome Modulation to Improve Clinical Outcomes in Pediatric Inflammatory Bowel Disease: A Multi-Omics and Interventional Approach.},
journal = {Microorganisms},
volume = {13},
number = {5},
pages = {},
doi = {10.3390/microorganisms13051047},
pmid = {40431220},
issn = {2076-2607},
support = {Without a Grant Number//"Victor Babes" University of Medicine and Pharmacy, Eftimie Murgu Square, No. 2, 300041 Timisoara, Romania; without a Grant Number/ ; },
abstract = {Inflammatory bowel disease (IBD) is a complex disorder influenced by genetic, environmental, and microbial factors, with emerging evidence highlighting the gut microbiome's role in disease pathogenesis. This study investigates the impact of microbiome-targeted interventions in pediatric IBD by integrating multi-omics analysis, including metagenomics, metabolomics, transcriptomics, and clinical biomarkers, to identify microbial dysbiosis patterns and potential therapeutic targets. A cohort of pediatric IBD patients underwent a personalized intervention involving dietary modifications, probiotic supplementation, and selective antibiotic therapy. Microbiome composition, inflammatory markers (fecal calprotectin, CRP), and disease activity scores (PCDAI/PUCAI) were assessed before and after treatment. At the 3-month follow-up, patients showed significant clinical improvement, with reduced stool frequency (p = 0.004) and improved stool consistency (p < 0.001). Symptoms such as bloating and abdominal pain decreased, while energy levels increased (p < 0.001). Dietary changes included higher fruit, meat, and dairy intake, and lower fast-food and sweets consumption (p < 0.001). Physician assessments classified 90% as "improved", reinforcing the effectiveness of personalized microbiome interventions. Microbiome-targeted interventions (diet, probiotics, and selective antibiotics) improved pediatric IBD outcomes by reducing pathogenic bacteria and increasing short-chain fatty acid (SCFA)-producing species, lowering inflammation and symptoms. Early-life factors (cesarean birth, and formula feeding) influence IBD risk. Personalized diets enhanced microbial balance. Integrating multi-omics supports precision medicine, offering microbiome-based biomarkers and reducing immunosuppressive reliance.},
}
@article {pmid40431212,
year = {2025},
author = {Belanche Monterde, A and Flores-Fraile, J and Pérez Pevida, E and Zubizarreta-Macho, &#xc1;},
title = {Biofilm Composition Changes During Orthodontic Clear Aligners Compared to Multibracket Appliances: A Systematic Review.},
journal = {Microorganisms},
volume = {13},
number = {5},
pages = {},
doi = {10.3390/microorganisms13051039},
pmid = {40431212},
issn = {2076-2607},
abstract = {Clear aligner treatment seems to be a good option for the periodontal patient by the reason of being removable. Multibracket appliances are more difficult to mantain clean and some bacteria might prefer to adhere on the archwire. A systematic review was carried out using 4 electronic databases (Pubmed-Medline, Scopus, Cochrane and Web of Science). The selected trials included quantitative (Shannon index, Simpson index, relative abundances) and/or qualitative (alpha and beta diversity) analysis in patients using clear aligners and multibracket appliances. Initially, a total of 123 articles were found after selecting clinical trials. The inclusion and exclusion criteria were applied by two authors. Finally, 20 articles were selected for the systematic review. The results showed that clear aligner treatment produced less dysbiosis in the selected bacteria compared to multibracket appliances. However, some microbiological changes were observed in some articles during clear aligner use. Oral dysibiosis was related with intestinal dysbiosis, inflammatory response and even cancer. The Firmicutes/Bacteroidetes ratio showed to have a very important role in this development. Periodontitis is also a bacterial disease and clear aligners were recommended to periodontal risk patients. Clear aligner treatment obtained less supra and subgingival biofilm changes compared with multibracket appliances but some bacteria were altered during treatment.},
}
@article {pmid40431187,
year = {2025},
author = {Gan, Y and Cai, R and Cai, G and Aweya, JJ and Xie, J and Chen, Z and Wang, H},
title = {Indole Acetic Acid: A Key Metabolite That Protects Marine Sulfitobacter mediterraneus Against Oxidative Stress.},
journal = {Microorganisms},
volume = {13},
number = {5},
pages = {},
doi = {10.3390/microorganisms13051014},
pmid = {40431187},
issn = {2076-2607},
support = {42206125, 32070113, 42306131//National Natural Science Foundation of China/ ; 2022B1515020017, 2021A1515110426, 2024A1515011054, 2023A1515010637//Basic and Applied Basic Research Foundation of Guangdong Province/ ; },
abstract = {For marine bacteria, the phycosphere is attractive as a major source of labile nutrients, but it also presents challenges due to the accumulation of stressors, such as reactive oxygen species (ROS) from algal metabolisms. Therefore, successful colonization of bacteria in the phycosphere requires an efficient mechanism to fight against oxidative stress, which is still a missing piece in studying bacteria-algae interactions. Here, we demonstrate that a common metabolite, indole acetic acid (IAA), enables the Roseobacter clade Sulfitobacter mediterraneus SC1-11, an IAA-producer, to resist hydrogen peroxide (H2O2) stress and that IAA biosynthesis can be activated by low concentrations of H2O2. Proteomics and metabolomics analyses revealed that bacteria consume high amino acid levels when exposed to H2O2 stress, while exogenous supplementation with IAA effectively protects bacteria from ROS damage and alleviates amino acid starvation by upregulating several proteins responsible for replication, recombination, and repair, as well as two proteins involved in amino acid transport and metabolism. Furthermore, the supplementation of some amino acids, such as arginine, also showed a significant protective effect on bacteria under H2O2 stress. This study highlights an unprecedented role of IAA in regulating amino acid metabolisms for resisting oxidative stress, which may be a specific strategy for adapting to the phycosphere.},
}
@article {pmid40431182,
year = {2025},
author = {Matsumoto, H and Gu, T and Yo, S and Sasahira, M and Monden, S and Ninomiya, T and Osawa, M and Handa, O and Umegaki, E and Shiotani, A},
title = {Fecal Microbiota Transplantation Using Donor Stool Obtained from Exercised Mice Suppresses Colonic Tumor Development Induced by Azoxymethane in High-Fat Diet-Induced Obese Mice.},
journal = {Microorganisms},
volume = {13},
number = {5},
pages = {},
doi = {10.3390/microorganisms13051009},
pmid = {40431182},
issn = {2076-2607},
support = {JP 19K11484//Japanese Grant-in-Aid Scientific Reserach/ ; },
abstract = {The gut microbiota plays an important role in the development of colorectal tumors. However, the underlying mechanisms remain unclear. In this study, we examined the effects of fecal microbiota transplantation (FMT) on azoxymethane (AOM)-induced colorectal tumors in obese mice. We divided the study subjects into the following five groups: high-fat diet (HFD), normal diet (ND), ND+exercise (Ex), HFD+FMT from ND-alone donor (HFD+FMT(ND alone)), and HFD+FMT from ND+Ex donor (HFD+FMT(ND+Ex)). The Ex group performed treadmill exercise for 15 weeks. Thereafter, fecal and colonic mucus samples were extracted for microbiome analysis. The deoxyribonucleic acid sample was collected from the feces and colonic mucosa, and V3-V4 amplicon sequencing analysis of the 16S rRNA gene was performed using MiSeq. The number of polyps was significantly lower in the ND (6.0 ± 1.6) and ND+Ex (1.8 ± 1.3) groups than in the HFD group (11.4 ± 1.5). The ND+Ex group had significantly fewer polyps than the ND group. The HFD+FMT(ND alone) (5.2 ± 0.8) and HFD+FMT(ND+Ex) (2.8 ± 2.6) groups also had significantly fewer polyps than the HFD group. The IL-15 mRNA levels in the colonic tissues were significantly higher in the HFD+FMT(ND alone) group than in the ND group. Fecal ω-muricholic acid concentrations were significantly higher in the HFD+FMT(ND alone) group than in the ND group and in the HFD+FMT(ND+Ex) group than in the ND+Ex group. The ND, ND+Ex, HFD+FMT(ND alone), and HFD+FMT(ND+Ex) groups had a significantly higher abundance of Lacyobacillaceae than the HFD group. In the FMT group, Erysipelotrichaceae and Tannerellaceae were significantly less abundant. Compared with the HFD group, the ND, ND+Ex, HFD+FMT(ND alone), and HFD+FMT(ND+Ex) groups had a significantly higher abundance of Muribaculaceae and a significantly higher abundance of Lactobacillaceae and Rikenellaceae in common among the ND and ND+Ex groups. The common and significantly less common species were Bacteroidaceae in the FMT group and Lactobacillaceae and Rikenellaceae in the ND alone and ND+Ex groups. Bacteroidaceae and Lachnospiraceae were significantly less common in the FMT group. We found that FMT inhibited AOM-induced colorectal tumorigenesis in obese mice. Furthermore, the fecal concentrations of short-chain fatty acids, bile acids, microbiota, and mucosa-associated microbiota differed between the FMT and diet/EX groups, suggesting that the inhibitory effect of FMT on colorectal tumorigenesis may be due to mechanisms different from those of ND alone and ND+Ex.},
}
@article {pmid40431165,
year = {2025},
author = {Properzi, M and Dimartino, V and Pietrucci, D and Fontana, C and Rotondo, C and Lembo, L and Ricci, F and Scatozza, F and Di Lella, G and Messina, F and Chillemi, G and Bartolini, B and Facchiano, A},
title = {Investigating Skin Microbial Community in Malignant Melanoma Lesions.},
journal = {Microorganisms},
volume = {13},
number = {5},
pages = {},
doi = {10.3390/microorganisms13050992},
pmid = {40431165},
issn = {2076-2607},
support = {Ricerca Corrente Linea 3 Progetto 2//Italian Ministry of Health/ ; },
abstract = {The skin microbiome is identified as one of the crucial factors in several pathological conditions, including its potential capacity in modulating cancer progression and response to treatment. A strong association of Bacilli and Betaproteobacteria classes and the Bacteroidetes phylum with melanoma is described in patients with cutaneous malignancies, while an imbalance of S. epidermidis and S. aureus is related to the progression of other skin cancers. In the present study, we characterized the microbial community in suspected lesions of 35 patients, classified, after histological analysis, as malignant melanoma lesions and benign non-melanoma lesions. Mirrored healthy skin were also included as negative control. No significant difference in alpha and beta diversity was observed when samples were categorized in four different groups (melanoma samples vs. contralateral healthy samples; melanoma samples vs. benign lesions; benign lesions vs. contralateral controls; melanoma controls vs. benign controls). The differential abundance analyses show that Corynebacterium urealyticum is more abundant in melanoma samples compared to their control, while Roseomonas gilardii is less abundant in melanoma. Staphylococcus massiliensis, Bacillus coagulans, Paracoccus yeei, Corynebacterium jeikeium, and Corynebacterium pyruviciproducens are present only in melanoma samples when compared with benign lesions.},
}
@article {pmid40431157,
year = {2025},
author = {Coates, N and John, DA and Jordan, S and Storey, M and Thornton, CA and Garaiova, I and Wang, D and Allen, SJ and Michael, DR and Plummer, SF and Facey, PD},
title = {The Impact of Probiotic Supplementation on the Development of the Infant Gut Microbiota: An Exploratory Follow-Up of a Randomised Controlled Trial.},
journal = {Microorganisms},
volume = {13},
number = {5},
pages = {},
doi = {10.3390/microorganisms13050984},
pmid = {40431157},
issn = {2076-2607},
support = {Collaborative Industrial Research (Project No. HE09 COL 1002)//Knowledge Exploitation Fund/ ; Accelerate Programme (Project code: PR-0228)//European Regional Development Fund (ERDF)/ ; N/A//Cultech Ltd/ ; },
abstract = {Early-life establishment of the gut microbiota plays a role in lifelong health, with disruptions linked to heightened risks of metabolic and immune disorders. Probiotic supplementation may be used to modulate the infant gut microbiome to promote favourable development. Here, we evaluate how Lab4B probiotic supplementation shapes the development of the infant gut microbiome over the first 6 months. Faecal samples collected from infants enrolled in PROBAT (ISRCTN26287422), a randomised, double-blind, placebo-controlled trial, were analysed using culture-dependent and -independent (16S rDNA and metagenomic shotgun sequencing) techniques to examine the composition, diversity, and metabolic capabilities of the microbiome, as well as the abundance of antimicrobial resistance genes (ARGs). Probiotic supplementation encouraged the development of a microbiome with a distinct composition characterised by elevated abundances of Bifidobacteriaceae in the first 6 weeks (p = 0.006) and Lactobacillaceae throughout the first 6 months (p < 0.05 at every 6-week time point), accelerated microbial diversification, reduced abundance of beta-lactam- and cephalosporin-resistance genes, and differences in predicted metabolic capabilities at the start and end points. Supplementation of this neonatal population, which is at high risk of atopy, with the Lab4B probiotic significantly influenced the development of the infant gut microbiota during the first 6 months.},
}
@article {pmid40431132,
year = {2025},
author = {Xue, Q and Liu, J and Cao, Y and Wei, Y},
title = {Host Lifeform Shapes Phyllospheric Microbiome Assembly in Mountain Lake: Deterministic Selection and Stochastic Colonization Dynamics.},
journal = {Microorganisms},
volume = {13},
number = {5},
pages = {},
doi = {10.3390/microorganisms13050960},
pmid = {40431132},
issn = {2076-2607},
support = {U23A20157//Key Project of the National Natural Science Foundation of China Joint Fund for Regional Innovation and Development/ ; 202304041101020//Key Cooperation Project of National Science and Technology in Shanxi Province/ ; },
abstract = {The phyllosphere microbiome of aquatic macrophytes constitutes an integral component of freshwater ecosystems, serving crucial functions in global biogeochemical cycling and anthropogenic pollutant remediation. In this study, we examined the assembly mechanisms of epiphytic bacterial communities across four phylogenetically diverse macrophyte species (Scirpus validus, Hippuris vulgaris, Nymphoides peltatum, and Myriophyllum spicatum) inhabiting Ningwu Mayinghai Lake (38.87° N, 112.20° E), a vulnerable subalpine freshwater system in Shanxi Province, China. Through 16S rRNA amplicon sequencing, we demonstrate marked phyllospheric microbiome divergence, as follows: Gammaproteobacteria dominated S. validus, H. vulgaris and N. peltatum, while Alphaproteobacteria dominated in M. spicatum. The nitrate, nitrite, and pH value of water bodies and the chlorophyll, leaf nitrogen, and carbon contents of plant leaves are the main driving forces affecting the changes in the β-diversity of epiphytic bacterial communities of four plant species. The partitioning of assembly processes revealed that deterministic dominance governed S. validus and M. spicatum, where niche-based selection contributed 67.5% and 100% to community assembly, respectively. Conversely, stochastic processes explained 100% of the variability in H. vulgaris and N. peltatum microbiomes, predominantly mediated by dispersal limitation and ecological drift. This investigation advances the understanding of microbial community structural dynamics and diversity stabilization strategies in aquatic macrophyte-associated microbiomes, while establishing conceptual frameworks between plant-microbe symbiosis and the ecological homeostasis mechanisms within vulnerable subalpine freshwater ecosystems. The empirical references derived from these findings offer novel perspectives for developing conservation strategies aimed at sustaining biodiversity equilibrium in high-altitude lake habitats, particularly in the climatically sensitive regions of north-central China.},
}
@article {pmid40431076,
year = {2025},
author = {Mendybayeva, A and Makhambetov, A and Yanin, K and Taskuzhina, A and Khusnitdinova, M and Gritsenko, D},
title = {Metagenomic Analysis of Wild Apple (Malus sieversii) Trees from Natural Habitats of Kazakhstan.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {10},
pages = {},
doi = {10.3390/plants14101511},
pmid = {40431076},
issn = {2223-7747},
support = {BR21882269//The Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; },
abstract = {Kazakhstan's rich biodiversity includes diverse apple populations, notably the wild apple tree (Malus sieversii) prized for traits like disease resistance and adaptability, potentially aiding breeding programs. Analyzing their microbiomes offers insights into bacterial diversity and how it influences apple tree development, making it a reliable method for understanding ecological interactions. In this research, 334 apple tree samples were collected from different mountain ranges in southeastern Kazakhstan. An analysis using nanopore-based 16S rRNA sequencing showed a distinct similarity in the microbiome compositions of samples from the Zhongar and Ile Alatau mountain ranges, with a predominance of Pseudomonadaceae, Enterobacteriaceae, and Microbacteriaceae. In contrast, samples from Ketmen ridge showed a higher prevalence of Enterobacteriaceae. Alongside the less represented Pseudomonadaceae family, in the Ketmen ridge region, bacteria of the Xanthomonadaceae, Alcaligenaceae, and Brucellaceae families were also present. Across all regions, beneficial plant-associated bacteria were identified, such as Pseudomonas veronii, Stenotrophomonas geniculata, and Kocuria rhizophila, potentially enhancing plant resilience. However, opportunistic phytopathogens were also detected, including Pseudomonas viridiflava and Serratia marcescens, particularly in the Ile Alatau region. These findings highlight the complex microbial interactions in M. sieversii, thus offering key insights into host-microbe relationships that can inform apple breeding and ecological preservation efforts.},
}
@article {pmid40431061,
year = {2025},
author = {Hu, J and Yang, S and Cornelis, WM and Zhang, M and Huang, Q and Qiu, H and Qi, S and Jiang, Z and Xu, Y and Zhu, L},
title = {Microstructure and Microorganisms Alternation of Paddy Soil: Interplay of Biochar and Water-Saving Irrigation.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {10},
pages = {},
doi = {10.3390/plants14101498},
pmid = {40431061},
issn = {2223-7747},
support = {52379038//National Natural Science Foundation of China/ ; BE2022390//the Jiangsu Province Key Research and Development Project/ ; B210204016//the Fundamental Research Funds for the Central Universities/ ; KYCX24_0889//Postgraduate Research &amp; Practice Innovation Program of Jiangsu Province/ ; 202306710108//China Scholarship Council/ ; },
abstract = {Biochar application and controlled irrigation (CI) enhance water conservation, lower emissions, and increase crop yields. However, the synergistic effects on the relationship between paddy soil microstructure and microbiome remain poorly understood. This study investigates the impact of different irrigation regimes and biochar applications on soil physicochemical properties, soil microstructure, and the composition and functions of soil microorganisms in paddy soil. The CA treatment (CI with 60 t/hm[2] biochar) showed higher abundances of Mycobacteriaceae, Streptomycetaceae, Comamonadaceae, and Nocardioidaceae than the CK treatment (CI without biochar), which was attributed to two main factors. First, CA increased the pore throat equivalent radius (EqR), throat surface area (SAR), total throat number (TTN), volume fraction (VF), and connected porosity (CP) by 1.47-9.61%, 7.50-25.21%, 41.55-45.99%, 61.12-73.04%, and 46.36-93.75%, respectively, thereby expanding microbial habitats and providing refuges for microorganisms. Second, CA increased the cation exchange capacity (CEC), mean weight diameter (MWD), soil organic carbon (SOC), and total nitrogen (TN) by 22.14-25.06%, 42.24-56.61%, 22.98-56.5%, and 9.41-87.83%, respectively, reinforcing soil structural stability and carbon storage, which promoted microbial community diversity. FK (flood irrigation without biochar) showed no significant correlations with these environmental factors. Compared to CK soil metabolites at Level 2 and Level 3, FK exhibited higher levels of the citrate cycle, indicating that changes in water and oxygen environments due to CI reduced soil organic matter decomposition and carbon cycle. CA and CK strongly correlated with the soil microstructure (VF, CP, TTN, SAR, EqR), and CA notably enhanced soil metabolites related to the synthesis and degradation of ketone bodies, suggesting that biochar can mitigate the adverse metabolomic effects of CI. These results indicate that biochar application in CI paddy fields highlights the critical role of soil microstructure in microbial composition and function and better supports soil sustainability.},
}
@article {pmid40430828,
year = {2025},
author = {Plewa, P and Kiełbowski, K and Mentel, O and Figiel, K and Bakinowska, E and Becht, R and Banach, B and Pawlik, A},
title = {Bacteria and Carcinogenesis and the Management of Cancer: A Narrative Review.},
journal = {Pathogens (Basel, Switzerland)},
volume = {14},
number = {5},
pages = {},
doi = {10.3390/pathogens14050509},
pmid = {40430828},
issn = {2076-0817},
mesh = {Humans ; *Neoplasms/microbiology/therapy/pathology ; *Carcinogenesis ; Tumor Microenvironment ; Gastrointestinal Microbiome ; *Bacteria ; Animals ; Helicobacter pylori ; },
abstract = {There is a widely known relationship between certain microbes and cancer progression. For instance, Helicobacter pylori is associated with the occurrence of gastric cancer, while HPV is associated with cervical and head and neck cancers. Recent studies have uncovered novel and important associations between bacterial presence and tumor formation and treatment response. Apart from the influence of the intestinal microbiome on cancer, the local activity of bacteria affects disease properties as well. Bacteria can localize within tumors in less vascularized niches. Their presence mediates the activity of signaling pathways, which contribute to tumorigenesis. Furthermore, they affect the composition of the tumor microenvironment, a highly complex structure composed of immunoregulatory cells and secreted inflammatory mediators. Recently, researchers have analyzed the properties of bacteria to develop novel anticancer strategies. The aim of this review is to discuss the latest findings regarding the relationships between bacteria and cancer and the properties of bacteria that could be used to kill cancer cells.},
}
@article {pmid40430796,
year = {2025},
author = {Klinsoda, J and Boonsoongnern, A and Thanantong, N and Kaminsonsakul, T and Treesuwan, K and Trevanich, S and Metzler-Zebeli, BU},
title = {The Microbiome Characterization of Edible Visceral Organs and Fresh Meat During Production in a Pig Processing Facility in Thailand.},
journal = {Pathogens (Basel, Switzerland)},
volume = {14},
number = {5},
pages = {},
doi = {10.3390/pathogens14050475},
pmid = {40430796},
issn = {2076-0817},
support = {Young Research Funding 2022-2024//National Research Council of Thailand/ ; },
mesh = {Animals ; Swine ; Thailand ; RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/isolation &amp; purification ; *Microbiota ; *Meat/microbiology ; Pilot Projects ; Food Microbiology ; DNA, Bacterial/genetics ; Gastrointestinal Microbiome ; Food Handling ; },
abstract = {Besides meat, pig organs are traditionally consumed in Asia. However, they can be a source of food poisoning. Less is known about the microbiome associated with different organ meats and the inter-animal variation in the microbiomes of organs. The aim of this pilot study was to characterize and compare the bacterial composition in fresh pig meat and organs (i.e., tonsils, lungs, and spleen) and blood from several carcasses using 16S rRNA amplicon sequencing as a screening method. We also investigated how closely the bacterial composition of the meat and organ samples was related to the gut bacterial community and the bacterial communities on the hands of the workers at different positions during meat processing. Meat, organ, blood, and gut (cecum and feces) samples were collected from 12 carcasses in two batches (n = 6/batch), along with swab samples (n = 4/batch) from the hands of the workers at different positions along the processing chain, from which DNA was extracted. The results for the bacterial diversity showed that each sample type (meat, organ, and blood) comprised a unique taxonomic composition (p < 0.05). Moreover, the data confirmed great inter-animal and batch variation for the meat, organs, and blood, which is helpful information for implementing strategies to enhance hygiene measures at pig farms and slaughterhouses, and hence food safety and quality. The genera associated with food safety and spoilage, such as Anoxybacillus, Acinetobacter, Pseudomonas, Campylobacter, and Streptococcus, were also different between the meat, organs, and blood. The bacterial communities in the gut samples distinctly clustered from communities in the pig organs and meat, whereas some overlaps in community clusters between lung, meat, and hand samples existed. This study demonstrates that the spleen, tonsils, and lungs contained more bacterial genera that comprise pathogenic strains than meat cuts, supporting the need to monitor their microbiome composition as potential contamination sources for food safety and spoilage reasons.},
}
@article {pmid40430465,
year = {2025},
author = {Hong, Y and Yang, Z and Liu, Z and Li, N and Qin, J and Ge, D and Peng, G and Wang, J and Wang, Q},
title = {Tuo-Min-Ding-Chuan Decoction Alleviates Asthma via Spatial Regulation of Gut Microbiota and Treg Cell Promotion.},
journal = {Pharmaceuticals (Basel, Switzerland)},
volume = {18},
number = {5},
pages = {},
doi = {10.3390/ph18050646},
pmid = {40430465},
issn = {1424-8247},
support = {82174113//National Natural Science Foundation of China/ ; 82374289//National Natural Science Foundation of China/ ; No. zyyzdxk-2023251//High level Key Discipline of National Administration of Traditional Chinese Medicine - Traditional Chinese constitutional medicine/ ; },
abstract = {Objective: Tuo-Min-Ding-Chuan decoction (TMDC), a traditional Chinese prescription, has demonstrated significant clinical efficacy in treating allergic asthma. This study aimed to investigate the mechanism of TMDC in treating asthma from the perspective of Treg cells and gut microbiota across distinct gut segments (jejunum, ileum, cecum, and colon). Methods: An ovalbumin (OVA)-induced asthma model was established in mice, followed by oral administration of TMDC at high, medium, and low dose. Immune cells and lung inflammation were examined to assess asthma severity. Microbial composition was determined by 16S rRNA sequencing. Antibiotic cocktail and Lactobacillus rhamnosus GG (LGG) were administrated to confirm the key role of specific bacteria. Results: TMDC attenuated lung inflammation (p < 0.01) and eosinophilic infiltration (p < 0.01) as well as IL-4 and IL-5 secretion (p < 0.01); it was also associated with an increase in Treg cells in the lung, small intestine (SI), and colon (p < 0.05). Meanwhile, TMDC restored the number of microbiota species and the Shannon index in the hindgut and reinstated beneficial bacteria, such as Allobaculum and Turicibacter, which were diminished in asthmatic mice. Notably, TMDC significantly enriched Bifidobacterium and Lactobacillus, particularly in the hindgut. Lactobacillus abundance was significantly correlated (p < 0.05) with Treg cells, IL-4, IL-5, and eosinophils. Furthermore, LGG supplementation restored elevated lung inflammation (p < 0.05) and decreased Treg cells (p < 0.01) due to antibiotic-induced microbiota depletion. Conclusion: TMDC alleviated asthma by promoting Treg cell expansion in a Lactobacillus-dependent manner across different gut segments, providing new insights into its therapeutic mechanisms.},
}
@article {pmid40430375,
year = {2025},
author = {Cichon, N and Szelenberger, R and Stela, M and Podogrocki, M and Gorniak, L and Bijak, M},
title = {Flavanones as Modulators of Gut Microbiota and Cognitive Function.},
journal = {Molecules (Basel, Switzerland)},
volume = {30},
number = {10},
pages = {},
doi = {10.3390/molecules30102203},
pmid = {40430375},
issn = {1420-3049},
mesh = {*Gastrointestinal Microbiome/drug effects ; *Flavanones/pharmacology/chemistry ; Humans ; *Cognition/drug effects ; Animals ; Neuroprotective Agents/pharmacology ; },
abstract = {Flavanones, a key subclass of flavonoids, exhibit a wide range of biological activities, including antioxidant, anti-inflammatory, and neuroprotective properties. Predominantly found in citrus fruits, they occur in both aglycone and glycosylated forms, undergoing extensive metabolic transformation upon ingestion. Recent evidence suggests that flavanones, such as naringenin and hesperidin, influence gut microbiota composition, fostering a balance between beneficial and pathogenic bacterial populations. The gut microbiota plays a pivotal role in regulating the gut-brain axis, impacting cognitive function through the production of short-chain fatty acids (SCFAs), neurotransmitters, and anti-inflammatory cytokines. The modulation of the gut microbiome by flavanones has been associated with improvements in cognitive performance and a reduced risk of neurodegenerative disorders. This review provides a comprehensive analysis of the characteristics of major flavanones, their metabolic pathways, and their impact on gut microbiota and cognitive function. It covers the fundamental mechanisms through which flavanones exert their effects, as well as their potential therapeutic applications for brain health and neuroprotection. Despite promising findings, further research is needed to determine optimal dosages, strategies to enhance bioavailability, and long-term safety profiles.},
}
@article {pmid40430199,
year = {2025},
author = {Li, Y and Ye, Y and Yuan, H and Yao, Z and Li, Y and Sun, Z and Wei, Y and Zhao, Y and Lai, Q},
title = {Dietary Melatonin Supplementation Improved Intestinal Health and Immune Function of Pacific White Shrimp (Litopenaeus vannamei) Under High Alkali Stress.},
journal = {Life (Basel, Switzerland)},
volume = {15},
number = {5},
pages = {},
doi = {10.3390/life15050772},
pmid = {40430199},
issn = {2075-1729},
support = {2023YFD2401001//the National Key Research and Development Plan/ ; },
abstract = {The intestinal tract serves as a critical immune regulator in aquatic species, maintaining homeostasis and environmental stress resistance. This study evaluates the protective effects of melatonin (MT) on Litopenaeus vannamei (L. vannamei) under acute alkaline stress through a comprehensive analysis of intestinal morphology, antioxidant responses, apoptosis regulation, and microbial community dynamics. A total of six groups of melatonin treatment groups were designed. After another 2 months of breeding, a 96 h acute alkalinity stress experiment was conducted. Experimental supplementation revealed dose-dependent outcomes: 82.7 mg/kg MT significantly improved survival rates without affecting growth parameters, while higher concentrations (329.2 mg/kg) induced elevated apoptosis (p < 0.05). Histological examination demonstrated mitigated intestinal structural damage in MT-treated groups compared to non-supplemented controls under alkaline stress. Antioxidant capacity initially increased and then stabilized at optimal MT doses (82.7-165.1 mg/kg), accompanied by enhanced immune marker expression (p < 0.05). Microbial profiling indicated MT-mediated enrichment of commensal bacteria associated with polysaccharide metabolism, energy utilization, and intestinal immunity. This study establishes that melatonin exerts dose-dependent protection in L. vannamei under alkaline stress, balancing antioxidant enhancement, apoptosis modulation, and microbiome regulation to fortify intestinal health, with 82.7-165.1 mg/kg identified as the optimal therapeutic range for mitigating environmental stress without compromising physiological homeostasis. The results of this study establish an empirical framework for optimizing MT application in crustacean aquaculture, particularly highlighting its role in maintaining intestinal barrier integrity and microbial homeostasis under alkaline environmental challenges.},
}
@article {pmid40430156,
year = {2025},
author = {Van den Ende, M and Van de Steen, L and Everaert, K and Hervé, F and Bou Kheir, G},
title = {Exploring Childhood Lower Urinary Tract Symptoms (LUTS), Urinary Tract Infections (UTIs) and the Microbiome-A Systematic Review.},
journal = {Life (Basel, Switzerland)},
volume = {15},
number = {5},
pages = {},
doi = {10.3390/life15050730},
pmid = {40430156},
issn = {2075-1729},
abstract = {UNLABELLED: Pediatric lower urinary tract symptoms (LUTS) are influenced by age and coexist with nocturnal enuresis (NE) and bladder-bowel dysfunction (BBD). Urinary tract infections (UTIs) are common and linked to LUTS, though the causal relationship remains unclear. This systematic review aims to analyze microbiome alterations in pediatric LUTS and UTIs.<br><br>METHODS: A systematic review was conducted following PRISMA guidelines. PubMed, Embase, and CINAHL databases were searched for studies analyzing gut and urinary microbiomes in pediatric patients with LUTS and UTIs. Quality assessment was performed using the QUADOMICS checklist.<br><br>RESULTS: Nine studies published between 2018 and 2024 were included; seven out of nine studies employed prospective designs. Six hundred nineteen patients (44.3% pathology groups, 55.7% controls) were analyzed, with microbiome sequencing performed on stool samples in four studies and urine samples in five studies. UTIs and BBD were associated with reduced alpha diversity and distinct bacterial compositions, while beta diversity analyses revealed distinct clustering of microbiome compositions between affected and healthy groups. The gut microbiome of UTI patients showed alterations in Actinobacteria and Proteobacteria abundance, while voiding dysfunction (VD) was linked to the presence of Fusobacterium nucleatum, Clostridium difficile, and Bacteroides clarus without significant VDSS correlation.<br><br>CONCLUSION: This systematic review reveals microbial alterations in pediatric LUTS and UTIs, with lower urinary diversity in UTI patients and sex-specific differences post-puberty. Microbiome-based interventions may offer novel therapeutic strategies for LUTS and UTIs.},
}
@article {pmid40430061,
year = {2025},
author = {López-López, J and Reuss, JM and Vinuesa-Aumedes, T and Egido-Moreno, S and Roselló-Llabres, X and Pereira-Riveros, T and Reuss, D and Alonso-Gamo, L and Rodríguez-Vilaboa, B},
title = {Rapid Reduction of Pro-Inflammatory Cytokines with an Oral Topical Composition Comprising Olive Oil, Trimethylglycine and Xylitol: A Randomized Double-Blind Controlled Trial.},
journal = {International journal of molecular sciences},
volume = {26},
number = {10},
pages = {},
doi = {10.3390/ijms26104920},
pmid = {40430061},
issn = {1422-0067},
mesh = {Humans ; Male ; Female ; Double-Blind Method ; Adult ; *Xylitol/administration &amp; dosage/pharmacology ; *Olive Oil/administration &amp; dosage/pharmacology ; Middle Aged ; *Cytokines/metabolism ; Interleukin-1beta/metabolism ; Saliva/metabolism ; Tumor Necrosis Factor-alpha/metabolism ; Obesity/metabolism ; Interleukin-4/metabolism ; *Glycine/analogs &amp; derivatives/administration &amp; dosage ; Overweight ; },
abstract = {An underlying pro-inflammatory status is related to recurrence and persistence of inflammatory susceptibility in obesity and periodontitis, two of the most prevalent chronic inflammatory diseases. Elevated levels of interleukin-1β (IL-1β) and tumor necrosis factor-α (TNF-α), part of the inflammatory network linking these two conditions, persist even after periodontal treatment, with high salivary cytokine levels being linked to overweight and obesity risk. This trial assessed the effect of a novel composition comprising olive oil, trimethylglycine and xylitol, delivered topically to the oral mucosa, on salivary cytokines in periodontally healthy normal and overweight/pre-obese individuals. In a randomized placebo-controlled double-blind clinical trial, adult patients were randomly assigned to use a test toothpaste (intervention group, IG) or a placebo toothpaste (control group, CG) three times a day for 1 month. Primary outcomes were levels of salivary cytokines IL-1β, TNF-α and interleukin-4 (IL-4). Significant differences between IG and CG were observed for IL-1β (p = 0.003; Z = 2.901; r = 0.62) and TNF-α (p = 0.001; Z = 3.23; r = 0.69), but not for IL-4 (p = 0.203; Z = 1.321; r = 0.28). A significant reduction in IL-1β (p = 0.008) and a near significant reduction in TNF-α (p = 0.059) was found in the IG at the end of the trial. Additionally, the effect of body mass index on cytokine levels response was analyzed. A significantly different behavior was shown between IG and CG in the overweight/pre-obesity subgroup for IL-1β (p = 0.014; Z = 2.430; r = 0.63) and TNF-α (p = 0.029; Z = 2.199; r = 0.57). Moreover, a significant decrease in IL-1β in the IG (p = 0.028) was observed. The rapid reduction in IL-1β and TNF-α after 1 month of use of the intervention composition suggests a safe and effective novel strategy for reducing pro-inflammatory cytokines that may offer an opportunity to diminish the inflammatory status in patients with overweight/pre-obesity.},
}
@article {pmid40430019,
year = {2025},
author = {Kozhakhmetov, S and Kossumov, A and Zhakupova, T and Polyakova, T and Imambayeva, N and Syzdykova, B and Rakhmankulova, A and Dalibayeva, G and Kovenskiy, A and Jarmukhanov, Z and Issilbayeva, A and Vinogradova, E and Kushugulova, A},
title = {Characterization of Gut Microbiome Composition in Depression and Completed Suicide.},
journal = {International journal of molecular sciences},
volume = {26},
number = {10},
pages = {},
doi = {10.3390/ijms26104880},
pmid = {40430019},
issn = {1422-0067},
support = {AP19676162//Science Committee of the Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; Male ; Female ; *Depression/microbiology ; Middle Aged ; Adult ; *Suicide, Completed/psychology ; Feces/microbiology ; Dysbiosis/microbiology ; Energy Metabolism ; },
abstract = {Growing evidence supports a bidirectional relationship between the gut microbiome and mental health. This study investigated the association between gut microbiota, depression, and suicidal behavior by analyzing fecal samples from 35 individuals with varying depression levels and 36 completed suicide cases. Standardized psychometric assessments were used for depression evaluation. Analysis revealed significant taxonomic differences between groups, with increased abundance of Firmicutes, Clostridia, Lachnospiraceae, Blautia, and Dorea in suicide cases, which also positively correlated with depression severity. Metabolic pathway analysis demonstrated a notable dichotomy: suicide cases showed elevated pathways related to infection processes, inflammation, and antibiotic resistance, while the control group exhibited higher energy metabolism and vitamin synthesis pathways. The findings establish specific microbiome profiles associated with both depression symptoms and suicidal behavior, suggesting that gut dysbiosis may influence mental health through altered energy metabolism and inflammatory processes, potentially offering new perspectives for diagnostic and therapeutic approaches.},
}
@article {pmid40430003,
year = {2025},
author = {Xu, JY and Rong, XJ and Shen, Z and Guo, YD and Zhang, YX and Ding, CC and Wang, Y and Han, YX and Gao, TL and Tie, C},
title = {Isochlorogenic Acid C Alleviates Allergic Asthma via Interactions Between Its Bioactive Form and the Gut Microbiome.},
journal = {International journal of molecular sciences},
volume = {26},
number = {10},
pages = {},
doi = {10.3390/ijms26104864},
pmid = {40430003},
issn = {1422-0067},
support = {2022D01E65//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; 2022-I2M-1-016, 2024-I2M-ZH-012//CAMS Innovation Fund for Medical Sciences/ ; 2023TSYCCX0065//Tianshan Talent Training Program/ ; 2024ZKPYHH01//Fundamental Research Funds for the Central Universities/ ; },
mesh = {*Gastrointestinal Microbiome/drug effects ; *Asthma/drug therapy/metabolism/microbiology ; Animals ; *Chlorogenic Acid/analogs &amp; derivatives/pharmacology/therapeutic use ; Mice ; Lung/drug effects/metabolism ; *Anti-Asthmatic Agents/pharmacology ; Male ; Lipid Peroxidation/drug effects ; Humans ; },
abstract = {The global prevalence of asthma is approximately 4.3%, and current asthma treatments focus on reducing symptoms, maintaining normal activity levels, and preventing the deterioration of lung function, rather than achieving a cure or complete prevention. We identified isochlorogenic acid C (ICGAC) as a potential natural medicine for the treatment of asthma. However, the bioavailability of ICGAC was low, ranging from 14.4% to 16.9%, suggesting the involvement of the gut microbiota. The full spectrum of ICGAC's anti-asthmatic mechanism remains to be elucidated. This study investigated the mechanism by which ICGAC alleviates allergic asthma through the gut-lung axis. We discovered anti-asthma pathways and targets based on the selective regulation of lipid peroxidation and employed pharmacological tools to preliminarily validate their mechanisms and efficacy. To study the role of ICGAC in regulating the gut microbiota, we performed 16S rRNA gene sequencing and metabolite analysis. Furthermore, by combining molecular biology and lipid metabolomics, we elucidated the underlying anti-asthma mechanisms of ICGAC. The effective form of ICGAC varies between single and long-term administration. The oral administration of ICGAC enhances the gut-microbiota-derived production of short-chain fatty acids (SCFAs) as the active substances, modulates immune cell activity, influences the differentiation of T- and B-cells, and reduces airway inflammation. ICGAC also regulates the metabolic network of lipid mediators (LMs) and polyunsaturated fatty acids (PUFAs), thus exerting anti-inflammatory effects by modulating arachidonate lipoxygenase (ALOX) activity and LM levels. In addition, ICGAC enhanced the antioxidant response by upregulating the expression of glutathione peroxidase 4 (GPX4), solute carrier family 7 member 11 (SLC7A11), and nuclear factor erythroid 2-related factor 2 (Nrf2), while inhibiting the release of interleukin-4 (IL-4), thereby suppressing asthma inflammation and IgE production. The anti-asthmatic mechanism of oral ICGAC involves the inhibition of lipid peroxidation by chlorogenic acid (CGA) and SCFAs produced by the gut microbiota. ICGAC suppresses asthma-associated inflammatory and oxidative stress responses through the upregulation of GPX4, SLC7A11, and Nrf2 in lung tissue. This study not only provides a solid foundation for the potential clinical use of ICGAC in asthma treatment but also offers novel insights for future research and therapeutic strategies targeting asthma.},
}
@article {pmid40429958,
year = {2025},
author = {San-Martin, MI and Chamizo-Ampudia, A and Sanchiz, &#xc1; and Ferrero, M&#xc1; and Martínez-Blanco, H and Rodríguez-Aparicio, LB and Navasa, N},
title = {Microbiome Markers in Gastrointestinal Disorders: Inflammatory Bowel Disease, Colorectal Cancer, and Celiac Disease.},
journal = {International journal of molecular sciences},
volume = {26},
number = {10},
pages = {},
doi = {10.3390/ijms26104818},
pmid = {40429958},
issn = {1422-0067},
mesh = {Humans ; *Celiac Disease/microbiology/metabolism ; *Inflammatory Bowel Diseases/microbiology/metabolism ; *Gastrointestinal Microbiome ; Biomarkers/metabolism ; *Colorectal Neoplasms/microbiology/metabolism ; Animals ; Metagenomics/methods ; },
abstract = {Intestinal microbiota and the host's immune system form a symbiotic alliance that sustains normal development and function in the human gut. Changes such as dietary habits among societies in developed countries have led to the development of unbalanced microbial populations in the gut, likely contributing to the dramatic increase in inflammatory diseases in the last few decades. Recent advances in DNA sequencing technologies have tremendously helped to characterize the microbiome associated with disease, both in identifying global alterations and discovering specific biomarkers that potentially contribute to disease pathogenesis, as evidenced by animal studies. Beyond bacterial alterations, non-bacterial components such as fungi, viruses, and microbial metabolites have been implicated in these diseases, influencing immune responses and gut homeostasis. Multi-omics approaches integrating metagenomics, metabolomics, and transcriptomics offer a more comprehensive understanding of the microbiome's role in disease pathogenesis, paving the way for innovative diagnostic and therapeutic strategies. Unraveling the metagenomic profiles associated with disease may facilitate earlier diagnosis and intervention, as well as the development of more personalized and effective therapeutic strategies. This review synthesizes recent and relevant microbiome research studies aimed at characterizing the microbial signatures associated with inflammatory bowel disease, colorectal cancer, and celiac disease.},
}
@article {pmid40429881,
year = {2025},
author = {Bauch, A and Baur, J and Honold, I and Willmann, M and Weber, GL and Müller, S and Sodenkamp, S and Peter, S and Schoppmeier, U and Laske, C},
title = {Prognostic Value of a Multivariate Gut Microbiome Model for Progression from Normal Cognition to Mild Cognitive Impairment Within 4 Years.},
journal = {International journal of molecular sciences},
volume = {26},
number = {10},
pages = {},
doi = {10.3390/ijms26104735},
pmid = {40429881},
issn = {1422-0067},
support = {374-1-0//University of T&#xfc;bingen/ ; 32-5400/58/3//Forum Gesundheitsstandort BW/ ; D3030814//Faber Foundation/ ; },
mesh = {Humans ; *Cognitive Dysfunction/microbiology/diagnosis ; *Gastrointestinal Microbiome ; Male ; Female ; Prognosis ; Disease Progression ; Aged ; *Cognition ; Alzheimer Disease/microbiology ; ROC Curve ; Middle Aged ; },
abstract = {Little is known about the dysbiosis of the gut microbiome in patients with mild cognitive impairment (MCI) potentially at risk for the development of Alzheimer's disease (AD). So far, only cross-sectional differences and not longitudinal changes and their prognostic significance have been in the scope of research in MCI. Therefore, we investigated the ability of longitudinal taxonomic and functional gut microbiome data from 100 healthy controls (HC) to predict the progression from normal cognition to MCI over a 4-year follow-up period (4yFU). Logistic regression models were built with baseline features that best discriminated between the two groups using an ANOVA-type statistical analysis. The best model for the discrimination of MCI converters was based on functional data using Gene Ontology (GO), which included 14 features. This model achieved an area under the receiver operating characteristic curve (AUROC) of 0.84 at baseline, 0.78 at the 1-year follow-up (1yFU), and 0.75 at 4yFU. This functional model outperformed the taxonomic model, which included 38 genera features, in terms of descriptive performance and showed comparable efficacy to combined analyses integrating functional, taxonomic, and clinical characteristics. Thus, gut microbiome algorithms have the potential to predict MCI conversion in HCs over a 4-year period, offering a promising innovative supplement for early AD identification.},
}
@article {pmid40429832,
year = {2025},
author = {Bardi, E and D'Arrigo, D and Pozzi, C and Gatti, A and Bertolino, L and Favaro, A and Rescigno, M and Bonanzinga, T},
title = {Current Methods in Synovial Fluid Microbiota Characterization: A Systematic Review.},
journal = {International journal of molecular sciences},
volume = {26},
number = {10},
pages = {},
doi = {10.3390/ijms26104690},
pmid = {40429832},
issn = {1422-0067},
support = {GR-2019-12371158//Ministero della Salute/ ; },
mesh = {*Synovial Fluid/microbiology ; Humans ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; High-Throughput Nucleotide Sequencing/methods ; DNA, Bacterial/genetics ; Gastrointestinal Microbiome ; Arthritis/microbiology ; Bacteria/genetics/classification/isolation &amp; purification ; },
abstract = {Evidence suggests that a cross-talk between the gut microbiota and joint health exists in a paradigm known as the gut-joint axis. Recent studies have also reported the presence of microorganisms potentially involved in the pathogenesis and progression of arthritis in synovial joints, previously believed to be sterile. This systematic review describes in detail the methodologies employed to characterize the microbiota in human synovial fluid (SF). A literature search was conducted in PubMed, Embase, and Web of Science up to 5 February 2025. Nine studies aimed to characterize the SF microbiome using next-generation sequencing or polymerase chain reaction. Eight studies detected bacterial DNA in SF. However, significant heterogeneity and incomplete reporting in methodologies, including sample collection and preparation, contamination management, DNA extraction and amplification, sequencing technology, targeted 16S rRNA or ITS regions, and bioinformatics processing, limit the comparability and significance of findings. Given the potential implications for understanding arthritis mechanisms and developing targeted treatments, a standardized methodological and reporting approach in SF microbiota characterization is needed to enhance the reproducibility and the relevance of results.},
}
@article {pmid40429741,
year = {2025},
author = {Ye, J and Raman, M and Taylor, LM and Yousuf, M and Panaccione, R and Turbide, C and Sinha, SR and Haskey, N},
title = {Reduced Sulfur Diet Reshapes the Microbiome and Metabolome in Mild-Moderate Ulcerative Colitis.},
journal = {International journal of molecular sciences},
volume = {26},
number = {10},
pages = {},
doi = {10.3390/ijms26104596},
pmid = {40429741},
issn = {1422-0067},
support = {NA//Nutricia North America/ ; NA//Alberta's Collaboration of Excellence for Nutrition in Digestive Diseases (Ascend), Cumming School of Medicine, University of Calgary, Calgary, Canada/ ; NA//Michael Smith Health Research BC Health Professional Investigator Award/ ; NA//TRIANGLE (TRaIning A New generation of researchers in Gastroenterology and LivEr) Fellowship Award/ ; },
mesh = {Humans ; *Colitis, Ulcerative/microbiology/diet therapy/metabolism ; *Gastrointestinal Microbiome ; Male ; Female ; *Metabolome ; Middle Aged ; Adult ; *Sulfur/metabolism/administration &amp; dosage ; Feces/microbiology ; Pilot Projects ; *Diet ; },
abstract = {This pilot study investigated the effects of a reduced sulfur (RS) diet on the gut microbiome composition and fecal metabolome in individuals with remitted or active ulcerative colitis (UC). Thirteen participants maintained their habitual diet (control), while nine followed an RS diet for eight weeks (Wk8). Stool and plasma samples were collected at the baseline and Wk8. The sulfur intake decreased in the RS group (-28 g/1000 kcal) versus the control group (-1.7 g/1000 kcal; p < 0.001). The RS group exhibited a significant decrease in lipopolysaccharide-binding protein (-5280 ng/mL), while these levels increased in the control group (620 ng/mL; p < 0.05). The microbiome analysis showed an increased alpha diversity at Wk8 (p < 0.01), suggesting a microbial shift with a RS intake. The metabolic alterations indicated enhanced nitrogen disposal (increased uric acid, methyluric acid, N-acetyl-L-glutamate) and a higher energy demand (elevated ubiquinol and glucose-pyruvate). The RS diet increased beneficial microbes Collinsella stercoris, Asaccharobacter celatus, and Alistipes finegoldii, while decreasing pathobionts Eggerthella lenta and Romboutsia ilealis. Methyluric acid correlated positively with C. stercoris (β = 0.70) and negatively with E. lenta (β = -0.77) suggesting these microbes utilized this metabolite and influenced the microbiome composition. In conclusion, a RS diet promoted microbial diversity, metabolic adaptations, and reduced inflammation, highlighting its potential as a novel strategy for UC management.},
}
@article {pmid40429679,
year = {2025},
author = {Joseph, YD and Ladd, AL and Bhutani, N},
title = {Hand Osteoarthritis: Molecular Mechanisms, Randomized Controlled Trials, and the Future of Targeted Treatment.},
journal = {International journal of molecular sciences},
volume = {26},
number = {10},
pages = {},
doi = {10.3390/ijms26104537},
pmid = {40429679},
issn = {1422-0067},
mesh = {Humans ; *Osteoarthritis/drug therapy/genetics/therapy/metabolism/pathology/etiology ; Randomized Controlled Trials as Topic ; *Hand/pathology ; Genome-Wide Association Study ; Molecular Targeted Therapy ; },
abstract = {Hand osteoarthritis (OA) is a prevalent and disabling condition, yet its pathogenesis remains less studied than OA in large weight-bearing joints. Emerging genetic, epigenetic, and microbiome research suggests that hand OA might be biologically distinct, involving joint-specific pathways not shared by knee or hip OA. This review integrates genome-wide association studies specific to hand OA, highlighting key molecular contributors such as inflammatory cytokines. These genetic insights, together with emerging data on epigenetic alterations and gut microbial dysbiosis, point to broader systemic and regulatory influences on hand OA onset and progression. We also assess pharmacologic interventions tested in randomized controlled trials that have attempted to target these pathways. While agents such as TNF and IL-6 inhibitors, hydroxychloroquine, and corticosteroids have shown limited success, emerging evidence supports the potential of methotrexate in synovitis-positive general hand OA, platelet-rich plasma in thumb carpometacarpal (CMC) OA, and prolotherapy in interphalangeal (IP) OA. These findings illustrate the persistent gap between mechanistic understanding and therapeutic success. Future work must prioritize multifactorial strategies for addressing pain and translational frameworks that link molecular mechanisms to treatment response. In summary, this review offers an update on hand OA and identifies key opportunities for more targeted and effective therapy.},
}
@article {pmid40429482,
year = {2025},
author = {Csecsei, P and Takacs, B and Pasitka, L and Varnai, R and Peterfi, Z and Orban, B and Czabajszki, M and Olah, C and Schwarcz, A},
title = {Distinct Gut Microbiota Profiles in Unruptured and Ruptured Intracranial Aneurysms: Focus on Butyrate-Producing Bacteria.},
journal = {Journal of clinical medicine},
volume = {14},
number = {10},
pages = {},
doi = {10.3390/jcm14103488},
pmid = {40429482},
issn = {2077-0383},
support = {NRDI Fund NKFI-FK-146159//National Research, Development and Innovation Office/ ; RRF-2.3.1-21-2022-00011//National Laboratory for Translational Neuroscience project/ ; },
abstract = {Background: Gut microbiome composition may influence the risk of intracranial aneurysm rupture. Methods: This study analyzed the gut microbiota of 48 patients-24 with ruptured aneurysms (RA) and 24 with unruptured intracranial aneurysms (UIA)-using next-generation sequencing. Results: While alpha diversity was similar between groups, beta diversity revealed significant taxonomic differences (Bray-Curtis: p = 0.02; unweighted UniFrac: p = 0.0291). Both groups were dominated by the phyla Bacillota, Bacteroidota, and Proteobacteria, but genus- and family-level differences were observed. RA patients showed higher abundances of Anaerotruncus, Coprobacillus, Sellimonas, Hungatella, and Ruthenibacterium, whereas UIA patients exhibited greater levels of Faecalibacterium, Brotolimicola, Clostridiaceae, Roseburia, and Agathobaculum. Linear discriminant analysis identified one class, 10 genera, and 17 species that differed significantly between groups. Notably, Faecalibacterium prausnitzii and Agathobaculum butyriciproducens-bacteria known for their anti-inflammatory and neuroprotective properties-were enriched in UIA patients. Conclusions: These findings suggest that gut microbiota, particularly short-chain fatty acid-producing bacteria, may contribute to vascular protection and aneurysm pathophysiology. Microbiome-based therapeutic strategies could offer new avenues for the prevention of cerebrovascular disease.},
}
@article {pmid40429412,
year = {2025},
author = {Duffy, HR and Ashton, NN and Stulce, P and Blair, A and Farnsworth, R and Ormiston, L and Kwok, AC and Williams, DL},
title = {Skin-Dwelling Bacteria Survive Preoperative Skin Preparation in Reconstruction Surgery.},
journal = {Journal of clinical medicine},
volume = {14},
number = {10},
pages = {},
doi = {10.3390/jcm14103417},
pmid = {40429412},
issn = {2077-0383},
support = {NA//L.S. Peery Foundation (University of Utah Orthopeadic Department)/ ; 2139322//U.S. National Science Foundation/ ; },
abstract = {Background/Objectives: Accurately determining the bacterial bioburden that survives preoperative skin preparation (PSP) is critical in understanding PSP efficacy and its limitations. Clinical PSP approval relies on a bacterial sampling method described in the American Society for Testing and Materials (ASTM) standard E1173-15. Though common, this technique may overlook deep-dwelling skin bacteria. The objective of this study was to test the hypothesis that deep-dwelling skin flora would survive PSP, and more growth would be detected using a destructive sampling method compared with ASTM E1173-15. Methods: Twelve female participants with a scheduled deep inferior epigastric perforator (DIEP) artery flap procedure at the Huntsman Cancer Institute in Salt Lake City, UT, were enrolled between January and August 2024. PSP was performed using three 26 mL ChloraPrep applicators (2% CHG), and excess tissue was collected. Bacteria in the skin were quantified using a destructive sampling method and ASTM E1173-15, and bioburden outcomes were compared. Two participants were excluded from the quantitative analysis. Results: Bacteria survived PSP in every participant. A greater diversity and more bacteria were quantified with destructive sampling than ASTM E1173-15 (p < 0.01). Generally, anaerobic bioburden values were higher than aerobic bioburden values. Higher bioburden correlated with processing more skin from a participant. Genotypic identification of select isolates identified Staphylococcus epidermidis and Cutibacterium acnes (formerly known as Propionibacterium acnes) as surviving bacteria, among others. Immunofluorescence revealed bacteria in all skin layers. No participant exhibited clinical signs of infection in the abdominal region. Human data corroborated previous porcine data collected using destructive skin sampling after PSP. Conclusions: Clinical PSP application does not create a sterile field. Destructive skin sampling techniques may be more effective than ASTM E1173-15 at resolving bacterial PSP survivors contributing to SSI risk.},
}
@article {pmid40429337,
year = {2025},
author = {Brożek-Mądry, E and Ziuzia-Januszewska, L and Misztal, O and Burska, Z and Sosnowska-Turek, E and Sierdziński, J},
title = {Nasal Rinsing with Probiotics-Microbiome Evaluation in Patients with Inflammatory Diseases of the Nasal Mucosa.},
journal = {Journal of clinical medicine},
volume = {14},
number = {10},
pages = {},
doi = {10.3390/jcm14103341},
pmid = {40429337},
issn = {2077-0383},
support = {RPWM.01.02.01-28-0027/18-00//European Regional Development Fund, European Social Fund, Regional Operational Program of the Warmian-Masurian Voivodeship - Research at Probios/ ; },
abstract = {Background/Objectives: The evidence regarding the efficacy of probiotics in chronic rhinosinusitis (CRS) is very limited, prompting the EPOS2020 steering group to advise against their use in CRS treatment. Therefore, further research to evaluate the impact of probiotics on microbial communities is particularly important. This study aimed to assess the influence of probiotic nasal rinses on nasal microbiota profiles in patients with primary CRS, granulomatosis with polyangiitis (GPA), and nasal septal perforation (NSP) using 16S rRNA sequencing. Methods: Thirty-six patients with nasal mucosal diseases, including sixteen with primary CRS, eleven with GPA, and nine with NSP, were randomly assigned to either a study group receiving nasal rinses with probiotics containing Lactobacillus plantarum and Bifidobacterium animalis, or a control group using nasal rinses with saline. Metagenomic analysis targeting the V3-V4 hypervariable region of the 16S rRNA gene was performed to characterize bacterial and archaeal populations. Results: At the genus level, the most abundant co-colonizers included Staphylococcus, Streptococcus, and Haemophilus. After one month of probiotic rinsing, a decrease in abundance of the genera Finegoldia (p = 0.010), Haemophilus (p = 0.020), Streptococcus (p = 0.027), Staphylococcus (p = 0.033), Micrococcus (p = 0.035), Corynebacterium (p = 0.049), Gemella (p = 0.055), Rubrobacter (p = 0.055), and Pseudonocardia (p = 0.058) was observed. Conversely, the abundance of probiotic species Lactobacillus plantarum and Bifidobacterium animalis increased. Moreover, increases in the genera Dolosigranulum and Stenotrophomonas were observed, although they did not reach statistical significance. Conclusions: Probiotic nasal rinses may contribute to restoring microbial homeostasis by reducing genera associated with inflammatory dysbiosis in nasal inflammatory diseases, warranting further research on their clinical benefits.},
}
@article {pmid40429183,
year = {2025},
author = {Zhou, J and Qin, W and Zeng, Y and Huang, X and Yuan, J and Yin, Y and Xu, P and Fan, X and Zhang, R and Li, G and Zhang, Y},
title = {Effects of Colony Breeding System and Nest Architecture on Soil Microbiome and Fertility in the Fungus-Growing Termite Macrotermes barneyi Light.},
journal = {Insects},
volume = {16},
number = {5},
pages = {},
doi = {10.3390/insects16050470},
pmid = {40429183},
issn = {2075-4450},
support = {31601891//National Natural Science Foundation of China/ ; 2023AFB1005//Natural Science Foundation of Hubei Province of China/ ; IWHR-2024TE003//Open Research Fund of Key Laboratory of Termite Control of Ministry of Water Resources, China Institute of Water Resources and Hydropower Research/ ; EWPL202408//Hubei Key Laboratory of Edible Wild Plants Conservation and Utilization/ ; },
abstract = {Macrotermes barneyi is a typical fungus-growing termite that forms both monogynous (single queen) and polygynous (multiple queen) colonies in nature. This species influences the local soil fertility in part by redistributing nutrients across the landscape in its habitats. However, how the colony structure of M. barneyi affects nutrient cycling and microbial communities within the nest is not well understood. In this study, we compared the physicochemical properties and microbial communities across nest parts between monogynous and polygynous colonies of M. barneyi. Our results showed that the fungus garden is the most nutrient-rich part of the nest, with higher soil moisture, organic matter, ammonium nitrogen, nitrate nitrogen, available sulfur, available potassium, available silicon, and available boron than other nest parts. Notably, the fungus garden in monogynous colonies had higher nitrate nitrogen, available sulfur, and available silicon than those in the polygynous colonies. The microbial α-diversity in the fungus garden was lower than that in other parts of the nest. β-diversity analysis revealed a clear separation of microbial communities between monogynous and polygynous colonies across nest parts. Furthermore, the relative abundance of functional genes associated with "cell cycle control, cell division, and chromosome partitioning" was higher in the fungus garden of polygynous colonies compared to monogynous colonies. Our results suggest that the fungus garden plays a crucial role in maintaining colony stability in M. barneyi colonies. The rapid depletion of nutrients in the fungus garden to sustain the larger population in polygynous colonies likely influences microbial community dynamics and nutrient cycling.},
}
@article {pmid40428846,
year = {2025},
author = {Torraco, A and Di Nicolantonio, S and Cardisciani, M and Ortu, E and Pietropaoli, D and Altamura, S and Del Pinto, R},
title = {Meta-Analysis of 16S rRNA Sequencing Reveals Altered Fecal but Not Vaginal Microbial Composition and Function in Women with Endometriosis.},
journal = {Medicina (Kaunas, Lithuania)},
volume = {61},
number = {5},
pages = {},
doi = {10.3390/medicina61050888},
pmid = {40428846},
issn = {1648-9144},
support = {SRA-882725/CCF/CCF/United States ; },
mesh = {Humans ; Female ; *Endometriosis/microbiology/physiopathology ; *Feces/microbiology ; *Vagina/microbiology ; *RNA, Ribosomal, 16S/analysis/genetics ; Dysbiosis/microbiology ; Adult ; Gastrointestinal Microbiome ; Metagenomics/methods ; },
abstract = {Background and Objectives: Dysbiosis of the oral-gut axis is related to several extraintestinal inflammatory diseases, including endometriosis. This study aims to assess the microbial landscape and pathogenic potential of distinct biological niches during endometriosis. Materials and Methods: A microbiome meta-analysis was conducted on 182 metagenomic sequences (79 of fecal and 103 of vaginal origin) from women with and without endometriosis. Fecal and vaginal microbial diversity, differential abundance, and functional analysis based on disease status were assessed. Random forest, gradient boosting, and generalized linear modeling were used to predict endometriosis based on differentially enriched bacteria. Results: Only intestinal microbes displayed distinctive taxonomic and functional characteristics in women with endometriosis compared to control women. Taxonomic differences were quantified using the microbial endometriosis index (MEI), which effectively distinguished between individuals with and without the disease. The observed functional enrichment pointed to proinflammatory pathways previously related to endometriosis development. Conclusions: Dysbiosis in the oral-gut microbial community appears to play a prevalent role in endometriosis. Our findings pave the ground for future studies exploring the potential mechanistic involvement of the oral-gut axis in disease pathogenesis.},
}
@article {pmid40428795,
year = {2025},
author = {Labunet, A and Objelean, A and Kui, A and Rusu, L and Vigu, A and Sava, S},
title = {Oral Manifestations in Menopause-A Scoping Review.},
journal = {Medicina (Kaunas, Lithuania)},
volume = {61},
number = {5},
pages = {},
doi = {10.3390/medicina61050837},
pmid = {40428795},
issn = {1648-9144},
support = {university budget 2025 - no grant//Iuliu Ha&#x21b;ieganu University of Medicine and Pharmacy/ ; },
mesh = {Humans ; Female ; *Menopause/physiology ; Xerostomia/etiology ; Saliva/metabolism ; *Mouth Diseases/etiology ; Middle Aged ; },
abstract = {Background and Objectives: Menopause is a natural physiological process involving hormone production changes, affecting many functions and systems. This scoping review offers a contemporary outlook on oral issues related to menopause, such as saliva production, periodontal and alveolar bone issues, and changes in the microbiome, and it also investigates the effects of hormonal therapy. Materials and Methods: A literature search from 2019 to 2024 was conducted according to PRISMA-ScR guidelines. Articles investigating the oral effects of menopause were included. Results: A total of 30 studies were covered; 8 focused on salivary alterations, 5 on periodontal issues, 7 on bone, 3 on the microbiome, and 7 on multiple oral problems, showing that xerostomia and altered taste are the most common oral manifestations, followed by indirect causal effects on periodontitis. Many of these alterations can be contained through regular consultations and adequate hygiene. Some alveolar bone changes may occur after menopause and are associated with osteoporosis. Conclusions: Postmenopausal women experience notable reductions in salivary flow, pH levels, and taste sensitivity, which are associated with hormonal fluctuations as well as factors such as age, medication use, and treatments for climacteric symptoms. This population is at increased risk for periodontitis, tooth loss, altered taste, lichen planus, candidiasis, and decreased bone mineral density, which also affect the peri-implant area. Osteoporosis and hormonal changes can play a significant role in causing these increased risks. Maintaining proper oral hygiene and consistently monitoring bone health are essential. While changes in the oral microbiome are more heavily influenced by reductions in salivary flow than by menopause itself, hormone therapy may help improve periodontal health by reducing harmful bacteria and fostering a more balanced microbial environment. The intricate impact of hormones on oral health highlights the necessity for further research.},
}
@article {pmid40428769,
year = {2025},
author = {Datkhayeva, Z and Iskakova, A and Mireeva, A and Seitaliyeva, A and Skakova, R and Kulniyazova, G and Shayakhmetova, A and Koshkimbayeva, G and Sarmuldayeva, C and Nurseitova, L and Koshenova, L and Imanbekova, G and Maxutova, D and Yerkenova, S and Shukirbayeva, A and Pernebekova, U and Dushimova, Z and Amirkhanova, A},
title = {The Multifactorial Pathogenesis of Endometriosis: A Narrative Review Integrating Hormonal, Immune, and Microbiome Aspects.},
journal = {Medicina (Kaunas, Lithuania)},
volume = {61},
number = {5},
pages = {},
doi = {10.3390/medicina61050811},
pmid = {40428769},
issn = {1648-9144},
mesh = {Humans ; *Endometriosis/physiopathology/microbiology/immunology/etiology ; Female ; *Gastrointestinal Microbiome/physiology/immunology ; Estrogens/metabolism ; Dysbiosis/complications ; Inflammation ; },
abstract = {Endometriosis (EM) is a common estrogen-dependent chronic inflammatory disorder affecting reproductive-aged women, yet its pathogenesis remains incompletely understood. Recent evidence suggests that the gut microbiota significantly influence immune responses, estrogen metabolism, and systemic inflammation, potentially contributing to EM progression. This narrative review explores the relationship between the gut microbiota and EM, emphasizing microbial dysbiosis, inflammation, estrogen regulation, and potential microbiome-targeted therapies. Studies published within the last 30 years were included, focusing on the microbiota composition, immune modulation, estrogen metabolism, and therapeutic interventions in EM. The selection criteria prioritized peer-reviewed articles, clinical trials, meta-analyses, and narrative reviews investigating the gut microbiota's role in EM pathophysiology and treatment. Microbial dysbiosis in EM is characterized by a reduced abundance of beneficial bacteria (Lactobacillus, Bifidobacterium, and Ruminococcaceae) and an increased prevalence of pro-inflammatory taxa (Escherichia/Shigella, Streptococcus, and Bacteroides). The gut microbiota modulate estrogen metabolism via the estrobolome, contributing to increased systemic estrogen levels and lesion proliferation. Additionally, lipopolysaccharides (LPS) from Gram-negative bacteria activate the TLR4/NF-κB signaling pathway, exacerbating inflammation and EM symptoms. The interaction between the gut microbiota, immune dysregulation, and estrogen metabolism suggests a critical role in EM pathogenesis. While microbiota-targeted interventions offer potential therapeutic benefits, further large-scale, multi-center studies are needed to validate microbial biomarkers and optimize microbiome-based therapies for EM. Integrating microbiome research with precision medicine may enhance the diagnostic accuracy and improve the EM treatment efficacy.},
}
@article {pmid40428567,
year = {2025},
author = {Ruban, M and Pozhidaeva, E and Bolotina, L and Kaprin, A},
title = {The Role of Diet and Nutrition in Cancer Development and Management: From Molecular Mechanisms to Personalized Interventions.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {10},
pages = {},
doi = {10.3390/foods14101788},
pmid = {40428567},
issn = {2304-8158},
abstract = {Diet plays a crucial role in cancer development and progression, beyond traditional risk factors. This review aims to summarize current evidence on the role of diet and specific nutrients in cancer development and progression, focusing on molecular mechanisms. We also discuss the potential of personalized dietary interventions, based on tumor and patient characteristics, in enhancing cancer prevention and treatment strategies. The review covers the impact of calories, protein, sugar, and other dietary components on signaling pathways and growth factors involved in carcinogenesis. We examine the influence of obesity, insulin resistance, and other metabolic factors on cancer risk and outcomes. The article also explores current dietary strategies, including calorie restriction, ketogenic diets, and the role of the gut microbiome in modulating response to anticancer therapies. Finally, we highlight the need for further research to develop targeted, personalized dietary recommendations based on an individual's tumor profile, stage of disease, and other clinical factors. Integrating such personalized dietary approaches into cancer prevention and treatment holds promise for improving patient outcomes and quality of life.},
}
@article {pmid40428305,
year = {2025},
author = {Guo, Q and Zhang, W and Xu, C and Li, X and Wang, B and Xiong, C and Duan, W and Luo, T and Wang, W and Zhou, J},
title = {Comparative Analysis of Gut Microbiome Community Structures in Different Populations of Asian Elephants in China and Their Correlation with Diet.},
journal = {Genes},
volume = {16},
number = {5},
pages = {},
doi = {10.3390/genes16050483},
pmid = {40428305},
issn = {2073-4425},
support = {202501AS070053//Key Project of Yunnan Basic Research Program/ ; },
mesh = {Animals ; *Elephants/microbiology/genetics ; *Gastrointestinal Microbiome/genetics ; *Diet ; China ; Metagenomics/methods ; Bacteria/genetics/classification ; },
abstract = {BACKGROUND: The interaction and co-evolution between the gut microbiome and the host play important roles in the host's physiology, nutrition, and health. Diet is considered an important driver of differences in the gut microbiota; however, research on the relationship between the gut microbiota and diet in Asian elephants remains limited.<br><br>METHODS: In this study, we explored the gut microbiota structure and its relationship with diet in different populations of Asian elephants through metagenomic sequencing, combined with previously published dietary data.<br><br>RESULTS: This study found that the dominant gut microbiota of Asian elephants includes the phyla Bacillota (29.85% in BP, 22.79% in RC, 21.89% in SM, 31.67% in ML, and 33.00% in NGH), Bacteroidota (25.25% in BP, 31.44% in RC, 16.44% in SM, 25.73% in ML, and 23.74% in NGH), and Spirochaetota (3.49% in BP, 6.18% in RC, 1.71% in SM, 2.69% in ML, and 3.52% in NGH), with significant differences in the gut microbiota among different populations. Correlation analysis between the gut microbiota and diet revealed that dietary diversity did not directly affect the alpha diversity of the gut microbiota. However, specific food types might play a key role in shaping the gut microbiota structure by regulating the abundance of certain microbiota.<br><br>CONCLUSIONS: This study reveals significant differences in the gut microbiota structure among different populations of Asian elephants and explores the impact of diet on the structure. The results provide foundational data for a deeper understanding of the gut microbiota structure of Asian elephants and offer important references for the scientific conservation and precise management strategies of this species.},
}
@article {pmid40428236,
year = {2025},
author = {Poddighe, D},
title = {Pancreatic Comorbidities in Pediatric Celiac Disease: Exocrine Pancreatic Insufficiency, Pancreatitis, and Diabetes Mellitus.},
journal = {Diagnostics (Basel, Switzerland)},
volume = {15},
number = {10},
pages = {},
doi = {10.3390/diagnostics15101243},
pmid = {40428236},
issn = {2075-4418},
abstract = {Celiac disease (CD) is a chronic and immune-mediated disorder triggered by the ingestion of gluten in some genetically predisposed individuals. CD can be associated with extra-gastrointestinal manifestations and diseases affecting several organs. In this review, the aim is to analyze and discuss the pancreatic alterations and/or comorbidities that could arise in the context of pediatric CD. Exocrine pancreatic insufficiency (EPI) can be observed in a variable fraction (up to 30%) of children diagnosed with CD at the diagnosis; indeed, it usually resolves after the implementation of a gluten-free diet (GFD). The main pathophysiological mechanisms of EPI could be represented by the impaired pattern of gastrointestinal hormones in CD patients. Conversely, pancreatitis seems to be a very rare comorbidity in CD children, since very few cases have been described in children. Therefore, there is no evidence that pancreatitis (including autoimmune forms) represents a relevant comorbidity in pediatric CD. Type 1 diabetes mellitus (T1DM) is a well-known and frequent comorbidity in CD children. The main determinant of this epidemiological association is the common HLA-related predisposing background, even if other (non-HLA-related) genetic and environmental factors (viruses, gut microbiome, and others) are likely to be also implicated in the development of both these autoimmune diseases. T1DM children with concomitant CD may experience specific challenges in the adherence to GFD, which has no negative impact on the glycemic and, in general, metabolic control of diabetes, if it is properly implemented and followed up.},
}
@article {pmid40427692,
year = {2025},
author = {Ogola, HJO and Selvarajan, R and Ncube, S and Madikizela, L},
title = {Thiocapsa, Lutimaribacter, and Delftia Are Major Bacterial Taxa Facilitating the Coupling of Sulfur Oxidation and Nutrient Recycling in the Sulfide-Rich Isinuka Spring in South Africa.},
journal = {Biology},
volume = {14},
number = {5},
pages = {},
doi = {10.3390/biology14050503},
pmid = {40427692},
issn = {2079-7737},
abstract = {Sulfur cycling is a fundamental biogeochemical process, yet its microbial underpinnings in environments like the Isinuka sulfur pool remain poorly understood. Using high-throughput Illumina 16S rRNA sequencing and PICRUSt-based functional inference, we analyzed bacterial diversity and metabolic potential in sediment and water samples. Sediments, characterized by high sulfide/sulfate/thiosulfate, salinity, alkalinity, and organic matter content under anoxic conditions, supported diverse sulfur-reducing and organic-degrading bacteria, primarily from the Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria phyla. In contrast, the anoxic water column harbored a less diverse community dominated by α-, γ-, and β-Proteobacteria, including Thiocapsa and Lutimaribacter. Sulfur oxidation genes (soxABCXYZ, sqr) were abundant in water, while sulfate reduction genes (dsrAB, aprAB, and sat/met3) were concentrated in sediments. Core microbiome analysis identified Thiocapsa, Lutimaribacter, and Delftia as functional keystones, integrating sulfur oxidation and nutrient recycling. Sediments supported dissimilatory sulfate-reducing bacteria (unclassified Desulfobacteraceae, Desulfosarcina, Desulfococcus, Desulfotignum, and Desulfobacter), while water samples were enriched in sulfur-oxidizing bacteria like Thiocapsa. Metabolic profiling revealed extensive sulfur, nitrogen, and carbon cycling pathways, with sulfur autotrophic denitrification and anoxygenic photosynthesis coupling sulfur-nitrogen and sulfur-carbon cycles. This study provides key theoretical insights into the microbial dynamics in sulfur-rich environments, highlighting their roles in biogeochemical cycling and potential applications in environmental management.},
}
@article {pmid40427657,
year = {2025},
author = {Karaman, T and Oktem Okullu, S and Bayram Akçapınar, G and Sezerman, OU},
title = {Pathway-Specific Insights into Colorectal Cancer Through Comprehensive Multi-Omics Data Integration.},
journal = {Biology},
volume = {14},
number = {5},
pages = {},
doi = {10.3390/biology14050468},
pmid = {40427657},
issn = {2079-7737},
support = {118C039//Scientific and Technological Research Council of Turkey/ ; },
abstract = {Thousands of biomarkers have been discovered to solve the mechanisms of cancer, but dynamic alterations in the parameters that affect cancer progression cause complex disease status. Therefore, it is essential when dealing with cancer to analyze all parameters, including pathway information, to understand the disease mechanism of action. In our study, we applied multi-omics data integration for microbiome, transcriptome, and microbial pathway datasets obtained from colorectal cancer patients. The Cldn7 gene and Fusobacteria, which both play roles in the stability of the intestinal barrier, were found to be highly associated with each other (r = 0.71). The Klf3 gene has been identified as a critical regulator in the activation of the WNT1 and WNT/β-catenin signaling pathways. Notably, it exhibited a strong positive correlation with the presence of Fusobacteria, which are also implicated in modulating these pathways. In addition, the glutaryl CoA degradation and p-cymene degradation pathways demonstrated a strong positive association with the expression of the Ahcy, Eis2s2, Hsp90ab1, Psma7, Lbr, Rpl7l1, Cse1l, Cbx3, Ncl, Hspd1, Tpx2, and Top2a genes (r > 0.65), suggesting their potential involvement in the regulation and metabolic integration of these pathways at the transcriptional level.},
}
@article {pmid40427639,
year = {2025},
author = {DeSantis, AH and Buss, K and Coker, KM and Pasternak, BA and Chi, J and Patterson, JS and Gu, H and Jurutka, PW and Sandrin, TR},
title = {Multiomics-Based Profiling of the Fecal Microbiome Reveals Potential Disease-Specific Signatures in Pediatric IBD (PIBD).},
journal = {Biomolecules},
volume = {15},
number = {5},
pages = {},
doi = {10.3390/biom15050746},
pmid = {40427639},
issn = {2218-273X},
support = {GR39923//Phoenix Children's Hospital Foundation Leadership Grant/ ; },
mesh = {Humans ; Child ; *Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; Male ; Female ; Metagenomics/methods ; *Inflammatory Bowel Diseases/microbiology/metabolism/genetics ; Metabolomics/methods ; Adolescent ; *Colitis, Ulcerative/microbiology/genetics/metabolism ; *Crohn Disease/microbiology/genetics/metabolism ; Biomarkers/metabolism ; Transcriptome ; Multiomics ; },
abstract = {Inflammatory bowel disease (IBD), which includes Crohn's Disease (CD) and Ulcerative Colitis (UC), is a chronic gastrointestinal (GI) disorder affecting 1 in 100 people in the United States. Pediatric IBD (PIBD) is estimated to impact 15 per 100,000 children in North America. Factors such as the gut microbiome (GM), genetic predisposition to the disease, and certain environmental factors are thought to be involved in pathogenesis. However, the pathophysiology of IBD is incompletely understood, and diagnostic biomarkers and effective treatments, particularly for PIBD, are limited. Recent work suggests that these factors may interact to influence disease development, and multiomic approaches have emerged as promising tools to elucidate the pathophysiology. We employed metagenomics, metabolomics- and metatranscriptomics-based approaches to examine the microbiome, its genetic potential, and its activity to identify factors associated with PIBD. Metagenomics-based analyses revealed pathways such as octane oxidation and glycolysis that were differentially expressed in UC patients. Additionally, metatranscriptomics-based analyses suggested enrichment of glycan degradation and two component systems in UC samples as well as protein processing in the endoplasmic reticulum, ribosome, and protein export in CD and UC samples. In addition, metabolomics-based approaches revealed patterns of differentially abundant metabolites between healthy and PIBD individuals. Interestingly, overall microbiome community composition (as measured by alpha and beta diversity indices) did not appear to be associated with PIBD. However, we observed a small number of differentially abundant taxa in UC versus healthy controls, including members of the Classes Gammaproteobacteria and Clostridia as well as members of the Family Rikenellaceae. Accordingly, when identifying potential biomarkers for PIBD, our results suggest that multiomics-based approaches afford enhanced potential to detect putative biomarkers for PIBD compared to microbiome community composition sequence data alone.},
}
@article {pmid40427581,
year = {2025},
author = {Mafe, AN and Büsselberg, D},
title = {The Effect of Microbiome-Derived Metabolites in Inflammation-Related Cancer Prevention and Treatment.},
journal = {Biomolecules},
volume = {15},
number = {5},
pages = {},
doi = {10.3390/biom15050688},
pmid = {40427581},
issn = {2218-273X},
support = {NPRP 14S0311-210033//Qatar National Research Fund/ ; },
mesh = {Humans ; *Neoplasms/prevention &amp; control/metabolism/microbiology/therapy ; *Inflammation/metabolism/microbiology/complications ; Animals ; *Microbiota ; Fatty Acids, Volatile/metabolism ; Bile Acids and Salts/metabolism ; Gastrointestinal Microbiome ; },
abstract = {Chronic inflammation plays a crucial role in cancer development, yet the mechanisms linking the microbiome to inflammation-related carcinogenesis remain unclear. Emerging evidence suggests that microbiome-derived metabolites influence inflammatory pathways, presenting both challenges and opportunities for therapy. However, a deeper understanding of how these metabolites regulate inflammation and contribute to cancer prevention is still needed. This review explores recent advances in microbiome-derived metabolites and their roles in inflammation-related carcinogenesis. It highlights key molecular mechanisms, emerging therapies, and unresolved challenges. Synthesizing current research, including clinical trials and experimental models, bridges the gap between microbiome science and cancer therapy. Microbial metabolites such as short-chain fatty acids (SCFAs), polyamines, indoles, and bile acids play vital roles in regulating inflammation and suppressing cancer. Many metabolites exhibit potent anti-inflammatory and immunomodulatory effects, demonstrating therapeutic potential. Case studies show promising results, but challenges such as metabolite stability, bioavailability, and individual variability remain. Understanding microbiome-metabolite interactions offers novel strategies for cancer prevention and treatment. This review identifies knowledge gaps and proposes future research directions to harness microbiome-derived metabolites for innovative cancer therapies. Addressing these issues may pave the way for microbiome-targeted cancer interventions.},
}
@article {pmid40427561,
year = {2025},
author = {Zaiou, M and Joubert, O},
title = {Racial and Ethnic Disparities in NAFLD: Harnessing Epigenetic and Gut Microbiota Pathways for Targeted Therapeutic Approaches.},
journal = {Biomolecules},
volume = {15},
number = {5},
pages = {},
doi = {10.3390/biom15050669},
pmid = {40427561},
issn = {2218-273X},
mesh = {Humans ; DNA Methylation ; *Epigenesis, Genetic ; Ethnicity/genetics ; *Gastrointestinal Microbiome/genetics ; Health Status Disparities ; *Non-alcoholic Fatty Liver Disease/genetics/therapy/microbiology/ethnology ; Racial Groups/genetics ; },
abstract = {Nonalcoholic fatty liver disease (NAFLD) is a growing global health concern, impacting approximately 32.4% of the worldwide population. As a disease linked to metabolic dysfunction, NAFLD continues to rise alongside global increases in obesity, type 2 diabetes mellitus (T2DM), and metabolic syndrome. There is considerable evidence indicating that NAFLD disproportionately affects racial, ethnic, and minority groups, although the exact reasons for these disparities remain elusive. Contributing factors to this disease may include socioeconomic status, cultural influences, stress, genetic factors, and lifestyle choices. Emerging evidence suggests that these causal factors could influence epigenetic mechanisms, particularly DNA methylation and histone modifications, as well as the composition and diversity of gut microbiota. Nevertheless, there is a scarcity of research that comprehensively examines the interplay between epigenetic changes and gut microbiome variations in relation to NAFLD disparities across different racial and ethnic populations globally. This paper intends to (i) explore the connections between NAFLD, ethnic disparities, gut microbiota composition, and epigenetic alterations, while reviewing pertinent studies that illustrate how these factors contribute to health inequities among various ethnic groups impacted by this disease; (ii) explore potential therapeutic targets and biomarkers to advance the management of NAFLD; and (iii) provide insights to enhance our understanding of the mechanisms associated with this disease, thereby promoting further research in this field. Advancements in this area are anticipated to enhance our understanding of disease susceptibilities in at-risk groups and to provide new therapeutic options for NAFLD and its associated complications.},
}
@article {pmid40427557,
year = {2025},
author = {Rossi, R and Mainardi, E},
title = {Prebiotics and Probiotics Supplementation in Pigs as a Model for Human Gut Health and Disease.},
journal = {Biomolecules},
volume = {15},
number = {5},
pages = {},
doi = {10.3390/biom15050665},
pmid = {40427557},
issn = {2218-273X},
mesh = {Animals ; *Probiotics/administration &amp; dosage ; *Prebiotics/administration &amp; dosage ; Humans ; Swine ; *Gastrointestinal Microbiome/drug effects ; Disease Models, Animal ; Dietary Supplements ; },
abstract = {Animal models are an essential part of translational research for the purpose of improving human health. The pig is a potential human research model that can be used to assess the effects of dietary interventions, pathologies, and drugs on gut health and the microbiome, due to its anatomical and physiological similarity to humans. It is recognised that a healthy gut is closely linked to the prevention of several chronic diseases, including obesity, diabetes, gastrointestinal inflammation, as well as neurological and cardiovascular diseases. The use of prebiotics and probiotics plays an important role in maintaining a healthy digestive system, which is responsible for modulating all other body functions. The present review focuses on the applications of prebiotics and probiotics in the pig as an animal model in healthy and diseased conditions, in order to highlight the efficacy of these molecules in the perspective of human health outcomes. The data support the use of prebiotics to improve intestinal health in both healthy and diseased states. In addition, the use of human microbiota-associated (HMA) gnotobiotic pigs provided a good model to study the intestinal and systemic immune response and microbiota composition following probiotic supplementation after a vaccine or virus challenge.},
}
@article {pmid40427529,
year = {2025},
author = {Daude, N and Machado, I and Arce, L and Yang, J and Westaway, D},
title = {Microbial Composition, Disease Trajectory and Genetic Background in a Slow Onset Model of Frontotemporal Lobar Degeneration.},
journal = {Biomolecules},
volume = {15},
number = {5},
pages = {},
doi = {10.3390/biom15050636},
pmid = {40427529},
issn = {2218-273X},
support = {N/A//Nanostring AD panel/ ; N/A//SynAD ADRD/ ; 16308/CAPMC/CIHR/Canada ; 173286/CAPMC/CIHR/Canada ; NIF 21633//Canada Foundation for Innovation/ ; NIF 39588//Canada Foundation for Innovation/ ; N/A//Campus Alberta Neuroscience/ ; APRIIEP201600033//Alberta Prion Research Institute/ ; N/A//Hope for Tomorrow/ ; },
mesh = {Animals ; Mice ; Mice, Transgenic ; Disease Models, Animal ; tau Proteins/metabolism/genetics ; *Frontotemporal Lobar Degeneration/genetics/microbiology/pathology/metabolism ; Mice, Inbred C57BL ; *Gastrointestinal Microbiome/genetics ; Genetic Background ; Humans ; Male ; },
abstract = {Slow-onset neurodegenerative disease in a low-expresser 2N4R P301L transgenic (Tg) mouse model is marked by neuroinflammation and by differing patterns of CNS deposition and accumulation of tau conformers, with such heterogeneities present even within inbred backgrounds. Gut microbial genotypes were notably divergent within C57BL6/Tac or 129SvEv/Tac congenic (Cg) sublines of TgTau[P301L] mice, and these sublines differed when challenged with antibiotic treatment and fecal microbial transplantation. Whereas aged, transplanted Cg 129SvEv/Tac TgTau[P301L] mice had neuroanatomical deposition of tau resembling controls, transplanted Cg C57BL6/Tac TgTau[P301L] mice had different proportions of rostral versus caudal tau accumulation (p = 0.0001). These data indicate the potential for environmental influences on tau neuropathology in this model. Furthermore, Cg C57BL6/Tac TgTau[P301L] cohorts differed from 129SvEv/Tac counterparts by showing 28% versus 9% net intercurrent loss (p = 0.0027). While the origin of this phenomenon is not established, it offers a parallel to differing patterns of frailty observed in C57BL6 versus 129 SvEv Tg mice expressing the 695 amino acid isoform of human amyloid precursor protein. We infer that generalized responses to protein aggregation might account for similar reductions in viability even when expressing different human proteins in the same inbred strain background.},
}
@article {pmid40427514,
year = {2025},
author = {Cabral, LGS and Martins, IM and Paulo, EPA and Pomini, KT and Poyet, JL and Maria, DA},
title = {Molecular Mechanisms in the Carcinogenesis of Oral Squamous Cell Carcinoma: A Literature Review.},
journal = {Biomolecules},
volume = {15},
number = {5},
pages = {},
doi = {10.3390/biom15050621},
pmid = {40427514},
issn = {2218-273X},
support = {88887.630761/2021-00//CAPES-Foundation Coordination for the Improvement of Higher Education Personnel/ ; },
mesh = {Humans ; *Mouth Neoplasms/pathology/immunology/microbiology/metabolism ; Tumor Microenvironment/immunology ; *Carcinogenesis/immunology/pathology ; *Carcinoma, Squamous Cell/pathology/immunology/microbiology ; Microbiota ; Animals ; },
abstract = {The tumor microenvironment (TME) plays a crucial role in the development, progression, and metastasis of oral squamous cell carcinoma (OSCC). The TME comprises various cellular and acellular components, including immune cells, stromal cells, cytokines, extracellular matrix, and the oral microbiome, all of which dynamically interact with tumor cells to influence their behavior. Immunosuppression is a key feature of the OSCC TME, with regulatory T cells (Tregs), myeloid-derived suppressor cells (MDSCs), and tumor-associated macrophages (TAMs) contributing to an environment that allows tumor cells to evade immune surveillance and supports angiogenesis. The oral microbiome also plays a pivotal role in OSCC pathogenesis, as dysbiosis, or imbalances in the microbiota, can lead to chronic inflammation, which promotes carcinogenesis through the production of pro-inflammatory cytokines and reactive oxygen species (ROS). Pathogens like Porphyromonas gingivalis and Fusobacterium nucleatum have, hence, been implicated in OSCC-driven tumor progression, as they induce inflammation, activate oncogenic pathways, and modulate immune responses. In this review, we discuss how the interplay between immunosuppression and microbiome-driven inflammation creates a tumor-promoting environment in OSCC, leading to treatment resistance and poor patient outcomes, and explore the potential therapeutic implication of a better understanding of OSCC etiology and molecular changes.},
}
@article {pmid40427392,
year = {2025},
author = {Zhong, C and Du, J and Zhu, H and Gao, J and Xu, G and Xu, P},
title = {Intestinal Microbiota and Gene Expression Alterations in Chinese Mitten Crab (Eriocheir sinensis) Under Deltamethrin Exposure.},
journal = {Antioxidants (Basel, Switzerland)},
volume = {14},
number = {5},
pages = {},
doi = {10.3390/antiox14050510},
pmid = {40427392},
issn = {2076-3921},
support = {2022YFD2400700//the National Key R&amp;D Program of China/ ; JBGS [2021] 125//Jiangsu Province seed industry revitalization "JBGS" project/ ; 2023JBFR04//the Central Public-interest Scientific Institution Basal Research Fund of China/ ; },
abstract = {The intestine is an important immune organ of aquatic animals and it plays an essential role in maintaining body health and anti-oxidative stress. To investigate the toxic effects of deltamethrin in intestinal tissue of Chinese mitten crabs (Eriocheir sinensis), 120 healthy crabs were randomly divided into two experimental groups (blank control group and deltamethrin-treated group), with three replicates in each group. After being treated with deltamethrin for 24 h, 48 h, 72 h, and 96 h, intestinal tissues were collected aseptically to assess the effects of deltamethrin on oxidative stress, immunity, apoptosis-related genes, and the structure of microflora in intestinal tissues. Additionally, correlations between gut microbiota composition and intestinal tissue damage-associated genes were analyzed. The results demonstrated that prolonged exposure to deltamethrin induced oxidative stress damage in intestinal tissue. Compared with the blank control group, the expression of autophagy-related genes B-cell lymphoma/Leukemia-2 (bcl-2), c-Jun N-terminal kinase (jnk), Microtuble-associated protein light chain 3 (lc3c), Cysteine-dependent Aspartate-specific Protease 8 (caspase 8), BECN1(beclin1), oxidative stress damage-related genes MAS1 proto-oncogene (mas), Glutathione Peroxidase (gpx), kelch-like ECH-associated protein 1 (keap1), Sequestosome 1 (p62), Interleukin-6 (il-6), and immune-related genes Lipopolysaccharide-induced TNF-alpha Factor (litaf), Heat shock protein 90 (hsp90) and prophenoloxidase (propo) in the deltamethrin treatment group were significantly up-regulated at 96 h (p < 0.05 or p < 0.01). Additionally, 16S rRNA sequencing showed that the diversity of intestinal flora in the deltamethrin-treated group was significantly higher compared with the blank control group (p < 0.01). Analysis of the differences in the composition of intestinal flora at the genus level showed that the relative abundance of Candidatus Bacilloplasma in the deltamethrin treatment group was significantly lower than that in the blank control group (p < 0.01). In contrast, the relative abundances of Flavobacterium, Lachnospiraceae_NK4A136_group, Acinetobacter, Chryseobacterium, Lacihabitans, Taibaiella, Hydrogenophaga, Acidovorax, and Undibacterium were significantly higher than those in the blank control group (p < 0.05 or p < 0.01). Pearson correlation analysis revealed that Malaciobacter, Shewanella, and Prevotella exhibited significant positive correlations with gene indicators (jnk, gpx, lc3c, litaf, hsp90), while Dysgonomonas, Vibrio, and Flavobacterium demonstrated significant negative correlations with multiple gene indicators (caspase 8, p62, il-16, keap1, jnk, etc). These results demonstrate that deltamethrin significantly impacts the gut microbiota, immune function, and antioxidant capacity of E. sinensis. The changes in gut microbiota have correlations with the biomarkers of intestinal tissue injury genes, indicating that gut microbiota plays a crucial role in deltamethrin-induced intestinal tissue damage. These insights contribute to a better understanding of the ecological risks associated with deltamethrin exposure in aquatic organisms.},
}
@article {pmid40427379,
year = {2025},
author = {Boggan, S and Awosile, B and Koziol, J},
title = {Correction: Boggan et al. Describing the Reproductive Microbiome of Tritrichomonas foetus Chronically Infected Bulls and Diagnostic Collection Device Performance. Animals 2024, 14, 2689.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {10},
pages = {},
doi = {10.3390/ani15101356},
pmid = {40427379},
issn = {2076-2615},
abstract = {In the original publication [...].},
}
@article {pmid40427322,
year = {2025},
author = {Oliaro, FJ and Ajileye, O and George, I and Lamsal, S and Mosley, IA and Ramirez, B and Sanders, TL and Vanitshavit, V and Van Bonn, W and Pinnell, LJ},
title = {The Role of Ammonia-Oxidizing Archaea During Cycling and Animal Introduction in a Newly Commissioned Saltwater Aquarium.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {10},
pages = {},
doi = {10.3390/ani15101446},
pmid = {40427322},
issn = {2076-2615},
abstract = {Closed recirculating aquatic systems (aquariums) offer a multitude of benefits including the ability to observe and research aquatic animals ex situ, and under controlled environmental conditions [...].},
}
@article {pmid40427319,
year = {2025},
author = {Xu, C and Guo, X and Li, L},
title = {Metagenomic Comparison of Gut Microbes of Lemur catta in Captive and Semi-Free-Range Environments.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {10},
pages = {},
doi = {10.3390/ani15101442},
pmid = {40427319},
issn = {2076-2615},
abstract = {In order to protect endangered species, many zoos adopt diverse rearing models to achieve optimal conservation outcomes. This study employed metagenomic approaches to assess differences in the fecal microbiome of captive and semi-free-ranging ring-tailed lemurs (Lemur catta). The results show that captivity significantly altered the microbial community structure. The inter-individual variability in the microbial community within the captive-bred (CB) group was lower than that in the semi-free-ranging (FR) group, yet these individuals harbored a higher abundance of potential pathogens (Treponema_D). In contrast, microbial genera associated with fiber degradation and short-chain fatty acid production in the FR group were significantly elevated (Faecalibacterium, Roseburia, and Megamonas) as compared to the CB group. Environmental variations between the two rearing systems led to distinct profiles in microbial functions and carbohydrate-active enzyme gene composition. Notably, the FR group of lemurs exhibited an increased abundance of enzyme genes associated with the degradation of complex polysaccharides (cellulose, hemicellulose, and pectin), suggesting that their diet, rich in natural plant fibers, enhances the capacity of their gut microbiota to extract essential energy and nutrients. Conversely, the CB group displayed a more homogeneous microbial community with a higher prevalence of potential pathogens, implying that a captive lifestyle may negatively impact gastrointestinal health. These findings offer valuable insights into the influence of rearing conditions on gut microbial ecology and its potential implications for the health management of ring-tailed lemurs.},
}
@article {pmid40427233,
year = {2025},
author = {Lee, AR and Woodward, MJ and Rymer, C},
title = {Prevalence and Characterisation of Antimicrobial Resistance, Virulence Factors and Multilocus Sequence Typing (MLST) of Escherichia coli Isolated from Broiler Caeca.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {10},
pages = {},
doi = {10.3390/ani15101353},
pmid = {40427233},
issn = {2076-2615},
abstract = {This study was undertaken to determine the effect of bird age and administering either Lactococcus lactis ssp. lactis 1 (LL) or Limosilactobacillus fermentum 1 (LF) in the drinking water on the prevalence of antimicrobial resistance by phenotypic test, multilocus sequence typing (MLST) and virulence genes of Escherichia coli (E. coli) isolated from broiler caeca by whole-genome sequencing (WGS) analysis. Male (Ross 308) day-old chicks (240) were reared for 28 days. Water was provided either untreated (CON) or with LL (10[7]/mL) or LF (10[7]/mL) via a nipple drinker on three days each week during the starter phase (days 1, 3, 5, 7, 9 and 11 d) in eight replicate pens per treatment, with initially ten chicks per pen. One chick from each pen was sacrificed when LL or LF was added to the water, and again on d 14 and 28. There was no evidence that LL and LF had any effect on the prevalence of antimicrobial resistance and virulence genes in E. coli isolates. The population density of Lactobacillus sp. and coliforms decreased with age (p < 0.001). The high resistance of E. coli to ampicillin and tetracycline was maintained throughout the life of the broilers. The prevalence of virulence genes was greatest during the starter phase but declined when birds were 28 days of age (p < 0.05). In birds < 14 d of age, E. coli MLST 457, 1640, 1485 and 155 were dominant, and these carried iucD, irp2, astA, iutA and iroN genes. When birds were 28 d of age, MLST 1286, 1112 and 973 predominated, and these carried few virulence genes. This suggests that young birds were more susceptible to putative pathogenic E. coli than older birds. Supporting the development of a healthy microbiome that might control the proliferation of potentially pathogenic E. coli is an area of future research.},
}
@article {pmid40427206,
year = {2025},
author = {Łyko, M and Maj, J and Jankowska-Konsur, A},
title = {The Role of the Gut Microbiome in Non-Hodgkin Lymphoma (NHL): A Focus on Diffuse Large B-Cell Lymphoma, Follicular Lymphoma, Cutaneous T-Cell Lymphoma, and NK/T-Cell Lymphoma.},
journal = {Cancers},
volume = {17},
number = {10},
pages = {},
doi = {10.3390/cancers17101709},
pmid = {40427206},
issn = {2072-6694},
support = {SUBK.C260.22.043.//Wroclaw Medical University/ ; },
abstract = {Non-Hodgkin lymphomas (NHLs) encompass a diverse group of neoplasms arising from the clonal proliferation of B-cell progenitors, T-cell progenitors, mature B-cells, mature T-cells, and natural killer (NK) cells. These malignancies account for over 90% of lymphoid neoplasms. The link between the gut microbiome and neoplasms has been extensively studied in recent years. Growing evidence suggests that the gut microbiome may be involved not only in the development of the disease, but also in modulating the efficacy of implemented therapies. In this review, we summarize the current knowledge on the potential involvement of the gut microbiome in the development of diffuse large B-cell lymphoma (DLBCL), follicular lymphoma (FL), mucosa-associated lymphoid tissue (MALT) lymphoma, and NK/T-cell lymphoma, including cutaneous T-cell lymphoma (CTCL). Moreover, we discuss the relationship between gut microbiome changes before and after treatment and their association with treatment outcomes, focusing on chemotherapy and CAR T-cell therapy.},
}
@article {pmid40427098,
year = {2025},
author = {Glapiński, F and Zając, W and Fudalej, M and Deptała, A and Czerw, A and Sygit, K and Kozłowski, R and Badowska-Kozakiewicz, A},
title = {The Role of the Tumor Microenvironment in Pancreatic Ductal Adenocarcinoma: Recent Advancements and Emerging Therapeutic Strategies.},
journal = {Cancers},
volume = {17},
number = {10},
pages = {},
doi = {10.3390/cancers17101599},
pmid = {40427098},
issn = {2072-6694},
abstract = {Pancreatic cancer (PC), with pancreatic ductal adenocarcinoma (PDAC) comprising about 90% of all cases, is one of the most aggressive and lethal solid tumors. PDAC remains one of the most significant challenges of oncology to this day due to its inadequate response to conventional treatment, gradual rise in incidence since 2004, and poor five-year survival rates. As cancer cells are the primary adversary in this uneven fight, they remain the primary research target. Nevertheless, increasing attention is being paid to the tumor microenvironment (TME). The most crucial TME constellation components are immune cells, especially macrophages, stellate cells and lymphocytes, fibroblasts, bacterial and fungal microflora, and neuronal cells. Depending on the particular phenotype of these cells, the composition of the microenvironment, and the cell ratio, patients can experience different disease outcomes and varying vulnerability to treatment approaches. This study aims to present the current knowledge and review the most up-to-date scientific findings regarding the microenvironment of PC. It contains detailed information on the structure and cellular composition of the stroma, including its impact on disease development, metastasis, and response to treatment, as well as the therapeutic opportunities that arise from targeting this tissue.},
}
@article {pmid40427090,
year = {2025},
author = {Kono, K and Kozu, Y and Yokota, S and Hatayama, K and Mizumura, K and Maruoka, S and Masuyama, H and Gon, Y},
title = {Gut Microbiota Dysbiosis in Japanese Female Patients with Nontuberculous Mycobacteria-Associated Lung Disease: An Observational Study.},
journal = {Biomedicines},
volume = {13},
number = {5},
pages = {},
doi = {10.3390/biomedicines13051264},
pmid = {40427090},
issn = {2227-9059},
abstract = {Background/Objectives: Nontuberculous mycobacterial pulmonary disease (NTM-PD) is treated using a combination of multiple antimicrobial agents and prolonged therapy; however, recurrence and reinfection rates remain high. Susceptibility to NTM-PD is not fully understood. We aimed to investigate the association between NTM-PD and gut microbiota and determine the impact of antimicrobial therapy on the composition of the gut microbiota. Methods: We analyzed the gut microbiota of 20 Japanese females with NTM-PD (mean age: 67.9 years; range: 50-80 years) at different treatment stages-before, during, and at recurrence-alongside 20 healthy individuals, using 16S rRNA gene amplicon sequencing. Results: Subgroup A (pre-treatment) showed a small difference in β-diversity when compared with the healthy control (HC) group, while no significant differences in α-diversity were observed. Subgroup B (during treatment) exhibited a larger difference in β-diversity compared with the HC group, along with a decrease in α-diversity. The α-diversity of the gut microbiota in Subgroup C (at recurrence) was lower than that in Subgroup A but higher than that in Subgroup B. In Subgroups A and C, the bacterial taxa Sutterella, Adlercreutzia, Odoribacter, and Prevotella had decreased relative abundance, while Erysipelatoclostridium, Massilimicrobiota, Flavonifractor, Eggerthella, and Fusobacterium had increased relative abundance compared to those in the HC group. Conclusions: The loss of normal resident gut bacteria may hinder reacquisition. Treatment may be associated with the persistence of a dysbiotic gut microbiota, fostering susceptibility to NTM-PD. Gut microbiota dysbiosis may heighten susceptibility to NTM-PD, complicate treatment outcomes, and increase the risk of microbiological recurrence following therapy.},
}
@article {pmid40427029,
year = {2025},
author = {Cianci, R and Caldarelli, M and Brani, P and Bosi, A and Ponti, A and Giaroni, C and Baj, A},
title = {Cytokines Meet Phages: A Revolutionary Pathway to Modulating Immunity and Microbial Balance.},
journal = {Biomedicines},
volume = {13},
number = {5},
pages = {},
doi = {10.3390/biomedicines13051202},
pmid = {40427029},
issn = {2227-9059},
abstract = {Bacteriophages are a unique and fascinating group of viruses, known for their highly specific ability to infect and replicate within bacterial cells. While their potential as antibacterial agents has been recognized for decades, recent research has revealed complex interactions between phages and the human immune system, offering new insights into their role in immune modulation. New evidence reveals a dynamic and intricate relationship between phages and cytokines, suggesting their ability to regulate inflammation, immune tolerance, and host-pathogen interaction. Herein, we review how phages affect the production of cytokines and the behavior of immune cells indirectly by lysis of bacterium or directly on mammalian cells. Phages have been shown to induce both pro- and anti-inflammatory responses and recently, they have been explored in personalized immunotherapy, cancer immunotherapy, and microbiome modulation, which are the focus of this review. Several challenges remain despite significant progress, including practical obstructions related to endotoxins along with host microbiome variability and regulatory issues. Nevertheless, the potential of bacteriophages to modulate immune responses makes them attractive candidates for the future of precision medicine.},
}
@article {pmid40427024,
year = {2025},
author = {Wu, P and Zhang, J and Zhang, W and Yang, F and Yu, Y and Zhang, Y and Wang, G and Zhang, H and Xu, Y and Yao, X},
title = {2bRAD-M Reveals the Characteristics of Urinary Microbiota in Overweight Patients with Urinary Tract Stones.},
journal = {Biomedicines},
volume = {13},
number = {5},
pages = {},
doi = {10.3390/biomedicines13051197},
pmid = {40427024},
issn = {2227-9059},
support = {22140903800//Science and Technology Commission of Shanghai Municipality/ ; },
abstract = {Background: Urinary tract stone (UTS) is a common disease significantly impacting human health. Obesity influences stone formation and increases UTS incidence, yet the differences in the urinary microbiota and pathways between overweight and healthy-weight UTS patients remain unclear. Methods: In this study, 16 patients were analyzed: 8 overweight and 8 healthy-weight UTS patients. Bladder urine samples were collected during surgery, and DNA was extracted for microbial analysis using 2bRAD markers. Microbial diversity and KEGG pathway differences were studied. Results: The results showed that overweight UTS patients had a significantly higher urinary microbial diversity than healthy-weight patients. The analysis identified differences in microbiota at various taxonomic levels. LEfSe analysis revealed Sphingomonas_paucimobilis as abundant in overweight patients, while Bifidobacterium_piotii dominated in healthy-weight patients. Key species, including Ralstonia_sp000620465, Sphingomonas_paucimobilis, and Campylobacter_D_coli, were identified. KEGG analysis highlighted enriched pathways in overweight UTS patients, including the porphyrin and chlorophyll metabolism, fatty acid metabolism, amino acid degradation, and renin-angiotensin and mineral absorption pathways. Conclusions: This study is the first to use 2bRAD-M microbiome analysis to compare the urinary microbiota between overweight and healthy-weight UTS patients. It identified significant microbiota and pathway differences, suggesting a link between microbiota imbalance, obesity, and stone formation. These findings provide potential targets for further research on obesity-related stone susceptibility mechanisms.},
}
@article {pmid40426941,
year = {2025},
author = {Mazzotta, C and Barkai, L},
title = {Obesity and Asthma in Children-Coexistence or Pathophysiological Connections?.},
journal = {Biomedicines},
volume = {13},
number = {5},
pages = {},
doi = {10.3390/biomedicines13051114},
pmid = {40426941},
issn = {2227-9059},
support = {2019-1.3.1-KK-2019-00007//Project no. 2019-1.3.1-KK-2019-00007 was implemented with the support provided from the National Research, Development and Innovation Fund of Hungary, financed under the 2019-1.3.1-KK funding scheme. This project has been supported by the National Researc/ ; },
abstract = {The aim of this narrative review is to explore possible connections that might lead to both obesity and asthma; it will explain factors and mechanisms involved in disease pathogenesis, focusing particularly on diet and nutrients, the microbiome, inflammatory and metabolic dysregulation, lung function, the genetics/genomics of obese asthma, risk of exacerbation, atopy, and response to treatment. It highlights the role that obesity plays as a risk factor for and disease modifier of asthma, understanding the evidence supporting lifestyle changes in influencing disease progression. Pathophysiological mechanisms in obesity-related asthma have influences on the course of disease pathology. Due to these factors, the child with obese asthma needs a specific therapeutic approach taking into account the common unresponsiveness to bronchodilators, increased requirements for controller medications, poorer steroid effectiveness, and better response to leukotriene receptor (LTR) inhibitors. Therapeutic strategies centered on prevention are suggested and the development of resources to assist families with weight loss strategies and lifestyle changes is shown to be useful for effective weight control and optimal asthma management. Obese children with asthma generally should receive interventions that encourage daily physical activity, weight loss, and normalization of nutrient levels, and monitoring of common obesity-related sequelae should be considered by healthcare providers managing obese children with difficult to control asthma. Recognizing and identifying an asthmatic patient is not always easy and a detailed medical history of the patient, with particular attention paid to their presenting and past symptoms, and a complete physical examination play pivotal and fundamental roles in determining the final diagnosis.},
}
@article {pmid40426930,
year = {2025},
author = {Loureiro, J and Costa-Pereira, JT and Pozza, DH and Tavares, I},
title = {The Power of Movement: How Exercise Influences Chemotherapy-Induced Peripheral Neuropathy.},
journal = {Biomedicines},
volume = {13},
number = {5},
pages = {},
doi = {10.3390/biomedicines13051103},
pmid = {40426930},
issn = {2227-9059},
support = {N/A//Catedra de Medicina da Dor (Faculdade de Medicina, Universidade do Porto)/ ; },
abstract = {As the number of cancer patients and survivors increases, we face a rising challenge: the long-term impact of the adverse effects of cancer treatment. One of the known adverse effects is chemotherapy-induced peripheral neuropathy (CIPN), which courses with pain complaints. The treatments of CIPN have reduced efficacy. The neurobiological causes of CIPN have been mainly ascribed to peripheral nerve damage, but recent studies show effects in the brain, namely in the descending pain modulatory systems. Physical exercise seems to be associated with better outcomes in CIPN patients, but the mechanisms underlying the effects have not been discussed, namely considering the recent results of the effects of CIPN in brain structures involved in pain modulation. In this critical review, we propose that the beneficial effects of exercise in CIPN also have central mechanisms, namely neuroinflammation and oxidative stress, as well as changes in the actions of neurotransmitters and neurotrophic factors, with a direct effect on optimizing the endogenous pain modulation, namely opioids, monoamines, and endocannabinoids. The effects are multifactorial, as mood improvement and the other psychological benefits of exercise should be considered. The emerging role of the microbiome, which is affected during CIPN, also needs to be considered. This review critically synthesizes the available literature to highlight how the neurobiological effects of physical exercise make it a promising strategy for managing CIPN, both from preventive and treatment perspectives.},
}
@article {pmid40426537,
year = {2025},
author = {Touaitia, R and Mairi, A and Ibrahim, NA and Basher, NS and Idres, T and Touati, A},
title = {Staphylococcus aureus: A Review of the Pathogenesis and Virulence Mechanisms.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {5},
pages = {},
doi = {10.3390/antibiotics14050470},
pmid = {40426537},
issn = {2079-6382},
support = {grant number IMSIU-DDRSP2501//Deanship of Scientific Research at Imam Mohammad Ibn Saud Islamic University (IMSIU)/ ; },
abstract = {Staphylococcus aureus is a formidable human pathogen responsible for infections ranging from superficial skin lesions to life-threatening systemic diseases. This review synthesizes current knowledge on its pathogenesis, emphasizing colonization dynamics, virulence mechanisms, biofilm formation, and antibiotic resistance. By analyzing studies from PubMed, Scopus, and Web of Science, we highlight the pathogen's adaptability, driven by surface adhesins (e.g., ClfB, SasG), secreted toxins (e.g., PVL, TSST-1), and metabolic flexibility in iron acquisition and amino acid utilization. Nasal, skin, and oropharyngeal colonization are reservoirs for invasive infections, with biofilm persistence and horizontal gene transfer exacerbating antimicrobial resistance, particularly in methicillin-resistant S. aureus (MRSA). The review underscores the clinical challenges of multidrug-resistant strains, including vancomycin resistance and decolonization strategies' failure to target single anatomical sites. Key discussions address host-microbiome interactions, immune evasion tactics, and the limitations of current therapies. Future directions advocate for novel anti-virulence therapies, multi-epitope vaccines, and AI-driven diagnostics to combat evolving resistance. Strengthening global surveillance and interdisciplinary collaboration is critical to mitigating the public health burden of S. aureus.},
}
@article {pmid40426509,
year = {2025},
author = {Wang, JH and Han, SY and Lee, K and Han, U and Cho, SK and Kim, H},
title = {Antibiotic Cocktail Exacerbates Esomeprazole-Induced Intestinal Dysmotility While Ameliorating Gastric Dyspepsia in Mice.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {5},
pages = {},
doi = {10.3390/antibiotics14050442},
pmid = {40426509},
issn = {2079-6382},
support = {NRF-2022M3A9E4017033//National Research Foundation of Korea/ ; },
abstract = {Background/Objectives: Esomeprazole, a proton pump inhibitor (PPI), is commonly prescribed for gastric-acid-related disorders but has been associated with impaired gastrointestinal (GI) motility with long-term use. However, the effect of concurrent antibiotic administration on this dysfunction remains unclear. Therefore, this study aimed to investigate the effects of antibiotics on esomeprazole-induced GI motility dysfunction and explore the underlying mechanisms in a mouse model. Methods: Male C57BL/6 mice were orally administered esomeprazole (160 mg/kg) five times per week for 4 weeks. Three days before initiating esomeprazole treatment, a broad-spectrum antibiotic cocktail (ABX) consisting of ampicillin (1 g/kg), neomycin (1 g/kg), metronidazole (1 g/kg), and vancomycin (0.5 g/kg) was provided in drinking water and maintained throughout the experimental period. Mosapride (3 mg/kg), a prokinetic agent, was used as a positive control. Results: Neither esomeprazole alone nor in combination with ABX affected body weight or food intake. Compared to normal controls, esomeprazole treatment significantly delayed both intestinal transit and gastric emptying. However, ABX co-administration further pronounced intestinal transit time and improved gastric motility. The potential mechanisms may involve interactions among gastric H[+]/K[+]-ATPase, CYP3A11, gastrointestinal hormones (secretin and motilin), and the gut microbiome. Conclusions: Long-term esomeprazole use can impair both gastric and intestinal motility, and ABX co-treatment further exacerbates intestinal transit delay while paradoxically enhancing gastric emptying. These findings highlight the critical role of the gut microbiota in esomeprazole-induced GI motility dysfunction and suggest that antibiotic use should be approached with caution, particularly when combined with PPI therapy.},
}
@article {pmid40426501,
year = {2025},
author = {Donia, M and Aref, NE and Zeineldin, M and Megahed, A and Blair, B and Lowe, J and Aldridge, B},
title = {Impact of Parenteral Ceftiofur on Developmental Dynamics of Early Life Fecal Microbiota and Antibiotic Resistome in Neonatal Lambs.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {5},
pages = {},
doi = {10.3390/antibiotics14050434},
pmid = {40426501},
issn = {2079-6382},
abstract = {Background: Early gut microbiome development is critical for neonatal health, and its dysbiosis may impact long-term animal productivity. This study examined the effects of parenteral Ceftiofur Crystalline Free Acid (CCFA) on the composition and diversity of the neonatal lamb fecal microbiome. The emergence of antimicrobial resistance genes associated with CCFA exposure was also investigated. Results: There were distinct microbial populations in the CCFA-treated lambs compared to the control group at each time point, with a highly significant decrease in alpha and beta diversity. The CCFA treatment showed a reduction in several key microbial taxa during nursing, but these differences were diminished by day 56. Unlike the control group, CCFA-treated lambs had core microbes potentially carrying multiple antibiotic resistance genes, including those for beta-lactam, fosfomycin, methicillin, and multidrug resistance. Methods: Twenty-four healthy neonatal lambs were randomly assigned to CCFA-treated (n = 12) and control (n = 12) groups. Fecal samples were collected on days 0, 7, 14, 28, and 56. Genomic DNA was extracted and sequenced using the Illumina MiSeq platform. Microbial composition was analyzed using the MG-RAST pipeline with the RefSeq database. Conclusions: Despite temporary reductions in critical bacterial populations during nursing, the early sheep fecal microbiome demonstrated resilience by repopulating after CCFA antibiotic disruption. While this highlights microbiota stability after short-course antibiotic exposure, the transient disturbance underscores potential risks to early gut health. Importantly, persistent CCFA resistance poses environmental dissemination risks, emphasizing the need for cautious antibiotic use in livestock to mitigate ecological impacts.},
}
@article {pmid40426500,
year = {2025},
author = {Tóth, AG and Tóth, DL and Remport, L and Tóth, I and Németh, T and Dubecz, A and Patai, &#xc1;V and Wagenhoffer, Z and Makrai, L and Solymosi, N},
title = {A One Health Approach Metagenomic Study on Antimicrobial Resistance Traits of Canine Saliva.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {5},
pages = {},
doi = {10.3390/antibiotics14050433},
pmid = {40426500},
issn = {2079-6382},
support = {SRF-001//University of Veterinary Medicine Budapest/ ; 874735 (VEO)//European Union's Horizon 2020/ ; 2024-2.1.2-EK&#xd6;P-2024-00018//Ministry of Culture and Innovation of Hungary/ ; },
abstract = {Background: According to the One Health concept, the physical proximity between pets and their owners facilitates the interspecies spread of bacteria including those that may harbor numerous antimicrobial resistance genes (ARGs). Methods: A shotgun sequencing metagenomic data-based bacteriome and resistome study of 1830 canine saliva samples was conducted considering the subsets of ARGs with higher public health risk, ESKAPE pathogen relatedness (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter species), and survey results on the physical and behavioral characteristics of the participating dogs. Results: A total of 318 ARG types achieved sufficiently high detection rates. These ARGs can affect 31 antibiotic drug classes through various resistance mechanisms. ARGs against tetracyclines, cephalosporins, and, interestingly, peptides appeared in the highest number of samples. Other Critically Important Antimicrobials (CIAs, WHO), such as aminoglycosides, fluoroquinolones, or macrolides, were among the drug classes most frequently affected by ARGs of higher public health risk and ESKAPE pathogen-related ARGs of higher public health risk. Several characteristics, including coat color, sterilization status, size, activity, or aggressiveness, were associated with statistically significant differences in ARG occurrence rates (p < 0.0500). Conclusions: Although the oral microbiome of pet owners is unknown, the One Health and public health implications of the close human-pet bonds and the factors potentially underlying the increase in salivary ARG numbers should be considered, particularly in light of the presence of ARGs affecting critically important drugs for human medicine.},
}
@article {pmid40426336,
year = {2025},
author = {Wang, Y and Zhou, K and Zhang, Y and Li, C and Zhang, Y and Ren, X and Mi, C and Ma, L and Duan, Y and Liu, M and Ping, G and Tian, X and Song, Z},
title = {The Systemic Impact of Helicobacter pylori Infection on the Microbiome of Whole Digestive Tract Based on Mucosal, Gastric Juice, and Fecal Specimens.},
journal = {Helicobacter},
volume = {30},
number = {3},
pages = {e70047},
doi = {10.1111/hel.70047},
pmid = {40426336},
issn = {1523-5378},
support = {82170562//National Natural Science Foundation of China/ ; 7232199//Beijing Natural Science Foundation/ ; BYSYZD2023008//Key Clinical Projects of Peking University Third Hospital/ ; },
mesh = {Humans ; *Feces/microbiology ; Cross-Sectional Studies ; *Helicobacter Infections/microbiology ; Male ; Middle Aged ; Female ; *Gastric Juice/microbiology ; Adult ; *Helicobacter pylori/physiology ; RNA, Ribosomal, 16S/genetics ; *Gastrointestinal Microbiome ; Bacteria/classification/genetics/isolation &amp; purification ; Aged ; *Gastrointestinal Tract/microbiology ; Dysbiosis/microbiology ; Metagenomics ; },
abstract = {BACKGROUND: Recent studies have found that in addition to directly impacting the gastric microbiome, Helicobacter pylori (H. pylori) infection may cause intestinal microbial dysbiosis. However, most existing studies on the influence of H. pylori infection on the intestinal microbiome used fecal specimens with inconsistent conclusions. Only one limited study on 8 H. pylori-infected patients has previously assessed the impact of H. pylori infection on the microbiome of the entire gastrointestinal tract, finding no significant effect on the bacterial composition of the lower gastrointestinal tract.<br><br>METHODS: This single-center cross-sectional study collected mucosa of the esophagus, stomach, small intestine, and colon, as well as gastric juice and feces from 120 participants of the H. pylori-infected group (HIG) and 30 of the healthy control group (HCG). 16S rRNA sequencing was applied to analyze the bacterial composition and functional pathways, and metagenomics was adopted to assess the composition of viruses, eukaryotes, and archaea in the feces, as well as the antibiotic resistance gene (ARG) and virulence factors of bacteria (VF).<br><br>RESULTS: Compared with the HCG, the alpha and beta diversity of bacteria in the mucosa of the whole digestive tract and the gastric juice of the HIG showed significant changes, with increased microbial dysbiosis index and significantly different compositions at the phylum and genus levels. Functional pathway analysis revealed that the metabolic characteristics of the flora changed in the HIG, with site-specific differences. Fecal specimens demonstrated no significant differences in the above indicators between the two groups. In addition, feces-based metagenomic analysis revealed that only eukaryotes had higher diversity in the HIG, whereas viruses and archaea showed no significant changes; the Shannon index of ARG increased; and VF showed no significant change.<br><br>CONCLUSIONS: This study revealed that H. pylori infection significantly influenced the diversity, composition, and metabolic functional pathway of bacteria in different parts of the digestive tract and the gastric juice. Moreover, fecal microbial composition may not fully represent the mucosal microbial composition of the gastrointestinal tract.<br><br>TRIAL REGISTRATION: Chinese Clinical Trial Registry: ChiCTR2300073419.},
}
@article {pmid40426143,
year = {2025},
author = {Zhao, X and Ren, Z and Li, W and Liu, Q and Dong, Y and Huang, Y},
title = {Alterations in ocular fungal microbiota in patients with fungal keratitis: a comparative study from coastal regions of Eastern China.},
journal = {BMC ophthalmology},
volume = {25},
number = {1},
pages = {316},
pmid = {40426143},
issn = {1471-2415},
support = {ts20190983//the Taishan Scholar Program/ ; 81970788//the National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Eye Infections, Fungal/microbiology/epidemiology ; China/epidemiology ; Male ; Female ; Middle Aged ; Adult ; *Keratitis/microbiology/epidemiology ; *Mycobiome ; *Fungi/genetics/isolation &amp; purification ; Conjunctiva/microbiology ; Aged ; *Cornea/microbiology ; Young Adult ; Dysbiosis/microbiology ; *Microbiota ; },
abstract = {OBJECTIVE: The understanding of the ocular microbiota, particularly in fungal keratitis (FK), is evolving with advancements in high-throughput sequencing technologies. Traditional culture-based methods may not fully capture the microbial diversity present in keratitis, highlighting the need for more comprehensive approaches to explore microbial dysbiosis in corneal infections. This study aimed to reveal the dysbacteriosis of the ocular fungal microbiome associated with FK.<br><br>METHODS: We analysed 105 samples, including conjunctival swabs from healthy eyes (HE) and conjunctival swabs (SW), as well as corneal scrapings (SC), from FK eyes. Positive results were observed in 58 samples, and detailed taxonomic categorization was carried out across multiple levels-phylum, class, order, family, and genus-using high-throughput ITS sequencing. Alpha and beta diversity indices were computed, and interaction networks at the genus level were predicted to elucidate changes in microbial communities. The analyses also included assessments of functional groups within the fungal microbiome.<br><br>RESULTS: Among the samples, the HE, SW, and SC groups presented differences in positivity rates and diversity indices. Compared with HE eyes, infected eyes (SW and SC) presented significantly greater Good's coverage estimator and lower Chao1, Shannon, and Simpson diversity indices, indicating reduced species richness and evenness. At multiple taxonomic levels, various taxa were significantly downregulated in the FK eyes. Functional analyses revealed differences, notably, an increase in the number of litter saprotrophs in FK eyes. Ascomycota and Basidiomycota were identified as core phyla in the ocular microbiota interaction network.<br><br>CONCLUSION: Fungal keratitis significantly alters the ocular surface microbiome, which is characterized by decreased microbial richness and evenness. High-throughput sequencing revealed a complex interaction network with significant variability between healthy and infected eyes. Additionally, these findings suggest potential benefits from early and aggressive debridement in managing FK due to its impact on functional microbial groups.},
}
@article {pmid40426050,
year = {2025},
author = {Kumar, ST and Zhang, Y and Zhang, Q and Azeem, RM and Jing, Z and Pan, L and Sun, WS and Zhao, Y and Zhang, SM},
title = {Breed-specific differences of gut microbiota and metabolomic insights into fat deposition and meat quality in Chinese Songliao Black Pig and Large White × Landrace Pig Breeds.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {334},
pmid = {40426050},
issn = {1471-2180},
support = {20240303075NC//The Key Technology Research and Development Program of Jilin Province of China/ ; 20240303066NC//The Key Technology Research and Development Program of Jilin Province of China/ ; 2023YFF1001000//National Key Research and Development Program of China/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; Swine/microbiology ; *Meat/analysis ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Metabolomics ; RNA, Ribosomal, 16S/genetics ; Breeding ; Cecum/microbiology ; },
abstract = {BACKGROUND: Gut microbiota ferment non-digestible substances to produce metabolites that accumulate in muscle and influence host metabolism. However, the regulatory mechanisms connecting gut microbiota, metabolites, and fat deposition across pig breeds remain unclear. This study explores the gut-muscle axis regulating fat deposition and meat quality in Chinese Songliao Black Pig (SBP) and Large White × Landrace Pigs (LWLDP). Digesta samples from the ileum, cecum, and rectum of both breeds were analyzed using 16 S rRNA sequencing for microbiome profiling and ultra-high-performance liquid chromatography (UHPLC) for metabolomics. Multi-omics data, including microbiota and metabolite profiles were integrated with our previously published data of transcriptomics and metabolomics insights into fat deposition in the longissimus dorsi (LD) muscle using the MixOmics DIABLO method.<br><br>RESULTS: Microbiome analysis revealed that Fibrobacter, Unidentified_Peptostreptococcaceae, Sutterella, and Unidentifed_Rickettsiales were enriched in SBP, while Ruminococcus, Corynebacterium, and Streptococcaceae in LWLDP. Metabolomic analysis indicated that SBP was enriched in fatty acid biosynthesis pathways, including linoleic acid, &#x3b1;-linolenic acid, and arachidonic acid, whereas LWLDP was associated with insulin signaling, starch and sucrose metabolism. Integrated analysis identified Peptostreptococcaceae and Rickettsiales in SBP, along with metabolites phosphatidylcholine (PC(22:4)), N-acylethanolamine (NAE(20:4)), and lysophosphatidylcholine (LysoPC(24:1)) were correlated with key genes (EIF4E, MSTN, PPARGC1A, NR4A3, and SOCS1) regulating fat deposition. In LWLDP, Corynebacterium and Streptococcaceae were linked to the PPP1R3B gene, which is involved in glycogen metabolism, as well as metabolites 2-methyl-3-hydroxybutyric acid and 5-keto-gluconic acid, suggesting a shift toward glycolysis over lipolysis.<br><br>CONCLUSION: This study concluded that cecum-associated microbes in LWLDP may enhance carbohydrate metabolism, leading to reduced fat deposition, whereas rectum-associated microbes in SBP contribute to docosahexaenoic acid (DHA) biosynthesis, thereby improving meat quality. These findings highlight gut microbiota-derived metabolites as potential biomarkers for optimizing meat production and livestock breeding strategies.},
}
@article {pmid40426042,
year = {2025},
author = {Dhakal, R and Neves, ALA and Sapkota, R and Khanal, P and Ellegaard-Jensen, L and Winding, A and Hansen, HH},
title = {Investigating dose-dependent effects of chemical compounds targeting rumen fermentation pathways using an in-vitro rumen fermentation system.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {330},
pmid = {40426042},
issn = {1471-2180},
mesh = {*Rumen/microbiology/metabolism/drug effects ; Animals ; *Fermentation/drug effects ; Methane/metabolism/biosynthesis ; Fatty Acids, Volatile/metabolism ; Bacteria/classification/drug effects/metabolism/genetics/isolation &amp; purification ; Dose-Response Relationship, Drug ; Alkanesulfonic Acids ; },
abstract = {BACKGROUND: Ruminal fermentation leads to the formation of methane (CH4) as a byproduct, which is one of the major greenhouse gases. Despite extensive research efforts involving the use of various anti-methanogenic and hydrogen sink compounds, the current understanding of the dose-response effects of these compounds on the rumen microbiome and fermentation profile is limited. In this study, potential methanogenesis inhibitors or electron acceptors were evaluated for their effects on methane production, fermentation, and prokaryotic community composition. Dose-response effects of sodium 2-bromoethanesulfonate (BES: 0, 2.5, 5, 10 mmol/L), p-hydrocinnamic acid (HoC: 0, 5, 10 mmol/L), and sodium fumarate dibasic (DFS: 0, 5, 10, 20 mmol/L) on dry matter degradation, total gas production, methane concentration and yield, composition and yield of volatile fatty acids, and prokaryote composition were studied during 48 h rumen fermentations.<br><br>RESULTS: The BES decreased the yield (ml/ g DM) and concentration (%) of CH4, acetic, isobutyric, and total VFA (t-VFA) concentrations (mmol/g DM), and increased propionic and butyric acid concentrations (mmol/g DM) without affecting dry matter degradability (dDM) as the dose increased. The HoC decreased dDM, total gas production (TGP), CH4 yield (ml/ g DM) and increased tVFA concentration (mmol/g DM) as the dose increased. The increasing dose of DFS increased the pH, propionic acid and tVFA concentrations (mmol/g DM) and decreased the yield (ml/ g DM) and concentration (%) of CH4 without affecting dDM. Sodium 2-bromoethanesulfonate, HoC, and DFS doses did not significantly change the alpha-diversity and beta-diversity indices of the prokaryotic communities at the amplicon sequence variant level, although the relative abundances of specific phyla were affected by the treatments. The major bacterial phyla across all samples were Bacteroidetes, Proteobacteria, Firmicutes, Spirochaetota, Verrucomicrobiota, and Patescibacteria.<br><br>CONCLUSIONS: This study demonstrated that (i) all the evaluated compounds affected the targeted metabolic pathways without influencing the structure of the rumen microbial community, (ii) BES inhibited methanogenesis without affecting dry matter degradability, and (iii) HoC and DFS shifted hydrogen utilization towards acetate and propionate production. The recommended doses, to reduce methane during in-vitro rumen fermentation for BES, HoC, and DFS were determined to be 2.5 mmol/L, 5 mmol/L, and 10 mmol/L, respectively. Further research is suggested to understand the interactive effects of methane inhibition compounds, such as BES, in conjunction with H2 sink compounds such as HoC and DFS. However, caution is advised when using halogenated compounds like BES, as some methanogens have developed resistance and BES is not approved for use as a feed additive for live animals.},
}
@article {pmid40425815,
year = {2025},
author = {Seira Curto, J and Dominguez Martinez, A and Perez Collell, G and Barniol Simon, E and Romero Ruiz, M and Franco Bordés, B and Sotillo Sotillo, P and Villegas Hernandez, S and Fernandez, MR and Sanchez de Groot, N},
title = {Exogenous prion-like proteins and their potential to trigger cognitive dysfunction.},
journal = {Molecular systems biology},
volume = {},
number = {},
pages = {},
pmid = {40425815},
issn = {1744-4292},
support = {FPU21/03897//MICIU/AEI/10.13039/501100011033 and by FSE+/ ; RYC2019-026752-I//MCIN/AEI/10.13039/501100011033 and by FSE invierte en tu futuro/ ; PID2020- 117454RA-I00//MCIN/AEI/10.13039/501100011033/ ; CNS2023-144437//MICIU/AEI/10.13039/501100011033 and by the European Union - NextGenerationEU/PRTR/ ; },
abstract = {The gut is exposed to a wide range of proteins, including ingested proteins and those produced by the resident microbiota. While ingested prion-like proteins can propagate across species, their implications for disease development remain largely unknown. Here, we apply a multidisciplinary approach to examine the relationship between the biophysical properties of exogenous prion-like proteins and the phenotypic consequences of ingesting them. Through computational analysis of gut bacterial proteins, we identified an enrichment of prion-like sequences in Helicobacter pylori. Based on these findings, we rationally designed a set of synthetic prion-like sequences that form amyloid fibrils, interfere with amyloid-beta-peptide aggregation, and trigger prion propagation when introduced in the yeast Sup35 model. When C. elegans were fed bacteria expressing these prion-like proteins, they lost associative memory and exhibited increased lipid oxidation. These data suggest a link between memory impairment, the conformational state of aggregates, and oxidative stress. Overall, this work supports gut microbiota as a reservoir of exogenous prion-like sequences, especially H. pylori, and the gut as an entry point for molecules capable of triggering cognitive dysfunction.},
}
@article {pmid40425685,
year = {2025},
author = {Sohrabi, R and Mousavi, SN and Shapouri, R and Nasiri, Z and Heidarzadeh, S and Shokri, R},
title = {The gut dysbiosis of mothers with gestational diabetes and its correlation with diet.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {18566},
pmid = {40425685},
issn = {2045-2322},
mesh = {Humans ; Female ; *Diabetes, Gestational/microbiology ; *Dysbiosis/microbiology ; Pregnancy ; Adult ; *Gastrointestinal Microbiome ; Case-Control Studies ; *Diet ; Young Adult ; Adolescent ; Iran ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The gut dysbiosis has been observed in gestational diabetes mellitus (GDM). However, changes in bacterial population are different among various countries due to genetic, environmental, and dietary differences. We compared the gut dominant phylum and some genus in GDM versus normo-glycemic pregnant in Iranian population, considering dietary intake. In this case-control study, 50 women diagnosed with GDM and 50 healthy pregnant, aged 18-35 yrs, during spring and summer, were participated. GDM was diagnosed based on the International Association of Diabetes and Pregnancy Groups criteria. The bacterial populations were determined based on 16SrRNA gene expression. Actinomycetota (p = 0.02), and Bifidobacterium spp. (p = 0.001) was significantly higher in the gut of healthy mothers than the GDM. However, bacteroides was significantly higher in the gut of GDM mothers than the healthies (p = 0.02). Daily calorie intake showed a negative correlation with population of Bacteroidota (p = 0.04) and Actinomycetota (p = 0.009), but dietary carbohydrate and fat showed a positive correlation. Increase in dietary intake of mono- and poly-unsaturated fatty acids (MUFAs and PUFAs) was associated with higher Bacteroidota in the gut (p = 0.02 and p = 0.04). However, dietary cholesterol showed a negative correlation with population of Bacteroidota and Bifidobacterium spp. (p = 0.003 and p = 0.02). GDM was correlated with the gut dysbiosis. Daily calorie and cholesterol intake was positively associated with dysbiosis. However total intake of carbohydrates, MUFAs and PUFAs showed a protective effect.},
}
@article {pmid40425571,
year = {2025},
author = {Bianco, DM and De Maio, F},
title = {Applying the theory of broken windows to microbiome studies.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {89},
pmid = {40425571},
issn = {2055-5008},
}
@article {pmid40425098,
year = {2025},
author = {Ye, Z and Gao, Y and Yuan, J and Chen, F and Xu, P and Liu, W},
title = {The Role of Gut Microbiota in Modulating Brain Structure and Psychiatric Disorders: A Mendelian Randomization Study.},
journal = {NeuroImage},
volume = {},
number = {},
pages = {121292},
doi = {10.1016/j.neuroimage.2025.121292},
pmid = {40425098},
issn = {1095-9572},
abstract = {The influence of the gut microbiome on the human brain, especially its associations with psychiatric disorders, has emerged as a focal area in contemporary neuroscience and psychiatry research. In this study, we employed a mediation Mendelian randomization approach to delve into the potential causal relationships between gut microbiota and psychiatric disorders, with a focus on the mediating role of brain structural changes. We harnessed genetic data from large - scale genome - wide association studies to analyze how 196 gut microbiota taxa affect ten psychiatric disorders via alterations in 3,143 brain structures. Our key findings revealed significant bidirectional causal relationships. In the gut microbiota - brain structure relationship, certain gut microbiota taxa, such as Bacteroides and Marvinbryantia, were associated with changes in brain activity and white matter integrity respectively. Conversely, brain structures like the right hippocampus and left superior cerebellar peduncle influenced gut microbiota composition. Regarding gut microbiota and psychiatric disorders, we identified numerous associations. For example, the genus Prevotellaceae was significantly associated with an increased risk of Autism Spectrum Disorder, while Ruminococcaceae UCG005 showed a protective effect. In Panic Disorder, Alistipes was positively associated, and for Schizophrenia, both protective (Barnesiella) and risk - associated (Phascolarctobacterium) genera were found. Moreover, through mediation analysis, we found that brain structures mediated the effects of gut microbiota on five psychiatric disorders, including bipolar disorder and anorexia nervosa. In these cases, the influence of gut microbiota on the disorders was fully transmitted through changes in brain structure. Overall, our research clarifies the role of the microbiota - gut - brain axis in mental health. It offers a new perspective on how intestinal microbes impact brain physiology and psychiatric pathology. These findings not only deepen our understanding of the biological interactions between the gut and brain but also suggest that targeted gut microbiota modifications could be novel therapeutic strategies for mental health disorders.},
}
@article {pmid40425058,
year = {2025},
author = {Ray, D and Bose, P and Mukherjee, S and Roy, S and Kaity, S},
title = {Recent drug delivery systems targeting the gut-brain-microbiome axis for the management of chronic diseases.},
journal = {International journal of pharmaceutics},
volume = {},
number = {},
pages = {125776},
doi = {10.1016/j.ijpharm.2025.125776},
pmid = {40425058},
issn = {1873-3476},
abstract = {In recent years, the study of microorganisms and the brain has become increasingly connected. The gut-brain-microbiome axis (GBMA), a bi-directional communication system, is the key part of how the body's bacteria and the brain interact. This system can influence the brain and behaviour. Changes in this relationship have been linked to various mental and physical health conditions. The immune system, tryptophan metabolism, the vagus nerve, and the enteric nervous system all facilitate connections between the gut and brain. Microbes produce Peptidoglycans, branched-chain amino acids, and short-chain fatty acids, which are involved in this communication. Studies suggest the gut microbiome may be involved in conditions like autism, anxiety, obesity, schizophrenia, Parkinson's disease, and Alzheimer's disease. Researchers are exploring the gut-brain connection to cure a variety of disorders, such as neurological disorders, cancers, metabolic problems, and liver diseases. Developing novel drug delivery systems is a key focus in GBMA for therapeutic targeting at various disease pathways. Notable platforms attracting significant interest include silica nanoparticle-based delivery systems for probiotic spores, composite hydrogels formulated from protein isolates and citrus pectin, and biomimetic nanosystems designed for targeted therapeutic delivery. This review summarizes different methods of delivering drugs and using dietary interventions to target the GBMA and treat these conditions in a less invasive way. By understanding how the gut and brain communicate, scientists aim to develop new and more effective therapies for these complex chronic diseases.},
}
@article {pmid40425055,
year = {2025},
author = {Ganamurali, N and Sabarathinam, S},
title = {Microbial Modulation of Digoxin Bioavailability: A Pharmacomicrobiome Perspective on Eggerthella lenta's Role in Steroid-Like Drug Metabolism and Precision Therapeutics.},
journal = {The Journal of steroid biochemistry and molecular biology},
volume = {},
number = {},
pages = {106792},
doi = {10.1016/j.jsbmb.2025.106792},
pmid = {40425055},
issn = {1879-1220},
abstract = {Digoxin is a cardiac glycoside used to treat heart failure and atrial fibrillation, but its narrow therapeutic index makes precise dosing critical. The effectiveness of digoxin is influenced by individual variations in drug metabolism, with recent studies showing that gut microbiota, particularly Eggerthella lenta (E. lenta), plays a key role. E. lenta can convert digoxin into its inactive form, dihydrodigoxin, potentially reducing its therapeutic efficacy. This paper explores how E. lenta affects the biotransformation of digoxin and other drugs like L-dopa and resveratrol. The aim is to investigate how the presence of E. lenta in the gut influences drug metabolism and therapeutic outcomes. The review also examines the broader implications of microbiome-driven drug interactions and highlights the need for precision dosing strategies based on an individual's microbiome composition which is also essential for patients with high E. lenta colonization. Further research into microbiome-driven drug and sterol interactions is needed to optimize treatment strategies, ensuring personalized and effective patient care.},
}
@article {pmid40424967,
year = {2025},
author = {Kipper, JA and Wiener, M and Horvath, A and Haidacher, F and Lackner, S and Holasek, S and Ramirez-Obermayer, A and Bengesser, S and Baranyi, A and Lahousen-Luxenberger, T and Leitner, M and Butler, MI and Wagner-Skacel, J and Mörkl, S},
title = {Beyond the surface: gut microbiome and implicit learning in anorexia nervosa - A pilot study.},
journal = {Journal of psychosomatic research},
volume = {194},
number = {},
pages = {112164},
doi = {10.1016/j.jpsychores.2025.112164},
pmid = {40424967},
issn = {1879-1360},
abstract = {BACKGROUND: Anorexia nervosa (AN) is characterized by high mortality, limited treatment options, altered gut microbiome composition, and impaired feedback (FB) learning. This pilot study explores the relationship between gut microbiome composition and reduced implicit FB learning in AN.<br><br>METHODS: Sixteen female patients with AN and fourteen healthy controls (HC) completed the Weather Prediction Task to assess implicit learning (feedback and paired-associate formats). Gut microbiome composition was analyzed via Illumina sequencing, with species differences identified using linear discriminant effect size (LEfSe) analysis.<br><br>RESULTS: Patients with AN had lower FB learning scores compared to HC (p&#xa0;=&#xa0;.012), while no significant difference in the paired-associate task was found (p&#xa0;=&#xa0;.905). Better feedback learning was associated with greater gut microbiome diversity, indicated by a larger number of observed species (r&#xa0;=&#xa0;0.45, p&#xa0;=&#xa0;.013), and a higher Shannon index (r&#xa0;=&#xa0;0.39, p&#xa0;=&#xa0;.035). LEfSe analysis revealed an increased abundance of Akkermansia muciniphila in AN, while short-chain fatty acid-producing species (such as phylum Firmicutes, including Roseburia, Agathobacter and Faecalibacterium) were more prevalent in HC. Participants with higher FB learning exhibited an increase in Actinobacteria, particularly Bifidobacteria, while those with low FB learning had an increase in the Lachnospirales of the phylum Firmicutes.<br><br>CONCLUSIONS: These findings highlight the gut microbiome's potential role in implicit learning in AN, which could play an important role in the success of treatments. Future research should focus on microbiome-targeted interventions, such as probiotics, particularly Bifidobacteria, to improve gut health and implicit learning in patients with AN.},
}
@article {pmid40424958,
year = {2025},
author = {Boyner, M and Ivarsson, E and Wattrang, E and Sun, L and Wistedt, A and Wall, H},
title = {Effects of early access to feed and water in hatchers on growth performance in broiler chickens.},
journal = {Animal : an international journal of animal bioscience},
volume = {19},
number = {6},
pages = {101519},
doi = {10.1016/j.animal.2025.101519},
pmid = {40424958},
issn = {1751-732X},
abstract = {Conventional hatchers do not provide feed or water to chicks during hatch, which may negatively affect chick development, especially in early hatchlings subjected to prolonged feed deprivation due to biological variation in hatch time. This study aimed to evaluate the effects of early access to feed, water and a synbiotic product on performance, caecal microbiota development, organ development, intestinal morphology, total serum immunoglobulin (Ig) Y and antibody response to vaccination in Ross-308 chickens. A total of 330 chicks hatched in a specialised hatcher were divided into three hatch treatment groups: access to feed, water and synbiotic additive (PS); access to feed and water (PosC); no access to feed and water (NegC). Ten birds per hatch treatment were euthanised for organ sampling at placement, and the remaining 300 chicks were randomly allocated to 30 pens. All chicks received feed and water, and half the chicks in each treatment group received the synbiotic additive for 3 consecutive days (giving three hatching treatments and two postplacement treatments). All chicks were vaccinated against avian pneumovirus (APV) at 10 days of age. Blood sampling was performed weekly on three focal birds per pen for analysis of total serum IgY and antibodies to APV. Organ sampling was performed on days 11 and 32. Feed intake (FI) and BW were recorded weekly. The NegC group exhibited reduced early growth and lower FI throughout the study. At 25 days, they also demonstrated an inferior feed conversion ratio (FCR) compared with the other groups. At 4 and 25 days chickens that did not receive any postplacement treatment, None had superior FCR compared to those receiving PS also postplacement. There was also an effect of postplacement treatment where the None group weighed more compared to the PS group on almost all occasions. The NegC group had higher concentrations of IgY in serum compared to the PosC group at 3 days of age, an effect that remained a tendency until 25 days of age. No differences between treatments were found for antibody responses to APV vaccination. Some differences in relative weights of digestive organs between hatching groups were detected at the end of study, while no persistent effects on caecal microbiota composition were observed. In conclusion, delayed access to feed and water had adverse effects on productivity traits, lasting throughout the study. These findings warrant further validation in a practical context with higher stocking densities and pathogen loads.},
}
@article {pmid40424934,
year = {2025},
author = {Fan, Y and Chen, Y and Yang, H and Chen, N and Gu, X and Feng, X and Fang, C and Yin, Y and Deng, H and Dai, L},
title = {Carvacrol attenuates mucosal barrier impairment and tumorigenesis by regulating gut microbiome.},
journal = {Translational oncology},
volume = {58},
number = {},
pages = {102431},
doi = {10.1016/j.tranon.2025.102431},
pmid = {40424934},
issn = {1936-5233},
abstract = {Colitis-associated colorectal cancer (CAC), which stems from inflammatory bowel disease (IBD), exhibits a high mortality rate. Chronic inflammation can drive the development of colorectal cancer via diverse mechanisms; however, proteomic-level studies in this regard are currently scarce. The chemical drugs conventionally employed for treating IBD carry significant side effects, accentuating the exigency for novel therapeutic agents. We focused on carvacrol, a traditional Chinese medicine-derived monoterpene phenol with anti-inflammatory and antioxidant traits, though its role in colitis and CAC was unclear. Employing TMT-based proteomics, we identified the oxidative stress pathway as crucial in CAC, with ALB, ADAM10, and APCDD1 (hub genes) being vital. Using DSS and AOM/DSS mouse models, carvacrol significantly restored colonic length (p < 0.01) and re-established key tight junction proteins like ZO-1. It also downregulated mRNA levels of inflammatory mediators such as iNOS and IL-6. Moreover, 16S rRNA sequencing and fluorescence in situ hybridization (FISH) assays indicated that the potential mechanism might be ascribed to carvacrol's modulation of the abundance of specific microbiota, such as Lactobacillus, Escherichia coli/Shigella, and Lachnoclostridium. In subsequent investigations, we ascertained that carvacrol exerted remarkable efficacy in the AOM/DSS models, as it markedly reduced the number of colonic tumors (p < 0.05) and concurrently suppressed the disease activity index scores (p < 0.05). These results jointly suggest its prospective role in thwarting the progression of colitis-associated colorectal cancer. Collectively, our study substantiates that carvacrol efficiently safeguards the mucosal barrier and curbs tumorigenesis, potentially via the modulation of gut microbiota.},
}
@article {pmid40424880,
year = {2025},
author = {Insawake, K and Songserm, T and Songserm, O and Rattanakreetakul, C and Theapparat, Y and Adeyemi, KD and Rassmidatta, K and Ruangpanit, Y},
title = {Influence of phytochemicals on growth performance, gut morphology and ceca microbiome in broilers fed aflatoxin-contaminated diet and raised under high stocking density and heat stress.},
journal = {Poultry science},
volume = {104},
number = {8},
pages = {105293},
doi = {10.1016/j.psj.2025.105293},
pmid = {40424880},
issn = {1525-3171},
abstract = {This study evaluated the effects of phytochemicals on growth performance, immune response, gut morphology, and cecal microbiome of broilers fed an aflatoxin-contaminated diet under high stocking density and heat stress. A total of 2,800 one-day-old male Ross 308 broiler chicks were raised at 18 birds/m[2] during the summer. The birds were assigned to seven dietary treatments: (1) corn-soybean meal basal diet (CON), (2) CON + 50 ppb aflatoxin (AFT), (3) AFT + 50 ppm bacitracin (BCT), (4) AFT + 300 ppm flavanone (FVN), (5) AFT + 80 ppm isoquinoline alkaloids (IQA), (6) AFT + FVN (1-10 days) and IQA (11-37 days) (FVN-IQA), and (7) AFT + IQA (1-10 days) and FVN (11-37 days) (IQA-FVN) for 37 days. The heat stress index exceeded 160 for most of the experimental period. Feed efficiency was significantly lower in the AFT group than in the CON, FVN, IQA, and combination groups, while the BCT group showed no significant difference from others. The heterophil-to-lymphocyte ratio was higher in the AFT group than in the CON, IQA, FVN-IQA, and IQA-FVN groups. The AFT group exhibited higher interleukin-6 levels than other groups. Serum malondialdehyde was lower in the CON, FVN, and IQA-FVN groups than in the AFT group. Duodenal and jejunal villi height and villi height-to-crypt depth ratio were reduced in the AFT group. The AFT group showed reduced α-diversity, evaluated by Chao1 and Shannon indices. Treatment groups significantly affected β-diversity and microbiota composition at the phylum, family, and species levels. Compared to the CON group, AFT altered 125 metabolic pathways, while BCT, FVN, IQA, FVN-IQA, and IQA-FVN altered 347, 91, 38, 153, and 396 metabolic pathways, respectively, relative to the AFT group. Exposure to 50 ppb aflatoxin under high stocking density and heat stress impaired feed efficiency, immune status, and gut health in broilers. Supplementation with FVN, IQA, or their combinations mitigated these effects, with the combinations showing the greatest efficacy.},
}
@article {pmid40424732,
year = {2025},
author = {Zancan, V and Nasello, M and Diamant, S and Marconi, M and Bigi, R and Reniè, R and Buscarinu, MC and Mechelli, R and Ristori, G and Salvetti, M and Bellucci, G},
title = {Influence of oral and skin microbiota on multiple sclerosis risk and severity: A mendelian randomization analysis.},
journal = {Multiple sclerosis and related disorders},
volume = {100},
number = {},
pages = {106535},
doi = {10.1016/j.msard.2025.106535},
pmid = {40424732},
issn = {2211-0356},
abstract = {Recent research on the impact of gut microbiota on multiple sclerosis (MS) has been extensive; however, the role of microbial composition in other body interfaces, such as the mouth and the skin, has received much less attention. In a first step towards addressing this gap, we used Mendelian Randomization (MR), an analytical approach using genetic variants as proxies for environmental exposures to estimate the causal relationship between a risk factor and an outcome. Here, we performed a two-sample MR analysis to assess the link between oral and skin microbiome composition and both MS risk and severity. Exposure data were extracted from summary statistics of two large genome-wide association studies (GWAS) assessing the influence of host genetics on the microbiome composition of the oral cavity and skin. Outcome data derived from the largest GWAS on MS susceptibility and the recent GWAS on MS severity. After stringent instrumental variant selection, we applied inverse-variance-weighted (IVW) and Wald's ratio as primary MR methods, MR EGGER to control for horizontal pleiotropy, and checked directionality through Steiger's test. We found that the relative abundance of Veillonella genus in the skin may enhance MS risk, while no significant association between oral composition and MS susceptibility emerged. Furthermore, we found the Gammaproteobacteria class in the skin is associated with MS severity. We also identified suggestive, protective signals from different oral microbial strains (Bacilli class, Porphyromonas genus, Proteobacteria phylum and Veillonella dispar species). Overall, our findings provide preliminary evidence supporting the hypothesis that skin microbiota might contribute to MS risk, and both oral and skin microbial composition could affect disease severity, broadening the relevance of dysbiosis beyond the gut in MS etiopathogenesis.},
}
@article {pmid40424724,
year = {2025},
author = {Duan, R and Zhang, Y and Dai, Q and Yang, L and Yang, H and Meng, F and Hu, W and Zhang, P},
title = {Phanerochaete chrysosporium reduces heavy metal uptake in rice by affecting rhizosphere microbes and root metabolism.},
journal = {Ecotoxicology and environmental safety},
volume = {299},
number = {},
pages = {118403},
doi = {10.1016/j.ecoenv.2025.118403},
pmid = {40424724},
issn = {1090-2414},
abstract = {The addition of functional microorganisms is a common approach for remediating farmland contaminated with heavy metals, but the mechanisms underlying their reduction of crop absorption of these metals require further investigation. Here, the effect of adding Phanerochaete chrysosporium (PC) on the accumulation of heavy metals, including antimony (Sb), arsenic (As), chromium (Cr), lead (Pb) and zinc (Zn), in rice was investigated, and the possible mechanisms behind these effects were explored. The results revealed that PC treatment significantly decreased the concentrations of Sb, As, Cr, Pb and Zn in rice grains, while increasing the abundance of four beneficial bacterial genera, including Mycobacterium, Desulfovirga, Methylosarcina, and Ferruginibacter. Ultra-performance liquid chromatography-mass spectrometry (UPLC-MS) analysis showed that adding PC significantly altered the concentrations of root metabolites, including organic acids, choline, and amino acids. The affected metabolic pathways were mainly concentrated in four pathways: (1) histidine metabolism, (2) pyrimidine metabolism, (3) alanine, aspartate, and glutamate metabolism, and (4) glycine, serine, and threonine metabolism. These findings suggest that PC reduces the uptake of heavy metals in rice by altering root metabolism and the composition of the rhizosphere microbiome, providing valuable insights for the remediation of farmland contaminated with heavy metals.},
}
@article {pmid40424714,
year = {2025},
author = {Yang, X and Guo, R and Tang, Z and Wang, D and Li, H and Huang, J and Xia, L and Lin, X and Huang, K and Yu, K},
title = {Compound Chinese herbal medicine improves immune function and alters intestinal microbiome composition of Hoplobatrachus rugulosus.},
journal = {Comparative biochemistry and physiology. Part D, Genomics &amp; proteomics},
volume = {55},
number = {},
pages = {101525},
doi = {10.1016/j.cbd.2025.101525},
pmid = {40424714},
issn = {1878-0407},
abstract = {BACKGROUND: The tiger frog (Hoplobatrachus rugulosus) is an economically important species extensively farmed in southern China. However, high-density farming is frequently challenged by infectious diseases such as ascites disease, red leg syndrome, and hepatomegaly disease.<br><br>OBJECTIVE: This study aims to develop and evaluate a compounded herbal medicine (CHM, composed of Taraxacum mongolicum Hand-Mazz., Canarium album (Lour.) Raeusch, Thlaspi arvense Linn., Metaplexis japonica (Thunb.) Makino, and seed of Vitis vinifera L.) for disease prevention in frog aquaculture.<br><br>METHODS: UPLC-MS/MS was performed to identify and analyze the pharmaceutical constituents of the CHM. Frogs were fed with diets containing 0&#xa0;% (Control) or graded levels of CHM (0.25&#xa0;%, 0.5&#xa0;%, 0.75&#xa0;%, 1&#xa0;%) under high-density farming conditions for 80&#xa0;days. Growth performance, physiology, histopathology and immune parameters were assessed. Subsequently, hepatic protein alterations were explored via iTRAQ-based proteomics, and gut microbial composition was evaluated using 16S rDNA sequencing.<br><br>RESULTS: A total of 64 bioactive compounds were identified in the CHM. Supplementation of CHM significantly improved growth performance and survival rate, and reduced feed conversion rate. CHM enhanced gut amylase and lipase activities, serum SOD and CAT activities, and decrease serum ASL, ALT, T-CHO, TG levels. Additionally, CHM increased serum immune indicators (IgG, IgM, LZM, ACP, and AKP) and levels of pro-inflammatory factors (IL-6, IL-8, and TNF-&#x3b1;). Proteomic analysis revealed 89 differentially abundant proteins between the CHM1 and Control, primarily associated with pathways related to immune system and infectious diseases: bacterial. Although no significant differences were detected in OTU richness and &#x3b1;-diversity among groups, 1&#xa0;% CHM supplementation markedly altered gut microbial composition, characterized by increased abundances of Firmicutes and Turicibacter, as well as higher Firmicutes/Bacteroidetes ratio. Functional predictions based on KEGG and COG analyses revealed the alterations of amino acid, lipid, and carbohydrate metabolism, particularly in the CHM1 group.<br><br>CONCLUSION: Dietary supplementation with 1&#xa0;% CHM regulates gut microbiota and hepatic protein expression, promoting growth and enhancing immune function in H. rugulosus. These findings suggest that CHM is a promising feed additive and alternative immunopotentiator for sustainable frog aquaculture.},
}
@article {pmid40424651,
year = {2025},
author = {Xia, Y and Zhou, X and Cai, P and Yan, R and Ocansey, DKW and Mao, F},
title = {Flos lonicerae polysaccharide alleviates inflammatory bowel disease by improving intestinal microbiota and inhibiting oxidative stress and the NF-κB pathway.},
journal = {International immunopharmacology},
volume = {159},
number = {},
pages = {114956},
doi = {10.1016/j.intimp.2025.114956},
pmid = {40424651},
issn = {1878-1705},
abstract = {Inflammatory bowel disease (IBD) is a chronic disease that is increasingly being recognized globally. IBD is difficult to cure and is in urgent need of more treatment options. Flos lonicerae polysaccharide (FLP) is an effective component extracted from traditional Chinese medicine flos lonicerae, and previous studies have demonstrated its therapeutic potential in treating inflammatory diseases such as rhinitis and dermatitis, but there has been few in-depth research on their regulation of IBD repair mechanisms. This study focuses on the regulatory mechanisms of FLP on the structure of the gut microbiome and immune homeostasis. Results have demonstrated that treatment with FLP effectively attenuates weight loss, reduces the release of proinflammatory cytokines, and restores spleen and colon structures in mice. These effects are achieved through modifying the intestinal microbial community structure, increasing beneficial bacteria, and decreasing harmful bacteria. Furthermore, FLP significantly impacts the levels of Coenzyme Q2, a lipid closely associated with mitochondrial function. This modulation possibly regulates oxidative stress levels and the NF-κB pathway, thereby contributing to the alleviation of IBD. Therefore, FLP as a natural product with multiple biological activities, exhibits potential therapeutic effects in regulating intestinal microbiota, reducing oxidative stress, and inhibiting the NF-κB pathway, suggesting it may serve as a novel strategy for IBD treatment.},
}
@article {pmid40424276,
year = {2025},
author = {Goldman, M and Zhao, C and Pollard, KS},
title = {Improved detection of microbiome-disease associations via population structure-aware generalized linear mixed effects models (microSLAM).},
journal = {PLoS computational biology},
volume = {21},
number = {5},
pages = {e1012277},
doi = {10.1371/journal.pcbi.1012277},
pmid = {40424276},
issn = {1553-7358},
abstract = {Microbiome association studies typically link host disease or other traits to summary statistics measured in metagenomics data, such as diversity or taxonomic composition. But identifying disease-associated species based on their relative abundance does not provide insight into why these microbes act as disease markers, and it overlooks cases where disease risk is related to specific strains with unique biological functions. To bridge this knowledge gap, we developed microSLAM, a mixed-effects model and an R package that performs association tests that connect host traits to the presence/absence of genes within each microbiome species, while accounting for strain genetic relatedness across hosts. Traits can be quantitative or binary (such as case/control). MicroSLAM is fit in three steps for each species. The first step estimates population structure across hosts. Step two calculates the association between population structure and the trait, enabling detection of species for which a subset of related strains confer risk. To identify specific genes whose presence/absence across diverse strains is associated with the trait, step three models the trait as a function of gene occurrence plus random effects estimated from step two. Applying microSLAM to 710 gut metagenomes from inflammatory bowel disease (IBD) samples, we discovered 56 species whose population structure correlates with IBD, meaning that different lineages are found in cases versus controls. After controlling for population structure, 20 species had genes significantly associated with IBD. Twenty-one of these genes were more common in IBD patients, while 32 genes were enriched in healthy controls, including a seven-gene operon in Faecalibacterium prausnitzii that is involved in utilization of fructoselysine from the gut environment. The vast majority of species detected by microSLAM were not significantly associated with IBD using standard relative abundance tests. These findings highlight the importance of accounting for within-species genetic variation in microbiome studies.},
}
@article {pmid40423982,
year = {2025},
author = {Politikos, I and Brown, S and Fein, JA and Eng, S and Casem, K and Chinapen, S and Quach, S and Scaradavou, A and Cho, C and Dahi, P and Giralt, SA and Gyurkocza, B and Hanash, AM and Jakubowski, AA and Papadopoulos, EB and Perales, MA and Ponce, DM and Shaffer, BC and Tamari, R and Young, JW and Devlin, S and Peled, JU and Barker, JN},
title = {Phase 2 trial of cyclosporine-A, mycophenolate mofetil, and tocilizumab GVHD prophylaxis in cord blood transplantation.},
journal = {Blood advances},
volume = {9},
number = {10},
pages = {2570-2584},
doi = {10.1182/bloodadvances.2024014177},
pmid = {40423982},
issn = {2473-9537},
mesh = {Humans ; *Graft vs Host Disease/prevention &amp; control/etiology ; *Antibodies, Monoclonal, Humanized/therapeutic use/administration &amp; dosage ; Middle Aged ; Adult ; *Cyclosporine/therapeutic use/administration &amp; dosage ; Female ; Male ; *Mycophenolic Acid/therapeutic use ; *Cord Blood Stem Cell Transplantation/adverse effects/methods ; *Immunosuppressive Agents/therapeutic use ; },
abstract = {Double-unit cord blood transplantation (dCBT) has been associated with high rates of progression-free survival (PFS) in adults with hematologic malignancies but also with relatively high rates of acute graft-versus-host disease (aGVHD). We conducted a single-arm, phase 2 clinical trial that investigated the addition of tocilizumab, an interleukin-6 receptor blocker, to cyclosporine-A (CSA) and mycophenolate mofetil (MMF) for aGVHD prophylaxis after intermediate-intensity dCBT. A total of 45 patients (median age, 47 years; range, 27-60 years; 80% acute leukemia; median hematopoietic cell transplant-comorbidity index, 2) were enrolled from March 2018 to March 2021. Transplant outcomes were compared with 39 previous CSA and MMF dCBT controls with similar inclusion criteria. Tocilizumab recipients had less pre-engraftment syndrome (38%; 95% confidence interval [CI], 24-52 vs 72%; 95% CI, 54-84; P < .001) but inferior day 45 neutrophil engraftment (93%; median, 25.5 days vs 97%; median, 22 days; P = .009]. The primary end point of day 100 grade 2 to 4 aGVHD was no different between groups (71%; 95% CI, 55-82 with tocilizumab vs 82%; 95% CI, 65-91; P = .11). However, there was a trend toward a lower day 100 incidence of stage 1 to 4 lower gastrointestinal aGVHD with tocilizumab (16%; 95% CI, 7-28 vs 33%; 95% CI, 19-48; P = .059). There were no significant differences in the 3-year incidences of relapse, transplant-related mortality, PFS, or overall survival between the groups. Tocilizumab recipients exhibited a distinct pattern of gut microbiome disruption. In summary, tocilizumab-based GVHD prophylaxis delayed neutrophil recovery without a significant reduction in aGVHD and had no survival benefit after dCBT. Investigation of alternative strategies to prevent severe aGVHD after dCBT is warranted. This trial was registered at www.clinicaltrials.gov as #NCT03434730.},
}
@article {pmid40423900,
year = {2025},
author = {Yang, W and Xu, X and Xie, R and Lin, J and Hou, Z and Xin, Z and Cao, X and Shi, T},
title = {Tryptophan metabolites exert potential therapeutic activity in graves' orbitopathy by ameliorating orbital fibroblasts inflammation and proliferation.},
journal = {Journal of endocrinological investigation},
volume = {},
number = {},
pages = {},
pmid = {40423900},
issn = {1720-8386},
support = {7232231//Natural Science Foundation of Beijing Municipality/ ; 7242181//Natural Science Foundation of Beijing Municipality/ ; 82470852//National Natural Science Foundation of China/ ; 82200937//National Natural Science Foundation of China/ ; 82270897//National Natural Science Foundation of China/ ; 82070850//National Natural Science Foundation of China/ ; },
abstract = {PURPOSE: Graves' orbitopathy (GO) is a sight-threatening organ-specific autoimmune disease with complicated pathogenesis. Gut microbiota-derived tryptophan (Trp) metabolites play important roles in immune-related diseases, but their role in GO remains unknown.<br><br>METHODS: Trp metabolism-associated gut flora was analyzed by 16&#xa0;S sequencing in GO patients and controls. Serum metabolomics profiling was performed to assess Trp metabolic pathway. Trp metabolites levels were measured by ELISA in 401 serum samples from a case-control study, and their effects on inflammation and proliferation in orbital fibroblasts were evaluated in vitro.<br><br>RESULTS: Trp metabolism-associated gut flora, including phylum Firmicutes and genus Anaerostipes, were significantly down-regulated in GO patients. Serum metabolomics revealed significant enrichment of Trp metabolic pathway in both GO and Graves' disease (GD) groups. Serum levels of indolepropionic acid (IPA), indole-3-lactate (ILA), and indoleacetic acid (IAA) were significantly decreased in both GD and GO patients compared to controls, with IAA levels further reduced in GO compared to GD patients. Notably, active GO patients had significantly lower IAA levels compared to inactive ones. Moreover, the levels of IAA were negatively correlated with clinical activity score and serum thyrotropin receptor antibody (TRAb) in GO patients. In vitro, IPA, ILA, and IAA mitigated TNF&#x3b1;-induced inflammation and proliferation in orbital fibroblasts by suppressing the Akt signaling pathway.<br><br>CONCLUSION: Trp metabolites IAA maybe a novel biomarker for GO progression. And IPA, ILA and IAA may play a protective role in GO by regulating inflammation and proliferation in orbital fibroblasts, suggesting their potential as therapeutic targets for GO treatment.},
}
@article {pmid40423805,
year = {2025},
author = {Meehan, DE and O'Toole, PW},
title = {A Review of Diet and Foraged Pollen Interactions with the Honeybee Gut Microbiome.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {54},
pmid = {40423805},
issn = {1432-184X},
support = {GOIPG/2024/5035//Taighde &#xc9;ireann/ ; 12/RC/2273_P2/SFI_/Science Foundation Ireland/Ireland ; },
mesh = {Bees/microbiology/physiology ; Animals ; *Gastrointestinal Microbiome ; *Pollen/metabolism ; *Diet ; },
abstract = {The honeybee Apis mellifera is a globally vital pollinator for flowering plants and crops, but it is currently facing mounting threats to survival due to habitat anthropization, emerging pathogens, and climate change. Over the past decade, increasing research efforts to understand and combat these challenges have led to an exploration of the honeybee gut microbiome-a relatively simple and highly conserved community of commensals which has a range of effects on the host. Researchers have now unravelled the main functional roles of this microbiome which include innate immune system stimulation, metabolism of dietary compounds, and mediation of host development and behaviour. Key amongst these is its role in aiding nutrition through the metabolism of complex carbohydrates and by degradation of otherwise indigestible pollen compounds. Increasingly, research is indicating that a diverse and high-quality pollen diet is key to maintaining healthy colonies and a stable microbiome. However, colonies can struggle to meet these dietary needs, particularly if they are located in anthropized ecosystems. Disruptions to honeybee diets or a reduction in the availability of diverse foraging options can significantly alter the composition of the microbiome, shifting it towards an abnormal state that leaves the honeybee more vulnerable to infection. Seasonal changes, primarily the overwintering period, also induce shifts in microbiome composition and are periods of time when a colony is particularly vulnerable to pathogenic infection. A comprehensive understanding of the effect these variables have on both microbiome composition and colony health is key to tackling the unprecedented environmental challenges that honeybees now face. This review summarises recent research which has elucidated the functional role of the gut microbiome in metabolism and how the composition of this bacterial community can alter due to seasonal change, anthropized landscapes, and dietary shifts. Finally, we also discuss recent studies investigating the effect that dietary supplementation has on the gut microbiome and the application of probiotic candidates for improving colony resilience and strength.},
}
@article {pmid40423653,
year = {2025},
author = {Sun, X and Wang, S and Lin, Z and Chen, Z and Huang, W and Kong, T and Huang, D and Li, B and Zhang, H and Sun, W},
title = {Plastic Biodegradation by Sediment Microbial Populations under Denitrifying Conditions.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c12187},
pmid = {40423653},
issn = {1520-5851},
abstract = {Biodegradation is critical for eliminating plastic contaminants from environments, and understanding its mechanisms under in situ conditions is crucial. The plastic biodegradation process in sediments, a major reservoir of plastic contamination with reduced redox conditions, remains elusive. This study compared the plastisphere communities and metabolic potentials of typical polyethylene (PE) contaminants collected from the Pearl River Estuary to their counterparts in the surrounding sediments. The results revealed a distinct plastisphere community composition, with the consistent enrichment of a group of core plastisphere populations compared to those of the sediments. Functional genes related to both potential aerobic and anaerobic PE biodegradation were encoded by the core plastisphere populations. Microcosm incubations were performed to assess the PE biodegradation potentials under denitrifying conditions. The results demonstrated that the polyethylene (PE) mineralization efficiencies were comparable under aerobic and denitrifying conditions through incubations with [13]C-PE. Development of functional groups on PE surfaces and the reduction in molecular weights further supported PE biodegradation under denitrifying conditions. The elevated laccase and lignin peroxidase activities implied their potential contribution to PE depolymerization under denitrifying conditions. Together, the sediment plastisphere microbiome holds the potential for plastic degradation under denitrifying conditions, which should be considered when assessing the fate of plastic contaminants.},
}
@article {pmid40423639,
year = {2025},
author = {Liu, Y and Yu, Y and Chen, Y and Zhuang, J and Sun, C},
title = {Tumor Immunosenescence Driven by Chronic Inflammation: Mechanisms, Microenvironment Remodeling and Therapeutic Strategies.},
journal = {Aging and disease},
volume = {},
number = {},
pages = {},
doi = {10.14336/AD.2025.0471},
pmid = {40423639},
issn = {2152-5250},
abstract = {The development of malignant tumors, as one of the most challenging public health issues today, is closely related to the interaction of chronic inflammation and immunosenescence. This review systematically analyzes the multidimensional mechanism of chronic inflammation driving immunosenescence. Chronic inflammation triggers immunosuppression and drives immunosenescence through interactions with inflammatory signals, the senescence-associated secretory phenotype (SASP), metabolic reprogramming, and microbiome. These processes remodel the tumor microenvironment via a multidimensional interaction network, which significantly weakens the anti-tumor immune response and accelerates tumor progression. This review proposes targeting strategies focusing on source intervention, SASP network blockade, and combination therapy optimization, as well as precise regulation with the help of novel technologies to break through the limitations of traditional immune checkpoint inhibition and provide new breakthroughs for overcoming tumor immune escape.},
}
@article {pmid40423631,
year = {2025},
author = {Morgado-Cáceres, P and Huerta, H and Bergman, C and Figueroa, R and Farias, P and Quiroz, G and Woehlbier, U and Mella, K and Díaz-Rivera, O and Linsambarth, S and Calderón-Romero, P and Court, FA and Sepulveda, D and Sauma, D and Luz-Crawford, P and Vargas, AA and Gonzalez-Seguel, C and Cárdenas, JC and Lovy, A},
title = {Postbiotic Parabacteroides Distasonis Supplementation Enhances Intestinal and Skeletal Muscle Function in Aged Mice.},
journal = {Aging and disease},
volume = {},
number = {},
pages = {},
doi = {10.14336/AD.2025.0188},
pmid = {40423631},
issn = {2152-5250},
abstract = {Parabacteroides distasonis (Pd), a core member of the human gut microbiota, is enriched in centenarians, suggesting a potential role in promoting organismal resilience. While Pd supplementation has been shown to alleviate cancer and inflammatory diseases, its ability to mitigate the decline associated with aging remains unexplored. Here, we demonstrate that postbiotic Pd supplementation induces multiple beneficial effects in 18- and 26-month-old mice following three months of treatment. Pd-treated mice exhibit lower blood glucose levels and increased ketone body production. In the gut, Pd reduces colon shortening observed in aged control mice and decreases the inflammatory mediator NFκB, in the colonic mucosa. Microbiome analysis further reveals enhanced gut microbiota diversity in Pd-supplemented mice. Additionally, FITC-dextran permeability assays indicate improved intestinal barrier function. Cell culture experiments in HCT116 colon cell line show that Pd reduces oxygen consumption and promotes mitochondrial networking, accompanied by upregulation of PGC1α and CHOP, suggesting a mitohormetic response. Beyond metabolic and gut-related benefits, Pd supplementation enhances skeletal muscle strength in both 18- and 26-month-old mice. Proteomic analysis of gastrocnemius muscle reveals that Pd increases the expression of mitochondrial proteins associated with mitochondrial fitness and survival. Notably, Pd-supplemented mice challenged with a high-fat diet gain weight at a slower rate, while maintaining better skeletal muscle coordination and strength. In summary, our findings suggest that postbiotic Pd supplementation enhances metabolic health, reduces inflammation, improves mitochondrial function, and preserves muscle strength in aged mice. These results position Pd as a promising therapeutic tool for promoting healthy aging and combating aging-related diseases.},
}
@article {pmid40433272,
year = {2024},
author = {van Bosse, HJP},
title = {Bone equilibria and disruptions.},
journal = {Journal of the Pediatric Orthopaedic Society of North America},
volume = {7},
number = {},
pages = {100059},
pmid = {40433272},
issn = {2768-2765},
abstract = {UNLABELLED: Osteoporosis is considered a disease of adulthood, but there is increasing recognition that poor bone density during childhood can have effects decades later. To understand the pathogenesis of osteoporosis, it is important to understand normal bone maintenance and remodeling, since disruptions of these processes lead to pathologic bone. Bone maintenance is a complex and highly regulated system, consisting of several homeostatic equilibria. This article highlights three homeostatic systems. The first, the interplay between the differentiation of osteoblasts from mesenchymal stem cells and osteoclasts from hematopoietic stem cells, is the most important. Estrogen has a direct effect on the system, and its absence is pivotal. The second is a lesser-known homeostasis that functions between bone and bone marrow adipose tissue, which can insidiously drive osteoporosis. Bone marrow adipose tissue acts as a regulator of bone metabolism, negatively affecting bone formation. The third homeostatic system covered is the microbiota-gut-bone axis, where the make-up of the gut microbiome can influence a balance between osteoblastic and osteoclastic T-cells. Understanding these systems has provided avenues of study for existing and future treatments.<br><br>KEY CONCEPTS: (1)The balance between bone formation and bone resorption is driven by factors that initiate the differentiation of mesenchymal stem cells to osteoblasts and hematopoietic stem cells to osteoclasts.(2)Bone marrow adipose tissue is formed by adipocytes that are the result of diversion of mesenchymal stem cells from the osteoblastic differentiation pathway.(3)The health of the gut microbiome has direct effects on the bone homeostatic processes.},
}
@article {pmid40423453,
year = {2025},
author = {Chi, Y and Zhang, H and Gao, J and Wan, L and Jiao, Y and Wang, H and Liao, M and Cuthbert, RN},
title = {Nanoplastics Elicit Stage-Specific Physiological, Biochemical, and Gut Microbiome Responses in a Freshwater Mussel.},
journal = {Toxics},
volume = {13},
number = {5},
pages = {},
doi = {10.3390/toxics13050374},
pmid = {40423453},
issn = {2305-6304},
support = {32471648; 32170383&#xff0c;HGKFZ08, HGKFZ04, HGKFZP009//the National Natural Science Foundation of China/ ; },
abstract = {Mussels are highly efficient filter feeders, playing a crucial role in managing eutrophication and assessing pollution. Although research on nanoplastic (NP) toxicity in marine organisms is expanding, studies on freshwater species remain limited despite freshwater ecosystems being disproportionately biodiverse and vulnerable to pollutants. Here, we quantified the effects of polystyrene nanoplastics (PS-NPs, 50 nm) at concentrations of 0, 2, 20, and 200 μg/L on different growth stages of the freshwater mussel Cristaria plicata. After a 45-day exposure, PS-NPs at concentrations ≥ 20 μg/L damaged intestinal epithelial cilia in both age groups. Exposure to 200 μg/L PS-NPs significantly increased malondialdehyde levels and decreased superoxide dismutase activity in both groups, with adults showing a significant rise in total protein content and juveniles exhibiting marked increases in respiratory and ammonia excretion rates. Additionally, PS-NP exposure significantly altered the relative abundance of gut microbial phyla, including Proteobacteria, Firmicutes, Verrucomicrobiota, and Bacteroidota, with Fusobacteriota also being affected in adults. Juveniles were more sensitive to physiological changes, whereas adults exhibited greater microbiota shifts in response to PS-NP exposure. Therefore, this study provides new insights into the stage-specific effects of PS-NPs on intestinal integrity and physiological and biochemical health in freshwater mussels, underscoring the need for targeted management strategies to protect freshwater ecosystems.},
}
@article {pmid40423333,
year = {2025},
author = {Llada, IM and Lourenco, JM and Dycus, MM and Carpenter, JM and Jarrell, ZR and Jones, DP and Suen, G and Hill, NS and Filipov, NM},
title = {Impact of Low-Level Ergot Alkaloids and Endophyte Presence in Tall Fescue Grass on the Metabolome and Microbiome of Fall-Grazing Steers.},
journal = {Toxins},
volume = {17},
number = {5},
pages = {},
doi = {10.3390/toxins17050251},
pmid = {40423333},
issn = {2072-6651},
support = {67015-31301//USDA, National Institute of Food and Agriculture (NIFA)/ ; },
mesh = {Animals ; *Ergot Alkaloids/toxicity/analysis ; *Endophytes ; Cattle ; Male ; *Metabolome ; *Epichloe/metabolism ; *Animal Feed/microbiology ; *Festuca/microbiology ; *Gastrointestinal Microbiome ; Rumen/microbiology/metabolism ; *Microbiota ; Feces/microbiology ; },
abstract = {Fescue toxicosis (FT) is a mycotoxin-related disease caused by the ingestion of tall fescue, naturally infected with the ergot alkaloid (EA)-producing endophyte Epichloë coenophiala. Some grazing on endophyte-free (E-) or non-toxic (NT), commercial endophyte-infected pastures takes place in the US as well. Earlier, we found that grazing on toxic fescue with low levels of EAs during fall affects thermoregulation, behavior, and weight gain. Building on these findings, the current study aimed to investigate how the presence of low EA-producing E+ or NT endophytes can influence animal metabolome, microbiome, and, ultimately, overall animal health. Eighteen Angus steers were placed on NT, E+, and E- fescue pastures for 28 days. Urine, rumen fluid (RF), rumen solid (RS), and feces were collected pre-exposure, and on days 2, 7, 14, 21, and 28. An untargeted high-resolution metabolomics approach was used to analyze urine and RF, while 16S rRNA-based next-generation sequencing (NGS) was used to examine RF, RS, feces, and fescue plant microbiomes. While alpha- or beta-microbiota diversity across all analyzed matrices were unaffected, there were specific effects of E+ on the relative abundance of some taxa (i.e., Prevotellaceae). Additionally, E+ grazing impacted aromatic amino acid metabolism in the urine and the metabolism of lipids in both the RF and urine. In both matrices, trace amine-related metabolic features differed markedly between E+ and the other groups. Compared to the endophyte-free group, endophyte presence, whether novel or toxic, influenced amino acid and carbohydrate metabolism, as well as unsaturated fatty acid biosynthesis. These findings suggest that low-EA-producing and non-toxic endophytes in fescue have more prominent effects on the metabolome than the microbiome, and this metabolome perturbation might be associated with decreased performance and reported physiological signs of FT.},
}
@article {pmid40423261,
year = {2025},
author = {Rotsaert, C and Minnebo, Y and Duysburgh, C and Liu, LS and Mahalak, KK and Firman, J and Mattei, LM and Moustafa, AM and Bittinger, K and Hu, W and Marzorati, M and Michiels, J and Van de Wiele, T},
title = {Digestive parameters and gut microbiota load and composition along the in vivo piglet gastrointestinal tract.},
journal = {Journal of animal science},
volume = {},
number = {},
pages = {},
doi = {10.1093/jas/skaf107},
pmid = {40423261},
issn = {1525-3163},
abstract = {The increased attention towards the role of the gut microbiome in health and disease for both animals and humans has fuelled the demand for more relevant and accurate research models. In this study, we present an overview of biochemical and microbial parameters measured throughout the digestive tract of ten TopigsNorsvin x German Piétrain piglets to better understand the in vivo dynamics of digestive and fermentative processes in different gastrointestinal segments, as pigs are suggested to be a representative animal model for the human gastrointestinal tract. Our key findings include region-specific and significantly differing (P < 0.001) pH profiles, with the stomach having the lowest pH (3.36 ± 0.72) and the ileum the highest (7.24 ± 0.18). Dry matter content also varied significantly (P < 0.001), with the stomach having the highest (27.8 ± 2.4%) and the duodenum the lowest (10.6 ± 0.7%). The average total transit time was 12 hours and 45 minutes ± 1 hour and 42 minutes. Enzyme activities (pepsin, trypsin, amylase) showed interindividual differences. Amino acid levels varied among piglets, with total concentrations averaging 7.04 x 102 ± 2.29 x 102 µg mL-1 in the duodenum, 1.19 x 103 ± 2.69 x 102 µg mL-1 in the jejunum and 9.39 x 102 ± 2.54 x 102 µg mL-1 in the ileum. Bile acid concentrations varied strongly between piglets, with high levels in the gall bladder and varying levels throughout the digestive tract. Short-chain fatty acid concentrations increased significantly (P < 0.001) along the digestive tract, with the highest levels in the large intestine. The microbial load increased consistently (P < 0.001) along the digestive tract, with the highest loads in the rectum (6.82 x 1010 ± 2.88 x 1010 cells mL-1). The highest microbial diversity was observed in the lower intestine (i.e. caecum, colon and rectum), with significant shifts in microbial community composition, especially from the ileum to the caecum. This study provides valuable insights into the digestive and microbiological parameters of the porcine gut, confirming the pig's relevance as a model for gastrointestinal research. The findings can inform the development of in vitro or ex vivo models, reducing ethical constraints of animal studies and aiding in the assessment of dietary interventions on gut health.},
}
@article {pmid40422917,
year = {2025},
author = {Hao, X and Shang, X and Zhang, Y and Hou, W and Chi, R and Pan, C and Liu, J and Deng, X and Zhang, J and Xu, T},
title = {Effects of Exercise on Gut Microbiome and Serum Metabolomics in Post-Traumatic Osteoarthritis Rats.},
journal = {Metabolites},
volume = {15},
number = {5},
pages = {},
doi = {10.3390/metabo15050341},
pmid = {40422917},
issn = {2218-1989},
support = {82272610//National Natural Science Foundation of China/ ; },
abstract = {Objective: The aim of this work is to investigate the impact of exercise on gut microbiome composition, serum metabolites, and their correlation with osteoarthritis (OA) severity. Methods: Thirty-six Sprague-Dawley (SD) rats were randomly divided into four groups: Sham rats without treadmill walking (Sham/Sed group, n = 9), Sham rats with treadmill walking 2 months (Sham/TW2M group, n = 9), PTOA rats without treadmill walking (PTOA/Sed group, n = 9), and PTOA rats with treadmill walking 2 months (PTOA/TW2M group, n = 9). The PTOA model was induced by transection of the anterior cruciate ligament (ACLT) and destabilization of the medial meniscus (DMM). Histological evaluation and micro-CT analysis were performed to observe the pathological changes in cartilage and subchondral bone, respectively. Additionally, we conducted 16S rDNA sequencing of fecal samples and untargeted metabolomic analysis using liquid chromatography-mass spectrometry (LC-MS) of serum samples to detect the alteration of gut microbiota composition and metabolites. Results: Exercise effectively mitigated OA-related pathological changes, including articular cartilage degeneration and subchondral bone loss. Moreover, 16S rDNA sequencing analysis of gut microbiome revealed a decreased abundance of Bacteroidetes (p < 0.01), Bacteroidia (p < 0.01), Rikenellaceae (p < 0.01), [Paraprevotellaceae] (p < 0.01), and Paraprevotella (p < 0.01) but an increase in Firmicutes (p < 0.01) in PTOA/TW2M group rats compared with PTOA/Sed group as a response to exercise. In addition, the results of metabolomics analysis showed that exercise treatment contributed to the upregulation of Daidzein and Anthranilic acid and downregulation of 1-Palmitoyllysophosphatidylcholine. Moreover, the correlation analysis showed that Rikenellaceae significantly positively correlated with both OARSI (r = 0.81, p < 0.01) and Mankin score (r = 0.83, p < 0.01) and negatively correlated with the serum level of Anthranilic acid (r = -0.56, p < 0.01) and Daidzein (r = -0.46, p < 0.01). Conclusions: Exercise can effectively mitigate OA through slowing down articular cartilage degeneration and subchondral bone loss, modulating gut microbiota composition, and increasing beneficial metabolites.},
}
@article {pmid40422911,
year = {2025},
author = {Lewis, N and Lagopoulos, J and Villani, A},
title = {Gut-Brain Inflammatory Pathways in Attention-Deficit/Hyperactivity Disorder: The Role and Therapeutic Potential of Diet.},
journal = {Metabolites},
volume = {15},
number = {5},
pages = {},
doi = {10.3390/metabo15050335},
pmid = {40422911},
issn = {2218-1989},
abstract = {Attention-deficit/hyperactivity disorder (ADHD) is a common childhood-onset neurodevelopmental disorder that often persists into adulthood, leading to various adverse outcomes. Its underlying pathology is multifactorial, involving neurotransmitter imbalances, gut microbiota alterations, and oxidative and inflammatory dysregulation. Diet, a key environmental modifier of gut ecology, is consistently poorer in individuals with ADHD, with multiple nutrients implicated in its pathophysiology. This review examines the role of specific nutrients such as omega-3 fatty acids, key micronutrients, and potentially harmful dietary components, as well as broader dietary patterns, particularly the Western diet and Mediterranean diet (MedDiet), in relation to ADHD symptoms. It also evaluates both whole-diet and supplement-based clinical interventions, supporting the growing recognition of nutrition as a safe and relatively affordable modifiable factor in ADHD management. Additionally, the biological mechanisms linking diet to ADHD are reviewed, highlighting strong evidence for the involvement of gut dysbiosis and inflammatory processes. Despite the well-documented antioxidant, anti-inflammatory, and microbiome benefits of the MedDiet, direct research investigating its role in ADHD remains limited. Most whole-diet approaches to date have focused on elimination diets, leaving a significant gap in understanding the potential role of the MedDiet in ADHD management. Therefore, this review outlines preliminary evidence supporting the MedDiet and its key components as modulators of ADHD-related biological pathways, indicating its potential as a therapeutic approach. However, further research is required to rigorously evaluate its clinical efficacy. Finally, the limitations of observational and interventional nutritional research in ADHD are discussed, along with recommendations for future research directions.},
}
@article {pmid40422666,
year = {2025},
author = {Gaspar, BS and Roşu, OA and Enache, RM and Manciulea Profir, M and Pavelescu, LA and Creţoiu, SM},
title = {Gut Mycobiome: Latest Findings and Current Knowledge Regarding Its Significance in Human Health and Disease.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {11},
number = {5},
pages = {},
doi = {10.3390/jof11050333},
pmid = {40422666},
issn = {2309-608X},
abstract = {The gut mycobiome, the fungal component of the gut microbiota, plays a crucial role in health and disease. Although fungi represent a small fraction of the gut ecosystem, they influence immune responses, gut homeostasis, and disease progression. The mycobiome's composition varies with age, diet, and host factors, and its imbalance has been linked to conditions such as inflammatory bowel disease (IBD) and metabolic disorders. Advances in sequencing have expanded our understanding of gut fungi, but challenges remain due to methodological limitations and high variability between individuals. Emerging therapeutic strategies, including antifungals, probiotics, fecal microbiota transplantation, and dietary interventions, show promise but require further study. This review highlights recent discoveries on the gut mycobiome, its interactions with bacteria, its role in disease, and potential clinical applications. A deeper understanding of fungal contributions to gut health will help develop targeted microbiome-based therapies.},
}
@article {pmid40422634,
year = {2025},
author = {Astuti, L and Masulili, SLC and Gunardi, I and Sulijaya, B and Soeroso, Y},
title = {Periodontal Pathogens Correlate with Rheumatoid Arthritis Disease Parameters: A Systematic Review Based on Clinical Studies.},
journal = {Dentistry journal},
volume = {13},
number = {5},
pages = {},
doi = {10.3390/dj13050214},
pmid = {40422634},
issn = {2304-6767},
abstract = {Background: Numerous studies have found higher levels of autoantibodies including anti citrullinated protein antibodies (ACPAs), anti-cyclic citrullinated peptides (aCCP), or rheumatoid factor (RF) against periodontal microorganisms in rheumatoid arthritis (RA). Objective: To evaluate the correlation between periodontal bacteria and RA disease parameters. Methods: We utilized PubMed, Scopus, ScienceDirect, and manual search databases up until March 2024 using PRISMA 2020 guidelines. The data were obtained from microbiological assays by RT-PCR/qPCR, sequencing, and serological testing of disease parameters (ACPA, aCCP, and RF) utilizing ELISA method. Results: A total of 1514 documents were discovered based on the inclusion criteria. Porphyromonas gingivalis, Aggregatibacter actinomycetemcomitans, and Prevotella_9 were associated with elevated levels of ACPA/aCCP and RF in RA with periodontitis. A positive correlation was found between Peptococcus simiae, Aminipila butyrica, Leptotrichia spp., Leptotrichia wadei, and Neisseria bacilliformis with ACPA, and Treponema sp. canine oral taxon 087 with RF. Conclusions: This study found that several oral microorganisms correlate with elevated ACPA/aCCP and RF in RA with periodontitis. Future studies of the oral microbiome and the molecular mechanisms are anticipated to discover new therapies and diagnostic methods for periodontitis and RA.},
}
@article {pmid40422281,
year = {2025},
author = {Rong, X and Zhu, L and Shu, Q},
title = {Synergistic gut microbiome-mediated degradation of Astragalus membranaceus polysaccharides and Codonopsis pilosula polysaccharides into butyric acid: a metatranscriptomic analysis.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0303924},
doi = {10.1128/spectrum.03039-24},
pmid = {40422281},
issn = {2165-0497},
abstract = {Astragalus membranaceus and Codonopsis pilosula are traditional Chinese medicines known for their tonifying effects, which are linked to the metabolism of their polysaccharide components in the gut. However, the role of gut microbiota in the degradation of these polysaccharides to butyric acid remains unclear. This study aims to investigate the in vitro degradation of polysaccharides from Astragalus membranaceus and Codonopsis pilosula by healthy mice fecal microbiota, focusing on butyric acid production and the associated microbial gene expression. We conducted an in vitro analysis of the degradation of homogeneous polysaccharides. from Astragalus membranaceus and Codonopsis pilosula using fecal microbiota cultures derived from healthy mice. The fecal microbiota was cultured with the polysaccharides for 48 hours, after which the degradation liquid was collected for butyric acid quantification and metatranscriptome analysis of the microbiota. The degradation of Astragalus membranaceus polysaccharide resulted in a significant increase in butyric acid levels compared to those produced from Codonopsis pilosula polysaccharide or fructooligosaccharide (control). Differential gene expression analysis indicated an upregulation of carbohydrate-active enzymes and genes associated with butyrate production during the degradation of Astragalus membranaceus polysaccharides. Additionally, the findings suggested that synergistic interactions between polysaccharide-degrading and butyrate-producing bacteria play a crucial role in the microbiota's response to specific polysaccharides. This study highlights the potential of Astragalus polysaccharides to enhance butyric acid production through specific gut microbiota interactions, suggesting their beneficial effects on gut health and metabolism. Further research may provide insights into the therapeutic applications of these traditional medicines in modulating gut microbiota and improving health outcomes.IMPORTANCEThis study significantly advances our understanding of the role of gut microbiota in the metabolism of traditional Chinese medicinal polysaccharides, specifically those from Astragalus membranaceus and Codonopsis pilosula. By demonstrating that Astragalus membranaceus polysaccharide enhances butyric acid production more effectively than Codonopsis pilosula polysaccharide or fructooligosaccharides, the research highlights the potential of these natural compounds in modulating gut health. The identification of upregulated carbohydrate-active enzymes and butyrate production genes provides valuable insights into the microbial mechanisms underlying polysaccharide degradation. This work not only contributes to the field of microbiome research but also supports the development of functional foods and therapeutics aimed at enhancing gut health through targeted polysaccharide consumption.},
}
@article {pmid40422223,
year = {2025},
author = {Pinco, P and Facciotti, F},
title = {Unconventional T Cells' Role in Cancer: Unlocking Their Hidden Potential to Guide Tumor Immunity and Therapy.},
journal = {Cells},
volume = {14},
number = {10},
pages = {},
doi = {10.3390/cells14100720},
pmid = {40422223},
issn = {2073-4409},
support = {IG 2019 22923//AIRC/ ; PNRR - M4C2-I1.3 Project PE_00000019 "HEAL ITALIA//European Union - NextGenerationEU through the Italian Ministry of University and Research/ ; },
mesh = {Humans ; *Neoplasms/immunology/therapy ; Tumor Microenvironment/immunology ; Animals ; *T-Lymphocytes/immunology ; },
abstract = {Unconventional T (UC T) cells, including invariant natural killer T (iNKT) cells, mucosal-associated invariant T (MAIT) cells, γδ T cells, and double-negative (DN) T cells, are key players in immune surveillance and response due to their properties combining innate-like and adaptive-like features. These cells are widely present in mucosal tissues, where they can rapidly respond to infections and tumor-associated changes. In fact, UC T cells can have both pro- and anti-tumoral effects, with their activity influenced by factors such as microbial composition and the tumor microenvironment. In particular, intratumoral microbiota significantly impacts the development, function, and activation of UC T cells, influencing cytokine production and shaping the immune response in various cancers. The complex crosstalk between UC T cells and the surrounding factors is discussed in this review, with a focus on how these cells might be interesting candidates to explore and exploit as anticancer therapeutic agents. However, the great potential of UC T cells, not only demonstrated in the context of adoptive cell transfer, but also enhanced through techniques of engineering, is still flanked by different challenges, like the immunosuppressive tumor microenvironment and heterogeneity of target molecules associated with some specific categories of tumors, like gastrointestinal cancers.},
}
@article {pmid40422211,
year = {2025},
author = {Harrington, K and Shah, K},
title = {Harmonizing the Gut Microbiome and Cellular Immunotherapies: The Next Leap in Cancer Treatment.},
journal = {Cells},
volume = {14},
number = {10},
pages = {},
doi = {10.3390/cells14100708},
pmid = {40422211},
issn = {2073-4409},
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; *Neoplasms/therapy/immunology/microbiology ; *Immunotherapy/methods ; Animals ; },
abstract = {The gut microbiome, a diverse community of microorganisms, plays a key role in shaping the host's immune system and modulating cancer therapies. Emerging evidence highlights its critical influence on the efficacy and toxicity of cell-based immunotherapies, including chimeric antigen receptor T cell, natural killer cell, and stem cell therapies. This review explores the interplay between gut microbiota and cellular immunotherapies, focusing on mechanisms by which microbial metabolites and microbial composition impact treatment outcomes. Furthermore, we discuss strategies to leverage the gut microbiome to optimize therapeutic efficacy and minimize adverse effects. A deeper understanding of the relationship between the gut microbiome and cellular immunotherapies can pave the way for more effective cell-based therapies for cancer.},
}
@article {pmid40422085,
year = {2025},
author = {Liu, L and Shi, J and Wang, H and Du, H and Yang, J and Wei, K and Zhou, Z and Li, M and Huang, S and Zhan, L and Li, G and Lv, Y and Shen, H and Cai, W},
title = {The characteristics of tissue microbiota in different anatomical locations and different tissue types of the colorectum in patients with colorectal cancer.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0019825},
doi = {10.1128/msystems.00198-25},
pmid = {40422085},
issn = {2379-5077},
abstract = {The gut microbiota is intricately associated with the onset and progression of colorectal cancer (CRC), leading to significant interest in developing prevention and treatment strategies that leverage gut microbiota. In this study, we collected 57 samples from 19 CRC patients, comprising cancerous tissue, paracancerous tissue, and normal mucosa. Utilizing metagenomic sequencing and bioinformatics analysis, we identified differences in the microbiomes and their functional characteristics across the various tissue types. The results indicated that species such as Alistipes putredinis were predominantly found in normal tissues, while Pseudomonas putida was enriched in paracancerous tissue, and Malassezia restricta was prevalent in cancerous tissues. Furthermore, the microbial functions exhibited variability among the different tissue types. Random forest analysis suggested that Moraxella osloensis may be implicated in the onset and progression of colorectal cancer. We also classified the patients into three subgroups based on the anatomical location of the colorectum: right-sided colon, left-sided colon, and rectum. The subgroup analysis revealed that the microbiota enriched in normal mucosa and paracancerous tissue varied across different anatomical sites. These findings not only elucidate the characteristics of the microbiomes in the normal mucosa, paracancerous tissue, and cancerous tissues of CRC patients, thereby providing new potential targets for clinical diagnosis and treatment, but also contribute to the existing microbiome data pertinent to CRC research.IMPORTANCEThis study provides crucial insights into the relationship between gut microbiota and colorectal cancer (CRC) by analyzing microbial communities in different tissue types and anatomical locations of CRC patients. We identified distinct microbial signatures, such as Alistipes putredinis in normal tissues and Malassezia restricta in cancerous tissues, indicating location-specific microbiomes with unique functional attributes. These findings suggest potential new biomarkers or therapeutic targets for CRC. The observed microbiota variations among right-sided colon, left-sided colon, and rectum cancers underscore the heterogeneity of CRC, pointing toward more personalized treatment strategies. By enhancing our understanding of the microbiome's role in CRC, this research paves the way for innovative diagnostic tools and targeted therapies tailored to individual patient profiles. This work is essential for advancing clinical approaches to CRC management.},
}
@article {pmid40421951,
year = {2025},
author = {Le, NN and Frater, I and Lip, S and Padmanabhan, S},
title = {Hypertension precision medicine: the promise and pitfalls of pharmacogenomics.},
journal = {Pharmacogenomics},
volume = {},
number = {},
pages = {1-24},
doi = {10.1080/14622416.2025.2504865},
pmid = {40421951},
issn = {1744-8042},
abstract = {Pharmacogenomics (PGx) has the potential to revolutionize hypertension management by tailoring antihypertensive therapy based on genetic profiles. Despite significant advances in genomic research, the clinical translation of PGx in hypertension remains challenging due to genetic complexity, variability in drug response, and implementation barriers. This review explores the genetic basis of hypertension, highlighting key pharmacogenomic markers that influence antihypertensive metabolism and efficacy, including CYP2D6, CYP3A4, UMOD, and ACE polymorphisms. We also examine the role of Mendelian randomization, polygenic risk scores in drug development and stratifying hypertension treatment response. While PGx offers opportunities for personalized medicine - such as reducing trial-and-error prescribing and improving adherence - several obstacles hinder its widespread adoption. These include limited clinical actionability, lack of large-scale randomized controlled trials, cost constraints, and concerns about equity and accessibility. Furthermore, drug-gene interactions and phenoconversion add complexity to implementation. Emerging technologies, including artificial intelligence-driven prescribing, microbiome integration, and pharmacoepigenomics, may enhance PGx precision in hypertension management. However, further research, clinical validation, and policy frameworks are necessary before PGx can be routinely incorporated into hypertension care. This review critically evaluates both the promise and limitations of PGx in hypertension, offering insights into the future of precision medicine in cardiovascular health.},
}
@article {pmid40421735,
year = {2025},
author = {Ghosh, S and Chorghade, R and Diehl, RC and Dodge, GJ and Bae, S and Dugan, AE and Halim, M and Wuo, MG and Bartlett, H and Herndon, L and Kiessling, LL and Imperiali, B},
title = {Tools for investigating host-microbe crosstalk using glycan analysis probes inspired by human lectins.},
journal = {Glycobiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/glycob/cwaf031},
pmid = {40421735},
issn = {1460-2423},
support = {R01AI055258//National Institute of Allergy and Infectious Diseases/ ; F32GM133116/NH/NIH HHS/United States ; F32GM134576/NH/NIH HHS/United States ; U01 CA231079/NH/NIH HHS/United States ; },
abstract = {Human lectins are critical carbohydrate-binding proteins that recognize diverse glycoconjugates from microorganisms and can play a key role in host-microbe interactions. Despite their importance in immune recognition and microbe binding, the specific glycan ligands and functions of many human lectins remain poorly understood. Using previous proof-of-concept studies on selected lectins as the foundation for this work, we present ten additional glycan analysis probes (GAPs) from a diverse set of human soluble lectins, offering robust tools to investigate glycan-mediated interactions. We describe a protein engineering platform that enables scalable production of GAPs that maintain native-like conformations and oligomerization states, equipped with functional reporter tags for targeted glycan profiling. We demonstrate that the soluble GAP reagents can be used in various applications, including glycan array analysis, mucin-binding assays, tissue staining, and microbe binding in complex populations. These capabilities make GAPs valuable for dissecting interactions relevant to understanding host responses to microbes. The tools can also be used to probe differential microbial and mammalian glycan interactions, which are crucial for understanding the interactions of lectins in a physiological environment where both glycan types exist. GAPs have potential as diagnostic and prognostic tools for detecting glycan alterations in chronic diseases, microbial dysbiosis, and immune-related conditions.},
}
@article {pmid40421710,
year = {2025},
author = {Kim, SH and Kang, W and Kim, M and Hong, S and Kim, H and Lee, JK},
title = {Temple stay diet and its impact on gut microbiome and irritable bowel syndrome: a prospective cohort study.},
journal = {Food &amp; function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d4fo06143h},
pmid = {40421710},
issn = {2042-650X},
abstract = {Background/Aims: Irritable Bowel Syndrome (IBS) significantly impacts quality of life, with effective treatment challenged by its multifactorial pathogenesis. A temple stay program incorporating a vegetarian diet may benefit IBS by modulating the gut microbiota. Methods: In this prospective cohort study, 61 patients with diarrhea-predominant IBS (IBS-D) or mixed bowel habit IBS (IBS-M) participated in a 4 day temple stay program following a 1 week washout period. IBS symptom severity, psychological stress, and fecal microbiota composition were assessed before, immediately after, and two weeks post-intervention using the IBS Severity Scoring System (IBS-SSS) and 16S rRNA gene sequencing. Results: A subset of participants demonstrated improvements in IBS symptom severity, particularly those who exhibited marked compositional shifts in their gut microbiota, as defined by beta-diversity (weighted UniFrac distance). These microbiome responders tended to show increased levels of beneficial bacteria such as Faecalibacterium and reduced levels of opportunistic taxa including Klebsiella and Enterococcus. A significant correlation was observed between the degree of microbiota change and improvement in IBS-SSS scores. Responders also differed from non-responders in baseline gut microbiota features, including lower alpha diversity and reduced abundance of commensal genera. Conclusions: The temple stay program may provide clinical and microbial benefits in a subset of individuals with IBS, particularly those with baseline gut dysbiosis. These findings support the potential role of personalized, microbiome-informed dietary interventions in managing IBS.},
}
@article {pmid40421693,
year = {2025},
author = {Jin, J and Lin, T and Liu, D and Wang, Y and Xu, X and Xu, Y and Siemann, E and Li, B},
title = {Changes in Soil Microbiome Mediated by Root Volatiles Enhanced Manganese Tolerance of an Invasive Plant Species.},
journal = {Plant, cell &amp; environment},
volume = {},
number = {},
pages = {},
doi = {10.1111/pce.15644},
pmid = {40421693},
issn = {1365-3040},
support = {//This study was financially supported by the National Key Research and Development Program of China (2022YFC2601100), the National Natural Science Foundation of China (Grant No.: U2102218, 32001204), the Science and Technology Department of Shanghai (Grant No.: 23015810100), the Department of Science and Technology of Yunnan Province (Grant No.: 202405AS350011) and the Yunnan Fundamental Research Projects (Grant No.: 202501AS070069)./ ; },
abstract = {Many invasive plants exhibit high heavy metal tolerance, but the roles of root-associated soil microbiomes in this process remain poorly understood. Heavy metal stress can alter the release of plant volatile organic compounds (VOCs), potentially influencing plant-soil feedbacks. This study utilised an aggressive invasive plant species Phytolacca americana as a study model, to assess the effects of different levels of soil manganese (Mn) stress on the emissions of root VOCs, and their subsequent influence on soil microbial communities. Results obtained here indicated that elevated Mn stress levels notably increased the quantity and altered the composition of root VOCs, subsequently influencing the diversity and composition of soil microbiomes. Specifically, a decrease in bacterial diversity and an increase in beneficial bacterial genera were observed. Limonene was identified as a key VOC compound influencing bacterial community composition, potentially promoting the accumulation of beneficial bacterial taxa such as Bacillus in soil. Reintroduction of inoculated soil collected from Mn-stressed plants significantly enhanced the tolerance of P. americana to Mn treatment. Elemental analysis suggested that the improved plant tolerance to Mn following soil reintroduction may be attributed to enhanced nutrient uptake that may be facilitated by beneficial microorganisms rather than reduced Mn accumulation in plant tissues.},
}
@article {pmid40421466,
year = {2025},
author = {Catalano Gonzaga, O and McKenna, S and O'Neill, I and Cotter, PD and McAuliffe, FM and Coffey, A and van Sinderen, D and Bottacini, F},
title = {Gene-trait matching among Bifidobacterium dentium strains reveals various glycan metabolism loci including a strain-specific fucosyllactose utilization cluster.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1584694},
pmid = {40421466},
issn = {1664-302X},
abstract = {In contrast to other human-associated bifidobacteria, Bifidobacterium dentium is commonly classified as an opportunistic pathogen as its presence in the oral cavity has been associated with the development of dental caries. While B. dentium is frequently isolated from the oral cavity of children with caries, recent microbiome investigations and preliminary genomic analyses have suggested that this species is also adapted to colonize the gastrointestinal tract. Understanding the genetic and metabolic adaptations that enable this flexible colonization ability is crucial to clarify its role in human health and disease. To assess B. dentium genomic diversity and metabolic potential, the current study presents analysis and characterization of 10 complete genome sequences from recently isolated B. dentium strains obtained from human fecal samples together with 48 publicly available genome sequences. We investigated genetic loci predicted to be involved in host interaction and carbohydrate utilization in this species by means of comparative genomics, pan-genome analysis, and gene-trait matching. These analyses identified gene clusters involved in the utilization of plant-derived glycans and, for the first time, revealed B. dentium strains capable of utilizing human milk oligosaccharides (HMOs) through a fucosyllactose utilization cluster homologous to the one found in several infant-derived bifidobacterial species. Moreover, additional investigations of strain-specific genetic features highlighted a taxon that is evolved to colonize multiple niches and to compete with other colonizers. These findings challenge the narrow classification of B. dentium as an opportunist and underscore its ecological versatility.},
}
@article {pmid40421334,
year = {2025},
author = {Ponce Alencastro, JA and Salinas Lucero, DA and Solis, RP and Herrera Giron, CG and Estrella López, AS and Anda Suárez, PX},
title = {Molecular Mechanisms and Emerging Precision Therapeutics in the Gut Microbiota-Cardiovascular Axis.},
journal = {Cureus},
volume = {17},
number = {4},
pages = {e83022},
pmid = {40421334},
issn = {2168-8184},
abstract = {A microbiome in the gut plays a significant role in cardiovascular health and disease. Dysbiosis is an imbalance in the gut microbiome, leading to multiple cardiovascular diseases (CVD) such as atherosclerosis, hypertension, and heart failure. Gut microbe-derived metabolites such as trimethylamine-N-oxide (TMAO) and short-chain fatty acids (SCFAs) are important mediators of the gut-heart axis. Evaluation of the relationship between the gut microbiome and host biomarkers with CVD requires the integration of metagenomics and metabolomics with meta-omics approaches. The literature review found that microbes and metabolic signatures are associated with the risk and progression of CVD. The development of precision therapeutic approaches for targeting gut microbiota includes preventing adverse microbial effects using probiotics, prebiotics, and the drug-as-bug approach to inhibit harmful metabolites of microbiomes, and fecal microbiota transplantation (FMT). However, the implication and practice of these findings in clinical settings face challenges due to the heterogeneity of study designs, difficulty in the determination of causality, and the impact of confounding factors such as diet, medication, and potential inter-individual gut microbiome variability. Future researchers are recommended to conduct longitudinal studies to further establish both gut microbiome associations with CVD and develop successful precision therapeutics approaches based on the microbiome for the treatment of CVD.},
}
@article {pmid40421256,
year = {2025},
author = {Carannante, A and Giustini, M and Rota, F and Bailo, P and Piccinini, A and Izzo, G and Bollati, V and Gaudi, S},
title = {Intimate partner violence and stress-related disorders: from epigenomics to resilience.},
journal = {Frontiers in global women's health},
volume = {6},
number = {},
pages = {1536169},
pmid = {40421256},
issn = {2673-5059},
abstract = {Intimate Partner Violence (IPV) is a major public health problem to be addressed with innovative and interconnecting strategies for ensuring the psychophysical health of the surviving woman. According to the World Health Organization, 27% of women worldwide have experienced physical and sexual IPV in their lifetime. Most of the studies on gender-based violence focus on short-term effects, while long-term effects are often marginally included even though they represent the most serious and complex consequences. The molecular mechanisms underlying stress-related disorders in IPV victims are multiple and include dysregulation of the hypothalamic-pituitary-adrenal axis, inflammatory response, epigenetic modifications, neurotransmitter imbalances, structural changes in the brain, and oxidative stress. This review aims to explore the long-term health consequences of intimate partner violence (IPV), emphasizing the biological and psychological mechanisms underlying stress-related disorders and resilience. By integrating findings from epigenetics, microbiome research, and artificial intelligence (AI)-based data analysis, we highlight novel strategies for mitigating IPV-related trauma and improving recovery pathways. Genome-wide environment interaction studies, enhanced by AI-assisted data analysis, offer a promising public health approach for identifying factors that contribute to stress-related disorders and those that promote resilience, thus guiding more effective prevention and intervention strategies.},
}
@article {pmid40420853,
year = {2025},
author = {Nchanji, GT and Fossi, BT and Fru-Cho, J and Shey, RA and Andoh, AA and Kemajou Tchamba, AL and Hasan, NA and Wanji, S},
title = {Bacterial Diversity in Aquacultured African Catfish and Source Pond Water in Buea, Cameroon.},
journal = {International journal of microbiology},
volume = {2025},
number = {},
pages = {6132661},
pmid = {40420853},
issn = {1687-918X},
abstract = {The catfish is a prominent freshwater fish species farmed in Cameroon to meet the escalating demand for fish products. Despite considerable growth potential, there are concerns about the occurrence of bacteria pathogenic to both fish and humans within aquaculture systems. Research on the microbiome of catfish and their habitats remains largely unexplored. Given the critical importance of understanding the microbial composition within aquaculture systems to ensure food safety and protect public health, this study aimed to generate vital preliminary data by investigating the bacteriome of catfish gills and intestines and pond water environment in Cameroon using 16S rRNA gene amplicon sequencing. The findings revealed a diverse bacterial community (30 phyla, 678 genera, and 1056 species), with Fusobacteria, Bacteroidetes, Proteobacteria, Firmicutes, and Verrucomicrobia collectively representing over 93% of the bacterial community observed. Notably, Fusobacteria emerged as the dominant phylum in catfish gills (49.98%) and intestines (65.3%), while Proteobacteria predominated in the pond water environment (40.24%). Bacteria of genus Cetobacterium dominated all three samples (gills, 49.93%; intestines, 65.19%; and pond water, 23.85%). Furthermore, this study identified many bacterial genera, including potential fish pathogens such as Edwardsiella, Aeromonas, Plesiomonas, and Flavobacterium, and human gut bacteria such as Clostridium and Bacteroides, alongside potential beneficial probiotic bacteria such as Lactococcus spp. The coexistence of both potentially pathogenic and probiotic species underscores ecological complex dynamics within freshwater fish aquaculture and highlights the need for thorough microbial management strategies. This study provides insights into the bacterial landscape of Cameroonian aquaculture, revealing potential risks and benefits of catfish farming.},
}
@article {pmid40420833,
year = {2025},
author = {Clasen, F and Yildirim, S and Arıkan, M and Garcia-Guevara, F and Hanoğlu, L and Yılmaz, NH and Şen, A and Celik, HK and Neslihan, AA and Demir, TK and Temel, Z and Mardinoglu, A and Moyes, DL and Uhlen, M and Shoaie, S},
title = {Microbiome signatures of virulence in the oral-gut-brain axis influence Parkinson's disease and cognitive decline pathophysiology.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2506843},
doi = {10.1080/19490976.2025.2506843},
pmid = {40420833},
issn = {1949-0984},
mesh = {Humans ; *Parkinson Disease/microbiology/physiopathology ; *Cognitive Dysfunction/microbiology/physiopathology ; *Gastrointestinal Microbiome ; *Mouth/microbiology ; *Brain/physiopathology/microbiology ; Male ; Female ; Aged ; *Bacteria/genetics/classification/pathogenicity/isolation &amp; purification ; Metagenomics ; Virulence ; Virulence Factors/genetics/metabolism ; Saliva/microbiology/chemistry ; Middle Aged ; },
abstract = {The human microbiome is increasingly recognized for its crucial role in the development and progression of neurodegenerative diseases. While the gut-brain axis has been extensively studied, the contribution of the oral microbiome and gut-oral tropism in neurodegeneration has been largely overlooked. Cognitive impairment (CI) is common in neurodegenerative diseases and develops on a spectrum. In Parkinson's Disease (PD) patients, CI is one of the most common non-motor symptoms but its mechanistic development across the spectrum remains unclear, complicating early diagnosis of at-risk individuals. Here, we generated 228 shotgun metagenomics samples of the gut and oral microbiomes across PD patients with mild cognitive impairment (PD-MCI) or dementia (PDD), and a healthy cohort, to study the role of gut and oral microbiomes on CI in PD. In addition to revealing compositional and functional signatures, the role of pathobionts, and dysregulated metabolic pathways of the oral and gut microbiome in PD-MCI and PDD, we also revealed the importance of oral-gut translocation in increasing abundance of virulence factors in PD and CI. The oral-gut virulence was further integrated with saliva metaproteomics and demonstrated their potential role in dysfunction of host immunity and brain endothelial cells. Our findings highlight the significance of the oral-gut-brain axis and underscore its potential for discovering novel biomarkers for PD and CI.},
}
@article {pmid40420533,
year = {2025},
author = {Hu, J and Zhang, Y and Liu, C and Gkaravella, A and Yu, J},
title = {Effects of microbiota-based interventions on depression and anxiety in children and adolescents-A systematic review.},
journal = {Journal of pediatric gastroenterology and nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1002/jpn3.70092},
pmid = {40420533},
issn = {1536-4801},
support = {//None/ ; },
abstract = {This study aims to systematically review evidence on gut microbiota-based interventions for reducing depression- and anxiety-like symptoms in children and adolescents with autism spectrum disorder, irritable bowel syndrome, Prader-Willi syndrome, below-average literacy skills or anorexia nervosa, where some individuals may exhibit indicators of depression or anxiety. This review includes evaluated evidence from randomized controlled trials (RCTs) involving children and adolescents aged 3-19 years, identified from PsycINFO, Medline (Ovid version), Web of Science, and the reference lists of existing reviews. Risk of bias were assessed using Risk of Bias Tool (RoB 2) in RevMan (version 5.4, Cochrane Collaboration). The results were qualitatively summarized by describing the main findings across the studies. Of the 1561 studies screened, 10 RCTs with 408 participants were included. Three gut microbiota-based interventions evaluated were probiotics, prebiotics, and dietary supplementation. Probiotics and dietary supplementation were identified as effective on reducing depression and anxiety in three studies; no significant effects were reported in the remaining seven studies. No evidence supported the effectiveness of prebiotics in reducing depression and anxiety in children and adolescents. Four studies presented low risk of bias, while others showed some bias in the randomization process, allocation concealment, selective reporting, and blinding of the outcome assessment. This review highlights the potential of probiotics and dietary supplements in treating depression and anxiety in children and adolescents. However, the current evidence is constrained by inadequate mental health measurements, participant heterogeneity, and small sample sizes in reviewed studies. Further well-designed studies are needed to confirm their effectiveness.},
}
@article {pmid40420336,
year = {2025},
author = {van Himbeeck, R and Geisen, S and van Schaik, C and van den Elsen, S and Berendsen, R and Bertran, A and Schepel, E and Helder, J},
title = {Patchy Distribution of Potato Cyst Nematodes Within Single Arable Fields Reveals Local Disease Suppressiveness Mediated by Disparate Microbial Communities.},
journal = {Environmental microbiology},
volume = {27},
number = {5},
pages = {e70113},
doi = {10.1111/1462-2920.70113},
pmid = {40420336},
issn = {1462-2920},
support = {LWV20338//Topconsortium voor Kennis en Innovatie/ ; 1083727//HORIZON EUROPE Food, Bioeconomy, Natural Resources, Agriculture and Environment/ ; },
mesh = {*Solanum tuberosum/parasitology/microbiology ; Animals ; *Soil Microbiology ; *Plant Diseases/parasitology/prevention &amp; control ; *Microbiota ; Rhizosphere ; *Nematoda ; Bacteria/genetics/classification/isolation &amp; purification ; *Tylenchoidea ; Fungi/genetics/isolation &amp; purification ; Soil/parasitology ; },
abstract = {Disease suppressiveness is a complex phenomenon that is assumed to be the resultant of the actions of local microbial antagonists. Exploitation of disease suppressiveness as a tool to manage pathogens is hindered by our poor understanding of this phenomenon. Here we investigated soil microbiome-based suppression of potato cyst nematodes (PCN), and to this end, four apparently homogeneous potato fields with an unexplained non-homogeneous PCN distribution were selected. We hypothesised that this patchy PCN distribution resulted from local variation in disease suppressiveness. Under controlled greenhouse conditions, we confirmed the overall suppressiveness of these soils vis-à-vis PCN and soils were gamma-irradiated to corroborate the biotic origin of this suppression. Subsequent DNA-based analysis of the microbial community in the potato rhizosphere revealed suppressiveness-related contrasts in community composition between suppressive and conducive patches. Elevated abundances of fungal (e.g., Metacordyceps chlamydosporia) and bacterial (e.g., Pseudomonas fluorescens) nematode antagonists were positively associated with PCN suppressive patches. Distinct sets of antagonists were found to be associated with PCN suppression despite the geographical closeness of the locations under investigation. Our findings confirm the biotic origin of local PCN suppressiveness and reveal that disparate microbial communities could achieve similar outcomes.},
}
@article {pmid40420312,
year = {2025},
author = {Peets, P and Litos, A and Dührkop, K and Garza, DR and van der Hooft, JJJ and Böcker, S and Dutilh, BE},
title = {Chemical characteristics vectors map the chemical space of natural biomes from untargeted mass spectrometry data.},
journal = {Journal of cheminformatics},
volume = {17},
number = {1},
pages = {82},
pmid = {40420312},
issn = {1758-2946},
support = {Germany's Excellence Strategy-EXC 2051-Project-ID 390713860//Deutsche Forschungsgemeinschaft/ ; BO 1910/23//Deutsche Forschungsgemeinschaft/ ; BO 1910/23//Deutsche Forschungsgemeinschaft/ ; Germany's Excellence Strategy-EXC 2051-Project-ID 390713860//Deutsche Forschungsgemeinschaft/ ; Alexander von Humboldt-Professorship//Alexander von Humboldt-Stiftung/ ; Alexander von Humboldt-Professorship//Alexander von Humboldt-Stiftung/ ; Consolidator grant 865694: DiversiPHI/ERC_/European Research Council/International ; },
abstract = {Untargeted metabolomics can comprehensively map the chemical space of a biome, but is limited by low annotation rates (< 10%). We used chemical characteristics vectors, consisting of molecular fingerprints or chemical compound classes, predicted from mass spectrometry data, to characterize compounds and samples. These chemical characteristics vectors (CCVs) estimate the fraction of compounds with specific chemical properties in a sample. Unlike the aligned MS1 data with intensity information, CCVs incorporate the chemical properties of compounds, allowing chemical annotation to be used for sample comparison. Thus, we identified compound classes differentiating biomes, such as ethers which are enriched in environmental biomes, while steroids enriched in animal host-related biomes. In biomes with greater variability, CCVs revealed key clustering compound classes, such as organonitrogen compounds in animal distal gut and lipids in animal secretions. CCVs thus enhance the interpretation of untargeted metabolomic data, providing a quantifiable and generalizable understanding of the chemical space of natural biomes.},
}
@article {pmid40420287,
year = {2025},
author = {Tancredi, A and Matthijs, T and Cox, E and Van Immerseel, F and Goossens, E},
title = {From mother to piglet: the lasting influence of the maternal microbiome.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {52},
pmid = {40420287},
issn = {2524-4671},
abstract = {BACKGROUND: Given their crucial roles in agriculture and biomedical research, promoting pig health is essential. A balanced gut microbiota is vital for immune development, metabolism and pathogen resistance, and requires optimal initial colonization by beneficial bacteria. This becomes particularly evident during early life stages, like suckling and weaning, where disruptions can lead to long-term health issues. Understanding the factors influencing microbiome development during these phases is fundamental for enhancing pig health. On these basis, rectal swab samples from eighteen sow-piglet pairs were collected at multiple time points from 7 days after birth to 10 days post-weaning, and analyzed through 16S rRNA gene sequencing. This study aims to understand the maternal influence on piglet microbiota development during the suckling-weaning period, exploring microbial diversity, composition and additional influencing factors such as age, piglet and weaning.<br><br>RESULTS: &#x3b1; diversity significantly increased with piglet age (p&#x2009;<&#x2009;0.001) and stabilized upon weaning, with maternal influence and differences between individual piglet affecting variability before weaning. Post-weaning &#x3b1; diversity was influenced by the pen environment (contributing to 14.5-16% of the variability between piglets) rather than age. Both the sow (~&#x2009;9.6%) and age of the piglets (20-30%) had a significant impact on the microbial &#x3b2; diversity over the entire timeframe. Moreover, at 10 days post-weaning a significant influence of the cage mates on piglets microbial &#x3b2; diversity was observed (~&#x2009;24.6%). Source-tracking analysis revealed a significant maternal contribution to piglet microbiome at 7 days (31.68%), which decreased over time but remained at 13.33% post-weaning. Piglet microbiome exhibited consistency across time, with 22.55-61.23% of bacteria retained from previous stages. Cage mates contributed 53.54% to the microbiome at 10 days post-weaning. Additionally, 68.32% of piglets microbiome at 7 days was derived from sources not included in the study, decreasing to 37.6% by 10 days post-weaning. ASV-level analysis showed that the majority of maternally transmitted ASVs pre-weaning persisted until the last time point, with both beneficial bacteria and pathobionts being transmitted.<br><br>CONCLUSIONS: This study highlights the significant influence of maternal microbiota on piglet gut microbiome development, affecting both diversity and composition. Beneficial bacteria are transmitted from mothers to offspring and persist through early developmental stages, thereby emphasizing the long-lasting impact of maternal microbiome and the importance of early microbial colonization for piglet health.},
}
@article {pmid40419960,
year = {2025},
author = {Shen, Q and Fan, X and Sun, Y and Gao, H and Su, X},
title = {TaxaCal: enhancing species-level profiling accuracy of 16S amplicon data.},
journal = {BMC bioinformatics},
volume = {26},
number = {1},
pages = {136},
pmid = {40419960},
issn = {1471-2105},
support = {2021YFF0704500//National Key Research and Development Program of China/ ; 32070086//National Natural Science Foundation of China/ ; },
mesh = {*RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Metagenomics/methods ; Algorithms ; Machine Learning ; Humans ; *Bacteria/genetics/classification ; Sequence Analysis, DNA/methods ; },
abstract = {BACKGROUND: 16S rRNA amplicon sequencing is a widely used method for microbiome composition analysis due to its cost-effectiveness and lower data requirements compared to metagenomic whole-genome sequencing (WGS). However, inherent limitations in 16S-based approach often lead to profiling discrepancies, particularly at the species level, compromising the accuracy and reliability of findings.<br><br>RESULTS: To address this issue, we present TaxaCal (Taxonomic Calibrator), a machine learning algorithm designed to calibrate species-level taxonomy profiles in 16S amplicon data using a two-tier correction strategy. Validation on in-house produced and public datasets shows that TaxaCal effectively reduces biases in amplicon sequencing, mitigating discrepancies between microbial profiles derived from 16S and WGS. Moreover, TaxaCal enables seamless cross-platform comparisons between these two sequencing approaches, significantly improving disease detection in 16S-based microbiome data.<br><br>CONCLUSIONS: Therefore, TaxaCal offers a cost-effective solution for generating high-resolution microbiome species profiles that closely align with WGS results, enhancing the utility of 16S-based profiling in microbiome research. As microbiome-based diagnostics continue to evolve, TaxaCal has the potential to be a crucial tool in advancing the utility of 16S sequencing in clinical and research settings.},
}
@article {pmid40419682,
year = {2025},
author = {Nishinarita, Y and Miyoshi, J and Kuronuma, S and Wada, H and Oguri, N and Hibi, N and Takeuchi, O and Akimoto, Y and Lee, STM and Matsuura, M and Kobayashi, T and Hibi, T and Hisamatsu, T},
title = {Characteristic gene expression profile of intestinal mucosa early in life promotes bacterial colonization leading to healthy development of the intestinal environment.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {18437},
pmid = {40419682},
issn = {2045-2322},
support = {19K23977//Japan Society for the Promotion of Science/ ; 21K07900//Japan Society for the Promotion of Science/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Mice ; *Intestinal Mucosa/microbiology/metabolism ; Fecal Microbiota Transplantation ; *Bacteria/genetics/growth &amp; development/classification ; Germ-Free Life ; *Transcriptome ; Male ; Gene Expression Profiling ; Female ; Feces/microbiology ; Mice, Inbred C57BL ; },
abstract = {The gut microbiome early in life plays a crucial role in development of the host and affects health throughout life. The definition of a healthy microbiome early in life has not been established, and the underlying mechanism of how a young host selects appropriate microbes for colonization remains unclear. Understanding the mechanism may provide insights into novel preventive and therapeutic strategies by correcting dysbiosis early in life. We employed germ-free mice early in life (4 weeks of age) and later in life (10 weeks of age) for fecal microbiota transfer (FMT) from specific pathogen-free mice. We performed age-unmatched FMT between recipients early in life and donors early or later in life, in addition to common age-matched FMT. Age-matched FMT resulted in significantly different bacterial compositions between recipients early vs. later in life. When the gut microbiome from donors early or later in life was transferred to recipients early in life, bacterial compositions of recipients from donors later in life were similar to those of recipients from donors early in life. This finding suggests that the host early in life has mechanisms to select microbes appropriate for age from the exposed microbiome. We hypothesized that the age-specific intestinal environment promotes age-appropriate intestinal microbiome colonization and examined gene expression in the intestinal mucosa of germ-free mice. We observed that gene expression profiles were different between early vs. later in life. Correlation analysis demonstrated that genera Lachnospiraceae NK4A136 group and Roseburia were positively correlated to genes expressed predominantly early in life, but negatively with genes expressed predominantly later in life. We confirmed that the relative abundance of these genera was significantly higher in specific pathogen-free mice early in life compared with mice later in life. The characteristic gene expression of the intestinal mucosa early in life might play roles in selecting specific bacteria in the intestinal microbiome early in life.},
}
@article {pmid40419398,
year = {2025},
author = {Manning, LP and Tuck, CJ and Biesiekierski, JR},
title = {Predicting response to the low FODMAP diet in irritable bowel syndrome: Current evidence and clinical considerations.},
journal = {Asia Pacific journal of clinical nutrition},
volume = {34},
number = {3},
pages = {373-385},
doi = {10.6133/apjcn.202506_34(3).0012},
pmid = {40419398},
issn = {1440-6047},
support = {APP2025943//Australian National Health and Medical Research Council Emerging Leadership Fellowship/ ; },
mesh = {*Irritable Bowel Syndrome/diet therapy ; Humans ; *Diet, Carbohydrate-Restricted ; Fermentation ; Gastrointestinal Microbiome ; Monosaccharides ; Polymers ; FODMAP Diet ; },
abstract = {BACKGROUND AND OBJECTIVES: The low fermentable oligo-, di-, mono-saccharides and polyols (FODMAP) diet is an effective dietary intervention for irritable bowel syndrome (IBS), yet up to 50% of patients fail to re-spond adequately. Identifying reliable predictors of response could optimize treatment selection and improve treatment outcomes while avoiding unnecessary dietary restrictions. This narrative review examines current evidence for predictors of response to the low FODMAP diet and highlights gaps in knowledge that must be addressed to develop clinically useful indicators for routine practice.<br><br>METHODS AND STUDY DESIGN: We re-viewed the literature on the low FODMAP diet, and studies investigating factors that may predict treatment response, including clinical, diagnostic, biological, biochemical, and microbial markers.<br><br>RESULTS: Several po-tential predictors to the low FODMAP diet have emerged, including baseline symptom severity, psychological factors (particularly depression), hydrogen breath test results, volatile organic compounds in fecal samples, and specific gut microbiota profiles. Clinical and psychological measures show the most immediate potential for implementation due to accessibility and established measurement tools. Biological markers, including breath testing, metabolomics, and microbiome analysis, show promise but require further validation in larger, diverse populations and standardization of methodologies.<br><br>CONCLUSIONS: Despite promising research, signifi-cant gaps remain in developing reliable, accessible predictors of response to the low FODMAP diet. Future research should focus on validating simple clinical tools that combine symptom profiles with psychological assessment to guide treatment decisions. A personalized approach to dietary management of IBS based on reliable response predictors would optimize clinical outcomes while minimizing unnecessary dietary restriction and healthcare resource utilization.},
}
@article {pmid40418963,
year = {2025},
author = {Tyson-Carr, J and Leng, J and Scott, M and Adams, S and Hoptroff, M and Murphy, B and Fallon, N and Paterson, S and Thomas, A and Giesbrecht, T and Roberts, C},
title = {Body-site specific associations between human skin microbiome composition and psychological wellbeing.},
journal = {The British journal of dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1093/bjd/ljaf177},
pmid = {40418963},
issn = {1365-2133},
abstract = {BACKGROUND/OBJECTIVES: There is increasing scientific interest in understanding the interplay between psychological wellbeing and the human microbiome, with a particular focus on the gut microbiome's impact on psychological health. However, the role of the skin microbiome remains underexplored. The current study addresses this gap by investigating the relationship between the human skin microbiome at various body sites (face, scalp, forearm, axilla) and psychological wellbeing. This unique multi body site investigation aims to provide an understanding of the skin microbiome's role in psychological health.<br><br>METHODS: Fifty-three participants underwent microbiome sampling via skin swabbing from four body regions (forearm, face, scalp, and axilla) and completed psychological measures of global/general wellbeing (Affect Grid, Sleep Quality, Stress NRS-11, PSS-10) and body site-related wellbeing (Hair &amp; ScalpCARE, SkinCARE, UnderarmCARE). All bacterial DNA extracts were analysed using quantitative polymerase chain reaction (qPCR) and Illumina sequencing of the V1 - V2 region of the 16S gene. Microbial diversity was computed as Shannon diversity and Faith's Phylogenetic diversity. Correlations were determined between psychological measures, microbial diversity, and genera for each body site.<br><br>RESULTS: The current study uncovered that specific bacterial genera were associated with aspects of wellbeing. Specifically, Cutibacterium showed consistent associations with psychological wellbeing across multiple body locations. Key findings showed increased Cutibacterium on the face and axilla was associated with reduced stress, increased Cutibacterium in the axilla was associated with increased mood pleasantness.<br><br>CONCLUSIONS: These findings highlight, for the first time, the nuanced relationship between skin microbiome and psychological wellbeing. Increased Cutibacterium across multiple body-sites was consistently associated with positive wellbeing outcomes. This underscores the need for further investigation into specific bacterial taxa that may be involved in a skin-brain axis, as well as the importance of specific microbial communities on the body and their potential influence on this connection.},
}
@article {pmid40418353,
year = {2025},
author = {Klátyik, S and Simon, G and Takács, E and Oláh, M and Zaller, JG and Antoniou, MN and Benbrook, C and Mesnage, R and Székács, A},
title = {Toxicological concerns regarding glyphosate, its formulations, and co-formulants as environmental pollutants: a review of published studies from 2010 to 2025.},
journal = {Archives of toxicology},
volume = {},
number = {},
pages = {},
pmid = {40418353},
issn = {1432-0738},
abstract = {Over the last decade and worldwide, an enormous investment in research and data collection has been made in the hope of better understanding the possible ecological and toxicological impacts triggered by glyphosate (GLY). This broad-spectrum, systemic herbicide became the most heavily applied pesticide ever in the 2000s. It is sprayed in many different ways in both agricultural and non-agricultural settings, resulting in multiple routes of exposure to organisms up and down the tree of life. Yet, relatively little is known about the environmental fate of GLY-based herbicide (GBH) formulations, and even less on how GBH co-formulants alter the absorption, distribution, metabolism, excretion, and toxicity of GLY. The environmental fate of GLY depends on several abiotic and biotic factors. As a result of heavy annual GBH use over several decades, GLY residues are ubiquitous, and sometimes adversely affect non-target terrestrial and aquatic organisms. GLY has become a frequent contaminant in drinking water and food chains. Human exposures have been associated with numerous adverse health outcomes including carcinogenicity, metabolic syndrome, and reproductive and endocrine-system effects. Nonetheless, the existence and magnitude of GLY-induced effects on human health remain in dispute, especially in the case of heavily exposed applicators. A wide range of biochemical/physiological modes of action have been elucidated. Various GBH co-formulants have long been considered as inert ingredients relative to herbicidal activity but clearly contribute to GLY-induced hazards and risk gradients. In light of already-identified toxicological and ecosystem impacts, the intensive research focuses on GLY and GBHs should continue, coupled in the interim with commonsense, low-cost changes in use patterns and label requirements crafted to slow the spread of GLY-resistant weeds and reduce applicator and general-population exposures.},
}
@article {pmid40418157,
year = {2025},
author = {Pajak, P and Teshome, S and Berton, A and Stobaugh, H and Fleet, A and Khatiwada, D and Cichon, B},
title = {A Global Scoping Review on Alternative Ready-to-Use Therapeutic Foods.},
journal = {Maternal &amp; child nutrition},
volume = {},
number = {},
pages = {e70035},
doi = {10.1111/mcn.70035},
pmid = {40418157},
issn = {1740-8709},
support = {//This research was supported by UNICEF./ ; },
abstract = {Alternative ready-to-use therapeutic foods (RUTF) formulations provide an opportunity to lower costs, facilitate local or national ingredient use, and enhance the availability and acceptability of RUTF. This scoping review aimed to identify and categorise the available evidence on alternative RUTF formulations developed and tested globally, assess their compliance with international standards and summarise evidence on acceptability, cost, effectiveness, cost-effectiveness and adverse events, highlighting evidence gaps to guide future research. Searches of three databases and extensive grey literature were conducted covering the period from 1999 to June 2023. Fifty-four articles, 42 peer-reviewed articles and 12 grey literature sources were included. Fifty-three RUTF formulations at various development stages for the treatment of severe acute malnutrition (SAM) without medical complications in children 6-59 months were identified. Numerous ingredients have undergone testing to replace primarily peanuts and/or milk, demonstrating consistent acceptance and promising results in terms of effectiveness. Evidence on outcomes beyond anthropometric recovery, such as higher iron status, and effects on cognitive and developmental outcomes or gut microbiome, is also limited. Few studies evaluated the cost implications, revealing potential savings in production costs while no significant differences were found in terms of safety. Additional evidence is required on how reduced or milk-free formulations within the innovation and novel categories can achieve compliance with the required protein digestibility-corrected amino acid score (PDCAAS) recommendations. Further research is also needed with specific focus on outcomes beyond anthropometric recovery such as cost-effectiveness, accessibility, macro and micronutrient deficiencies, sustainability of recovery and longer term health outcomes.},
}
@article {pmid40418139,
year = {2025},
author = {Pilipenko, VI and Perova, IB and Eller, KI and Morozov, SV and Isakov, VA and Bezrukov, EV},
title = {[The influence of dietary pattern on the production of volatile organic compounds in patients with hydrogen-producing small intestinal bacterial overgrowth syndrome].},
journal = {Voprosy pitaniia},
volume = {94},
number = {2},
pages = {106-116},
doi = {10.33029/0042-8833-2025-94-2-106-116},
pmid = {40418139},
issn = {0042-8833},
support = {FGMF-2025-0003//The research was carried out using subsidies for the implementation of a state task/ ; },
mesh = {Humans ; Female ; Male ; *Hydrogen/metabolism ; *Volatile Organic Compounds/metabolism ; Middle Aged ; *Intestine, Small/microbiology/metabolism ; *Gastrointestinal Microbiome ; Adult ; *Blind Loop Syndrome/metabolism/microbiology ; Breath Tests ; Methane/metabolism ; Feces/chemistry/microbiology ; },
abstract = {Antibacterial therapy of the small intestine bacterial overgrowth (SIBO) is not effective enough and has a high relapse rate after treatment. Diet is a well-modifiable factor that plays a major role in shaping the composition, diversity, metabolic activity and stability of the intestinal microbiota. Intestinal bacteria ferment undigested food residues to form species-specific carbon-chain volatile organic compounds (VOCs). The aim of this research was to study possible correlations between dietary variables and the level of stool VOCs in patients with hydrogen-producing SIBO. Material and methods. The material of the study was the data of 100 patients referred for a hydrogen-methane breath test with lactulose in case of suspected presence of SIBO. Excessive bacterial growth of hydrogen-producing flora in the small intestine was determined by changes in the content of hydrogen and methane in exhaled air after consuming a portion of lactulose using the GastroCheck Gastrolyzer apparatus. The assessment of actual nutrition at home was carried out by 24-hour dietary recall. The determination of VOCs in patients' feces was carried out using gas chromatographymass spectrometry (a gas chromatograph equipped with a vapor-phase autosampler in combination with a triple quadrupole mass spectrometer). Results. Of the 100 patients examined, 41 were found to have a overgrowth of hydrogen- producing flora, 15 had an excess of methanogenic flora, and 10 had an excess of both hydrogen-producing and methanogenic flora. No signs of SIBO were found in 34 patients and they formed a control group. When comparing dietary parameters expressed in absolute values, significant differences were found only in relation to dietary fiber: patients with SIBO differed in a lower level of their consumption (19.8±9.1 vs 25.5±12.3 g/ day, p=0.023). At the same time, the index of healthy nutrition HEI-2020 in the control group was significantly higher (52.9±11.1 vs 44.4±14.4%, p=0.003). Due to the high variability of VOC levels, no significant differences between the groups for individual VOCs have been established. The results of the analysis of the structure of correlations between 84 variables of the nutrition assessment of the studied participants and 80 VOCs in their stool showed significant interdependence differences between patients of the studied groups. In patients with SIBO, the metabolic activity of the microbiota changed most significantly when eating leafy greens, berries, oatmeal and sausages, and in the control group when eating potatoes, tropical fruits, buckwheat and eggs. Conclusion. Thus, significant differences in the structure of correlations between dietary variables and the level of stool VOCs in patients with SIBO and the control group have been established.},
}
@article {pmid40418015,
year = {2025},
author = {Woodmartin, S and McGovern, F and Smith, PE and Boland, TM and McGrane, L and Monaghan, A and Dunne, E and Creighton, P},
title = {The inclusion of a companion legume or herb, in combination with perennial ryegrass increased growth performance and reduced enteric methane emissions in lambs post-weaning.},
journal = {Journal of animal science},
volume = {},
number = {},
pages = {},
doi = {10.1093/jas/skaf139},
pmid = {40418015},
issn = {1525-3163},
abstract = {Increasing lamb growth rates directly from pasture and reducing enteric methane (CH4) emissions are key drivers to enhancing production efficiency and achieving more sustainable lamb finishing systems. The objective of this study was to assess the influence of binary sward mixtures of perennial ryegrass (Lolium perenne L.) plus a companion forage on growth performance, enteric CH4 output, reticulo-rumen content weight (RRcw), rumen fermentation parameters and the composition of the rumen microbiome in growing lambs. A randomized block design was employed to investigate five treatments, namely, perennial ryegrass (PRG), PRG plus white clover (Trifolium repens L.; PRG+WC), PRG plus red clover (Trifolium pratense L.; PRG+RC), PRG plus chicory (Chicorium intybus L.; PRG+Chic) and PRG plus plantain (Plantago lanceolate L.; PRG+Plan). At weaning, 120 lambs (n = 24 per treatment) were selected in both 2021 and 2022 for CH4 measurement using portable accumulation chambers. A further subset of 60 lambs (n = 12 per treatment) were selected from the initial 120 lambs in each year for rumen measurements and sampling. Lambs were weighed fortnightly and drafted for slaughter upon reaching their target live weight (LW). Rumen fluid was harvested using a transoesophageal sampling device post-weaning and manually immediately post-mortem. Average sward companion forage content was 28% on a dry matter basis. Lambs grazing PRG+WC, PRG+RC or PRG+Chic had a higher post-weaning average daily gain (ADG) (P < 0.001) and an increased lifetime ADG (P < 0.001), compared with lambs grazing PRG. The addition of any companion forage resulted in a reduction in age at slaughter of 16-50 days (P < 0.001). Methane production (g/day) and CH4 intensity (g/kg LW and g/kg ADG) were reduced for lambs grazing PRG+WC, PRG+RC, and PRG+Plan (P < 0.001), compared with those grazing PRG. There was a lower relative abundance of Methanobrevibacter (P < 0.001) in lambs grazing PRG+RC over those grazing PRG, PRG+Chic and PRG+Plan. The presence of Prevotella was more abundant in lambs grazing the legume treatments, PRG+WC and PRG+RC, than those grazing PRG (P < 0.001). The RRcw of the PRG lambs was heavier than lambs grazing PRG+WC, PRG+RC and PRG+Plan (P < 0.001). These results suggest that the manipulation of pasture species composition is a promising, practical and feasible strategy to enhance production efficiency and mitigate CH4 from pasture-based lamb production systems.},
}
@article {pmid40417982,
year = {2025},
author = {Brown, SE and He, X and Magder, L and Johnston, ED and Morgan, D and Ravel, J and Mark, K and Ghanem, KG and Brotman, RM},
title = {Bacterial vaginosis incidence following a single hyperosmolal vaginal lubricant exposure: A comparison of two observational cohorts.},
journal = {Sexually transmitted diseases},
volume = {},
number = {},
pages = {},
doi = {10.1097/OLQ.0000000000002184},
pmid = {40417982},
issn = {1537-4521},
abstract = {BACKGROUND: Hyperosmolal lubricants may negatively affect the vaginal microenvironment, increasing the risk for bacterial vaginosis (BV). We compared the incidence of Amsel-defined BV in reproductive-age women exposed to hyperosmolal lubricant during transvaginal ultrasound to those without recent lubricant exposure.<br><br>METHODS: We analyzed two observational cohorts over 10 weeks: 58 lubricant-exposed women from the Gynecology and Lubricants Effects study and 59 lubricant-unexposed women from a University of Alabama Birmingham cohort linked to the University of Maryland Human Microbiome Project. BV was diagnosed using Amsel criteria at baseline, mid-study (lubricant-exposed: week 2, lubricant-unexposed: week 5), and final visit (week 10), and categorized by symptomatology. Risks for incident BV and Amsel criteria were assessed using modified Poisson regression with robust standard errors. An additional outcome of new-onset/newly-symptomatic BV included those with baseline asymptomatic BV. A secondary analysis focused on Black participants (N = 73) due to an observed higher BV incidence.<br><br>RESULTS: Baseline demographics and behaviors were similar between the cohorts. Among all participants, lubricant was not associated with new-onset BV (adjusted relative risk (aRR):1.32, 95% CI:0.58-3.01). 88% (23/26) of all new-onset/newly-symptomatic BV cases occurred in Black participants. Among Black participants, exposure to lubricant doubled the risk of developing new-onset BV (aRR:2.18, 95% CI:1.16-4.11) and new-onset/newly-symptomatic BV (aRR:1.91, 95% CI: 1.04-3.51), and increased the risk for new-onset clue cells (aRR:2.18, 95% CI:1.17 - 4.06) versus no lubricant exposure.<br><br>CONCLUSION: Hyperosmolal lubricants was associated with BV incidence in Black women. Factors contributing to this elevated risk require further research.},
}
@article {pmid40417664,
year = {2025},
author = {Govorov, I and Komlichenko, E and Ulrikh, E and Dikareva, E and Pervunina, T and Vazhenina, O and Dzharbaeva, A and Kalinina, O and Zaikova, E and Razumova, Z and Mints, M and Sitkin, S},
title = {The microbiome in endometrial cancer: vaginal milieu matters.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1533344},
pmid = {40417664},
issn = {2296-858X},
abstract = {Endometrial cancer remains one of the most common malignancies in women, and its incidence is particularly increasing in developed countries. Despite the well-known promotive role of excessive exposure to estrogen, many other details of the pathogenesis of endometrial cancer remain unknown. Recent studies have elucidated the emerging role of the resident microbiota in the progression of various diseases, including cancer. Next-generation sequencing demonstrated that the uterine cavity, previously considered sterile, contains a composition-rich microbiota. In this work, we determined the differences in the composition of the intrauterine microbiota between patients with endometrial cancer and its precursor-endometrial hyperplasia.},
}
@article {pmid40417391,
year = {2025},
author = {Cyphert, EL and Nand, S and Franco, G and Hajkowski, M and Soto, L and Lee, DM and Ferner, MC and Zabin, CJ and Blumenthal, J and Deck, AK and Boyer, KE and Burrus, LW and Hernandez, CJ and Anand, A},
title = {Combinatorial characterization of bacterial taxa-driven differences in the microbiome of oyster beds.},
journal = {Sustainable microbiology},
volume = {2},
number = {2},
pages = {qvaf006},
pmid = {40417391},
issn = {2755-1970},
abstract = {Oyster reefs and beds provide crucial ecosystem services, including water filtration, coastal protection, and habitat provision for marine species. However, these habitats face significant threats from climate change and anthropogenic stressors. To address these challenges, numerous oyster restoration initiatives have been undertaken globally. Intertidal microbial communities, comprising diverse bacteria, archaea, and unicellular eukaryotes, drive key biogeochemical processes, but remain poorly understood in ecosystems targeted for oyster restoration. We investigated the microbiome associated with the Olympia oyster (Ostrea lurida), a key restoration target in the western USA, by characterizing microbial abundance and diversity in sediment, oyster-associated biofilm, and oysters at four sites in San Francisco Bay. Our findings revealed distinct microbial assemblages in oysters and sediment compared to biofilm. Diversity, measured by the Shannon index, was highest at Heron's Head (5.47), followed by Brickyard Park (5.35), Dunphy Park (5.17), and Point Pinole (4.85). Notably, microbes Ruminococcus, Streptococcus, Staphylococcus, Prevotella, Porphyromonas, Parvimonas, Neisseria, Lactococcus, Haemophilus, Fusobacterium, Dorea, Clostridium, Campylobacter, Bacteroides, and Akkermansia were positively associated with biofilm collected from hard surfaces where oysters were attached at most sites. Potential implications of these microbial associations for oyster growth, survival, and interactions with environmental factors remain largely unexplored. Future research is warranted on culturing specific microbes to assess their functions and investigating environmental and ecological drivers of microbial diversity to determine relationships indicative of oyster health and potential for enhancing oyster recruitment.},
}
@article {pmid40415961,
year = {2025},
author = {Inui, I and Mochizuki, S and Hirabayashi-Nishimuta, F and Yoshioka, Y and Takahashi, O and Sasaguri, M and Habu, M and Ariyoshi, W and Yamasaki, R},
title = {In vitro impact of Streptococcus mitis on the inhibition of oral cancer cell proliferation via mitotic modulation.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1524820},
pmid = {40415961},
issn = {2235-2988},
mesh = {Humans ; Cell Line, Tumor ; *Streptococcus mitis/physiology ; *Cell Proliferation ; *Mouth Neoplasms/microbiology/pathology ; *Mitosis ; *Carcinoma, Squamous Cell/microbiology ; Cell Survival ; },
abstract = {INTRODUCTION: Recent studies have elucidated a potential correlation between oral carcinogenesis and the oral microbiome. However, few reports exist on the interaction between Streptococcus spp., the most common oral microflora bacterium, and oral cancer. In this study, we aimed to elucidate the effects of Streptococcus spp. on oral squamous cell carcinoma (OSCC) cells in vitro.<br><br>METHODS: HSC-3 (tongue carcinoma) and Ca9-22 (gingival carcinoma) cells were used as models of OSCC cells, and their responses were examined after adding major oral Streptococcus species-S. mitis, S. sanguinis, S. anginosus, S. salivarius, and S. mutans-to the culture medium. Cell viability was assessed using the CCK-8 assay. Gene expression changes were analyzed using RNA sequencing and RT-qPCR followed by Gene Ontology analysis. Flow cytometry was used to observe the effects of bacteria on the cell cycle.<br><br>RESULTS: Among all examined Streptococcus species, S. mitis had the strongest inhibitory effect on the growth of OSCC cells. RNA sequencing and RT-qPCR revealed an increase in the number of genes involved in mitotic nuclear division, especially DUSP1, in HSC-3 cells treated with S. mitis. Flow cytometry showed that S. mitis caused a decreased number of HSC-3 cells in the G0/G1 phase and an increased number in the G2/M phase, suggesting cell cycle arrest in the G2/M phase. Various treatments of S. mitis were used to examine the effects of intact bacteria and bacterial components on cancer cells, indicating the involvement of structural bacterial proteins.<br><br>CONCLUSIONS: This study, investigating the association between oral cancer cells and bacteria of the genus Streptococcus, revealed that S. mitis may play an important role in the inhibition of cancer cells.},
}
@article {pmid40415946,
year = {2025},
author = {Leclercq, L and Debarre, S and Lloret, E and Taminiau, B and Daube, G and Rambaud, C and Drider, D and Siah, A and Desprez, B and Hilbert, JL and Lucau-Danila, A},
title = {Unveiling the hidden allies of industrial chicory-a metagenomic exploration of rhizosphere microbiota and their impact on productivity and plant health.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1509094},
pmid = {40415946},
issn = {1664-302X},
abstract = {BACKGROUND: As industrial chicory is significant for food, fodder, and medicinal purposes, its cultivation is increasingly crucial for producers. To enhance productivity, resistance, and the nutritional and functional values of this plant, we aimed to investigate its interactions with the microbial environment. We performed the first comprehensive taxonomic and functional characterization of the rhizosphere microbiota associated with industrial chicory, investigating how environmental factors influence its composition.<br><br>METHODS: Six different land plots were simultaneously cultivated with the same chicory genotype in northern France. Using soil analyses and metagenomic approaches, we characterized the diversity of bacterial and fungal communities in the soil microbiome associated with chicory plants and discussed their functional traits.<br><br>RESULTS: We observed significant taxonomic variability, influenced by soil composition and cultivation history across each plot. The presence of chicory plants distinctly shaped the microbial community. Specifically, chicory was found to recruit Streptomyces species that produce plant hormones and Penicillium species that facilitate phosphate solubilization and promote plant growth. Moreover, the plant demonstrated an ability to repel pathogens and adapt to local microbial communities by selectively favoring beneficial microorganisms according to local stresses and nutritional needs.<br><br>DISCUSSION: Our study represents a comprehensive taxonomic and functional analysis of the Cichorium intybus rhizosphere microbiome, underscoring the pivotal role of soil composition and land-use history. The specific microbial recruitment by chicory was also addressed.},
}
@article {pmid40415934,
year = {2025},
author = {Liu, L and Zhao, W and Zhang, H and Shang, Y and Huang, W and Cheng, Q},
title = {Relationship between pediatric asthma and respiratory microbiota, intestinal microbiota: a narrative review.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1550783},
pmid = {40415934},
issn = {1664-302X},
abstract = {Pediatric asthma is a common chronic airway inflammatory disease that begins in childhood and its impact persists throughout all age stages of patients. With the continuous progress of detection technologies, numerous studies have firmly demonstrated that gut microbiota and respiratory microbiota are closely related to the occurrence and development of asthma, and related research is increasing day by day. This article elaborates in detail on the characteristics, composition of normal gut microbiota and lung microbiota at different ages and in different sites, as well as the connection of the gut-lung axis. Subsequently, it deeply analyzes various factors influencing microbiota colonization, including host factor, delivery mode, maternal dietary and infant feeding patterns, environmental microbial exposure and pollutants, and the use of antibiotics in early life. These factors are highly likely to play a crucial role in the onset process and disease progression of asthma. Research shows that obvious changes have occurred in the respiratory and gut microbiota of asthma patients, and these microbiomes exhibit different characteristics according to the phenotypes and endotypes of asthma. Finally, the article summarizes the microbiota-related treatment approaches for asthma carried out in recent years, including the application of probiotics, nutritional interventions, and fecal microbiota transplantation. These treatment modalities are expected to become new directions for future asthma treatment and bring new hope for solving the problem of childhood asthma.},
}
@article {pmid40415931,
year = {2025},
author = {Murtskhvaladze, M and Ninua, L and Budagashvili, N and Tevdoradze, E and Gurgenidze, Z and Kotorashvili, A and Kotaria, N and Gavashelishvili, A and Javakhishvili, Z},
title = {Tracheal and cloacal bacterial diversity of red listed Eastern Imperial Eagle (Aquila heliaca).},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1477032},
pmid = {40415931},
issn = {1664-302X},
abstract = {This study aimed to improve knowledge of raptor microbiomes by providing the first description of tracheal and cloacal bacterial diversity of Eastern Imperial Eagles (Aquila heliaca). To date, only few studies are available and they are carried out mainly on captive birds. The Eastern Imperial Eagle is species of significant conservation concern and, therefore, characterization microbiota contributes valuable information to the field of avian microbiology and aids in conservation efforts for this threatened species, moreover, identification of avian and human pathogens within microbial communities and evaluation of potential threats to birds, humans, and other species are crucial for sustainably balancing the wellbeing of ecosystems, 3,500 OTUs were identified from each sample supported by ∼2.8 Million sequence reads. The tracheal and cloacal microbiomes were dominated by Gammaproteobacteria (67.5%), Bacilli (43.8%), and Negativicutes (22.0%). We detected dissimilarities between cloacal (unique 440 OTUs) and tracheal (337 unique OTUs) samples, and significant evidence of moderate positive monotonic relationship between cloacal and tracheal bacterial communities. No significant differences between individuals from different nests. Aquila heliaca can serve as an indicator of presence of bacterial species in its respective habitats. Efforts aiming at protection of red-listed birds may not presently prioritize microbiome considerations but integrating microbiome research into conservation strategies could yield significant benefits.},
}
@article {pmid40415928,
year = {2025},
author = {Karimianghadim, R and Satokari, R and Yeo, S and Arkkila, P and Kao, D and Pakpour, S},
title = {Prolonged effect of antibiotic therapy on the gut microbiota composition, functionality, and antibiotic resistance genes' profiles in healthy stool donors.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1589704},
pmid = {40415928},
issn = {1664-302X},
abstract = {INTRODUCTION: Fecal microbiota transplantation (FMT) is highly effective in preventing Clostridioides difficile recurrence by restoring gut microbiota composition and function. However, the impact of recent antibiotic use, a key exclusion criterion for stool donors, on gut microbiota recovery is poorly understood.<br><br>METHODS: We investigated microbial recovery dynamics following antibiotic use in three long-term stool donors from Canada and Finland. Using longitudinal stool sampling, metagenomic sequencing, and qPCR, we assessed changes in bacterial diversity, community composition, microbial functions, the gut phageome, and the risk of transmitting antibiotic-resistant genes (ARGs).<br><br>RESULTS: Antibiotics caused lasting disruption to bacterial communities, significantly reducing important taxa like Bifidobacterium bifidum, Blautia wexlerae, Akkermansia muciniphila, Eubacterium sp. CAG 180, and Eubacterium hallii, with effects persisting for months. Functional analyses revealed alterations in housekeeping genes critical for energy production and biosynthesis, with no direct links to key health-related pathways. Antibiotics also disrupted viral populations, decreasing diversity and increasing crAssphage abundance, reflecting disrupted host-bacteriophage dynamics. No significant increase in clinically important ARGs was detected.<br><br>DISCUSSION: These findings highlight the unpredictable and complex recovery of gut microbiota post-antibiotics. Individualized suspension periods in donor programs, guided by metagenomic analyses, are recommended to optimize FMT outcomes in various indications by considering antibiotic spectrum, duration, and host-specific factors.},
}
@article {pmid40415923,
year = {2025},
author = {Sánchez-Gallego, J and Curtis, NP and Paerl, HW and Paerl, RW},
title = {New perspectives on picocyanobacteria and understudied cyanobacterial diversity in the Albemarle Pamlico sound system, North Carolina, USA.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1539050},
pmid = {40415923},
issn = {1664-302X},
abstract = {Cyanobacteria are important primary producers, sources of secondary metabolites, and sentinels of environmental change in aquatic ecosystems - including large estuaries. Here, we newly investigated cyanobacterial diversity within the Albemarle Pamlico Sound System (APES) using (16S rRNA) gene amplicon sequencing analyses. Substantial cyanobacterial diversity including lineages lacking current isolates were recovered (46 genera, 17 potentially cyanotoxic), with oligohaline waters of the Albemarle Sound and its tributaries being notable regional hotspot for diversity. Salinity and temperature were influential drivers of cyanobacterial community composition. Picocyanobacteria (cells <3 µm in diameter) were abundant in amplicon sequence libraries (72% of cyanobacterial sequences) - especially populations within Synechococcus SubClade 5.2. Picocyanobacteria along with picoeukaryotes were large contributors to total phytoplankton biomass comprising ~47% of chlorophyll a. Further, the picocyanobacterial genera Synechococcus, Cyanobium, and Synechocystis (55.4%, 14.8%, and 12.9% of cyanobacterial sequences, respectively) formed a core community spanning from freshwater regions (eastern AST, D949) to polyhaline environments (NRE100 downstream stations to PS5), suggesting resilience to significant salinity fluctuations and associated environmental changes. Amplicon sequence variant (ASV) and environmental data indicate the presence of several putative ecotypes, as well as distinct abundance patterns among closely related populations, highlighting substantial fitness variability among subspecies. Notably, potentially cyanotoxic genera, Synechocystis, Planktothrix, Plectonema, and Dolichospermum were the four more abundant detected in polyhaline APES regions, far beyond conspicuous freshwater sources. These findings reveal previously unrecognized potential sources of cyanotoxics in estuarine food webs and habitats, underscoring the ecological significance of cyanobacterial community dynamics across salinity gradients.},
}
@article {pmid40415693,
year = {2025},
author = {Fontaine, SS and Kennedy-Gold, SR and Regester, KJ and Sheridan, JA and Kohl, KD},
title = {The Impact of Whole-Animal Fluid Preservation on the Observed Gut Microbiome of Vertebrates: Implications for the Use of Museum Specimens in Microbiome Research.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {e14127},
doi = {10.1111/1755-0998.14127},
pmid = {40415693},
issn = {1755-0998},
support = {//University of Pittsburgh/ ; //University of Pittsburgh's Pymatuning Laboratory of Ecology Pape Endowment Award/ ; },
abstract = {The vertebrate gut houses diverse microbial communities that provide insights into their host's ecological and evolutionary histories. Nevertheless, microbiome research has not been distributed equally across host taxonomy, geography and timescales. The millions of fluid-preserved specimens stored in natural history museums worldwide represent a potentially untapped resource for microbiome information. However, it is unknown how fluid preservation and long-term storage change the composition and diversity of the original microbial community across a variety of host taxa. Here, we present the largest study to date aimed at addressing this question. Specifically, we identified an optimal method for extracting DNA from preserved samples using commercially available kits. Next, for 11 host species representing four vertebrate classes, we compared the gut microbiomes between animals dissected freshly and those collected simultaneously but subsequently fixed in formalin and stored in 70% ethanol for 1 year, similar to museum conditions. In a secondary analysis in amphibians, we compared our collected samples with those from decades-old historical museum specimens. We found that while fluid preservation altered the community composition and reduced the diversity of the recovered microbiome inventories, host species identity predominated in shaping the gut microbiome, and differences across species and geographic localities were retained after preservation. Historical specimens had microbiomes that were the most different from fresh specimens, suggesting that over time, changes in the microbiome of populations have occurred, or preservation effects have compounded. Considering these findings, we discuss the potential for use of fluid-preserved museum specimens in future microbiome studies.},
}
@article {pmid40415338,
year = {2025},
author = {Shen, W and de Boer, JF and Kuipers, F and Fu, J},
title = {New insights in amino sugar metabolism by the gut microbiome.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2510462},
doi = {10.1080/19490976.2025.2510462},
pmid = {40415338},
issn = {1949-0984},
mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; *Bacteria/metabolism/genetics/classification ; Animals ; *Amino Sugars/metabolism ; Acetylgalactosamine/metabolism ; Gastrointestinal Tract/microbiology ; },
abstract = {Gut microorganisms inhabiting the intestinal tract play key roles in host's health and disease. A properly functioning gut microbiome requires the availability of adequate carbon, nitrogen and energy sources. One of the main sources of energy for intestinal bacteria are glycans, of which amino sugars are important components. Amino sugars are a class of carbohydrates in which one or more hydroxyl groups are substituted with amino groups. However, bacterial utilization of amino sugars and their impact on the gut microbiome and host health have not been thoroughly assessed. In this review, we summarize the latest discoveries about amino sugar metabolism by gut microbes, paying particular attention to the metabolism of N-acetyl-galactosamine (GalNAc), one of the most abundant amino sugars in the intestine, and its potential implications for microbial functionality and host health.},
}
@article {pmid40415193,
year = {2025},
author = {Othón-Martínez, D and Peña-Muñoz, SV and Riojas Barret, M and Vidales-Lopez, GG and Sánchez Guzmán, JM and Kwapisz, L},
title = {EXPRESS: Cardiovascular Disease in Inflammatory Bowel Disease Pathophysiology and Risk Factors: A Review.},
journal = {Journal of investigative medicine : the official publication of the American Federation for Clinical Research},
volume = {},
number = {},
pages = {10815589251346966},
doi = {10.1177/10815589251346966},
pmid = {40415193},
issn = {1708-8267},
abstract = {Inflammatory Bowel Disease (IBD), including Crohn's disease (CD) and ulcerative colitis (UC), are chronic systemic immune dysregulated disorders affecting the gastrointestinal tract that often have extraintestinal manifestations. Limited data exists on the cardiovascular (CV) implications of IBD, but a higher prevalence of cardiovascular disease (CVD) has been observed compared to the general population, resulting in increased mortality risk. Although IBD's etiology remains unclear, research has shown that it involves a complex interplay between factors such as enteric neural activity, inflammatory mediators, microbiome imbalance, intestinal barrier dysfunction, and environmental stressors. This proinflammatory environment in IBD may contribute significantly to the development of CVD, including myocarditis, pericarditis, thromboembolism, arrhythmia, and heart failure. Furthermore, certain IBD-specific medications have been associated with either the development or worsening of CVD. Despite this potential risk to CV health, drugs like anti-integrins, amino-salicylates, corticosteroids, immunomodulators, and advanced therapies including biologics have proven effective for managing and achieving remission in patients with IBD. This literature review analyzes existing data on IBD's pathophysiology and its potential effect on CVD development and progression, along with examining IBD drugs linked to CV health risks and those with less harmful cardiac involvement.},
}
@article {pmid40414991,
year = {2025},
author = {Rashid, MH and Pascottini, OB and Xie, L and Niazi, M and Lietaer, L and Comlekcioglu, U and Opsomer, G},
title = {Shotgun metagenomic composition, microbial interactions and functional insights into the uterine microbiome of postpartum dairy cows with clinical and subclinical endometritis.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {18274},
pmid = {40414991},
issn = {2045-2322},
support = {2(3)/HRD/OSS-III/2022/HEC/83//Higher Education Commission, Pakistan/ ; KP 2020; FFB200048//Ghent University, Belgium/ ; BOF17/DOC/269//Ghent University, Belgium/ ; 12Y5220N//University of Antwerp, Belgium/ ; CSC; 202206300032//China Scholarship Council/ ; },
mesh = {Animals ; Cattle ; Female ; *Endometritis/microbiology/veterinary ; *Cattle Diseases/microbiology ; *Microbiota/genetics ; Metagenomics/methods ; Postpartum Period ; *Uterus/microbiology ; Bacteria/genetics/classification/isolation &amp; purification ; *Microbial Interactions ; Metagenome ; },
abstract = {Clinical endometritis (CE) is associated with bacterial pathogens while the same has not been proved about subclinical endometritis (SCE). We aimed to use shotgun metagenomic sequencing to investigate the associations between potentially unidentified pathogens and SCE. Uterine cytobrush samples from multiparous Holstein cows (n = 23) were taken at 21 days in milk (DIM) and sequenced via the Illumina shotgun platform. At 36 DIM, the cows were diagnosed as CE (n = 7), SCE (n = 7), or healthy (n = 9). We did not find differences in the alpha and beta diversity of bacteria and eukaryotes among the health groups. Relative abundance of typical pathogens i.e. Fusobacterium, Peptoniphilus, Peptostreptococcus, and Trueperella was greater in CE than healthy controls. We did not find evidence of eukaryotic or viral association in infection, yet, distinct patterns of bacterial co-occurrence were observed among pathogenic and non-pathogenic bacteria. In CE cows, Wnt/catenin pathway had lower abundance than SCE or healthy cows. Our findings support that CE is characterized by domination of pathogenic bacteria that intercorrelate, whereas SCE is not associated with bacterial colonization.},
}
@article {pmid40414843,
year = {2025},
author = {Thompson, TP and Rice, CJ and Athanasakis, E and Mawhinney, J and Gilmore, BF and Fitzgerald, P and Skvortsov, T and Kelly, SA},
title = {The effect of sample type and location on industrial workplace sink and hand dryer microbiomes.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {325},
pmid = {40414843},
issn = {1471-2180},
mesh = {*Microbiota/genetics ; *Bacteria/genetics/classification/drug effects/isolation &amp; purification ; Humans ; Workplace ; Drug Resistance, Bacterial ; Anti-Bacterial Agents/pharmacology ; Hand Disinfection ; Hand/microbiology ; Metagenomics ; },
abstract = {One major issue in tackling antimicrobial resistance (AMR) is the ability to effectively track resistance spread in environments where surveillance is limited. Such environments include those experiencing high volumes of hand washing and drying from multiple users. This study characterised the microbial populations and antimicrobial resistomes of two different sample types from a pharmaceutical industrial site as part of an AMR environmental surveillance programme. Paired samples were collected from hand dryers and adjacent sinks in distinct sampling locations: from toilets adjacent to 'wet' labs, and locations associated with 'dry' activities. Microbial populations in hand dryers were significantly different to those of sinks, whereas there was no significant difference based on sample location. The opposite effect was observed for resistomes, where profiles differed significantly based on sample location, but not sample type. When both sample type and location were considered together, differences in microbiomes were driven primarily by hand dryer profiles from different locations. Analysis of metagenomically-assembled genomes revealed the presence of many poorly characterised organisms, and suggested no specific families predominated in terms of ARG carriage. This study emphasises the impact of human activities in determining the resistome of commonly used appliances, and the need for continued AMR surveillance programmes.},
}
@article {pmid40358579,
year = {2025},
author = {Luo, M and Xing, Z and Gou, Y and Yang, X and Zhang, X and Yu, W and Lv, H},
title = {Associations Between the Gut Microbiota and Its Related Metabolic Pathways and Uveitis: A Bidirectional Two-Sample Mendelian Randomization Study.},
journal = {Translational vision science &amp; technology},
volume = {14},
number = {5},
pages = {15},
doi = {10.1167/tvst.14.5.15},
pmid = {40358579},
issn = {2164-2591},
abstract = {PURPOSE: Some experimental reports have proposed an interaction between gut microbiota (GM) and uveitis. However, the exact association between GM and its metabolic pathways and uveitis remains unknown. This study was conducted to explore the bidirectional causal relationship between GM and its metabolic pathways and uveitis.<br><br>METHODS: Summary data of the GM and its metabolic pathways and uveitis were leveraged from the Dutch Microbiome Project and the Genome-Wide Association Studies (GWAS) Catalog, respectively. We then conducted Mendelian randomization (MR) analysis to explore whether the GM and its metabolic pathways have a corresponding causal relationship with uveitis. To confirm the credibility of the findings, we utilized MR Egger, the MR-PRESSO global test, and the Cochran Q test to detect pleiotropy and heterogeneity.<br><br>RESULTS: According to the inverse variance weighting method, the species Bacteroides faecis (odds ratio [OR] = 0.598, 95% confidence interval [CI] = 0.390&#x2013;0.919, P = 0.019) and the superpathway of sulfate assimilation and cysteine biosynthesis (OR = 0.179, 95% CI = 0.038&#x2013;0.843, P = 0.029) had beneficial effects on uveitis. In contrast, the genus Sutterellaceae (OR = 3.493, 95% CI = 1.121&#x2013;10.879, P = 0.030); the species Parabacteroides distasonis (OR = 5.932, 95% CI = 1.321&#x2013;26.635, P = 0.020), Faecalibacterium prausnitzii (OR = 4.838, 95% CI = 1.067&#x2013;21.936, P = 0.040), and Bacteroides caccae (OR = 3.818, 95% CI = 1.010&#x2013;14.437, P = 0.048); and the L1,2&#x2013;propanediol degradation (OR = 2.084, 95% CI = 1.098&#x2013;3.954, P = 0.024), galactose degradation I (Leloir pathway; OR = 3.815, 95% CI = 1.108&#x2013;13.135, P = 0.033), TCA cycle VI (obligate autotrophs; OR = 2.955, 95% CI = 1.015&#x2013;8.606, P = 0.046) and UMP biosynthesis (OR = 4.979, 95% CI = 1.000&#x2013;24.782, P = 0.049) pathways had adverse effects on uveitis. No pleiotropy or heterogeneity was found. Leave-one-out analysis showed the reliability of the above findings.<br><br>CONCLUSIONS: Our analysis revealed a causality between certain GM species and metabolic pathways and uveitis via genetic prediction, which may provide new perspectives into the etiology and therapies of uveitis.<br><br>TRANSLATIONAL RELEVANCE: This study provides evidence that modulating the intestinal flora and its metabolic pathways is effective in treating uveitis.},
}
@article {pmid40414644,
year = {2025},
author = {Manusha, S and Varsha, N and Varshini, R and Sivamani, Y and Pokkuluri, KS and Elayaperumal, S},
title = {Altered microbiome influence on the enteric neuromuscular system in amyotrophic lateral sclerosis (ALS).},
journal = {International review of neurobiology},
volume = {180},
number = {},
pages = {95-123},
doi = {10.1016/bs.irn.2025.04.006},
pmid = {40414644},
issn = {2162-5514},
mesh = {*Amyotrophic Lateral Sclerosis/microbiology/physiopathology ; Humans ; *Gastrointestinal Microbiome/physiology ; *Enteric Nervous System/physiopathology/microbiology ; *Dysbiosis/physiopathology ; Animals ; },
abstract = {Amyotrophic lateral sclerosis (ALS) is a neurological disease marked by the degeneration of motor neurons, leading to muscle weakness and paralysis. While the cause of ALS is uncertain, research indicates that changes in the gut microbiome may influence the disease's progression. This chapter explores how alterations in gut microbiota affect the enteric neuromuscular system (ENS) in ALS. In ALS patients, disrupted gut microbiota are linked to the brain-gut axis, impacting both gastrointestinal function and neuronal health. Studies show that microbial changes are associated with inflammation, immune instability, and neurodegeneration, which exacerbate the disease. Gastrointestinal issues like constipation and dysphagia in ALS are tied to ENS dysregulation. Understanding the connections between the gut microbiome, ENS, and central nervous system (CNS) may lead to novel therapies targeting neurodegeneration and microbial dysbiosis in ALS.},
}
@article {pmid40414643,
year = {2025},
author = {Acharjee, P and Prasad, SK and Singh, VV and Ray, M and Acharjee, A},
title = {Microbiota dysbiosis impact on the immune system dysregulation in Huntington's disease (HD).},
journal = {International review of neurobiology},
volume = {180},
number = {},
pages = {57-94},
doi = {10.1016/bs.irn.2025.04.002},
pmid = {40414643},
issn = {2162-5514},
mesh = {Humans ; *Huntington Disease/immunology/microbiology ; *Dysbiosis/immunology/microbiology ; *Gastrointestinal Microbiome/immunology/physiology ; Animals ; },
abstract = {Huntington's disease (HD) is a neurodegenerative disorder characterized by motor, cognitive, and psychiatric impairments caused by Huntingtin (HTT) gene mutations, resulting in the mutant huntingtin (mHTT) protein. Both innate and adaptive immunities play crucial roles in the pathogenesis of HD. In this chapter, we explore the vital role of the gut microbiota in HD, emphasizing its impact on the immune response and brain health via the gut-brain axis. Dysbiosis influences immune responses and HD pathogenesis through microbial metabolites such as short-chain fatty acids (SCFAs) and pathogen-associated molecular patterns (PAMPs). We discuss advanced mathematical models, telemedicine, and biosensors for tracking HD progression and detecting gut dysbiosis. Nutritional interventions to restore microbiota balance and using artificial intelligence and machine learning to predict disease prognosis and personalized treatments have been highlighted. Based on their unique immune profiles and gut microbiota, personalized medicine has been proposed as a promising strategy for effective HD treatment.},
}
@article {pmid40414637,
year = {2025},
author = {Upadhyay, R and Mani, S and Sevanan, M},
title = {Microbiome-based dietary supplements for better development and healthy brain.},
journal = {International review of neurobiology},
volume = {180},
number = {},
pages = {329-368},
doi = {10.1016/bs.irn.2025.03.009},
pmid = {40414637},
issn = {2162-5514},
mesh = {Humans ; *Dietary Supplements ; *Brain/growth &amp; development ; *Gastrointestinal Microbiome/physiology ; *Probiotics/administration &amp; dosage ; Prebiotics/administration &amp; dosage ; Animals ; },
abstract = {Microbiome-based dietary supplements have gained attention for their role in enhancing brain development and cognitive health. The gut microbiome influences neurological functions through the gut-brain axis, impacting neurotransmitter production, immune regulation, and metabolic pathways. Dysbiosis is linked to neurological disorders such as Alzheimer's, Parkinson's, and autism spectrum disorders. This chapter explores dietary interventions targeting the microbiome, emphasising probiotics, prebiotics, and postbiotics. Additionally, AI and machine learning are transforming microbiome research by enabling personalised supplementation strategies tailored to individual gut profiles. Ethical challenges, including data privacy and algorithmic bias, are also discussed. Advances in big data analytics and predictive modelling are paving the way for precision-targeted interventions to optimise brain health. While microbiome-based therapies hold great promise, further clinical validation and regulatory frameworks are needed to ensure their efficacy and accessibility. This chapter highlights the future potential of microbiome-targeted strategies in neuroprotection and cognitive well-being.},
}
@article {pmid40414636,
year = {2025},
author = {Parthasarathy, S and Giridharan, B and Panigrahi, J and Konyak, LM and Jamir, N and Tharumasivam, SV},
title = {Abnormal microbiota due to prenatal antibiotic as a possible risk factor for Attention-Deficit / Hyperactivity Disorder (ADHD).},
journal = {International review of neurobiology},
volume = {180},
number = {},
pages = {299-328},
doi = {10.1016/bs.irn.2025.03.007},
pmid = {40414636},
issn = {2162-5514},
mesh = {Humans ; *Attention Deficit Disorder with Hyperactivity/chemically induced/microbiology/etiology ; Pregnancy ; *Anti-Bacterial Agents/adverse effects ; Female ; *Prenatal Exposure Delayed Effects/chemically induced ; *Dysbiosis/chemically induced ; Risk Factors ; *Microbiota/drug effects ; *Gastrointestinal Microbiome/drug effects ; },
abstract = {One of the major issues modern medicine faces is the increasing use of antibiotics in reaction to the increased incidence of infectious agents. The current trend of antibiotic overuse contributes to microbial dysbiosis. Recent studies have hypothesized that antibiotic exposure during pregnancy, which alters the composition of the microbiome, might increase the likelihood of attention deficit hyperactivity disorder (ADHD). In addition to the ongoing discussion about the potential links between antibiotic usage, microbiome dysbiosis, and ADHD, there is a rising interest in integrating AI and ML into healthcare practices. Diagnosis, treatment plans, and prognoses are all enhanced by these technological advancements. Remote monitors or telemedicine monitoring are among the management techniques described in this chapter for effectively managing illnesses. Also discussed are ways to halt the progression of diseases by preventative measures that use biosensor technology and dietary approaches. Personalized treatment programs, disease progression stages, and prognosis evaluations are all made possible with the use of artificial intelligence and machine learning. By using these technologies to provide individualized therapy, healthcare practitioners may get a better understanding of ADHD and perhaps improve patient outcomes.},
}
@article {pmid40414634,
year = {2025},
author = {Singh, S and Saini, V and Jha, HC},
title = {The role of secondary genomes in neurodevelopment and co-evolutionary dynamics.},
journal = {International review of neurobiology},
volume = {180},
number = {},
pages = {245-297},
doi = {10.1016/bs.irn.2025.03.008},
pmid = {40414634},
issn = {2162-5514},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Neurodevelopmental Disorders/genetics/microbiology ; *Biological Evolution ; Animals ; *Brain/growth &amp; development ; },
abstract = {This chapter examines how human biology and microbial "secondary genomes" have co-evolved to shape neurodevelopment through the gut-brain axis. Microbial communities generate metabolites that cross blood-brain and placental barriers, influencing synaptogenesis, immune responses, and neural circuit formation. Simultaneously, Human Accelerated Regions (HARs) and Endogenous Retroviruses (ERVs) modulate gene expression and immune pathways, determining which microbes thrive in the gut and impacting brain maturation. These factors converge to form a dynamic host-microbe dialogue with significant consequences for neurodevelopmental disorders (NDD), including autism spectrum disorder (ASD), attention-deficit/hyperactivity disorder (ADHD), and schizophrenia. Building on evolutionary perspectives, the chapter elucidates how genetic and immune mechanisms orchestrate beneficial and pathological host-microbe interactions in early brain development. It then explores therapeutic strategies, such as probiotics, prebiotics, fecal microbiota transplantation, and CRISPR-driven microbial engineering, targeting gut dysbiosis to mitigate or prevent neurodevelopmental dysfunctions. Furthermore, innovative organ-on-chip models reveal mechanistic insights under physiologically relevant conditions, offering a translational bridge between in vitro experiments and clinical applications. As the field continues to evolve, this work underscores the translational potential of manipulating the microbiome to optimize neurological outcomes. It enriches our understanding of the intricate evolutionary interplay between host genomes and the microbial world.},
}
@article {pmid40414633,
year = {2025},
author = {Mi, J and Morys, J and Nowacka-Chmielewska, M and Burek, M},
title = {The role of microbiome in gut-brain-axis dysbiosis causing depression: From mechanisms to treatment.},
journal = {International review of neurobiology},
volume = {180},
number = {},
pages = {189-244},
doi = {10.1016/bs.irn.2025.03.006},
pmid = {40414633},
issn = {2162-5514},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Dysbiosis/metabolism/complications/microbiology ; Animals ; *Blood-Brain Barrier/metabolism ; *Brain/metabolism ; *Depression/microbiology/metabolism ; *Brain-Gut Axis/physiology ; },
abstract = {Gut microbiota not only affects the function of the gastrointestinal tract but also the function of other organs, including the brain. The microbiota-gut-brain axis reflects the constant bidirectional communication between the central nervous system and the gastrointestinal tract. Gut microbiota metabolites can cross brain barriers, the blood-brain barrier (BBB) and the blood-cerebrospinal fluid barrier (BCSF) and influence neuropsychiatric disorders, including depression. In recent years, the communication between the microbiome and brain in depression has been extensively studied in humans and animal models. In this chapter, we summarise the current literature on the role of gut microbiota in depression, focusing in particular on brain barriers and bidirectional gut-brain communication.},
}
@article {pmid40414632,
year = {2025},
author = {Srinivasan, S},
title = {Disruption in the human microbiome causing behavioural changes in bipolar disorder.},
journal = {International review of neurobiology},
volume = {180},
number = {},
pages = {157-187},
doi = {10.1016/bs.irn.2025.04.001},
pmid = {40414632},
issn = {2162-5514},
mesh = {Humans ; *Bipolar Disorder/microbiology/physiopathology/psychology ; *Gastrointestinal Microbiome/physiology ; *Microbiota/physiology ; },
abstract = {This chapter explores the intriguing and complex relationship between the human microbiome and Bipolar Disorder (BD). The microbiome, notably the gut microbiota, has been increasingly recognised as a key performer in brain health and disease. This is due to its role in the gut-brain axis, a bidirectional communication between the gastrointestinal tract and the central nervous system. Disruptions in the gut microbiota due to factors such as diet, and stress, may influence this axis and potentially trigger or exacerbate psychiatric conditions. Hence, we investigate into the present interpretation of the microbiome's role in mental health, concentrating on its impact on mood regulation and cognitive function. Consequently, we also explore the possible mechanisms through which microbiome disruption may pay to the behavioural changes observed in BD. Further exploration understand the complex interplay between the microbiome and BD and translate these findings into effective therapeutic plans.},
}
@article {pmid40414631,
year = {2025},
author = {Krishnan, D and Ghosh, P and Lakshman, N and Justin, A and Ramasamy, S},
title = {Oro-pharyngeal mucosal microbiome alternations causing immune system dysregulation in schizophrenia.},
journal = {International review of neurobiology},
volume = {180},
number = {},
pages = {125-156},
doi = {10.1016/bs.irn.2025.03.003},
pmid = {40414631},
issn = {2162-5514},
mesh = {Humans ; *Schizophrenia/immunology/microbiology ; *Microbiota/immunology/physiology ; *Oropharynx/microbiology/immunology ; *Mouth Mucosa/microbiology/immunology ; },
abstract = {Schizophrenia is a chronic and thoughtful psychological disorder that affects a person's thinking, feelings, and behaviours. Multi-factorial genetic, environmental, and neurological variables cause it. Recently, more research focused on the human microbiome, which alters the immune system and develops adverse health effects on the human body. The study discusses a possible relationship between the oropharyngeal microbiome and schizophrenia. According to recent studies, the oropharyngeal microbiome may alter the immune system in the human body and cause various psychiatric disorders, including schizophrenia. The oropharyngeal microbiome can cause schizophrenia either by affecting the genes, chromosomes, and immune system in the human body. Additionally, it examines the combined mechanism of how the oropharyngeal microbiome's alterations lead to genetic abnormalities and immune dysregulation in schizophrenia. By combining the various approaches, this chapter offers a comprehensive view of the oropharyngeal microbiome's role in schizophrenia and suggests that microbial alterations could serve as biomarkers or therapeutic targets for the disorder.},
}
@article {pmid40414257,
year = {2025},
author = {Bostanci, N and Manoil, D and Van Holm, W and Belibasakis, GN and Teughels, W},
title = {Microbial Markers for Diagnosis and Risk Assessment for Periodontal Diseases: A Systematic Literature Search and Narrative Synthesis.},
journal = {Journal of clinical periodontology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jcpe.14183},
pmid = {40414257},
issn = {1600-051X},
support = {01-11-2021//Vetenskapsr&#xe5;det/ ; 01-11-2024//Vetenskapsr&#xe5;det/ ; //Funding for "Senior Clinical Associates" from the Faculty of Medicine of the University of Geneva/ ; FoUI-966140//Steering Group for Odontological Research/ ; FoUI-978687//Steering Group for Odontological Research/ ; },
abstract = {AIM: To examine the accuracy of microbiological biomarkers in diagnosing periodontal diseases, specifically addressing three focus questions: (FQ1) distinguishing health from disease; (FQ2) predicting disease progression; and (FQ3) assessing treatment outcomes.<br><br>MATERIALS AND METHODS: A PRISMA-guided search in MEDLINE, EMBAS and WEB OF SCIENCE included cross-sectional and longitudinal studies (e.g., randomised controlled trials, cohort studies) with &#x2265;&#x2009;20 participants per group. Eligible studies involved individuals diagnosed with periodontal health, gingivitis or periodontitis, based on well-defined clinical criteria, and utilised microbiological analyses of oral fluids and/or dental plaque. Diagnostic accuracy had to be evaluated using sensitivity, specificity or area under the receiver operating characteristic (ROC) curve (AUC), or alternatively, data for their computation had to be provided.<br><br>RESULTS: Thirty-one studies were included, mostly cross-sectional or case-control, with significant variability in sampling sites, microbial analyses and diagnostic definitions, complicating direct comparisons. Frequently investigated biomarkers included Aggregatibacter actinomycetemcomitans (JP2 genotype), Porphyromonas gingivalis, Tannerella forsythia and Treponema denticola. The highest diagnostic accuracy (AUC >&#x2009;0.95) was achieved through composite microbiome-based metrics such as the subgingival microbial dysbiosis index. However, methodological heterogeneity and inconsistent criteria limited reliability.<br><br>CONCLUSION: Although microbiological biomarkers hold promise for periodontal disease diagnostics and monitoring, current evidence is insufficient for clinical implementation. Future research should standardise methodologies, sampling protocols and diagnostic criteria to ensure robust validation and facilitate integration into precision dentistry.},
}
@article {pmid40414140,
year = {2025},
author = {Kolev, M and Kremer, AE and Sokollik, C and Gershwin, ME and Terziroli Beretta-Piccoli, B and , },
title = {Unmet needs in autoimmune liver diseases.},
journal = {Current opinion in immunology},
volume = {95},
number = {},
pages = {102565},
doi = {10.1016/j.coi.2025.102565},
pmid = {40414140},
issn = {1879-0372},
abstract = {Autoimmune hepatitis, primary biliary cholangitis, and primary sclerosing cholangitis are well-defined autoimmune liver diseases, the pathophysiology of which remains enigmatic. While major therapeutic advances have been achieved for many other autoimmune diseases, precision therapy for these diseases has lagged. For example, limited data exist on the use of innovative drugs targeting the immune system, such as monoclonal antibodies that block immune checkpoint, mRNA vaccines, the influence of infections, the microbiome, and drugs on loss of tolerance in liver autoimmunity. The knowledge on recent radiological techniques, on the expanding role of artificial intelligence in medicine, and on the relationship between the pediatric and adult phenotypes also urgently needs to be advanced in liver autoimmunity. Increased patient involvement focusing on individual symptom burden is also crucial for improving long-term quality of treatment. The fourth Swiss Autoimmune Liver Disease Meeting provided a unique interdisciplinary platform for experts and patients to discuss critical gaps. This opinion paper highlights the discussions on unmet needs and potential solutions in autoimmune liver diseases.},
}
@article {pmid40413951,
year = {2025},
author = {Li, Z and Liu, H},
title = {Microbe-dependent and independent effects of diet on metabolic inflammation in glucose metabolism regulation.},
journal = {Food chemistry},
volume = {488},
number = {},
pages = {144852},
doi = {10.1016/j.foodchem.2025.144852},
pmid = {40413951},
issn = {1873-7072},
abstract = {Diet can contribute to the development of metabolic disease including type 2 diabetes (T2D) by inducing metabolic inflammation. While the gut microbiota mediates the effects of diet, the diet can also exert its effects independent of gut microbes. The microbe-dependent and -independent effects of diet on inflammation remain to be elucidated. This review examines recent advances and dissects the specifics of both gut microbe-dependent and independent mechanisms through which diet impacts inflammation and glucose metabolism. We delineate how diet interacts with the gut microbiome and induces metabolic inflammation. We also describe the direct effects of dietary components and their related metabolites on the immune system, and explore how diet-induced sterile inflammation may contribute to metabolic disorders. It is important to consider both microbe-dependent and independent pathways when developing therapeutic approaches aimed at preventing T2D.},
}
@article {pmid40413912,
year = {2025},
author = {Li, Z and Zhou, Y and Lv, L and Long, Y and Dong, M and Xiao, Q and Jia, X and Ju, D and Sun, X and Huang, F and Cai, M and Zhang, J and Yu, Z and Zheng, L},
title = {Host-mediated environmental microbiome recruitment by black soldier fly (Hermetia illucens) enhances waste biotransformation.},
journal = {Waste management (New York, N.Y.)},
volume = {204},
number = {},
pages = {114886},
doi = {10.1016/j.wasman.2025.114886},
pmid = {40413912},
issn = {1879-2456},
abstract = {The black soldier fly larvae (BSFL) have demonstrated the ability to convert organic waste into high-quality proteins, lipids, and chitin on an industrial scale. This study aimed to examine the influence of exogenous microbes on the growth and development of BSFL by comparing Germ-free and normal BSFL that were reared on different substrates. Furthermore, the research evaluated the effects of microbes associated with the eggs. The results demonstrated that BSFL actively recruited specific functional microbes from their environment to facilitate growth and developmental processes. These recruited exogenous microbial consortia, originating from artificial substrates, kitchen waste, chicken manure, and egg-carrying microbiota, significantly enhanced Germ-free BSFL performance through improved larval viability, increased material conversion efficiency, elevated average body weight, and reduced pupal stage duration compared to Germ-free groups. The isolation and functional validation of intestinal microbiota identified Enterococcus, Bacillus, and Lactobacillus as core taxa for consortium formulation. This synthetic microbial community exhibited robust growth-promoting effects on BSFL, with maximal efficacy observed in chicken manure bioconversion systems, achieving 72.1 %, 193.6 % and 439.59 % enhancements in larval survival, biomass accumulation and feed conversion rate, respectively, alongside a 62.4 % reduction in prepupal development time compared to non-inoculated controls. Mechanistic analysis revealed a host-driven microbial recruitment strategy wherein BSFL selectively enriched functional symbionts to optimize environmental adaptation. These mutualistic interactions enhanced larval niche specialization and waste metabolic capacity, demonstrating scalable potential for circular waste valorization and sustainable bioremediation protocols.},
}
@article {pmid40413833,
year = {2025},
author = {Wu, M and Li, G},
title = {Mycoviruses and their ecological impacts on fungi.},
journal = {Virology},
volume = {610},
number = {},
pages = {110562},
doi = {10.1016/j.virol.2025.110562},
pmid = {40413833},
issn = {1096-0341},
abstract = {Mycoviruses, as components of the endohyphal microbiome, have been extensively identified in major fungal and oomycetous groups. While most mycoviral infections are asymptomatic, quite a few mycoviruses significantly affect biological characteristics of their hosts. This review emphasizes the roles of mycoviruses in the ecological adaptation of host fungi and oomycetes. Traditional views suggest that mycoviruses are primarily transmitted vertically through spores or horizontally among different individuals via hyphal fusion or anastomosis. However, recent studies have documented instances of mycoviral transmission between species, even across different kingdoms, as well as through specific vectors, suggesting the presence of additional transmission pathways. Although the majority of mycoviruses exert little to no influence on host phenotypes, certain mycoviral infections can significantly impact host fitness. Notably, recent research indicates that mycoviruses can alter interactions between fungi and plants. These findings may offer innovative strategies for the application of mycoviruses in management of plant diseases caused by fungi and oomycetes.},
}
@article {pmid40413742,
year = {2025},
author = {Fernández-Pato, A and Sinha, T and Garmaeva, S and Gulyaeva, A and Kuzub, N and Roux, S and Fu, J and Kurilshikov, A and Zhernakova, A},
title = {Early-life development of the gut virome and plasmidome: A longitudinal study in cesarean-born infants.},
journal = {Cell reports},
volume = {44},
number = {6},
pages = {115731},
doi = {10.1016/j.celrep.2025.115731},
pmid = {40413742},
issn = {2211-1247},
abstract = {Mobile genetic elements (MGE) are critical yet understudied determinants of gut microbiome composition. In this secondary analysis of a randomized controlled trial (NCT06030713), we characterized the gut virome and plasmidome in 195 samples from 28 mother-infant dyads delivered by cesarean section. Infant mobilome increases in richness over the first 6 postnatal weeks, demonstrating high individual-specificity and temporal stability, establishing a personal persistent mobilome. Formula-fed infants exhibit greater mobilome richness than breastfed infants, with plasmid composition being influenced by antibiotic exposure and birth weight. Plasmids constitute a reservoir of antibiotic resistance genes (ARG), with around 5% of infant gut plasmid taxonomic units carrying ARG. Notably, ARG profiles do not differ with antibiotic exposure at birth. Mother-infant sharing of viral and plasmid strains primarily occurs after 6 months of age. Overall, our integrative analysis offers insights into the dynamics, modulation, and origin of MGE in the developing gut microbiome.},
}
@article {pmid40413728,
year = {2025},
author = {Kousgaard, SJ and Dall, SM and Albertsen, M and Nielsen, HL and Thorlacius-Ussing, O},
title = {Fecal microbiota transplantation from a healthy pouch donor for chronic pouchitis: a proof-of-concept study.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2510464},
doi = {10.1080/19490976.2025.2510464},
pmid = {40413728},
issn = {1949-0984},
mesh = {Humans ; *Pouchitis/therapy/microbiology ; *Fecal Microbiota Transplantation/adverse effects/methods ; Male ; Female ; Adult ; Middle Aged ; Feces/microbiology ; Quality of Life ; Chronic Disease/therapy ; Gastrointestinal Microbiome ; Proof of Concept Study ; Treatment Outcome ; Tissue Donors ; Denmark ; },
abstract = {Chronic pouchitis is a common complication after ileal pouch-anal anastomosis (IPAA) with limited treatment options. In this case series, we aimed to investigate clinical and microbiome changes, as well as adverse events, associated with using fecal microbiota transplantation (FMT) from a donor with a normal functioning IPAA to induce remission in patients with chronic pouchitis. Methods The study was a case-series including a 4-week intervention period and 12-month follow-up. Patients with chronic pouchitis who met the inclusion criteria were recruited from the Department of Gastrointestinal Surgery at Aalborg University Hospital, Denmark. Participants received FMT derived from a donor with a normal functioning IPAA. Treatment was administered by enema daily for two weeks, then every other day for two more weeks. Disease severity and quality of life (QoL) were accessed at baseline and 30-day follow-up. Clinical remission was defined as Pouchitis Disease Activity Index (PDAI) <7. Fecal samples from participants, healthy donors, and the IPAA donor were analyzed using shotgun metagenomic sequencing. Results Three patients with chronic pouchitis were included and completed the treatment protocol and follow-up visits. At the 30-day follow-up, all participants achieved clinical remission with reduced endoscopic inflammation. The median total PDAI score decreased from 8 (range 10-8) at baseline to 6 (range 6-5) at 30 days. Two participants reported improved QoL, while one reported no change. Few mild, self-limited adverse events were reported by all participants during treatment, with no serious events. Principal component analysis of fecal samples distinguished two clusters: healthy donors and the IPAA donor, with participant samples forming a separate cluster Conclusion We observed that all participants achieved clinical remission with reduced endoscopic inflammation following a 4-week FMT intervention. Adverse events were mild and self-limited. Metagenomic analysis revealed distinct microbiome clusters between IPAA donor and recipients, both of which differed from those of healthy donors.},
}
@article {pmid40413516,
year = {2025},
author = {Hashimoto, R and Nishiyama, K and Namai, F and Suzuki, K and Sakuma, T and Fukuda, I and Sugiyama, Y and Okano, K and Shanoh, T and Toyoshi, E and Ohgi, R and Saha, S and Tsuchida, S and Nishiyama, E and Mukai, T and Furukawa, M and Nochi, T and Villena, J and Ikeda-Ohtsubo, W and Yoshioka, G and Nakazaki, E and Suda, Y and Kitazawa, H},
title = {Milk sialyl-oligosaccharides mediate the early colonization of gut commensal microbes in piglets.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {135},
pmid = {40413516},
issn = {2049-2618},
support = {23K27051//Japan Society for the Promotion of Science/ ; 23K19327//Japan Society for the Promotion of Science/ ; 23K18072//Japan Society for the Promotion of Science/ ; 2023//Japanese Dairy Science Association/ ; JPJ007097//Development of Innovative Technology grants BRAIN/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; *Oligosaccharides/metabolism/chemistry ; Swine/microbiology ; *Milk/chemistry ; *Lactobacillus/metabolism/isolation &amp; purification/classification/growth &amp; development ; Fatty Acids, Volatile/metabolism ; Symbiosis ; },
abstract = {BACKGROUND: The suckling period in pigs is a key phase in development for shaping the gut microbiota, which is essential for maintaining biological homeostasis in neonates. In piglets fed sow milk, the gut microbiota comprises predominantly lactobacilli, indicating a host-gut microbiota symbiosis that is influenced by sow milk components. In this study, we sought to elucidate the mechanisms underlying the establishment and maintenance of the gut microbiome in suckling piglets, with a specific focus on the metabolism of sialyl-oligosaccharides by lactobacilli.<br><br>RESULTS: Based on liquid chromatography-mass spectrometry analysis, we identified 3'-sialyl-lactose (3'SL) as the major oligosaccharide in porcine milk, and microbiome profiling revealed the predominance of Ligilactobacillus salivarius during the suckling period, with a subsequent transition to Limosilactobacillus reuteri dominance post-weaning. Notably, sialic acid metabolism was established to be exclusively attributable to L. salivarius, thereby highlighting the pivotal role of 3'SL in determining species-specific bacterial segregation. L. salivarius was found to metabolize 3'SL when co-cultured with Bacteroides thetaiotaomicron, resulting in a shift in the predominant short-chain fatty acid produced, from lactate to acetate. This metabolic shift, in turn, inhibits the growth of enterotoxigenic Escherichia coli. Furthermore, the comparison of the gut microbiota between suckling piglets and those fed a low-3'SL formula revealed distinct diversity profiles. We accordingly speculate that an absence of sialyl-oligosaccharides in the formula-fed piglets may have restricted the growth of sialic acid-utilizing bacteria such as L. salivarius, thereby leading to a higher abundance of Enterobacteriaceae.<br><br>CONCLUSIONS: Our findings reveal the influence of sialyl-oligosaccharides in promoting microbial diversity and gut homeostasis, thereby highlighting the importance of sialic acid as a key factor in shaping milk-driven microbial colonization during the early stages of piglet development. Video Abstract.},
}
@article {pmid40413401,
year = {2025},
author = {Qi, Y and Lei, Y and Ahmed, T and Cheng, F and Lei, K and Yang, H and Ali, HM and Li, Z and Qi, X},
title = {Low-intensity laser exposure enhances rice (Oryza sativa L.) growth through physio-biochemical regulation, transcriptional modulation, and microbiome alteration.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {698},
pmid = {40413401},
issn = {1471-2229},
support = {ZJ2024084//Postdoctoral Research Funding Project of Zhejiang Province/ ; RSP2025R123//King Saud University/ ; 2024SNJF009//Zhejiang Agriculture and Rural Affairs Project/ ; 2023C1S02002//Project of Xianghu Laboratory/ ; 2024SSYS0100//Science and Technology Planning Project of Zhejiang Province/ ; },
mesh = {*Oryza/growth &amp; development/radiation effects/microbiology/genetics/physiology ; *Microbiota/radiation effects ; Gene Expression Regulation, Plant/radiation effects ; *Lasers ; Rhizosphere ; Seedlings/growth &amp; development/radiation effects ; Photosynthesis/radiation effects ; Plant Roots/growth &amp; development/radiation effects/microbiology ; },
abstract = {Environmental stressors significantly impact plant growth and agricultural productivity, necessitating innovative approaches to enhance crop resilience and yield. While high-intensity laser applications in agriculture have traditionally been limited to destructive purposes due to their harmful effects on plant growth, the emergence of low-intensity laser technology presents new opportunities for crop improvement. However, the molecular mechanisms underlying the beneficial effects of low-intensity laser treatment remain largely unexplored. This study investigated the effects of low-intensity laser treatment on rice seedling growth, physiological and molecular responses, and rhizosphere microbial communities. Low-intensity laser treatment (2 µmol/m[2]/s PPFD) significantly enhanced root and shoot growth, enhanced biomass accumulation, and improved yield parameters, with a 16.8% increase in effective panicles and 9.01% higher yield per plant. Physiological analyses revealed elevated antioxidant enzyme activities (POD and SOD) and reduced ROS levels in treated plants. Transmission electron microscopy showed improved chloroplast structure, correlating with enhanced photosynthetic efficiency. Transcriptomic analysis identified 623 differentially expressed genes, with significant enrichment in pathways related to photosynthesis, carbon metabolism, and hormone signaling. Notably upregulation was observed in photosynthesis-related genes (OsPsbB and OsCYF) and hormone signaling genes (OsWRKY114 and OsWRI1). Additionally, 16S rRNA sequencing revealed significant restructuring of rhizosphere bacterial communities in laser-treated plants, with enrichment of beneficial genera including Pseudomonas and Enterobacter. These findings establish low-intensity laser treatment as a promising tool for enhancing rice productivity through coordinated regulation of photosynthetic efficiency, stress responses, and beneficial microbiome interactions.},
}
@article {pmid40413198,
year = {2025},
author = {Brandão Gontijo, J and Huang, L and Levintal, E and Prieto García, C and Erikson, CB and Coyotl, A and Horwath, WR and Dahlke, HE and Mazza Rodrigues, JL},
title = {Depth-dependent Metagenome-Assembled Genomes of Agricultural Soils under Managed Aquifer Recharge.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {858},
pmid = {40413198},
issn = {2052-4463},
support = {7975//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; 2021-38420-34070//United States Department of Agriculture | National Institute of Food and Agriculture (NIFA)/ ; },
mesh = {*Soil Microbiology ; *Groundwater ; Agriculture ; *Metagenome ; Microbiota ; Bacteria/genetics/classification ; Metagenomics ; California ; Archaea/genetics ; Soil ; },
abstract = {Managed Aquifer Recharge (MAR) systems, which intentionally replenish groundwater aquifers with excess water, are critical for addressing water scarcity exacerbated by demographic shifts and climate variability. To date, little is known about the functional diversity of the soil microbiome at different soil depth inhabiting agricultural soils used for MAR. Knowing the functional diversity is pivotal in regulating nutrient cycling and maintaining soil health. Metagenomics, particularly Metagenome-Assembled Genomes (MAGs), provide a powerful tool to explore the diversity of uncultivated soil microbes, facilitating in-depth investigations into microbial functions. In a field experiment conducted in a California vineyard, we sequenced soil DNA before and after water application of MAR. Through this process, we assembled 146 medium and 14 high-quality MAGs, uncovering a wide array of archaeal and bacterial taxa across different soil depths. These findings advance our understanding of the microbial ecology and functional diversity of soils used for MAR, contributing to the development of more informed and sustainable land management strategies.},
}
@article {pmid40412609,
year = {2025},
author = {Zhu, W and Yuan, Y and Guan, X and Xie, Q and Sun, X and Dong, Z},
title = {Gut microbiota-derived extracellular vesicles: Exploring the pathogenesis and treatment of neuropsychiatric disorders.},
journal = {Life sciences},
volume = {},
number = {},
pages = {123750},
doi = {10.1016/j.lfs.2025.123750},
pmid = {40412609},
issn = {1879-0631},
abstract = {The gut microbiome is connected to the pathogenesis of various neuropsychiatric disorders, including cognitive impairment and depression. The gut microbiota can act on the brain through multiple pathways along the gut-brain axis. However, the specific mechanisms are unclear. Bacterial extracellular vesicles (BEVs), bacteria-derived membrane-bound vesicles that can carry a variety of bioactive substances and cross various barriers in the host, are used by bacteria to communicate and interact with the host. Recent studies have shown that BEVs from the gut microbiota are involved in gut-brain communication and may play a role in the pathogenesis and treatment of neuropsychiatric disorders. This review provides an overview of the biogenesis, structure, and function of BEVs and emphasizes their role in the development and treatment of neuropsychiatric disorders.},
}
@article {pmid40412571,
year = {2025},
author = {Saco, A and Rey-Campos, M and Panebianco, A and Novoa, B and Figueras, A},
title = {Comparative transcriptomics reveals different grades of susceptibility to a bacterial infection in bivalves.},
journal = {Fish &amp; shellfish immunology},
volume = {},
number = {},
pages = {110443},
doi = {10.1016/j.fsi.2025.110443},
pmid = {40412571},
issn = {1095-9947},
abstract = {Because of their filtering activity, bivalve species are constantly exposed to the wide presence of pathogenic microorganisms in seawater. In this work, the transcriptomic response after a waterborne bacterial infection with Vibrio splendidus was analyzed in hemolymph hemocytes from three bivalve species present in the same environment in Galicia: mussels (Mytilus galloprovincialis), cockles (Cerastoderma edule) and clams (Ruditapes decussatus). A clear transcriptomic immune modulation was observed in mussels and cockles, with shared responses such as immune recognition, inflammation, and oxidative stress. However, there were apparent differences, such as retrotransposons' regulation and apoptosis inhibition, exclusive to mussels. On the contrary, clams had very few modulated genes and almost no response to the infection. Metatranscriptomics showed each species' bacterial microbiome signature and a very high prevalence of Vibrio in the non-responsive clam individuals. These Vibrio reads were retrieved and used for a dual transcriptomics approach that revealed modulated bacterial genes related to their virulence in the clam samples, indicating that the bacteria could be in control of this interaction. This work showed that there are clear differences between the innate immune systems of different bivalves to the same infection and could indicate a greater vulnerability of the clam to certain bacterial pathogens.},
}
@article {pmid40412567,
year = {2025},
author = {Yang, R and Xu, Y and Zhu, F and Ma, X and Fan, T and Wang, HL},
title = {Gut microbiome, a potential modulator of neuroepigenome.},
journal = {The Journal of nutritional biochemistry},
volume = {},
number = {},
pages = {109961},
doi = {10.1016/j.jnutbio.2025.109961},
pmid = {40412567},
issn = {1873-4847},
abstract = {Gut microbiome has a considerable impact on the central nervous system via the "gut-brain axis". Neuroepigenome emerges as the interface between environment and genes, potentially help conveying the signals derived from the microbiome to the brain tissue. While only a limited number of studies have implicated epigenetic roles in the gut-brain axis, this review explores how gut microbiome might impact various brain-based epigenetic mechanisms, including DNA methylation, histone modification, ncRNA and RNA methylation, notably in the context of the specific neural complications. Among the epigenetic mechanisms, histone acetylation was most well-studied with respect to its relationships with gut microbiome, exerting a dynamic influence on gene expression in the brain. Furthermore, the pathways connecting gut bacteria to neuroepigenome were summarized, highlighting the roles of metabolites such as butyrate, propionate, acetate, lactate, and folate. Of particular interest, the roles of butyrate are emphasized due to their outstanding inhibitory activity towards histone deacetylases (HDACs), among other mechanisms. It is worth noting that some indirect gut-brain pathways may also be associated with the interplay between microbiome and neuroepigenome, while IL-6 has been found to effectively transmit microbe-derived signals to histone methylation in brains. Finally, we recapitulate the future perspectives critical to understanding this gut-brain crosstalk, such as clarifying the cause-and-effect relationship, bacterial cross-feeding within the gut, and the mechanisms underlying the site-specific histone modification in the brain. Together, this review attempts to consolidate our current knowledge about the "microbiome-neuroepigenome interplay" and propose a conceptual pathway to decipher the gut-brain axis in various neurological conditions.},
}
@article {pmid40412325,
year = {2025},
author = {Ding, Y and Zheng, JT and Du, S and Wu, D and Hu, F and Zhu, D},
title = {Pivotal role of earthworm gut protists in mediating antibiotic resistance genes under microplastic and sulfamethoxazole stress in soil-earthworm systems.},
journal = {Journal of hazardous materials},
volume = {494},
number = {},
pages = {138681},
doi = {10.1016/j.jhazmat.2025.138681},
pmid = {40412325},
issn = {1873-3336},
abstract = {Microplastics (MPs) are currently receiving widespread attention worldwide, and their co-occurrence with antibiotics is unavoidable. However, our understanding of how protists respond to co-pollution and mediate antibiotic resistance genes (ARGs) profiles remains exceedingly limited, particularly within non-target animals' guts. To bridge these gaps, we investigated the individual and combined effects of polyethylene and sulfamethoxazole (SMZ) on microbial communities and ARGs in soil and earthworm guts. We found that the MP-SMZ combination significantly elevated the abundance and richness of ARGs in the soil and earthworm. Protistan compositions (particularly consumers) responded more strongly to pollutants than did bacterial and fungal communities, especially under combined pollution. Interkingdom cooccurrence network analysis revealed that protists had stronger and more effective interactions with the resistome in the earthworm guts, suggesting that the impact of these protists on ARGs compositional changes was potentially modulated through the "top-down" regulation of bacteria and fungi. Meta-cooccurrence networks further confirmed that protist-related networks had more keystone pollution-sensitive ASVs (psASVs) and these psASVs were mostly associated with protistan consumers. Our study highlights protists as promising agents for regulating and monitoring microbial functions, as well as the ecological risks of the antibiotic resistome associated with MPs and SMZ pollution in agricultural ecosystems.},
}
@article {pmid40412269,
year = {2025},
author = {Zhang, R and Gao, Y and Fan, X and Zhu, S and Wang, T and Gao, L and Zhao, X and Ma, Z and Fan, Y and Jiang, D and Liu, S},
title = {Deciphering the preservative effects of protamine from Xinjiang Coregonus peled on grass carp (Ctenopharyngodon idellus) fillets during refrigerated storage: a perspective from the microbiome.},
journal = {International journal of food microbiology},
volume = {440},
number = {},
pages = {111222},
doi = {10.1016/j.ijfoodmicro.2025.111222},
pmid = {40412269},
issn = {1879-3460},
abstract = {Protamine is a natural cationic peptide which has been utilized as a food preservative, since its antibacterial capability against a wide range of Gram-negative and -positive bacteria. Despite the antibacterial mechanism has been well uncovered, its role in complex food microbial communities is largely elusive. In the present study, grass carp (Ctenopharyngodon idellus) fillets were treated with protamine and a protamine-based compound preservative, and stored at 4 °C for 15 days. The pH, total viable count (TVC), and total volatile base nitrogen (TVB-N) were monitored during the refrigerated storage, as well as the bacterial communities by 16S rRNA amplicon sequencing. Protamine, especially the protamine compound preservative, reduced the pH, TVC and TVB-N during the storage, and prolonged the shelf life of fish fillets. Bacterial communities on fillets during the refrigerated storage challenged by protamine and its compound preservative significantly differed from that in control. Prevalent genera including Aeromonas, Pseudomonas, and Myroides were significantly altered by protamine treatment. A group of 18 genera were closely associated with the antibacterial activity of protamine. The fillets treated with protamine possessed a more complex and stable bacterial community. Our study depicted a dynamic alteration of bacterial communities during the refrigerated storage of fish fillets, and offered an insight into the understanding of the antibacterial mechanisms of protamine from a microbiota perspective.},
}
@article {pmid40412026,
year = {2025},
author = {Lahouty, M and Fadaee, M and Aghaei, R and Alizadeh, F and Jafari, A and Sharifi, Y},
title = {Gut microbiome and colorectal cancer: From pathogenesis to treatment.},
journal = {Pathology, research and practice},
volume = {271},
number = {},
pages = {156034},
doi = {10.1016/j.prp.2025.156034},
pmid = {40412026},
issn = {1618-0631},
abstract = {Colorectal cancer (CRC) continues to rank among the most prevalent cancers worldwide. A growing body of research indicates that the microbiome significantly influences the onset, development, and progression of CRC, in addition to affecting the efficacy of various systemic therapies. The composition of the microbiome, shaped by factors such as bacterial strains, geography, ethnicity, gender, and dietary habits, provides essential information for CRC screening, early diagnosis, and the prediction of treatment responses. Modulating the microbiome presents a highly promising medical strategy for improving individual health. This review aims to present a thorough overview of recent research concerning the interplay between host microbiota and CRC, along with its implications for screening and the immune response against tumors in the context of cancer treatment.},
}
@article {pmid40411603,
year = {2025},
author = {Georgakis, N and Premetis, GE and Pantiora, P and Varotsou, C and Bodourian, CS and Labrou, NE},
title = {The impact of metagenomic analysis on the discovery of novel endolysins.},
journal = {Applied microbiology and biotechnology},
volume = {109},
number = {1},
pages = {126},
pmid = {40411603},
issn = {1432-0614},
support = {4036//HFRI/ ; },
mesh = {*Metagenomics/methods ; *Endopeptidases/genetics/isolation &amp; purification/pharmacology/metabolism ; Bacteriophages/enzymology/genetics ; Anti-Bacterial Agents/pharmacology ; Computational Biology ; Humans ; },
abstract = {Metagenomics has revolutionized enzyme discovery by enabling the study of genetic material directly from environmental samples, bypassing the need for microbial cultivation. This approach is particularly effective for identifying novel endolysins, phage-derived enzymes with antibacterial properties suited for therapeutic and industrial applications. Diverse ecosystems, such as biofilms, human microbiome, hot springs, and geothermal areas, serve as rich reservoirs for endolysins with traits like thermostability, broad-spectrum activity, specificity and resistance to harsh conditions. Functional metagenomics, complemented by bioinformatics, enables the discovery and annotation of previously uncharacterized endolysins. Examples of endolysins discovered from metagenomics analysis are discussed. Despite the challenges of analyzing complex microbial ecosystems and isolating target genes, metagenomics holds immense potential for uncovering innovative endolysins, paving the way for developing new biotechnological applications. KEY POINTS: • Endolysins offer antibacterial potential for therapeutic and industrial use. • Metagenomics enables discovery of novel endolysins from diverse ecosystems. • Advances in tools and methods have accelerated novel endolysins discovery.},
}
@article {pmid40411594,
year = {2025},
author = {Dash, HR and Patel, A},
title = {Genealogically bewildered individuals and forensic identification: a review of current and emerging solutions.},
journal = {International journal of legal medicine},
volume = {},
number = {},
pages = {},
pmid = {40411594},
issn = {1437-1596},
abstract = {The increasing use of assisted reproductive technologies (ART) with donor gametes is driven by rising infertility rates, delayed parenthood, and the need to prevent hereditary diseases. Greater social acceptance of diverse family structures, advancements in reproductive medicine, and improving success rates also contribute. Accessibility, affordability, and cross-border reproductive care further expand ART's reach, making donor gametes a preferred option for many individuals and couples worldwide. The widespread application of ART has led to an increasing number of donor-conceived individuals, many of whom are now reaching reproductive maturity. This demographic shift introduces significant challenges for traditional forensic genetic identification methods, which rely on biological reference samples from genetically related individuals. The absence of such samples complicates the identification process, particularly for individuals conceived via gamete donation or adoption, where biological and legal parentage are incongruent. Conventional forensic genetic analyses, including short tandem repeat (STR) and single nucleotide polymorphism (SNP) profiling of autosomal, Y-chromosome, X-chromosome, and mitochondrial DNA, exhibit limited efficacy in these scenarios. While these methods can sometimes identify individuals conceived using a single donor gamete, they are insufficient for cases involving dual donor gametes or mitochondrial replacement therapy. Emerging methodologies such as forensic genetic genealogy, DNA methylation profiling, and human microbiome analysis offer innovative approaches but necessitate further clinical validation and standardization.},
}
@article {pmid40411560,
year = {2025},
author = {Xu, J and Yang, J and Sun, Q and Chang, J and Wang, F},
title = {Analyses of single-cell RNA sequencing uncover the role of intratumoral Helicobacter pylori in shaping tumor progression and immunity in gastric cancer.},
journal = {Cancer immunology, immunotherapy : CII},
volume = {74},
number = {7},
pages = {218},
pmid = {40411560},
issn = {1432-0851},
support = {2024-QN-17//Institutional Foundation of The First Affiliated Hospital of Xi'an Jiaotong University/ ; QT264//Cancer Precision Medical Science System and Service Platform Building National Major Disease Multidisciplinary Collaborative Diagnosis and Treatment Capacity Building Program/ ; 81902680//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Stomach Neoplasms/immunology/microbiology/pathology/genetics ; *Helicobacter pylori/immunology/isolation &amp; purification ; Single-Cell Analysis/methods ; *Helicobacter Infections/immunology/microbiology/complications ; Disease Progression ; Sequence Analysis, RNA/methods ; Female ; Male ; Prognosis ; Middle Aged ; },
abstract = {The intratumoral microbiota is closely associated with tumor initiation and progression in multiple solid tumors, including gastric cancer (GC). Single-cell analysis of host-microbiome interactions (SAHMI) is a pipeline used to systematically recover and denoise microbial signals in human clinical tissues and examine tumor-microbiome interactions at the single-cell transcriptome level. In a large GC cohort, we used SAHMI to detect 12 bacteria, among which Helicobacter pylori (H. pylori) was widely present in multiple tumor and normal samples. Meanwhile, we verified the presence of H. pylori in GC tissues via fluorescence in situ hybridization and immunohistochemistry. We performed single-cell RNA sequencing to analyze 11 cell populations, including B cells, T cells, and epithelial cells, and these cell types contained large numbers of H. pylori. We detected obvious enrichment of H. pylori in cancer cells and identified 13 upregulated differentially expressed genes exhibiting significantly negative correlations with patient survival in the H. pylori-positive tumor group compared with the findings in the other groups, indicating that these genes could represent prognostic biomarkers or therapeutic targets for H. pylori-infected patients with GC. Moreover, H. pylori-enriched immune cells, including T cells, B cells, and macrophages, were associated with cell-type-specific gene expression and pathway activities, including cell fate and immune signaling. In summary, tumor-microbiome interactions might reflect or influence tumorigenesis in GC, which has implications for clinical practice.},
}
@article {pmid40411542,
year = {2025},
author = {Guo, Z and Liu, S and Hu, Z and Pan, X and Zhang, W and Zhang, Z},
title = {Potential associations between gut and skin microbiota and lung cancer: a bidirectional Mendelian randomization analysis.},
journal = {Discover oncology},
volume = {16},
number = {1},
pages = {906},
pmid = {40411542},
issn = {2730-6011},
support = {2022J011000//Natural Science Foundation of Fujian Province/ ; },
abstract = {BACKGROUND: Recent research has demonstrated that microbes have a vital impact on cancer by governing immune responses, managing inflammation, and employing other methods. However, the specific relationship between the microbiome and lung cancer requires further investigation to be fully understood.<br><br>METHODS: Summary data regarding lung cancer outcomes and skin bacteria were sourced from the GWAS and GWAS catalog databases, respectively. Data on gut microbiota were acquired from the MiBioGen database. Using these datasets, we performed Mendelian randomization (MR) and linkage disequilibrium score regression (LDSC) analysis to evaluate the genetic relationships and possible relationships between gut and skin microbiota and lung cancer.<br><br>RESULTS: The LDSC analysis indicated that Bifidobacteria have a negative genetic correlation with lung cancer across order, family, and genus levels. Similarly, the Eubacterium Coprostanoligenes group displayed a negative genetic correlation at the genus level. Mendelian randomization analysis of gut and skin microbiome data further identified several microbiotas positively associated with lung cancer risk, including Eubacterium brachy group, Coprobacter genus, Adlercreutzia, Flavonifractor, Holdemanella, Anaerotruncus, Erysipelatoclostridium, and ASV045 [Acinetobacter]. Conversely, microbiota such as Bacteroidetes (phylum), Eubacterium rectale group, Prevotella 9, Ruminococcus1, Lachnospiraceae NK4A136 group, Gordonibacter, Eubacterium hallii group, Streptococcus genus, and ASV009 [D. nitroreducens] demonstrated a protective effect against lung cancer. Notably, the Coprobacter genus exhibited contrasting associations with lung cancer subtypes. Reverse Mendelian randomization did not reveal any potential effects of lung cancer on these microbiota abundances. Heterogeneity and pleiotropy analyses confirmed the robustness and reliability of these findings.<br><br>CONCLUSION: Our Mendelian randomization analysis identified multiple microbial communities that may be associated with lung cancer risk, highlighting the complex interactions between the microbiota and lung cancer development, providing valuable insights and promising research directions for microbiota-targeted prevention and treatment strategies for lung cancer.},
}
@article {pmid40411534,
year = {2025},
author = {Thomas, ZO and Holm, J and McCarthy, M and Nguyen, W and Pang, Y and Chrisman, LP and Guitart, J and Burns, MB and Zhou, XA},
title = {Decreased gut short-chain fatty acids in cutaneous T-cell lymphoma: a novel insight.},
journal = {Archives of dermatological research},
volume = {317},
number = {1},
pages = {781},
pmid = {40411534},
issn = {1432-069X},
support = {5KL2TR001424/NH/NIH HHS/United States ; },
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; Male ; Female ; *Fatty Acids, Volatile/metabolism ; Middle Aged ; *Dysbiosis/immunology/microbiology ; *Skin Neoplasms/immunology/microbiology/pathology/metabolism ; Aged ; Adult ; *Mycosis Fungoides/immunology/microbiology/pathology/metabolism ; Feces/microbiology/chemistry ; Case-Control Studies ; Pilot Projects ; Propionates/metabolism ; },
abstract = {Short-chain fatty acids (SCFAs) are critical metabolites produced by gut microbiota that play a key role in modulating inflammation and regulating systemic immunity, including against cancer. Decreases in SCFAs can foster a permissive tumor immune environment. Recent studies have shown that cutaneous T-cell lymphoma (CTCL) patients exhibit increasing gut dysbiosis and loss of bacteria predicted to produce SCFAs with increasing disease severity. To investigate this functional connection, we collected stool swab samples from 15 individuals- 8 mycosis fungoides (MF) patients and 7 matched healthy controls (HC)- and quantified concentrations of four SCFAs (acetate, propionate, isovalerate, butyrate) via liquid chromatography-mass spectrometry. Our results demonstrated significantly reduced acetate and propionate concentrations in MF patients when compared to HC (both p = 0.027). Total measured SCFA concentrations were on average lower in MF versus HC, but did not achieve statistical significance (p = 0.063). Both propionate and acetate have been previously demonstrated to promote tumor apoptosis, inhibit tumor proliferation, and enhance antitumor immunity. Thus, dysbiosis-associated reductions in SCFAs may be another contributive factor in the immune dysfunction observed in CTCL. Our pilot findings add to the growing body of knowledge implicating the gut microbiota-SCFA axis in CTCL pathogenesis and offer potential new avenues for therapeutic intervention.},
}
@article {pmid40410872,
year = {2025},
author = {Heyer, R and Wolf, M and Benndorf, D and Uzzau, S and Seifert, J and Grenga, L and Pabst, M and Schmitt, H and Mesuere, B and Van Den Bossche, T and Haange, SB and Jehmlich, N and Di Luca, M and Ferrer, M and Serrano-Villar, S and Armengaud, J and Bode, HB and Hellwig, P and Masselot, CR and Léonard, R and Wilmes, P},
title = {Metaproteomics in the One Health framework for unraveling microbial effectors in microbiomes.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {134},
pmid = {40410872},
issn = {2049-2618},
support = {ANR-20-CE34-0012//R&#xe9;gion Occitanie (DeepMicro grant)/ ; ANR-20-CE34-0012//R&#xe9;gion Occitanie (DeepMicro grant)/ ; ANR-24-INBS-0015//Agence Nationale de la Recherche/ ; ANR-24-INBS-0015//Agence Nationale de la Recherche/ ; 1286824N//Research Foundation Flanders (FWO)/ ; MICIU/AEI/10.13039/501100011033//Agencia Estatal de Investigaci&#xf3;n/ ; PID2023-153370OB-I00//NextGenerationEU/PRTR/ ; INMUNOBIOTA//CSIC (COCREA program)/ ; },
mesh = {*Proteomics/methods ; *Microbiota ; Humans ; Animals ; *One Health ; *Bacteria/metabolism/genetics ; Virulence Factors ; },
abstract = {One Health seeks to integrate and balance the health of humans, animals, and environmental systems, which are intricately linked through microbiomes. These microbial communities exchange microbes and genes, influencing not only human and animal health but also key environmental, agricultural, and biotechnological processes. Preventing the emergence of pathogens as well as monitoring and controlling the composition of microbiomes through microbial effectors including virulence factors, toxins, antibiotics, non-ribosomal peptides, and viruses holds transformative potential. However, the mechanisms by which these microbial effectors shape microbiomes and their broader functional consequences for host and ecosystem health remain poorly understood. Metaproteomics offers a novel methodological framework as it provides insights into microbial dynamics by quantifying microbial biomass composition, metabolic functions, and detecting effectors like viruses, antimicrobial resistance proteins, and non-ribosomal peptides. Here, we highlight the potential of metaproteomics in elucidating microbial effectors and their impact on microbiomes and discuss their potential for modulating microbiomes to foster desired functions.},
}
@article {pmid40410854,
year = {2025},
author = {Fan, L and Chen, J and Zhang, Q and Ren, J and Chen, Y and Yang, J and Wang, L and Guo, Z and Bu, P and Zhu, B and Zhao, Y and Wang, Y and Liu, X and Wang, W and Chen, Z and Gao, Q and Zheng, L and Cai, J},
title = {Fecal microbiota transplantation for hypertension: an exploratory, multicenter, randomized, blinded, placebo-controlled trial.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {133},
pmid = {40410854},
issn = {2049-2618},
support = {82300564//National Natural Science Foundation of China/ ; 81630014//National Natural Science Foundation of China/ ; BRWEP2024W012060100//Beijing Research Ward Excellence Program/ ; BRWEP2024W012060100//Beijing Research Ward Excellence Program/ ; 2024ZD0526804//National Science and Technology Major Project for the Prevention and Treatment of Cancer, Cardiovascular and Cerebrovascular Diseases, Respiratory Diseases and Metabolic Diseases/ ; 2024ZD0526800//National Science and Technology Major Project for the Prevention and Treatment of Cancer, Cardiovascular and Cerebrovascular Diseases, Respiratory Diseases and Metabolic Diseases/ ; BRWEP2024W012060105//Beijing Research Ward Excellence Program&#xff0c;BRWEP/ ; CIFMS, 2021-I2M-1-007//CAMS Innovation Fund for Medical Sciences/ ; 81825002//National Outstanding Youth Science Fund Project of National Natural Science Foundation of China/ ; BJJWZYJH01201910023029//Beijing Outstanding Young Scientist Program/ ; Z231100004623009//Beijing Municipal Science &amp; Technology Commission/ ; CI2021A00920//Key project of Science and Technology Innovation Project of China Academy of Chinese Medical Sciences/ ; ZLRK202511//Beijing Hospitals Authority Clinical medicine Development of special funding support/ ; L248105//Beijing Natural Science Foundation/ ; },
mesh = {Humans ; *Fecal Microbiota Transplantation/methods/adverse effects ; Male ; Female ; *Hypertension/therapy/microbiology ; Adult ; *Gastrointestinal Microbiome/physiology ; Middle Aged ; Feces/microbiology ; Blood Pressure ; China ; Treatment Outcome ; },
abstract = {BACKGROUND: On the basis of the contribution of the gut microbiota to hypertension development, a novel strategy involving fecal microbiota transplantation (FMT) has been proposed to treat hypertension, but its efficacy has not been investigated in the clinic.<br><br>METHODS: In a randomized, blinded, placebo-controlled clinical trial (2021/03-2021/12, ClinicalTrials.gov, NCT04406129), hypertensive patients were recruited from seven centers in China, and received FMT or placebo capsules orally at three visits. The patients were randomized at a 1:1 ratio in blocks of four and stratified by center by an independent statistician. The intention-to-treat principle was implemented, as all randomized participants who received at least one intervention were included. The primary outcome was the decrease in office systolic blood pressure (SBP) from baseline to the day 30 visit. Adverse events (AEs) were recorded through the 3-month follow-up to assess safety measures. Alterations in BP, the fecal microbiome, and the plasma metabolome were assessed via exploratory analyses.<br><br>RESULTS: This study included 124 patients (mean age 43&#xa0;years, 73.4% men) who received FMT (n&#x2009;=&#x2009;63) or placebo (n&#x2009;=&#x2009;61) capsules. The numbers of participants who experienced AEs (13 (20.6%) vs. 9 (14.8%), p&#x2009;=&#x2009;0.39) and the primary outcome (6.28 (11.83) vs. 5.77 (10.06) mmHg, p&#x2009;=&#x2009;0.62) were comparable between the groups. The FMT group presented a decrease in SBP after 1&#xa0;week of FMT, with a between-arm difference of&#x2009;-&#x2009;4.34 (95% CI,&#x2009;-&#x2009;8.1 to&#x2009;-&#x2009;0.58; p&#x2009;=&#x2009;0.024) mmHg, but this difference did not persist even after repeated intervention. After FMT, shifts in microbial richness and structure were identified and the abundance of the phyla Firmicutes and Bacteroidetes was altered. Decreases in the abundances of Eggerthella lenta, Erysipelatoclostridium ramosum, Anaerostipes hadrus, Gemella haemolysans, and Streptococcus vestibularis and increases in the abundances of Parabacteroides merdae, Prevotella copri, Bacteroides galacturonicus, Eubacterium sp. CAG 180, Desulfovibrio piger, Megamonas hypermegale, Collinsella stercoris, Coprococcus catus, and Allisonella histaminiformans were identified and correlated with office SBP. Those species were also correlated with responding and inversely office SBP-associated metabolites including tyrosine, glutamine, aspartate, phenylalanine, methionine, serine, sarcosine, and/or asparagine.<br><br>CONCLUSIONS: Safety but unsustainable BP reduction was observed in the first trial of the effects of FMT on hypertension. Additional intervention studies on specific microbes with metabolite-targeting and BP-modulating features are needed. Video Abstract.},
}
@article {pmid40410722,
year = {2025},
author = {Liu, YH and Lee, YL and Han, CL and Lo, YC and Liao, ZA and Shih, YS and Lin, YW and Peng, SW and Lee, KY and Ho, SC and Wu, SM and Lin, CW and Chung, KF and Chang, JH and Chuang, HC},
title = {ITIH4 alleviates OVA-induced asthma by regulating lung-gut microbiota.},
journal = {Molecular medicine (Cambridge, Mass.)},
volume = {31},
number = {1},
pages = {204},
pmid = {40410722},
issn = {1528-3658},
support = {112-2628-B-038-010-MY3//National Science and Technology Council/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Asthma/drug therapy/metabolism/etiology/pathology/chemically induced ; Mice ; Male ; *Lung/drug effects/metabolism/pathology/microbiology ; Ovalbumin/adverse effects ; Disease Models, Animal ; Cytokines/metabolism ; Mice, Inbred BALB C ; Bronchoalveolar Lavage Fluid ; },
abstract = {BACKGROUND: Inter-alpha-trypsin inhibitor heavy chain 4 (ITIH4), a Type 2 acute phase protein, is critical for resolving inflammation and promoting tissue repair. While its role in chronic respiratory diseases is recognized, its effects on asthma remain unclear. This study investigated the effects of ITIH4 on the modulation of lung and gut microbiota, the attenuation of allergic inflammation, and the improvement of respiratory outcomes in an asthma mouse model.<br><br>METHODS: Six-week-old male Balb/c mice were divided into five groups: control, ITIH4, ovalbumin (OVA), and two OVA&#x2009;+&#x2009;ITIH4 treatment groups at different doses. Lung function and oxygen saturation were measured, and bronchoalveolar lavage fluid (BALF) was analyzed for white blood cell counts and cytokines. Lung and gut microbiota were profiled using 16&#xa0;S rRNA gene sequencing, and short-chain fatty acids (SCFAs) were measured using gas chromatography-mass spectrometry (GC-MS). Proteomic profiling of intestinal tissues was conducted to identify ITIH4-associated signaling pathways.<br><br>RESULTS: ITIH4 administration significantly mitigated OVA-induced asthma symptoms by reducing weight loss, airway resistance, and tissue damping (p&#x2009;<&#x2009;0.05). Histological analysis showed decreased airway wall thickening and lung injury scores (p&#x2009;<&#x2009;0.05). ITIH4 also lowered BALF eosinophils and lymphocytes, IgE, and Th2 cytokines (IL-4, IL-5, and IL-13) (p&#x2009;<&#x2009;0.05). ITIH4 treatment modulated microbiome composition, enriching Gram-positive taxa (Nocardioidaceae and Acholeplasmataceae) and depleting Gram-negative Helicobacteraceae (p&#x2009;<&#x2009;0.05). SCFAs correlated with microbiome alterations, notably reduced 4-methylpentanoic acid levels (p&#x2009;<&#x2009;0.05). Proteomic analysis revealed a dose-dependent activation of granzyme A signaling and suppression of metabolic and solute transport pathways.<br><br>CONCLUSIONS: ITIH4 ameliorates asthma symptoms by modulating lung and gut microbiota, dampening Th2-driven inflammation, and restoring mucosal immune balance. These findings support ITIH4 as a potential candidate for microbiome-targeted asthma therapy.},
}
@article {pmid40410556,
year = {2025},
author = {Chen, Y and Fu, KX and Cotton, R and Ou, Z and Kwak, JW and Chien, JC and Kesler, V and Nyein, HYY and Eisenstein, M and Tom Soh, H},
title = {A biochemical sensor with continuous extended stability in vivo.},
journal = {Nature biomedical engineering},
volume = {},
number = {},
pages = {},
pmid = {40410556},
issn = {2157-846X},
support = {OT2OD025342//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; },
abstract = {The development of biosensors that can detect specific analytes continuously, in vivo, in real time has proven difficult due to biofouling, probe degradation and signal drift that often occur in vivo. By drawing inspiration from intestinal mucosa that can protect host cell receptors in the presence of the gut microbiome, we develop a synthetic biosensor that can continuously detect specific target molecules in vivo. The biomimetic multicomponent sensor features the hierarchical nano-bio interface design with three-dimensional bicontinuous nanoporous structure, polymer coating and aptamer switches, balancing small-molecule sensing and surface protection in complex biological environments. Our system is stable for at least 1 month in undiluted serum in vitro or 1 week implanted within the blood vessels of free-moving rats, retaining over 50% baseline signal and reproducible calibration curves. We demonstrate that the implanted system can intravenously track pharmacokinetics in real time even after 4 days of continuous exposure to flowing blood within rat femoral vein. In this way, our work provides a generalizable design foundation for biosensors that can continuously operate in vivo for extended durations.},
}
@article {pmid40410461,
year = {2025},
author = {},
title = {Research links Fusobacterium nucleatum to microbiome imbalance and periodontal disease.},
journal = {British dental journal},
volume = {238},
number = {10},
pages = {753},
doi = {10.1038/s41415-025-8787-z},
pmid = {40410461},
issn = {1476-5373},
}
@article {pmid40410196,
year = {2025},
author = {Li, C and Li, X and Liu, K and Xu, J and Yu, J and Liu, Z and Mach, N and Ni, W and Liu, C and Zhou, P and Wang, L and Hu, S},
title = {Multiomic analysis of different horse breeds reveals that gut microbial butyrate enhances racehorse athletic performance.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {87},
pmid = {40410196},
issn = {2055-5008},
support = {32360016//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32400045//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Horses/microbiology/physiology ; Mice ; *Bacteria/metabolism/classification/genetics/isolation &amp; purification ; *Butyrates/metabolism ; *Athletic Performance ; Physical Conditioning, Animal ; *Butyric Acid/metabolism ; Muscle, Skeletal/physiology ; Humans ; Male ; },
abstract = {Gut microbes play a vital role in host physiology, but whether specific bacterial functions contribute to the exceptional athletic performance of racehorses needs to be better understood. Here, we identify an association of gut butyrate-producing bacteria with athletic performance in racehorses (Thoroughbred horse). Butyrate-producing bacteria and microbial butyrate synthesis genes were significantly enriched in the racehorse gut, and the GC-MS results confirmed this conclusion. Using a mouse model, we demonstrated that sodium butyrate is sufficient to increase treadmill run time performance. We also show that butyrate improves the host response to exercise, significantly altering muscle fibre type in skeletal muscle, and increasing muscle mitochondrial function and activity. In addition, in-depth analysis of the published data showed that the gene for the synthesis of butyrate was also significantly enriched in the gut microbes of human athletes. Overall, our study indicates that gut microbial butyrate improves run time via the gut-muscle axis, providing novel insights into gut microbial functions and paving the way for improving athletic performance by targeted gut microbiome manipulation.},
}
@article {pmid40410194,
year = {2025},
author = {Lin, H and Shao, X and Gu, H and Yu, X and He, L and Zhou, J and Zhong, Z and Guo, S and Li, D and Chen, F and Song, Y and Xu, L and Wang, P and Meng, L and Chi, J and Lian, J},
title = {Akkermansia muciniphila ameliorates doxorubicin-induced cardiotoxicity by regulating PPARα-dependent mitochondrial biogenesis.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {86},
pmid = {40410194},
issn = {2055-5008},
support = {82174204//National Natural Science Foundation of China/ ; 81870255//National Natural Science Foundation of China/ ; 82000252//National Natural Science Foundation of China/ ; 81870255//National Natural Science Foundation of China/ ; 2022A14009//Science and Technology Projects of Shaoxing city/ ; ZCLTGD24H0201//Natural Science Foundation of Zhejiang Province/ ; LHDMZ24H020001//Natural Science Foundation of Zhejiang Province/ ; 2023-BZDS//Ningbo Key Laboratory of Molecular Target Screening and Application/ ; },
mesh = {Animals ; *Doxorubicin/adverse effects ; *PPAR alpha/metabolism/genetics ; Mice ; *Cardiotoxicity/prevention &amp; control/microbiology ; *Probiotics/administration &amp; dosage ; Humans ; Mice, Inbred C57BL ; *Akkermansia ; *Organelle Biogenesis ; *Mitochondria/metabolism/drug effects ; Feces/microbiology ; RNA, Ribosomal, 16S/genetics ; Signal Transduction ; Male ; Gastrointestinal Microbiome ; Peroxisome Proliferator-Activated Receptor Gamma Coactivator 1-alpha/metabolism/genetics ; },
abstract = {Doxorubicin (DOX) is a key chemotherapeutic agent but is also a leading cause of DOX-induced cardiotoxicity (DIC), limiting its clinical use. Akkermansia muciniphila (A. muciniphila), known for its benefits as a probiotic in treating metabolic syndrome, has uncertain effects in the context of DIC. Here, 16S rRNA sequencing of fecal samples from anthracycline-treated patients and DIC mice revealed marked depletion of A. muciniphila. Cardiac transcriptomics, supported by in vitro experiments, showed that A. muciniphila colonization improved mitochondrial function and alleviated DIC by activating the PPARα/PGC1α signaling pathway in both normal and antibiotic-treated C57BL/6 mice. Further analysis uncovered a restructured microbiome-metabolome network following A. muciniphila administration, which contributed to DIC protection. Notably, A. muciniphila supplementation increased serum levels of the tryptophan metabolite indole-3-propionic acid (IPA), which binds to the cardiac aryl hydrocarbon receptor (AhR), leading to the activation of the PPARα/PGC1α signaling pathway. In conclusion, our study sheds light on the potential of A. muciniphila as a probiotic in mitigating DIC.},
}
@article {pmid40410138,
year = {2025},
author = {Chen, AS and Kim, H and Nzabarushimana, E and Shen, J and Williams, K and Gurung, J and McGoldrick, J and Burke, KE and Yarze, JC and Nguyen, LH and Staller, K and Chung, DC and Xavier, RJ and Khalili, H},
title = {Association of distinct microbial and metabolic signatures with microscopic colitis.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {4644},
pmid = {40410138},
issn = {2041-1723},
support = {R01AG068390//U.S. Department of Health &amp; Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; P30DK043351//U.S. Department of Health &amp; Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes &amp; Digestive &amp; Kidney Diseases)/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Male ; Female ; Middle Aged ; *Metabolome ; Feces/microbiology ; *Colitis, Microscopic/microbiology/metabolism ; Aged ; Adult ; Case-Control Studies ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Diarrhea/microbiology/metabolism ; Metabolomics ; Metagenomics ; Biomarkers/metabolism ; },
abstract = {Microscopic colitis (MC) is a chronic inflammatory disease of the large intestine that primarily affects older adults and presents with chronic diarrhea. The etiology is unknown and there are currently no FDA approved medications or biomarkers for treatment or monitoring of the disease. Emerging evidence have implicated the gut microbiome and metabolome disturbances in MC pathogenesis. We conduct a comprehensive analysis of gut microbial and metabolic changes in a cohort of 683 participants, including 131 patients with active MC, 159 with chronic diarrhea, and 393 age- and sex-matched controls without diarrhea. Stool microbiome and metabolome are profiled using whole-genome shotgun metagenomic sequencing and ultra-high performance liquid chromatography-mass spectrometry, respectively. Compared to controls, eight microbial species including pro-inflammatory oral-typical Veillonella dispar and Haemophilus parainfluenzae, and 11 species, including anti-inflammatory Blautia glucerasea and Bacteroides stercoris are enriched and depleted in MC, respectively. Pro-inflammatory metabolites, including lactosylceramides, ceramides, lysophospholipids, and lysoplasmalogens, are enriched in active MC. Multi-omics analyses reveal robust associations between microbial species, metabolic pathways, and metabolites, suggesting concordant disruptions in MC. Here, we show distinct shifts in gut microbiome and metabolome in MC that can inform the development of non-invasive biomarkers and novel therapeutics.},
}
@article {pmid40409517,
year = {2025},
author = {Gui, F and Zhang, L and Xiao, J and Zeng, C},
title = {Decoding the role of intratumoral microbiota in gastric cancer.},
journal = {Biochimica et biophysica acta. Reviews on cancer},
volume = {1880},
number = {3},
pages = {189355},
doi = {10.1016/j.bbcan.2025.189355},
pmid = {40409517},
issn = {1879-2561},
abstract = {Intratumoral microbiota are increasingly recognized for their impact on gastric cancer, with growing evidence highlighting their complexity and significance. This review synthesizes current knowledge on the origins, heterogeneity, detection, and mechanistic roles of intratumoral microbiota in gastric carcinogenesis. In gastric cancer, intratumoral microbiota can originate from mucosal disruption and may migrate from normal adjacent tissues or be influenced by the TME. It exhibits spatial and functional heterogeneity within gastric cancer. Despite challenges in the detection of intratumoral microbiota, advances in deep sequencing and spatial omics have enhanced our understanding of microbial diversity and functionality. Mechanistically, intratumoral microbiota influence gastric cancer development through genetic and epigenetic alterations, signaling pathway modulation, metabolic reprogramming, and regulation of chronic inflammation and immune responses. These insights underscore the microbiota's dual function in both promoting and hindering tumor advancement. Therapeutically, the microbiota's impact on chemotherapy resistance and immune modulation presents opportunities for novel interventions. Integrating microbiome analysis into cancer research and leveraging microbial therapies may enable more effective, personalized treatment strategies. Future research should further elucidate the intricate microbe-tumor interactions to advance clinical applications and improve outcomes for gastric cancer patients.},
}
@article {pmid40409481,
year = {2025},
author = {Chen, E and Zhou, W},
title = {Immunotherapy in microsatellite-stable colorectal cancer: Strategies to overcome resistance.},
journal = {Critical reviews in oncology/hematology},
volume = {212},
number = {},
pages = {104775},
doi = {10.1016/j.critrevonc.2025.104775},
pmid = {40409481},
issn = {1879-0461},
abstract = {Colorectal cancer (CRC) is among the foremost causes of cancer-related mortality worldwide; however, individuals with microsatellite-stable (MSS) disease-who constitute most CRC diagnoses-derive limited benefit from existing immunotherapeutic approaches. Here, we outline emerging methods designed to address the inherent resistance of MSS CRC to immune checkpoint inhibitors (ICIs). Recent findings emphasize how the immunosuppressive tumor microenvironment (TME) in MSS CRC, marked by diminished immunogenicity and high levels of regulatory T cells and myeloid-derived suppressor cells, restricts effective antitumor immune activity. Combination regimens that merge ICIs with chemotherapy, anti-angiogenic agents, or targeted blockade of pathways such as TGF-β and VEGF have shown encouraging early outcomes, including enhanced antigen presentation and T-cell penetration. Novel immunomodulatory platforms-such as epigenetic modifiers, oncolytic viruses, and engineered probiotic vaccines-are under assessment to further reprogram the TME and boost therapeutic efficacy. Concurrently, progress in adoptive cell therapies (for example, chimeric antigen receptor (CAR) T cells) and the development of cancer vaccines targeting tumor-associated and neoantigens promise to extend immune control over MSS CRC. In parallel, improving patient selection through predictive biomarkers-from circulating tumor DNA (ctDNA) to gene expression signatures and specific molecular subtypes-could refine individualized treatment strategies. Finally, interventions that alter the gut microbiome, including probiotics and fecal transplantation, serve as complementary tools to strengthen ICI responses. Taken together, these insights and combined treatment strategies lay the foundation for more successful immunotherapeutic interventions in MSS CRC, ultimately aiming to provide sustained clinical benefits to a broader spectrum of patients.},
}
@article {pmid40409472,
year = {2025},
author = {Zhang, H and Atefi, N and Surendran, A and Han, J and Goodlett, DR and Jassal, DS and Shah, A and Ravandi, A},
title = {Conjugated bile acids are elevated in severe calcific aortic valve stenosis.},
journal = {Journal of lipid research},
volume = {},
number = {},
pages = {100830},
doi = {10.1016/j.jlr.2025.100830},
pmid = {40409472},
issn = {1539-7262},
abstract = {INTRODUCTION: Calcific aortic valve stenosis (CAVS) is a disease associated with significant morbidity and mortality in the aging population. Recently, bile acids have been shown to play a significant role in many disease processes, and untargeted metabolomic analyses of CAVS patient valves has shown a disrupted bile acid pathway.<br><br>AIM: We aimed to understand the changes in human valvular bile acids in relation to CAVS severity.<br><br>METHODS: A total of 100 human aortic valves were collected from patients undergoing aortic valve replacement surgery. Bile acids were quantified by ultrahigh performance liquid chromatography coupled to tandem mass spectrometry.<br><br>RESULTS: Patients with mild aortic stenosis (AS) showed a distinct valvular bile acid composition compared to moderate and severe AS groups, with five bile acids being significantly elevated in patients with moderate and severe AS. These included norcholic, nordeoxycholic, glycodeoxycholic, glycocholic and taurodeoxycholic acid. When classified by calcification score, five species were significantly different between mild and severe AS groups; four bile acids were similar when stratified based on AS severity. Using k means clustering we were able to distinguish valve severity by their bile acid composition. Grouping bile acids by conjugation and by primary versus secondary revealed that conjugated primary and secondary bile acids were significantly increased in stenotic valves compared to the mild AS group.<br><br>CONCLUSION: Conjugated bile acids are significantly elevated in the valvular tissue of patients with severe calcific aortic stenosis. These findings suggest a potential link between liverand gut microbiome physiologyand bile acid pathways in contributing to the pathophysiology of valvular stenosis.},
}
@article {pmid40409234,
year = {2025},
author = {Pontes, KSDS and Guedes, MR and Souza, PG and Neves, MFT and Klein, MRST},
title = {Effects of multi-strain probiotics supplementation on body adiposity and metabolic profile in individuals with hypertension and overweight following an energy-restricted diet: A randomized clinical trial.},
journal = {Clinical nutrition (Edinburgh, Scotland)},
volume = {50},
number = {},
pages = {117-127},
doi = {10.1016/j.clnu.2025.05.005},
pmid = {40409234},
issn = {1532-1983},
abstract = {BACKGROUND &amp; AIMS: Recent evidence suggests that gut microbiota has a potential role in the pathophysiology of obesity and other cardiovascular disease (CVD) risk factors, including hypertension, dyslipidemia, and type 2 diabetes. However, clinical trials evaluating the effects of probiotics supplementation on these outcomes have found inconsistent results, probably due to the wide heterogeneity in trial designs. In addition, there is a lack of studies investigating whether probiotics can enhance the beneficial effects of caloric restriction in individuals with increased risk of CVD as individuals with hypertension and excess body adiposity. Thus, the aim of this study was to evaluate the effects of multi-strain probiotics supplementation on body adiposity, glycemic homeostasis, lipid profile, and serum adipokine levels in individuals with hypertension and excess body weight following an energy restricted diet.<br><br>METHODS: A randomized, double-blind, placebo controlled clinical trial was conducted for 12 weeks. Were included 66 individuals aged between 40 and 65 years; both sexes; body mass index (BMI) &#x2265; 25 and < 40 kg/m[2] and diagnosis of hypertension. Were excluded smokers; individuals using probiotics, prebiotics, symbiotics and antibiotics in the last 3 months; presenting diabetes, chronic kidney disease or liver failure; and pregnant and lactating women. Participants were allocated into 2 groups: group with supplementation of 8 probiotic strains in capsules (3 &#xd7; 10[10] CFU/day) or control group (placebo capsules). Both groups followed a low-calorie diet. Participants underwent anthropometric, body composition (dual-energy radiological absorptiometry) and biochemical (glucose metabolism, lipid profile, adiponectin, and leptin) evaluation at baseline and at the end of the study.<br><br>RESULTS: After 12 weeks of intervention, the probiotics group presented: a) reduction of body weight, BMI, circumferences of waist, hip and neck and waist-to-height ratio; b) decrease in total fat mass (kg); and c) reduction of glycated hemoglobin (HbA1c). In the control group, it was observed: a) significant reduction in all anthropometric variables; b) significant reduction in total fat mass (kg and %), trunk fat mass (kg), visceral fat and load capacity index. In the comparison between groups, there was a higher decrease in HbA1c in the probiotics group (p < 0.05).<br><br>CONCLUSION: Multi-strain probiotics supplementation associated with energy restriction in individuals with excess body weight and hypertension promoted a significant improvement in glucose homeostasis assessed by HbA1c. The clinical trial was registered at www.ensaiosclinicos.gov.br: RBR-7jw4ry.},
}
@article {pmid40409220,
year = {2025},
author = {Klein Meuleman, SJM and van Houdt, R and Schuster, HJ and de Leeuw, RA and Post Uiterweer, ED and Huirne, JAF},
title = {Effect of laparoscopic niche resection on vaginal microbiota and its relation to pregnancy rate.},
journal = {European journal of obstetrics, gynecology, and reproductive biology},
volume = {311},
number = {},
pages = {114046},
doi = {10.1016/j.ejogrb.2025.114046},
pmid = {40409220},
issn = {1872-7654},
abstract = {OBJECTIVE: To study the impact of a laparoscopic niche resection on vaginal microbiota in relation to pregnancy rate.<br><br>METHODS: A explorative prospective cohort study that included women with a large niche (residual myometrium&#xa0;&#x2264;&#xa0;3 mm), actual wish to conceive who were scheduled for laparoscopic niche resection. Pre- and three months post-operatively, a vaginal swab was collected during the mid-luteal phase (cycle day 19 to 24). The microbiota composition was determined using 16S rDNA sequencing. Microbiota profiles were assigned to community state types (CST) based on the dominant bacterial species.<br><br>RESULTS: In total, 55 women completed sequential sampling. In all women, laparoscopic niche resection significantly reduced niche volume, withmean paireddifference of 1766.6&#xa0;mm[3] (95&#xa0;% CI: 640.4 - 2892.8). CST-IV was the dominant type both pre- and post-operatively (38.2&#xa0;% vs 36.4&#xa0;%, respectively). In ten (18.2&#xa0;%) women the dominant CST changed after surgery. Three (5.5&#xa0;%) women experienced a favourable change linked to fertility, while two (3.6&#xa0;%) had unfavourable change and five (9.1&#xa0;%) showed neutral shift. Women with favourable change had a greater reduction in niche volume (median reduction 1067.4&#xa0;mm[3] (p&#xa0;=&#xa0;0.014)). Within a year, 23 (54.8&#xa0;%) women became pregnant. The highest pregnancy rate (90.0&#xa0;%, n&#xa0;=&#xa0;9) was observed in women with post-operative CST-I, while the lowest rate (38.5&#xa0;%, n&#xa0;=&#xa0;5) was seen in those with CST-III.<br><br>CONCLUSION: Laparoscopic niche resection resulted in a more than 10-fold reduction in niche volume. However, no significant changes in vaginal microbiota were observed postoperatively. Notably, women who experienced the largest reduction in niche volume also demonstrated a favourable shift in their microbiome profile, which is associated with improved fertility.Postoperatively, the highest pregnancy rate (90&#xa0;%) was observed in women with Lactobacillus crispatus-dominant microbiota (p&#xa0;=&#xa0;0.78). These results provide valuable insights into the pathophysiology of uterine niches and suggest potential therapeutic approaches for women experiencing niche-related infertility, however lager studies are needed to confirm these findings.},
}
@article {pmid40408818,
year = {2025},
author = {Xu, J and Zou, H and Shu, C and Liu, Y and Yin, Y and Ni, B},
title = {Research progress and hotspots of the impact of Mediterranean diet on aging from 2004 to 2023: A bibliometric analysis.},
journal = {Geriatric nursing (New York, N.Y.)},
volume = {64},
number = {},
pages = {103375},
doi = {10.1016/j.gerinurse.2025.05.014},
pmid = {40408818},
issn = {1528-3984},
abstract = {OBJECTIVE: This study aims to identify research hotspots and trends by conducting a bibliometric report regarding the impact of MD on aging.<br><br>METHODS: Publications on MD and aging were extracted from the Web of Science Core Collection. R software, VOSviewer and CiteSpace were employed to detect research hotspots and frontiers.<br><br>RESULTS: The number of annual articles has grown rapidly. The core research content in this field are the mechanism of the antiaging action of MD (inflammation, oxidative stress and gut microbiome) and age-related diseases (particularly cardiovascular diseases, Alzheimer's disease and metabolic syndrome). The interplay between MD and the gut microbiome or physical activity impacting healthy aging has been the recent hotspot and research frontier.<br><br>CONCLUSION: This study quantitatively and objectively described the research status and research focus of the impact of MD on aging, which provides reference for future research in this field.},
}
@article {pmid40408396,
year = {2025},
author = {Borriello, G and Valentini, F and Ferrini, S and Di Muro, G and Cagnotti, G and Grego, E and Catania, AM and Stella, MC and Ala, U and Nebbia, P and D'Angelo, A and Bellino, C},
title = {Characterization of blood microbial population in beef calves with clinical signs of sepsis using 16S rRNA gene sequencing.},
journal = {PloS one},
volume = {20},
number = {5},
pages = {e0324469},
pmid = {40408396},
issn = {1932-6203},
mesh = {Animals ; Cattle ; *RNA, Ribosomal, 16S/genetics ; *Sepsis/microbiology/veterinary/blood/diagnosis ; DNA, Bacterial/genetics/blood ; *Cattle Diseases/microbiology/blood ; *Bacteria/genetics/classification/isolation &amp; purification ; },
abstract = {Sepsis, a dysregulated host response to infection, severely affects calf health. To date, sepsis diagnosis relies on clinical examination and positive blood culture. Differently, in humans 16S rRNA gene analysis is a valuable adjunct to blood culture as it allows for broader assessment of bacterial DNA in whole blood and its fractions. However, its efficacy in cattle remains unknown. Therefore, this study characterized and compared the bacterial DNA detected in whole blood and its fractions between healthy calves and those showing clinical signs of sepsis. The study sample was 18 Piedmontese calves classified according to their clinical status as suspected septic (S, 8/18) or healthy (H, 10/18). Aseptic blood samples were collected into EDTA tubes for 16S rRNA gene analysis of whole blood (WB), plasma (PL), buffy coat (BC), and red blood cells (RBC). Aseptic samples were additionally taken only from the S calves for blood culture. Clinical and microbiological parameters were compared between the two groups and between the blood fractions within each group. The S calves were diagnosed with pneumonia (3/8, 37.5%), enteritis (3/8, 37.5%), and omphalitis (2/8, 25%). Microbiome analysis revealed significant intra-group differences in α and β diversity indices between PL and the other blood fractions for both groups. Comparison between the S and the H calves showed differences in β diversity indices for PL and WB. DNA of known pathogens (e.g., Escherichia coli) and species not commonly associated with sepsis (e.g., Cutibacterium acnes) were more abundant in the S calves. Moreover, in S calves, 16S rRNA gene sequencing detected E. coli DNA more often (8/8, 100%) than blood culture (2/8, 25%). While the DNA of several bacteria can be detected in calves showing clinical signs of sepsis, further studies are needed to clarify its origin, role, and distribution in blood fractions.},
}
@article {pmid40408283,
year = {2025},
author = {Hauschild, K and Giongo, A and Liu, B and Babin, D and Bloem, E and Beerhues, L and Winkelmann, T and Smalla, K},
title = {Catch crop amendments and microbial inoculants differently modulate apple rhizosphere microbiomes and plant responses.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiaf055},
pmid = {40408283},
issn = {1574-6941},
abstract = {Plant-soil feedback and soil microbial legacies play crucial roles in replanting success of apple. This study investigated how different soil amendment strategies influence these factors in replant disease-affected soil. Two approaches were tested: (i) the pre-culture and amendment of catch crops-either a single species, Tagetes patula, or a diverse catch crop mixture (CCM), and (ii) the inoculation of plant-beneficial microbes- bacteria, arbuscular mycorrhizal fungi, or their combination (SynC). Apple rootstock M.26 was grown for seven weeks in a greenhouse, and plant growth, soil nutrients, root phytoalexins, and microbial communities in rhizosphere and root-affected soil were analyzed. Catch crop amendments but not microbial inoculations, significantly altered soil nutrients. Root length increased significantly under CCM, and in tendency in Tagetes and SynC. Phytoalexin contents were lowest in Tagetes and highest in CCM, both differing from the control in specific compounds. Microbiome analysis revealed that catch crops strongly modulated fungal communities in rhizosphere and root-affected soil, favoring potentially beneficial Linnemannia and Mortierella, while microbial inoculations predominantly modulated bacterial/archaeal rhizosphere communities. Our results suggest that catch crops and microbial inoculants induced distinct shifts in soil-plant-microbe interactions under replanting conditions.},
}
@article {pmid40408276,
year = {2025},
author = {Ketehouli, T and Sossah, FL and Panwala, R and Suazo Tejada, AK and Goss, EM and Garcia, FHS and Vallad, GE and Martins, SJ},
title = {Secondary metabolites in plant-microbe interactions.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxaf124},
pmid = {40408276},
issn = {1365-2672},
abstract = {As sessile organisms, plants are constantly exposed to various abiotic and biotic factors in their environment. Among the biotic factors, beneficial microorganisms, pathogens, and insects cause metabolic changes that affect growth and productivity. In response to these interactions and stress conditions, plants have developed sophisticated metabolic plasticity, adjusting their primary and secondary metabolic pathways. Secondary metabolites are specialized compounds that serve various ecological functions, such as defense against herbivores and pathogens, allelopathy, interaction with beneficial microorganisms, and attraction of pollinators and seed dispersers. These metabolites also act as signaling molecules in plant-microbe interactions, regulating the relationship between plants and microbes. Recent genetic and chemical research has revealed that secondary metabolites have multiple functions, acting as powerful regulators of both plant growth and defense beyond their roles in primary metabolism. This review explored the microbiome's complexity and emerging trends in understanding how microbiome composition and/or synthetic microbial community (SynCom) influence microbial and plant metabolic activities. Addressing the correlation between the varieties of microorganisms or SynCom and their metabolic profiles is crucial for elucidating the biological mechanisms that induce alterations in microbial communities and their metabolic functions within the rhizosphere and plant microbiomes. This knowledge will contribute to developing strategies to enhance beneficial interactions and mitigate the effects of pathogens that can reduce plant growth and productivity.},
}
@article {pmid40408146,
year = {2025},
author = {Fontanarrosa, P and Clare, C and Fedorec, AJH and Barnes, CP},
title = {MIMIC: A Python Package for Simulating, Inferring, and Predicting Microbial Community Interactions and Dynamics.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btaf174},
pmid = {40408146},
issn = {1367-4811},
abstract = {SUMMARY: The study of microbial communities is vital for understanding their impact on environmental, health, and technological domains. The Modelling and Inference of MICrobiomes Project (MIMIC) introduces a Python package designed to advance the simulation, inference, and prediction of microbial community interactions and dynamics. Addressing the complex nature of microbial ecosystems, MIMIC integrates a suite of mathematical models, including previously used approaches such as Generalized Lotka-Volterra (gLV), Gaussian Processes (GP), and Vector Autoregression (VAR) plus newly developed models for integrating multi-omic data, to offer a versatile framework for analysing microbial dynamics. By leveraging Bayesian inference and machine learning techniques, MIMIC provides the ability to infer the dynamics of microbial communities from empirical data, facilitating a deeper understanding of their complex biological processes, unveiling possible unknown ecological interactions, and enabling the design of microbial communities. Such insights could help to advance microbial ecology research, optimizing biotechnological applications, and contribute to environmental sustainability and public health strategies. MIMIC is designed for flexibility and ease of use, aiming to support researchers and practitioners in microbial ecology and microbiome research.<br><br>MIMIC is freely available under the MIT License at https://github.com/ucl-cssb/MIMIC. It is implemented in Python (version 3.7 or higher) and is compatible with Windows, macOS, and Linux operating systems. MIMIC depends on standard Python libraries including NumPy, SciPy, and PyMC. Comprehensive examples and tutorials (including the main text demonstrations) are provided as Jupyter notebooks in the examples/directory and at the MIMIC Docs website, along with detailed installation instructions and real-world data use cases. The software will remain freely available for at least two years following publication. A code snapshot for this publication is also available at Zenodo: https://doi.org/10.5281/zenodo.15149003.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
}
@article {pmid40311947,
year = {2025},
author = {Heckmann, ND and Culler, MW and Atallah, LM and Mont, MA and Lieberman, JR and Parvizi, J},
title = {Emerging Concepts in Periprosthetic Joint Infection Research: Intracellular Organisms.},
journal = {The Journal of arthroplasty},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.arth.2025.04.052},
pmid = {40311947},
issn = {1532-8406},
abstract = {Despite advances in the treatment of periprosthetic joint infection (PJI), recurrence is a concern for both patients and orthopaedic surgeons. Staphylococcal species are commonly implicated in PJI and are associated with more instances of treatment failure and recalcitrance relative to other organisms. A possible explanation for this is the ability of staphylococci to undergo phenotypic transformation into a quasidormant small colony variant (SCV) phenotype. These SCVs are difficult to culture and demonstrate increased resistance to targeted antibiotic therapy. Most importantly, SCVs are capable of intracellular invasion and may reside and proliferate within a variety of host cell types, including osteoblasts, osteocytes, fibroblasts, and circulating immune cells, such as neutrophils. In doing so, virulent organisms may interfere with normal host cell function while also converting these cells into reservoirs of bacteria that are sequestered from the extracellular environment and thus less vulnerable to standard antibiotic regimens. Additionally, these intracellular organisms may emerge from dormancy under certain conditions, including dysregulation or suppression of the host immune system, to return to their virulent state and cause recurrence of an infection. This phenomenon has been observed clinically, with reports in the literature describing cases of recurrent PJI and osteomyelitis, often many years later, caused by organisms previously thought to be eradicated. Furthermore, circulating immune cells containing intracellular organisms may also transport bacteria to other body sites before undergoing cellular lysis, leading to metastatic infection via a "Trojan Horse" mechanism. Previous reports have demonstrated intraosteoblastic infection with Staphylococcus aureus in clinical cases of recurrent osteomyelitis, while a recent study identified the same pathogen in osteocytes obtained from patients who have culture-positive PJI. While the translational application of these findings warrants further exploration, a better understanding of the clinical relevance of intracellular invasion could lead to the development of more optimal treatment strategies for eradicating infection and improving patient outcomes.},
}
@article {pmid40407923,
year = {2025},
author = {Pastuszka, A and Tobor, S and Łoniewski, I and Wierzbicka-Woś, A and Sielatycka, K and Styburski, D and Cembrowska-Lech, D and Koszutski, T and Kurowicz, M and Korlacka, K and Podkówka, A and Lemiński, A and Brodkiewicz, A and Hyla-Klekot, L and Skonieczna-Żydecka, K},
title = {Rewriting the urinary tract paradigm: the urobiome as a gatekeeper of host defense.},
journal = {Molecular biology reports},
volume = {52},
number = {1},
pages = {497},
pmid = {40407923},
issn = {1573-4978},
mesh = {Humans ; *Urinary Tract Infections/microbiology/immunology ; *Urinary Tract/microbiology/immunology ; *Microbiota/immunology ; Urothelium/microbiology/immunology ; Dysbiosis/microbiology ; Host-Pathogen Interactions/immunology ; Animals ; },
abstract = {The urobiome, or urinary tract microbiome, has emerged as a crucial component in maintaining urinary health and defending against infections. Recent advances in next-generation sequencing (NGS) have debunked the long-held belief that the urinary tract is sterile, revealing a unique ecosystem of microorganisms. The urobiome interacts with the urothelium and mucosa-associated lymphoid tissue (MALT) to support local immunity, playing an integral role in defending the urinary tract against pathogens. Through complex communication processes like quorum sensing, the urobiome regulates microbial behavior and controls interactions with host tissues, helping to prevent pathogen colonization and infection. However, dysbiosis in the urobiome can disrupt this balance, making the urinary tract more susceptible to infections, including urinary tract infections (UTIs). Studies have highlighted specific microbial compositions associated with both healthy and disease states, suggesting that shifts in the urobiome may correlate with various urological diseases. Furthermore, microbial diversity within the urinary tract differs by factors such as age and gender, reflecting the dynamic nature of the urobiome. Future research focusing on the interplay between the urobiome, host immune defenses, and pathogenic mechanisms may lead to innovative diagnostic and therapeutic approaches. Understanding how microbial composition changes during disease states could enable targeted treatments, potentially reducing reliance on antibiotics and minimizing resistance issues. The urobiome thus represents a promising frontier in urology, with implications for enhancing urinary health and treating infections more effectively.},
}
@article {pmid40407765,
year = {2025},
author = {Camera, E and Di Nardo, A},
title = {A Microbial Shield: Interactions between UVR, cis-Urocanic Acid, and the Skin Microbiome.},
journal = {The Journal of investigative dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jid.2025.04.010},
pmid = {40407765},
issn = {1523-1747},
}
@article {pmid40407722,
year = {2025},
author = {Flaherty, KT and Aplin, AE and Davies, MA and Hacohen, N and Herlyn, M and Hoon, D and Hwu, P and Lotem, M and Mulé, J and Wargo, JA and Fisher, DE},
title = {Facts &amp; Hopes: towards the next quantum leap in melanoma.},
journal = {Clinical cancer research : an official journal of the American Association for Cancer Research},
volume = {},
number = {},
pages = {},
doi = {10.1158/1078-0432.CCR-25-0278},
pmid = {40407722},
issn = {1557-3265},
abstract = {Outcomes from advanced melanoma, the deadliest of the skin cancers arising from melanocytes and capable of widely metastasizing, have greatly improved with death rates decreasing for AJCC stage 4 melanoma patients by 3-5 percent annually over the past 10 years (1,2). This improvement is a result of advances in both targeted therapy and immunotherapy (Fig 1). BRAF and MEK inhibitors for advanced melanoma have led the way for targeted cancer strategies and first- in-class approvals for immune checkpoint blockers targeting CTLA4, PD1, and LAG3, T cell engager therapy targeting the antigen gp100 and tumor-infiltrating lymphocyte therapy (3). All of the preceding have contributed to enhanced outcomes including long-term durable responses in up to half of patients with advanced disease. In addition, adjuvant and neoadjuvant approaches are reducing the risk of relapse in patients with stage II and III disease. Because of its immunogenicity and defined targetable mutations, melanoma drug development has led the way for novel approaches in cancer research. Yet additional approaches are needed for patients with recurrent or non-responsive disease or rare subtypes including mucosal, acral and uveal melanomas. Progress in modified T cells, including TCR, CAR-T and CRISPR gene editing strategies holds promise for future therapeutics. Continued understanding of the molecular and immune tumor microenvironment and heterogeneity, understanding the microbiome and numerous diverse approaches to topics ranging from prevention, to mechanisms of treatment resistance and novel therapeutic approaches, will optimize opportunities to further decrease melanoma mortality.},
}
@article {pmid40407702,
year = {2025},
author = {Hendrickx, DM and Savova, MV and Zhu, P and An, R and Boeren, S and Klomp, K and Mutte, SK and Presto Study Team, and Wopereis, H and van der Molen, RG and Harms, AC and Belzer, C},
title = {A multi-omics machine learning classifier for outgrowth of cow's milk allergy in children.},
journal = {Molecular omics},
volume = {},
number = {},
pages = {},
pmid = {40407702},
issn = {2515-4184},
abstract = {Cow's milk protein allergy (CMA) is one of the most common food allergies in children worldwide. However, it is still not well understood why certain children outgrow their CMA and others do not. While there is increasing evidence for a link of CMA with the gut microbiome, it is still unclear how the gut microbiome and metabolome interact with the immune system. Integrating data from different omics platforms and clinical data can help to unravel these interactions. In this study, we integrate clinical, microbial, (meta)proteomics, immune and metabolomics data into machine learning (ML) classification, using multi-view learning by late integration. The aim is to group infants into those that outgrew their CMA and those that did not. The results show that integration of microbiome data with clinical, immune, (meta)proteomics and metabolomics data could considerably improve classification of infants on outgrowth of CMA, compared to only considering one type of data. Moreover, pathways previously linked to development of CMA could also be related to outgrowth of this allergy.},
}
@article {pmid40407371,
year = {2025},
author = {Li, S and Wu, J and Wang, Q and Cao, H and Zhang, L},
title = {The landscape of bacterial contractile injection systems across large-scale metagenomes.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0321324},
doi = {10.1128/spectrum.03213-24},
pmid = {40407371},
issn = {2165-0497},
abstract = {UNLABELLED: Bacterial contractile injection systems (CISs) have evolved as sophisticated mechanisms that enable bacteria to interact with and manipulate their hosts. Resembling bacteriophage tails, these systems inject effector proteins directly into target cells, facilitating complex bacterial-host interactions. Despite significant advances in understanding CISs, exploration has largely been constrained by the availability of completely sequenced microbial genomes, potentially underrepresenting their diversity in natural environments. In this study, we identified 1,129 CISs from metagenome-assembled genomes spanning 14 bacterial phyla and 1 archaeal phylum. Notably, CISs were identified in many uncultured microorganisms and were highly enriched in the phylum Bacteroidota. Structural gene composition varied across ecosystems, with Bacteroidetes injection systems (BISs) from the human digestive system lacking typical tail fiber proteins and Cis6. However, all BISs encoded homologs of Aasi_0556, suggesting functional similarities with T6SS[iv]. Furthermore, we identified a candidate CIS cargo protein, BDI_2459, containing the toxin-associated DUF4157 domain, which exhibited moderate toxin potential. We cloned and heterologously expressed BDI_2459 in Escherichia coli. The standalone BDI_2459 did not exhibit its activity. However, there was activity when fused with a periplasmic translocation tag.<br><br>IMPORTANCE: Overall, this study expands our understanding of the ecological diversity, evolutionary adaptations, and functional roles of contractile injection systems (CISs) in microbial communities. The findings particularly highlight their adaptations to human-associated microbiomes. In addition, we conducted preliminary functional studies targeting the cargo protein BDI_2459 in CIS from Parabacteroides distasonis (CIS[Pd]). These results provide new insights into CIS-mediated bacterial interactions and pave the way for future microbiome engineering and antibacterial strategies.},
}
@article {pmid40407311,
year = {2025},
author = {Li, H and Wang, Z and He, S and Zhao, X and Wu, Q and Sun, Y and Fan, Y and Hu, X and Tian, Z and Zhang, S},
title = {Unraveling gut microbiome alterations and metabolic signatures in hereditary transthyretin amyloidosis.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0230224},
doi = {10.1128/spectrum.02302-24},
pmid = {40407311},
issn = {2165-0497},
abstract = {UNLABELLED: Hereditary transthyretin amyloidosis (hATTR) is a rare, often fatal disease characterized by the abnormal aggregation of atypical transthyretin fibrils. Given the variability in the penetrance and clinical manifestations of hATTR, the role of nongenetic factors, particularly those related to the gut microbiota, warrants investigation. We conducted a cross-sectional study, examining the untargeted serum metabolome and gut metagenome in 13 patients with hATTR and 22 healthy controls. Significant disparities were observed in both the serum metabolome and gut microbiome of individuals with hATTR when compared to healthy controls. Notably, the serum levels of gamma-aminobutyric acid (GABA) and taurine were markedly decreased in the hATTR group, with the most pronounced reduction in those exhibiting hATTR-related cardiac amyloidosis. Additionally, commensals such as Bifidobacterium pseudocatenulatum, Lactobacillus rogosae, and Hungatella hathewayi were significantly diminished in hATTR patients and were positively correlated with the metabolite module containing GABA and taurine. Metagenomic and metabolomic pathway enrichment analyses collectively revealed disruptions in glutamate and taurine metabolism in hATTR. Our findings imply that patients with hATTR may exhibit metabolic irregularities in glutamate and taurine, potentially associated with an imbalance in the gut microbiota.<br><br>IMPORTANCE: Hereditary transthyretin amyloidosis (hATTR) is influenced not only by genetic factors but also by environmental or host factors during its onset and progression. Previous studies have independently examined the metabolome or gut microbiome in hATTR, but the interplay between the microbiota and metabolism under this condition remains largely unknown. Our cross-sectional study represents the first comprehensive integration of gut metagenome and serum metabolome analyses in hATTR patients. We observed disturbances in glutamate and taurine metabolism among these patients, which correlated with distinctive shifts in the gut microbiota. This study offers insights into the intricate dynamics among gut dysbiosis, metabolic imbalances, and the progression of hATTR, suggesting directions for future research into the underlying mechanisms and therapeutic strategies.},
}
@article {pmid40407228,
year = {2025},
author = {Rawstern, AH and Carbajal, LJ and Slade, TJ and Afkhami, ME},
title = {Non-Additive Interactions Between Multiple Mutualists and Host Plant Genotype Simultaneously Promote Increased Plant Growth and Pathogen Defence.},
journal = {Plant, cell &amp; environment},
volume = {},
number = {},
pages = {},
doi = {10.1111/pce.15631},
pmid = {40407228},
issn = {1365-3040},
support = {//This study was funded by the University of Miami research funds awarded to M. Afkhami and the Mycological Society of America graduate fellowship awarded to A. Rawstern. A. Rawstern was additionally supported by the University of Miami Department of Biology and the Lisa D. Anness Graduate Fellowship./ ; },
abstract = {Understanding the impact of microbial interactions on plants is critical for maintaining healthy native ecosystems and sustainable agricultural practices. Despite the reality that genetically distinct plants host multiple microbes of large effect in the field, it remains unclear the extent to which host genotypes modulate non-additive microbial interactions and how these interactions differ between benign/pathogenic environments. Our study fills this gap by performing a large-scale manipulative microbiome experiment across seven genotypes of the model legume Medicago truncatula. We combine plant performance metrics, survival analyses, predictive modelling, RNA extractions and targeted gene expression to assess how host genotype and microbes non-additively interact to shape plant growth and disease ecology. Our results reveal three important findings: (1) host genotypes with high tolerance to pathogens benefit more from multiple mutualist interactions than susceptible genotypes, (2) only high-tolerance genotypes retain the same beneficial host performance outcomes from the benign environment within the pathogenic environment and (3) the quality of the symbiotic relationship with mutualists is a strong predictor of host survival against pathogenic disease. By applying these findings towards developing crops that promote synergistic microbial interactions, yields and pathogen defence could be simultaneously increased while reducing the need for toxic fertilisers and pesticides.},
}
@article {pmid40407188,
year = {2025},
author = {Batarseh, TN and Koskella, B},
title = {Distinguishing among evolutionary and ecological processes shaping microbiome dynamics.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf107},
pmid = {40407188},
issn = {1751-7370},
abstract = {Evolution is defined as the change in allele frequency over time as a result of either neutral processes, such as genetic drift, or as an adaptive process in response to selection. In contrast, ecological dynamics describe changes in population densities, species distributions, species interactions, and/or relative abundances within communities, all of which can also be the result of either stochastic or deterministic processes. Although the distinction between these patterns has long held for plants and animals, microbial community dynamics can blur the line between ecological and evolutionary processes, especially as they can occur on very similar timescales. Despite the importance of differentiating changes occurring within a population or strain from those occurring among populations, many common methodologies used to study microbiomes are not able to differentiate among them. In this review, we summarize the forces known to generate genetic diversity in bacterial genomes and describe the approaches used to study bacterial evolution from simple to more complex systems. We then explore how current methodologies and conceptual understanding can be applied to both understand and differentiate between the ecological and evolutionary processes in microbial communities. By highlighting lessons from longitudinal microbiome studies and experimental evolution, we explore the unique opportunities afforded by newer sequencing approaches and better sequencing resolution. Throughout, we identify the unique and outstanding challenges in studying these processes in microbiome systems and emphasize the great benefits in doing so to move forward our ability to better predict and manipulate microbiomes.},
}
@article {pmid40407119,
year = {2025},
author = {Theys, C and Verheyen, J and Janssens, L and Tüzün, N and Fajgenblat, M and Stoks, R},
title = {The Gut Microbiome Causally Contributes to Interspecific Differences in Pesticide Sensitivity.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c01615},
pmid = {40407119},
issn = {1520-5851},
abstract = {Explaining interspecific differences in pesticide sensitivity is key to increasing the predictive power of ecotoxicology. Besides species traits, the gut microbiome may provide an untested additional predictive factor since it often plays a role in host defense against stressors. Therefore, we investigated the gut microbiome's causal role in shaping differences in pesticide sensitivity between two congeneric damselfly species. After an antibiotic treatment, reciprocal gut microbiome transplants were performed between pesticide-sensitive Ischnura elegans and more tolerant Ischnura pumilio larvae, with donor larvae first preexposed to either chlorpyrifos or a solvent control to match the subsequent pesticide treatments of the recipients. The gut microbiome, determined by 16S rRNA gene amplicon sequencing, of both species included pesticide-degrading bacteria, but also showed shared and species-specific responses to the pesticide. Notably, the most pesticide-sensitive combination, with the highest pesticide-induced mortality, consisted of I. elegans larvae receiving I. elegans donor gut microbiota, whereas the least sensitive combination consisted of I. pumilio larvae receiving I. pumilio donor gut microbiota, whereby the pesticide did not increase larval mortality. The two mixed donor-recipient gut microbiome combinations resulted in an intermediate sensitivity. Remarkably, I. elegans recipient larvae experienced a lower chlorpyrifos-induced mortality when they received an I. pumilio donor gut microbiome than when they received their conspecific I. elegans donor gut microbiome. Our results provide, to our knowledge, the first proof-of-evidence that the gut microbiome causally contributes to species differences in pesticide sensitivity.},
}
@article {pmid40407098,
year = {2025},
author = {Cortés-Martín, A and Buttimer, C and Maier, JL and Tobin, CA and Draper, LA and Ross, RP and Kleiner, M and Hill, C and Shkoporov, AN},
title = {Adaptations in gut Bacteroidales facilitate stable co-existence with their lytic bacteriophages.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2507775},
doi = {10.1080/19490976.2025.2507775},
pmid = {40407098},
issn = {1949-0984},
mesh = {*Bacteriophages/physiology/genetics ; *Gastrointestinal Microbiome ; *Bacteroides/virology/genetics/physiology/metabolism ; Proteomics ; Adaptation, Physiological ; Humans ; *Bacteroidetes/virology/genetics/physiology ; },
abstract = {Bacteriophages (phages) and bacteria within the gut microbiome persist in long-term stable coexistence. These interactions are driven by eco-evolutionary dynamics, where bacteria employ a variety of mechanisms to evade phage infection, while phages rely on counterstrategies to overcome these defenses. Among the most abundant phages in the gut are the crAss-like phages that infect members of the order Bacteroidales, in particular, genus Bacteroides. In this study, we explored some of the mechanisms enabling the co-existence of four phage-Bacteroidales host pairs in vitro using a multi-omics approach (transcriptomics, proteomics and metabolomics). These included three Bacteroides species paired with three crAss-like phages (Bacteroides intestinalis and фcrAss001, Bacteroides xylanisolvens and фcrAss002, and an acapsular mutant of Bacteroides thetaiotaomicron with DAC15), and Parabacteroides distasonis paired with the siphovirus фPDS1. We show that phase variation of individual capsular polysaccharides (CPSs) is the primary mechanism promoting phage co-existence in Bacteroidales, but this is not the only strategy. Alternative resistance mechanisms, while potentially less efficient than CPS phase variation, can be activated to support bacterial survival by regulating gene expression and resulting in metabolic adaptations, particularly in amino acid degradation pathways. These mechanisms, also likely regulated by phase variation, enable bacterial populations to persist in the presence of phages, and vice versa. An acapsular variant of B. thetaiotaomicron demonstrated broader transcriptomic, proteomic, and metabolomic changes, supporting the involvement of additional resistance mechanisms beyond CPS variation. This study advances our understanding of long-term phage-host interaction, offering insights into the long-term persistence of crAss-like phages and extending these observations to other phages, such as фPDS1. Knowledge of the complexities of phage-bacteria interactions is essential for designing effective phage therapies and improving human health through targeted microbiome interventions.},
}
@article {pmid40407096,
year = {2025},
author = {Creskey, M and Silva Angulo, F and Wu, Q and Tamming, L and Fekete, EEF and Cheng, K and Ning, Z and Wang, A and Brito Rodrigues, P and de Rezende Rodovalho, V and Ramirez Vinolo, MA and Figeys, D and Li, X and Trottein, F and Zhang, X},
title = {Metaproteomics reveals age-specific alterations of gut microbiome in hamsters with SARS-CoV-2 infection.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2505117},
doi = {10.1080/19490976.2025.2505117},
pmid = {40407096},
issn = {1949-0984},
mesh = {Animals ; *Gastrointestinal Microbiome ; *COVID-19/microbiology/virology ; Cricetinae ; *Proteomics/methods ; SARS-CoV-2 ; Feces/microbiology ; Age Factors ; Metagenomics ; Disease Models, Animal ; Mesocricetus ; Male ; },
abstract = {The gut microbiome's pivotal role in health and disease is well established. SARS-CoV-2 infection often causes gastrointestinal symptoms and is associated with changes of the microbiome in both human and animal studies. While hamsters serve as important animal models for coronavirus research, there exists a notable void in the functional characterization of their microbiomes with metaproteomics. In this study, we present a workflow for analyzing the hamster gut microbiome, including a metagenomics-derived hamster gut microbial protein database and a data-independent acquisition metaproteomics method. Using this workflow, we identified 32,419 protein groups from the fecal microbiomes of young and old hamsters infected with SARS-CoV-2. We showed age-specific changes in the expressions of microbiome functions and host proteins associated with microbiomes, providing further functional insight into the interactions between the microbiome and host in SARS-CoV-2 infection. Altogether, this study established and demonstrated the capability of metaproteomics for the study of hamster microbiomes.},
}
@article {pmid40407013,
year = {2025},
author = {Patige Madhusudhan, A and Pandey, S and Wang, PC and Chen, SC and Byadgi, OV},
title = {Impact of Streptococcus iniae Infection on Gut Microbiome Diversity and Immune Response in Four-Finger Threadfin (Eleutheronema tetradactylum).},
journal = {Journal of fish diseases},
volume = {},
number = {},
pages = {e14149},
doi = {10.1111/jfd.14149},
pmid = {40407013},
issn = {1365-2761},
support = {NSTC 112-2313-B-020-007-MY3//National Science and Technology Council/ ; },
abstract = {Streptococcus iniae is one of the key etiological agents of Streptococcosis and is a significant pathogen affecting four-finger Threadfin (Eleutheronema tetradactylum), leading to severe clinical manifestations, such as ascitic fluid accumulation in the abdominal cavity and intestinal haemorrhages. Understanding the interplay between fish infections, gut microbiota dysbiosis and immune responses is critical for effective management in aquaculture. This study investigates the impact of the acute infection caused by S. iniae on the gut microbiome composition and immune response of Threadfin fish. Following experimental infection, we observed significant differences in taxonomic richness and diversity between healthy and infected fish during the acute phase of the disease. The gut microbiota was primarily dominated by Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes. Notably, infection led to a marked decline in microbiota richness and diversity in the gut, accompanied by an increase in the relative abundance of pathogenic genera such as Streptococcus and Vibrio. Immune modulation, as evidenced by altered gene expression of selected immune parameters, was observed in tissue samples following clinical infection. Also, histological examinations revealed significant disruptions to intestinal villi architecture in infected fish. These findings suggest that S. iniae alters the gut microbiota composition, which may compromise immune function and elevate the risk of intestinal inflammation. This research underscores the importance of monitoring gut microbiota dynamics as a potential diagnostic tool for managing bacterial infections in aquaculture settings.},
}
@article {pmid40406671,
year = {2025},
author = {Benedetti, G and Seraidarian, E and Pralas, T and Jeba, A and Borman, T and Lahti, L},
title = {iSEEtree: interactive explorer for hierarchical data.},
journal = {Bioinformatics advances},
volume = {5},
number = {1},
pages = {vbaf107},
pmid = {40406671},
issn = {2635-0041},
abstract = {MOTIVATION: Hierarchical data structures are prevalent across several research fields, as they represent an organized and efficient approach to study complex interconnected systems. Their significance is particularly evident in microbiome analysis, where microbial communities are classified at various taxonomic levels using phylogenetic trees. In light of this trend, the R/Bioconductor community has established a reproducible analytical framework for hierarchical data, which relies on the generic and optimized TreeSummarizedExperiment data container. However, this framework requires basic programming skills.<br><br>RESULTS: To reduce the entry requirements, we developed iSEEtree, an R package, which provides a visual interface for the analysis and exploration of TreeSummarizedExperiment objects, thereby expanding the interactive graphics capabilities of related work to hierarchical structures. This way, users can interactively explore several aspects of their data without the need for an extensive knowledge of R programming. We describe how iSEEtree enables the exploration of hierarchical multi-table data and demonstrate its functionality with applications to microbiome analysis.<br><br>iSEEtree was implemented in the R programming language and is available on Bioconductor at https://bioconductor.org/packages/iSEEtree under an Artistic 2.0 license.},
}
@article {pmid40406527,
year = {2025},
author = {Li, Y and Wu, S and Zhang, Y and Zhang, T and Hu, C and Zhang, P and Yang, W and Xiong, S and Liu, Y},
title = {Analysis of the diversity and function of the microbiota in infected root canals of type 2 diabetes mellitus with apical periodontitis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1514510},
pmid = {40406527},
issn = {2235-2988},
mesh = {Humans ; *Periapical Periodontitis/microbiology/complications ; *Diabetes Mellitus, Type 2/complications/microbiology ; *Microbiota/genetics ; *Dental Pulp Cavity/microbiology ; RNA, Ribosomal, 16S/genetics ; Male ; Female ; Middle Aged ; *Bacteria/classification/genetics/isolation &amp; purification ; DNA, Bacterial/genetics ; Adult ; DNA, Ribosomal/genetics/chemistry ; Phylogeny ; Sequence Analysis, DNA ; Aged ; Biodiversity ; Computational Biology ; },
abstract = {PURPOSE: This study aimed to compare the compositional differences and functions of microbial communities in infected root canals of teeth with apical periodontitis (AP) and/or type 2 diabetes mellitus (T2DM) using 16S rDNA sequencing.<br><br>METHODS: Eighteen participants were categorized into two groups based on their health conditions: AP and AP complicated with T2DM (APDM). Infected root canal microbiota was clinically collected for 16S rDNA sequencing. Subsequent statistical and bioinformatics analyses were conducted after sequencing by NovaSeq, encompassing diversity analysis, intergroup difference analysis, and functional prediction analysis.<br><br>RESULTS: The core microbiome of root canal microorganisms was similar in the two groups, which mainly consisted of Bacteroidota, Firmicutes, Synergistota, Actinobacteriota, Proteobacteria, Fusobacteriota, Spirochaetota. The root canals of the affected teeth of APDM had significantly higher abundance of Olsenella_uli, Peptostreptococcaceae_bacterium _oral_taxon_113_str_W5053, W5053, Pyramidobacter_piscolen, Pyramidobacte, Synergistaceae, Synergistales was significantly higher than AP group (P<0.05). Under the condition of T2DM, root canal microbial metabolism was predominantly enriched towards functions of the phosphotransferase system, ABC system, amino acid metabolism, and carbohydrate metabolism.<br><br>CONCLUSION: The microbial community in the infected root canals of APDM showed similarities to AP yet exhibited differences in certain species and microbial functions.},
}
@article {pmid40406520,
year = {2025},
author = {Zhai, Q and Zhao, L and Wang, M and Li, L and Li, LA and Ye, M and Li, M and Xu, C and Meng, Y},
title = {Integrated analysis of microbiome and metabolome reveals insights into cervical neoplasia aggravation in a Chinese cohort.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1556153},
pmid = {40406520},
issn = {2235-2988},
mesh = {Humans ; Female ; *Uterine Cervical Neoplasms/microbiology/pathology/metabolism ; *Microbiota ; *Metabolome ; Adult ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; *Uterine Cervical Dysplasia/microbiology/pathology ; China ; Metabolomics ; Dinoprostone/metabolism/analysis ; Cervix Uteri/microbiology ; Case-Control Studies ; Cohort Studies ; Bacteria/classification/genetics/isolation &amp; purification ; Asian People ; Biomarkers, Tumor ; East Asian People ; },
abstract = {INTRODUCTION: Cervical carcinoma (CC) remains one of the significant cancers threatening women's health globally. Increasing evidence suggests that alterations in the microbiota are closely associated with cancer development. However, the understanding of reliable biomarkers and underlying mechanisms during the aggravation of cervical neoplasia such as cervical intraepithelial neoplasia (CIN) and CC is still relatively limited.<br><br>METHODS: In this study, cervical swab samples from 53 healthy controls, 51 high-grade squamous intraepithelial lesion (HSIL), and 52 CC patients were subjected to 16S rDNA sequencing and metabolomics analysis.<br><br>RESULTS: We observed significant differences in the cervical microbiota between CC patients and healthy controls or HSIL groups. Compared to the healthy controls, CC patients exhibited increased microbial diversity, decreased abundance of Lactobacillus, and notable changes in microbial composition. Metabolomics analysis revealed significantly elevated levels of the inflammatory mediator Prostaglandin E2 (PGE2) in CC samples. Through random forest modeling and ROC curve analysis, we identified a combination of key microbiota (Porphyromonas, Pseudofulvibacter) and metabolites (Cellopentaose, PGE2) as diagnostic biomarkers with high diagnostic value for CC. Furthermore, we found a significant correlation between the cervical microbiota Porphyromonas and the metabolite PGE2, suggesting a potential role of key microbiota in inducing inflammation.<br><br>DISCUSSION: These findings indicate that alterations in cervical microbiota and metabolites may be closely associated with the occurrence and aggravation of cervical neoplasia, providing new insights for further understanding the mechanisms of cervical neoplasia progression and developing novel diagnostic markers and therapeutic approaches.},
}
@article {pmid40406514,
year = {2025},
author = {Kehrmann, J and Dostmohammadi, A and Stumpf, AL and Best, L and Consten, L and Sievert, H and Maischack, F and Sammet, S and Albayrak-Rena, S and Doerr, AK and Bohlen, K and von Velsen, O and Kraiselburd, I and Karsten, CB and Farahpour, F and Meyer, F and Esser, S and Buer, J},
title = {Gut microbiota differences linked to weight gain and ART in people living with HIV are enterotype specific and minor compared to the large differences linked to sexual behavior.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1568352},
pmid = {40406514},
issn = {2235-2988},
mesh = {Humans ; *HIV Infections/drug therapy/microbiology ; Male ; *Gastrointestinal Microbiome/drug effects ; *Weight Gain/drug effects ; RNA, Ribosomal, 16S/genetics ; Adult ; Middle Aged ; Female ; *Sexual Behavior ; Bacteria/classification/genetics/isolation &amp; purification ; Prevotella ; Cohort Studies ; Homosexuality, Male ; DNA, Bacterial/genetics/chemistry ; Phylogeny ; Sequence Analysis, DNA ; DNA, Ribosomal/genetics/chemistry ; *Anti-Retroviral Agents/therapeutic use/adverse effects ; },
abstract = {INTRODUCTION: Specific antiretroviral therapy (ART) regimens are associated with weight gain in people living with HIV (PLWH). Gut microbiota is involved in weight gain in humans and animals. Human gut microbiota can be classified into enterotypes with distinct microbial and functional profiles.<br><br>METHODS: In a cohort of 118 PLWH, we analyzed the gut microbiome in relation to weight gain and ART regimen using 16S rRNA gene sequencing, taking enterotype classification into account.<br><br>RESULTS: The enterotype was strongly associated with sexual orientation. Of the 67 individuals forming a Prevotella-dominated enterotype cluster in principal coordinates analysis, 93% were men who had sex with men (MSM), while 31% of individuals in the Bacteroides-dominated enterotype cluster were MSM and 69% were non-MSM. Forty-nine genera differed significantly between the MSM and non-MSM individuals. When stratified by dominant genus, only six taxa were associated with weight gain. Of these, five were restricted to Bacteroides-dominated individuals. Among them, the class Actinobacteria and genus Bifidobacterium differed between individuals gaining more than 5% weight and less than 5% weight 1 year after ART switch. Additionally, three taxa were significantly different between 15% of individuals with the highest weight gain (&#x2265;6.3%) and the highest weight loss (&#x2264;3.19%) 1 year after ART switch, including the phyla Firmicutes, Verrucomicrobia, and Synergistetes. Distinct functional properties in Bacteroides, but not Prevotella-dominated enterotype individuals, linked to weight gain were observed, particularly for glycan and lipid metabolism. Additionally, ART regimen-associated differences were observed for the phylum Actinobacteria, although this was limited to Prevotella-dominated enterotype individuals.<br><br>DISCUSSION: Differences in the composition and functional characteristics of the gut microbiome associated with weight gain and ART regimens were enterotype-specific and relatively small compared with differences linked to sexual orientation. Due to the substantial differences in gut microbiome structure among many MSM, categorization into enterotypes is useful for identifying differences in microbiome composition associated with variables such as weight gain or ART, which may be limited to a single enterotype. This may further advance the identification of microbes that contribute to weight gain or alter the gut microbiome composition in the context of the enterotype.},
}
@article {pmid40406347,
year = {2025},
author = {Teng, JLL and Bopegamage, S and Yeung, ML},
title = {Editorial: Molecular pathogenesis of enteroviruses: insights into viral-host interactions, pathogenic mechanisms, and microbiome dynamics.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1608481},
pmid = {40406347},
issn = {1664-302X},
}
@article {pmid40406150,
year = {2025},
author = {Griffard-Smith, R and Schueddig, E and Mahoney, DE and Chalise, P and Koestler, DC and Pei, D},
title = {micRoclean: an R package for decontaminating low-biomass 16S-rRNA microbiome data.},
journal = {Frontiers in bioinformatics},
volume = {5},
number = {},
pages = {1556361},
pmid = {40406150},
issn = {2673-7647},
abstract = {In 16S-rRNA microbiome studies, cross-contamination and environmental contamination can obscure true biological signal. This contamination is particularly problematic in low-biomass studies, which are characterized by samples with a small amount of microbial DNA. Although multiple methods and packages for decontaminating microbiome data exist, there is no consensus on the most appropriate tool for decontamination based on the individual research study design and how to quantify the impact of removing identified contaminants to avoid over-filtering. To address these gaps, we introduce micRoclean, an open-source R package that contains two distinct microbiome decontamination pipelines with guidance on which to select based on the downstream goals of the research study and study design. This package integrates and expands on existing packages for microbiome decontamination and analysis for convenience of users. Furthermore, micRoclean also implements a filtering loss statistic to quantify the impact of decontamination on the overall covariance structure of the data. In this paper, we demonstrate the utility of micRoclean through implementation on example data, illustrating that micRoclean effectively and intuitively decontaminates microbiome data. Further, we demonstrate through a multi-batch simulated microbiome sample that micRoclean matches or outperforms tools with similar objectives. This package is freely available from GitHub repository rachelgriffard/micRoclean.},
}
@article {pmid40406136,
year = {2025},
author = {Duhamel, M and Salzet, M},
title = {Self or nonself: end of a dogma?.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1595764},
pmid = {40406136},
issn = {1664-3224},
mesh = {Humans ; Animals ; *Immune Tolerance ; Immunity, Innate ; *Autoimmunity ; *Immune System/immunology ; *Self Tolerance ; },
abstract = {Immunologists generally view the notion of self and non-self as part of a broader, more contextual understanding of immune function, rather than a rigid dogma. While the classical paradigm that the primary role of the immune system is to recognize and eliminate anything foreign once provided a unifying basis for explaining tolerance and rejection, numerous discoveries have focused attention on how immune responses are finely tuned by a range of contextual cues, including tissue signals, hygienist theory, molecular mimicry, symbiotic microbes, metabolic factors and epigenetic modifications. Maternal-fetal tolerance and the persistence of microchimeric cells in adults demonstrate that genetically foreign cells can be actively integrated into the host, challenging the simple assumption that 'foreign' equals unconditional attack. Similarly, research into the microbiome, the virome and the phenomenon of trained innate immunity has shown that there can be beneficial or even essential relationships between the body and what has traditionally been labelled 'non-self'. Over the last decade, the idea that the immune system strictly enforces a binary distinction has instead evolved towards a model in which it continuously interprets signals of damage or perturbation, manages complex ecological relationships with commensal or latent organisms, and recalibrates according to the organism's life stage and environment. There remains a recognition that clonal deletion and negative selection in the thymus, together with MHC-bound peptide recognition, still underlie many core processes, and in certain clinical contexts, such as acute transplant rejection or the prevention of autoimmunity, an approximate self-non-self-categorization is directly relevant. Overall, however, the field recognizes that 'self' is not a static attribute defined once and for all, but rather a dynamic and context-dependent state that continues to be shaped by microbial symbioses, epigenetic reprogramming and immunoregulatory networks throughout an individual's lifespan.},
}
@article {pmid40406096,
year = {2025},
author = {Zhang, J and Song, Z and Zhang, Y and Zhang, C and Xue, Q and Zhang, G and Tan, F},
title = {Recent advances in biomarkers for predicting the efficacy of immunotherapy in non-small cell lung cancer.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1554871},
pmid = {40406096},
issn = {1664-3224},
mesh = {Humans ; *Carcinoma, Non-Small-Cell Lung/therapy/immunology/metabolism/drug therapy/diagnosis/genetics ; *Lung Neoplasms/therapy/immunology/metabolism/diagnosis/drug therapy/genetics ; *Biomarkers, Tumor/genetics ; *Immunotherapy/methods ; *Immune Checkpoint Inhibitors/therapeutic use ; Treatment Outcome ; Lymphocytes, Tumor-Infiltrating/immunology ; B7-H1 Antigen ; Prognosis ; Animals ; },
abstract = {Lung cancer continues to be the primary cause of cancer-related deaths globally, with non-small cell lung cancer (NSCLC) accounting for approximately 85% of all instances. Recently, immune checkpoint inhibitors (ICIs) have transformed the treatment approach for NSCLC, however, only a subset of patients experiences significant benefits. Therefore, identifying reliable biomarkers to forecast the efficacy of ICIs is crucial for ensuring the safety and effectiveness of treatments, becoming a major focus of current research efforts. This review highlights the recent advances in predictive biomarkers for the efficacy of ICIs in the treatment of NSCLC, including PD-L1 expression, tertiary lymphoid structures (TLS), tumor-infiltrating lymphocytes (TILs), tumor genomic alterations, transcriptional signatures, circulating biomarkers, and the microbiome. Furthermore, it underscores the pivotal roles of liquid biopsy, sequencing technologies, and digital pathology in biomarker discovery. Special attention is given to the predictive value of TLS, circulating biomarkers, and transcriptional signatures. The review concludes that the integration of multiple biomarkers holds promise for achieving more accurate efficacy predictions and optimizing personalized immunotherapy strategies. By providing a comprehensive overview of the current progress, this review offers valuable insights into biomarker-based precision medicine for NSCLC and outlines future research directions.},
}
@article {pmid40406094,
year = {2025},
author = {Eslami, M and Naderian, R and Bahar, A and Babaeizad, A and Rezanavaz Gheshlagh, S and Oksenych, V and Tahmasebi, H},
title = {Microbiota as diagnostic biomarkers: advancing early cancer detection and personalized therapeutic approaches through microbiome profiling.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1559480},
pmid = {40406094},
issn = {1664-3224},
mesh = {Humans ; Precision Medicine/methods ; *Gastrointestinal Microbiome/immunology ; *Neoplasms/diagnosis/therapy/microbiology ; *Early Detection of Cancer/methods ; *Biomarkers, Tumor ; Animals ; Fecal Microbiota Transplantation ; },
abstract = {The important function of microbiota as therapeutic modulators and diagnostic biomarkers in cancer has been shown by recent developments in microbiome research. The intricate interplay between the gut microbiota and the development of cancer, especially in colorectal and breast cancers, emphasizes how microbial profiling may be used for precision treatment and early diagnosis. Important microbial signatures, including Bacteroides fragilis and Fusobacterium nucleatum, have been linked to the development and progression of cancer, providing important information on the processes behind carcinogenesis. Additionally, the influence of microbiota on the effectiveness of treatments such as immunotherapy and chemotherapy highlights its dual function in improving treatment outcomes and reducing side effects. To optimize treatment results, strategies including dietary changes and fecal microbiota transplantation (FMT) are being investigated. Despite these developments, there are still issues, such as individual variations in microbial composition, a lack of standardized procedures, and the requirement for reliable biomarkers. Integrating microbiome-based diagnostics with conventional approaches, such as liquid biopsies and machine learning algorithms, could revolutionize cancer detection and management. This review provides an overview of the current understanding of the host-microbe immunological axis and discusses emerging therapeutic strategies centered on microbiota modulation to support human health. Further research is essential to overcome existing challenges and fully realize the promise of microbiota-driven innovations in oncology.},
}
@article {pmid40405772,
year = {2025},
author = {Onghena, L and Heldens, A and De Paepe, K and Antwi, M and Van Vlierberghe, H and Raevens, S and Verhelst, X and Hoorens, A and Devisscher, L and van Nieuwenhove, Y and Van de Wiele, T and Geerts, A and Lefere, S},
title = {The double-edged sword of metabolic and bariatric surgery: extending the biliary limb can trigger bacterial translocation, sepsis, and liver inflammation - an experimental study.},
journal = {International journal of surgery (London, England)},
volume = {},
number = {},
pages = {},
doi = {10.1097/JS9.0000000000002502},
pmid = {40405772},
issn = {1743-9159},
abstract = {BACKGROUND: Metabolic and bariatric surgery (MBS) procedures with extended biliary limb length are gaining popularity to expedite weight loss but can induce liver failure. We aimed to investigate the underlying pathophysiology for this potentially fatal complication.<br><br>MATERIALS AND METHODS: We compared mouse models of vertical sleeve plication, sleeve gastrectomy, Roux-en-Y gastric bypass (RYGB), and one-anastomosis gastric bypass with three biliary limb lengths (25%&#xa0;=&#xa0;&#x3a9;1, 50%&#xa0;=&#xa0;&#x3a9;2, 75%&#xa0;=&#xa0;&#x3a9;3) by analyzing mortality, weight loss, metabolic and liver health, bacterial translocation, inflammation, and biliary and fecal microbiome. Gut decontamination with oral antibiotics (amoxicillin, vancomycin, neomycin, and metronidazole) was performed in a subset of &#x3a9;3 mice. Liver histology from mice with different biliary limb lengths was compared to samples from human patients who developed liver failure following biliopancreatic diversion or RYGB.<br><br>RESULTS: RYGB and &#x3a9;1&amp;2 significantly improved glucose intolerance and liver steatosis compared to sham surgery. However, extending the biliary limb (&#x3a9;3) resulted in 100% mortality. The &#x3a9;3 procedure induced bacterial translocation of enterococcus genus to the spleen and biliary fluid, consistent with increased serum lipopolysaccharide levels and terminal ileum, biliary limb, and hepatic inflammation. Liver histology in &#x3a9;3 mice was characterized by mediovesicular steatosis, closely resembling the histological picture observed in patients with liver failure after MBS. Oral gut decontamination significantly improved &#x3a9;3 one-week-survival from 31.3% to 80.0%, prevented bacterial overgrowth in biliary fluid and spleen, and decreased liver damage.<br><br>CONCLUSION: Mortality in longer biliary limb MBS surgery is caused by bacterial overgrowth, translocation, and gut-liver axis inflammation, which were reversed by oral gut decontamination with antibiotics.},
}
@article {pmid40405437,
year = {2025},
author = {Matloubieh, JE and Patel, RD and Fram, E and Lowe, FC},
title = {Factors associated with Fournier's gangrene survival in a diverse urban community: a 15-year review.},
journal = {BJU international},
volume = {},
number = {},
pages = {},
doi = {10.1111/bju.16766},
pmid = {40405437},
issn = {1464-410X},
abstract = {OBJECTIVE: To assess risk factors, scoring systems, microbiology, and outcomes associated with Fournier's gangrene (FG) in a diverse urban community.<br><br>METHODS: A retrospective review of patients with FG medical data from 2007 to 2021 was performed. Means were compared via t-tests, associations via chi-square analysis, and survival probability via Kaplan-Meier analysis. Statistical findings were considered significant if P&#x2009;&#x2264;&#x2009;0.05.<br><br>RESULTS: Of the 132 patients with FG, 14% died of FG, 47% were discharged home, and 39% were discharged to a nursing facility. Orchidectomies, thigh pouches, flap/graft wound closure, and immediate wound closure were performed in 9%, 12%, 22%, and 29% of cases, respectively. Escherichia coli, Bacteroides, Streptococcus, Enterococcus, and Candida were most frequently isolated. Candida and Proteus species were associated with lower survival probability, whereas Streptococcus and Staphylococcus species were associated with higher survival probability. Lower haemoglobin A1c was associated with orchidectomy and FG death, while higher A1c was associated with flap/graft use during wound closure. Compared to culture-concordant empiric antibiotics, culture-discordant empiric antibiotics were associated with longer hospital stay and worse outcomes. The Uludag Fournier's Gangrene Severity Index (UFGSI) was significantly associated with the most surgical and clinical outcomes of interest.<br><br>CONCLUSIONS: The microbiome responsible for the FG disease process evolved with the emergence of fungal FG. Along with causative organisms, this study also highlights comorbid conditions that adversely affect patient outcomes, especially mental illness. We also note the relative superiority of the UFGSI compared to other scoring systems. There is a need to reassess empiric antibiotic selection and surgical management.},
}
@article {pmid40405394,
year = {2025},
author = {Shannon, OM and Mathers, JC and Stevenson, E and Siervo, M},
title = {Healthy dietary patterns, cognition and dementia risk: current evidence and context.},
journal = {The Proceedings of the Nutrition Society},
volume = {},
number = {},
pages = {1-11},
doi = {10.1017/S0029665125100050},
pmid = {40405394},
issn = {1475-2719},
abstract = {Approximately 60 million individuals worldwide are currently living with dementia. As the median age of the world's population rises, the number of dementia cases is expected to increase markedly, and to affect ∼150 million individuals by 2050. This will create a huge and unsustainable economic and social burden across the globe. Although promising pharmacological treatment options for Alzheimer's disease - the most common cause of dementia - are starting to emerge, dementia prevention and risk reduction remain vital. In this review, we present evidence from large-scale epidemiological studies and randomised controlled trials to indicate that adherence to healthy dietary patterns could improve cognitive function and lower dementia risk. We outline potential systemic (e.g. improved cardiometabolic health, lower inflammation, modified gut microbiome composition/metabolism, slower pace of aging) and brain-specific (e.g. lower amyloid-β load, reduced brain atrophy and preserved cerebral microstructure and energetics) mechanisms of action. We also explore current gaps in our knowledge and outline potential directions for future research in this area. Our aim is to provide an update on current state of the knowledge, and to galvanise research on this important topic.},
}
@article {pmid40405262,
year = {2025},
author = {Nixon, MP and Gloor, GB and Silverman, JD},
title = {Incorporating scale uncertainty in microbiome and gene expression analysis as an extension of normalization.},
journal = {Genome biology},
volume = {26},
number = {1},
pages = {139},
pmid = {40405262},
issn = {1474-760X},
support = {1R01GM148972-01/NH/NIH HHS/United States ; 1R01GM148972-01/NH/NIH HHS/United States ; },
mesh = {*Microbiota ; Software ; Humans ; Uncertainty ; *Gene Expression Profiling/methods ; },
abstract = {Statistical normalizations are used in differential analyses to address sample-to-sample variation in sequencing depth. Yet normalizations make strong, implicit assumptions about the scale of biological systems, such as microbial load, leading to false positives and negatives. We introduce scale models as a generalization of normalizations, which allows researchers to model potential errors in these modeling assumptions, thereby enhancing the transparency and robustness of data analyses. In practice, scale models can drastically reduce false positives and false negatives rates. We introduce updates to the popular ALDEx2 software package, available on Bioconductor, facilitating scale model analysis.},
}
@article {pmid40405248,
year = {2025},
author = {Cornejo-Granados, F and Gallardo-Becerra, L and Romero-Hidalgo, S and Lopez-Zavala, AA and Cota-Huízar, A and Cervantes-Echeverría, M and Sotelo-Mundo, RR and Ochoa-Leyva, A},
title = {Host genome drives the microbiota enrichment of beneficial microbes in shrimp: exploring the hologenome perspective.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {50},
pmid = {40405248},
issn = {2524-4671},
support = {Fronteras de la Ciencia CF2019-G-263986//Consejo Nacional de Innovaci&#xf3;n, Ciencia y Tecnolog&#xed;a/ ; Fronteras de la Ciencia CF2019-G-263986//Consejo Nacional de Innovaci&#xf3;n, Ciencia y Tecnolog&#xed;a/ ; Fronteras de la Ciencia CF2019-G-263986//Consejo Nacional de Innovaci&#xf3;n, Ciencia y Tecnolog&#xed;a/ ; Fronteras de la Ciencia CF2019-G-263986//Consejo Nacional de Innovaci&#xf3;n, Ciencia y Tecnolog&#xed;a/ ; IN219723//Direcci&#xf3;n General de Asuntos del Personal Acad&#xe9;mico (DGAPA)/ ; IN219723//Direcci&#xf3;n General de Asuntos del Personal Acad&#xe9;mico (DGAPA)/ ; IN219723//Direcci&#xf3;n General de Asuntos del Personal Acad&#xe9;mico (DGAPA)/ ; IN219723//Direcci&#xf3;n General de Asuntos del Personal Acad&#xe9;mico (DGAPA)/ ; },
abstract = {BACKGROUND: Pacific Whiteleg shrimp (Litopenaeus vannamei) is an important model for breeding programs to improve global aquaculture productivity. However, the interaction between host genetics and microbiota in enhancing productivity remains poorly understood. We investigated the effect of two shrimp genetic lines, Fast-Growth (Gen1) and Disease-Resistant (Gen2), on the microbiota of L. vannamei.<br><br>RESULTS: Using genome-wide SNP microarray analysis, we confirmed that Gen1 and Gen2 represented distinct genetic populations. After confirming that&#xa0;the rearing pond did not significantly influence the microbiota composition, we determined that genetic differences explained 15.8% of the microbiota variability, with a stronger selective pressure in the hepatopancreas than in the intestine. Gen1, which exhibited better farm productivity, fostered a microbiota with greater richness, diversity, and resilience than Gen2, along with a higher abundance of beneficial microbes. Further, we demonstrated that a higher abundance of beneficial microbes was associated with healthier shrimp vs. diseased specimens, suggesting that Gen1 could improve shrimp's health and productivity by promoting beneficial microbes. Finally, we determined that the microbiota of both genetic lines was significantly different from their wild-type counterparts, suggesting farm environments and selective breeding programs strongly alter the natural microbiome.<br><br>CONCLUSIONS: This study highlights the importance of exploring the hologenome perspective, where integrating host genetics and microbiome composition can enhance breeding programs and farming practices.},
}
@article {pmid40405192,
year = {2025},
author = {Wang, W and Lu, Y and Wu, B and Peng, S and Cai, W and Xiao, Y},
title = {Multi-omics analysis reveals Lactobacillus and Indolelactic acid involved in small intestinal adaptation of piglet with short bowel syndrome.},
journal = {Nutrition &amp; metabolism},
volume = {22},
number = {1},
pages = {47},
pmid = {40405192},
issn = {1743-7075},
support = {82270537, 81974058//National Natural Science Foundation of China/ ; SHDC2020CR2010A//Clinical Research Plan of SHDC/ ; 22Y31900600//Shanghai Science and Technology innovation Program/ ; },
abstract = {BACKGROUND: Short bowel syndrome (SBS) is a condition characterized by malabsorption that occurs when a patient loses a significant amount of bowel length or function, often necessitating lifelong parenteral nutrition support. This study utilized multi-omics analysis to investigate alterations in gut microbiota, metabolism, and transcriptome during the progression of intestinal adaptation in SBS using a piglet model.<br><br>METHODS: We established a model of SBS in Bama mini piglets by performing a 75% jejunoileal resection. Fifteen piglets were randomized into EN, PN, and PN-SBS groups. Fecal samples were collected for 16&#xa0;S rRNA gene-based microbiota analysis. Ileal mucosa and serum were collected for untargeted liquid chromatography-mass spectrometry. Transcriptomic analysis on ileal mucosa was performed.<br><br>RESULTS: The PN-SBS model was established in the newborn piglets. A significant decrease in species-level diversity was observed in piglets with SBS, accompanied by alterations in their microbiome compositions. The beneficial anaerobes from Bacillota and Bacteroidota were depleted while microorganisms from Verrucomicrobiota and Fusobacteriota were enriched in feces from SBS piglets. The dysregulation of metabolites and metabolic pathways was observed in the metabolic profiles of ileal mucosa and serum in SBS piglets. Indolelactic acid (ILA) levels were found to be reduced in the ileal mucosa and serum of SBS piglets. Transcriptomic analysis revealed an extensive functional alteration in SBS, primarily manifested as metabolic changes and intestinal proliferation. The multi-omics analysis revealed that the decreased abundance of Lactobacillus may result in a diminished production of their metabolite ILA, thereby influencing intestinal proliferation and anti-inflammatory responses.<br><br>CONCLUSION: Disrupted homeostasis of gut microbiota, metabolism, and transcriptome were reported in the SBS piglets. Multi-omics analysis demonstrated Lactobacillus and its metabolite ILA may be involved in small intestinal adaptation of SBS. These alterations may contribute to the proinflammatory state and the delay of intestinal adaptation in SBS, which in turn provide promising targets for therapies.},
}
@article {pmid40405096,
year = {2025},
author = {Yasmin, A and Rahman, MS and Kador, SM and Ahmed, MM and Moon, MEK and Akhter, H and Sultana, M and Begum, A},
title = {Metagenomic insights into microbial diversity and potential pathogenic transmission in poultry farm environments of Bangladesh.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {318},
pmid = {40405096},
issn = {1471-2180},
mesh = {Bangladesh ; Animals ; *Bacteria/genetics/classification/isolation &amp; purification/drug effects/pathogenicity ; RNA, Ribosomal, 16S/genetics ; Farms ; *Poultry/microbiology ; *Microbiota/genetics ; *Metagenomics ; *Poultry Diseases/transmission/microbiology ; Biodiversity ; Soil Microbiology ; DNA, Bacterial/genetics ; },
abstract = {The microbiome plays a critical role in poultry health and productivity, influencing growth, immunity, and the overall farm ecosystem. This study investigated microbial diversity, antibiotic resistance pathways, and functional potential across various components of poultry ecosystems-cloacal swabs, droppings, feed, hand swabs, soil, and water-in different districts of Bangladesh. Using 16S rRNA gene amplicon sequencing, we identified 2,745 Operational Taxonomic Units (OTUs) and analyzed microbial richness, community structure, and functional pathways. Alpha diversity metrics revealed that droppings exhibited the highest microbial richness (726 OTUs in Noakhali), while feed samples showed the lowest diversity (211 OTUs). Beta diversity analysis indicated significant differences in microbial composition across sample sources, with PERMANOVA confirming that sample origin accounted for 51.45% of the variability (p < 0.001). Proteobacteria dominated the microbial communities (48.36%), followed by Firmicutes (19.83%) and Cyanobacteria (12.02%). Key genera of concern, such as Enterobacter (26.62% in hand swabs), Acinetobacter (30.87% in cloacal swabs), and Shigella (22.89% in cloacal swabs), were identified, highlighting potential contamination and zoonotic risks. Conversely, beneficial genera like Lactobacillus (36.89% in feed) and Enterococcus (10.78% in droppings) were prevalent, suggesting roles in gut health and nutrient cycling. Functional pathway analysis (KEGG) revealed that carbohydrate and amino acid metabolism were highly active in droppings and feed, reflecting nutrient utilization. Antimicrobial resistance (AMR) pathways, such as 23S rRNA-methyltransferase and multidrug efflux pumps, were widespread, with pathogenic genera (Enterobacter, Acinetobacter, Shigella, Pseudomonas) showing strong positive correlations with AMR pathways. These findings underscore the influence of environmental factors on microbial diversity and functional potential in poultry farming. The study highlights the need for improved management practices and biosecurity measures to mitigate risks associated with microbial pathogens and antimicrobial resistance, ultimately supporting healthier and more sustainable poultry production in Bangladesh.},
}
@article {pmid40405038,
year = {2025},
author = {Zhang, F and Lo, EKK and Chen, C and Lee, JC and Felicianna, and Ismaiah, MJ and Leung, HKM and Tsang, DHL and El-Nezami, H},
title = {Probiotics Mixture, Prohep: a Potential Adjuvant for Low-Dose Sorafenib in Metabolic Dysfunction-Associated Steatotic Liver Disease-Associated Hepatocellular Carcinoma Suppression Through Modulating Gut Microbiota.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {40405038},
issn = {1867-1314},
abstract = {Targeting gut microbiota is an innovative approach to mitigate the development of metabolic dysfunction-associated steatotic liver disease-associated hepatocellular carcinoma (MASLD-HCC). This study aims to investigate the effects of Prohep, a probiotic mixture, both as a prophylactic measure and as an adjuvant therapy for low-dose sorafenib. A MASLD-HCC mice model was established by diethylnitrosamine (DEN) injection with feeding of a high-fat high-cholesterol (HFHC) diet. Gut microbiome profiles were later identified through shotgun sequencing. Our findings demonstrated that Prohep supplementation effectively suppressed MASLD-HCC development in mice. This protective effect was attributed to the modulation of gut microbiota and the increased production of short-chain fatty acids (SCFAs), propionate, and valerate. Prohep also activated AMPK, which decreased lipogenesis, reduced lipid uptake, and enhanced antioxidant enzyme expressions. Additionally, the cancer proliferation pathway PI3K/mTOR was inhibited in response to Prohep treatment. As an adjuvant therapy, Prohep improved the efficacy of low-dose sorafenib, as indicated by reduced tumor counts, alleviated inflammation, and increased hepatic superoxide dismutase (SOD) expression. The combination led to enhanced butyrate production, contributing to the overall therapeutic effects, thanks to the gut microbiota modulatory effects of Prohep. These results underscore Prohep's anti-tumorigenic properties and its potential to enhance the therapeutic outcomes of low-dose sorafenib in MASLD-HCC treatment. The study highlights the importance of gut microbiota modulation for developing effective neoadjuvant therapies and long-term management strategies for MASLD-HCC.},
}
@article {pmid40404925,
year = {2025},
author = {Xu, Z and Wang, Y and Cai, W and Chen, Y and Wang, Y},
title = {Single microorganism RNA sequencing of microbiomes using smRandom-Seq.},
journal = {Nature protocols},
volume = {},
number = {},
pages = {},
pmid = {40404925},
issn = {1750-2799},
support = {32200073//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32250710678//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82200977//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Bacteria colonize nearly every part of the human body and various environments, displaying remarkable diversity. Traditional population-level transcriptomics measurements provide only average population behaviors, often overlooking the heterogeneity within bacterial communities. To address this limitation, we have developed a droplet-based, high-throughput single-microorganism RNA sequencing method (smRandom-seq) that offers highly species specific and sensitive gene detection. Here we detail procedures for microbial sample preprocessing, in situ preindexed cDNA synthesis, in situ poly(dA) tailing, droplet barcoding, ribosomal RNA depletion and library preparation. The main smRandom-seq workflow, including sample processing, in situ reactions and library construction, takes ~2 days. This method features enhanced RNA coverage, reduced doublet rates and minimized ribosomal RNA contamination, thus enabling in-depth analysis of microbial heterogeneity. smRandom-seq is compatible with microorganisms from both laboratory cultures and complex microbial community samples, making it well suited for constructing single-microorganism transcriptomic atlases of bacterial strains and diverse microbial communities. This Protocol requires experience in molecular biology and RNA sequencing techniques, and it holds promising potential for researchers investigating bacterial resistance, microbiome heterogeneity and host-microorganism interactions.},
}
@article {pmid40404677,
year = {2025},
author = {Biada, I and Santacreu, MA and Blasco, A and Pena, RN and Ibáñez-Escriche, N},
title = {Gut microbiota variations over the lifespan and longevity in rabbit's maternal lines.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {17874},
pmid = {40404677},
issn = {2045-2322},
support = {PID2020-115558GB-C21//Ministerio De Educacion Espa&#xf1;a/ ; AICO/2020/349//Generalitat Valenciana/ ; },
mesh = {Animals ; *Longevity/genetics ; Rabbits ; *Gastrointestinal Microbiome ; Female ; },
abstract = {In rabbit breeding, selection for production efficiency traits has been successful but has reduced rabbit functional longevity. The gut microbiota, which influences host health, is linked to longevity and undergoes significant changes with age. While previous studies have focused on young rabbits, research on gut microbiota changes in adult rabbits is limited. Understanding how gut microbiota evolves with age and its impact on longevity of does during reproductive life could offer insights into improving productivity, health and welfare. This study aims to investigate the evolution of gut microbiota through age and to compare different functional longevity groups between and within two maternal rabbit lines with different longevities; a standard commercial line (A) and another founded using longevity criteria (LP). Our analysis demonstrated a significant impact of age on the gut microbiome of does during their reproductive lifespan, with a decline in alpha diversity and change in beta diversity composition as age progressed. Differential abundance analysis revealed that 20% and 16% of taxa in lines A and LP, respectively, were influenced by age, predominantly showing a negative correlation. In terms of functional longevity, differences in abundance between groups were more pronounced within line A, with up to 16% of taxa differing between high-longevity HL (females with more than 10 parities) and low-longevity LL (females died/culled before 5th parity) groups, compared to only 4% within line LP, highlighting the role of genetic background in shaping microbiota composition and its potential influence on longevity. Finally, differences in microbiome between the two lines A and LP were consistent and maintained through their lifespan independently from their longevity. This study reveals that age significantly influences gut microbiome diversity and composition in adult female rabbits, leading to decreased alpha diversity and notable shifts in composition. Microbiome also differs according to functional longevity, with differences varying by genetic line. This suggests that using microbiome through selection or using specific taxa within it as biomarkers could be a promising avenue for improving longevity. Moreover, microbiome differences between genetic lines persist throughout life, even among animals with the same longevity.},
}
@article {pmid40404666,
year = {2025},
author = {Le Cosquer, G and Pannier, M and Meunier, E and Thevenin, J and Pyhourquet, E and Guyonnet, S and Vellas, B and Santin, Y and Guiard, B and Parini, A and Buscail, L and Bournet, B and Guillemet, D and Deraison, C and Vergnolle, N and Motta, JP and , },
title = {Pathogenicity of commensal gut biofilm in prefrail aging.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {84},
pmid = {40404666},
issn = {2055-5008},
support = {IHU HealthAge Open Science initiative//ANR-23-IAHU-0011/ ; IHU HealthAge Open Science initiative//ANR-23-IAHU-0011/ ; PARCURE PRCE-CE18, 2020//ANR/ ; dysBIOFILM ANR-22-CE14-0041-01//ANR/ ; national program "Microbiote"//INSERM/ ; national program "Microbiote"//INSERM/ ; AMIGO//INSPIRE-Grant/ ; },
mesh = {*Biofilms/growth &amp; development/drug effects ; *Gastrointestinal Microbiome/drug effects ; Animals ; Humans ; Mice ; *Aging ; Feces/microbiology ; *Bacteria/pathogenicity/classification/genetics/drug effects/isolation &amp; purification ; Female ; Male ; Virulence ; Frailty/microbiology ; Aged ; Plant Extracts/pharmacology ; Vitis/chemistry ; },
abstract = {Pathophysiological mechanisms of unhealthy aging, particularly the transition from robustness to frailty, remain poorly understood. Despite extensive microbiome research on taxonomy, the behavior of early prefrail gut bacteria in their natural community-host mucosal tissue context remains unexplored. Using fecal samples from the INSPIRE-T aging human cohort, we characterized gut microbiota phenotype during prefrailty stages using a polymicrobial biofilm model. Results revealed that prefrail-derived biofilms exhibited distinct taxonomic and physical alterations, enhanced dispersal, and increased epithelial virulence compared to robust counterparts. Multiparametric analyses linked biofilm characteristics to clinical traits, suggesting their potential as aging status indicators. Polyphenol-rich grape pomace extract partially reversed prefrail biofilm alterations and reduced proinflammatory prefrail biofilm responses in vitro. Microbiota from prefrail-aged mice induced colon damage in antibiotic-treated recipients, establishing a prefrail microbiome-inflammation causality. Overall, the findings identified novel prefrail microbiome characteristics, established causal inflammatory links, and supported microbiota-targeted geroprotective interventions for the prefrail populations.},
}
@article {pmid40404643,
year = {2025},
author = {Jimenez, NR and Herman, CR and Łaniewski, P and Cope, E and Lee, K and Mahnert, ND and Chase, DM and Caporaso, JG and Herbst-Kralovetz, MM},
title = {Navigating complexities of polymorphic microbiomes in endometrial cancer.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {85},
pmid = {40404643},
issn = {2055-5008},
mesh = {Humans ; Female ; *Endometrial Neoplasms/microbiology/pathology ; *Vagina/microbiology ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; *Bacteria/classification/genetics/isolation &amp; purification ; Middle Aged ; Rectum/microbiology ; Aged ; },
abstract = {The microbiome is key to understanding endometrial cancer (EC) etiology and prevention strategies, implicated in the regulation of estrogen in estrogen-driven cancers. Utilizing robust methodologies in the QIIME 2 platform, we examined 16S rRNA vaginal and rectal microbiome data from an EC cohort: 192 women with benign gynecologic conditions, endometrial hyperplasia, or endometrial cancer. Distinct microbial compositions and community networks specific to EC were identified and related to histological grade with adjustments for EC risk factors. Vaginal health-associated Lactobacillus and Limosilactobacillus, and rectal Prevotella and Peptoniphilus, were depleted in EC, while detrimental vaginal Anaerococcus, Porphyromonas, Prevotella, Peptoniphilus, and rectal Buttiaxella were enriched. Significant bacterial features were shared between rectal and vaginal sites in EC, such as Prevotella timonensis and Peptoniphilus A. Vaginal Lactobacillus abundance contributed to less feature sharing from the rectum. Putative microbial metabolic analysis identified dysregulation of amino acid, complex carbohydrate, and hormone metabolism amongst patients with EC.},
}
@article {pmid40404632,
year = {2025},
author = {Dillard, LR and Glass, EM and Kolling, GL and Thomas-White, K and Wever, F and Markowitz, R and Lyttle, D and Papin, JA},
title = {Genome-scale metabolic network reconstruction analysis identifies bacterial vaginosis-associated metabolic interactions.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {4768},
pmid = {40404632},
issn = {2041-1723},
support = {R01-AI154242//Foundation for the National Institutes of Health (Foundation for the National Institutes of Health, Inc.)/ ; R01-AT010253//Foundation for the National Institutes of Health (Foundation for the National Institutes of Health, Inc.)/ ; NRT-ROL 2021791//Foundation for the National Institutes of Health (Foundation for the National Institutes of Health, Inc.)/ ; 1 T 32 GM 145443-1//Foundation for the National Institutes of Health (Foundation for the National Institutes of Health, Inc.)/ ; 5T32GM136615-03//U.S. Department of Health &amp; Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; 1842490//National Science Foundation (NSF)/ ; },
mesh = {*Vaginosis, Bacterial/microbiology/metabolism ; Humans ; Female ; *Metabolic Networks and Pathways/genetics ; Vagina/microbiology ; Microbiota/genetics ; *Bacteria/genetics/metabolism/classification/isolation &amp; purification ; Metabolomics ; Metagenomics ; Genome, Bacterial ; Computer Simulation ; },
abstract = {Bacterial vaginosis (BV) is the most prevalent vaginal condition among reproductive-age women presenting with vaginal complaints. Despite its significant impact on women's health, limited knowledge exists regarding the microbial community composition and metabolic interactions associated with BV. In this study, we analyze metagenomic data obtained from human vaginal swabs to generate in silico predictions of BV-associated bacterial metabolic interactions via genome-scale metabolic network reconstructions (GENREs). While most efforts to characterize symptomatic BV (and thus guide therapeutic intervention by identifying responders and non-responders to treatment) are based on genomic profiling, our in silico simulations reveal functional metabolic relatedness between species as quite distinct from genetic relatedness. We grow several of the most common co-occurring bacteria (Prevotella amnii, Prevotella buccalis, Hoylesella timonensis, Lactobacillus iners, Fannyhessea vaginae, and Aerrococcus christenssii) on the spent media of Gardnerella species and perform metabolomics to identify potential mechanisms of metabolic interaction. Through these analyses, we identify BV-associated bacteria that produce caffeate, a compound implicated in estrogen receptor binding, when grown in the spent media of other BV-associated bacteria. These findings underscore the complex and diverse nature of BV-associated bacterial community structures and several of these mechanisms are of potential significance in understanding host-microbiome relationships.},
}
@article {pmid40404216,
year = {2025},
author = {Thng, KX and Tiew, PY and Mac Aogáin, M and Narayana, JK and Jaggi, TK and Ivan, FX and Shuttleworth, M and Long, MB and Richardson, H and Lind, H and Alferes de Lima Headley, D and Robertson, K and Pollock, J and Goeminne, PC and Shteinberg, M and De Soyza, A and Aliberti, S and Altenburg, J and Haworth, CS and Sibila, O and Polverino, E and Loebinger, MR and Ringshausen, FC and Lorent, N and Dimakou, K and Shoemark, A and Chalmers, JD and Chotirmall, SH},
title = {Sputum metagenomics in bronchiectasis reveals pan-European variation: an EMBARC-BRIDGE study.},
journal = {The European respiratory journal},
volume = {},
number = {},
pages = {},
doi = {10.1183/13993003.00054-2025},
pmid = {40404216},
issn = {1399-3003},
abstract = {BACKGROUND: The EMBARC registry shows considerable variation in culturable microbes in sputum between different European countries. The additive role of next generation metagenomic sequencing remains unexplored and association with antimicrobial resistomes unknown.<br><br>METHODS: We prospectively assessed sputum from N=349 individuals recruited into the EMBARC-BRIDGE study with next-generation shotgun metagenomic sequencing including three European regions: Northern and Western Europe, Southern Europe and the United Kingdom, including samples from ten European countries. Microbiome and resistome profiles were assessed in relation to clinical outcomes.<br><br>RESULTS: Next generation metagenomic sequencing reproduced differences between countries in microbial profiles previously shown by culture in the EMBARC study. Metagenomics provided enhanced detection for some bronchiectasis pathogens including P. aeruginosa, H. influenzae and S. pneumoniae. Three metagenomic microbial clusters dominated by the genera Pseudomonas, Streptococcus and Haemophilus demonstrated pan-European but variable distribution. Diverse resistomes, linked to underlying microbiomes, were identified across Europe, with significantly higher diversity of resistance gene determinants in Southern Europe. Resistome composition significantly differed between regions characterised by regionally contrasting multi-drug-resistant profiles. The EMBARC-BRIDGE cohort validated established bronchiectasis resistotypes: RT1 and RT2, which occur at varying frequency across regions. Despite geographic variation in microbiome and resistome profiles in bronchiectasis across Europe, analogous antimicrobial resistance gene profiles associate with the key bronchiectasis genera Pseudomonas, Streptococcus and Haemophilus, independent of country or region.<br><br>CONCLUSION: Sputum metagenomics confirms and extends prior observations of regional variation in bronchiectasis microbiology. Important variation in the distribution of pathogens and antimicrobial resistance genes has implications for antimicrobial practices across Europe.},
}
@article {pmid40404081,
year = {2025},
author = {Wang, X and Wei, Z and Ma, R and Wang, J and Liu, Z and Liu, Y and Xu, X and Chu, P and Zhu, L},
title = {Dysregulation of gut barrier and microbiota in Asiatic hard clams (Meretrix petechialis) exposed to environmentally relevant Bisphenol A.},
journal = {Environmental research},
volume = {},
number = {},
pages = {121913},
doi = {10.1016/j.envres.2025.121913},
pmid = {40404081},
issn = {1096-0953},
abstract = {Bisphenol A (BPA), recognized as an endocrine disruptor, is widely present in various aquatic ecosystems. Marine bivalves constitute a significant portion of molluscan diversity and occupy a crucial niche in marine ecosystems. Nonetheless, toxicological studies focusing on the dysregulation of the intestinal barrier and microbiota in marine bivalves under BPA exposure still need to be refined and deepened. This research aims to assess the toxicity of BPA at concentrations of 1, 10, 100 μg/L on the intestinal tissues of Meretrix petechialis, focusing on behavioral responses, intestinal morphology, intestinal oxidative stress and antioxidant homeostasis, intestinal barrier function and intestinal microbial community. Our results demonstrated that BPA exposure caused behavioral changes in M. petechialis, significantly increased the number of buried clams and decreased the ingestion rate. Furthermore, BPA exposure disrupted the intestinal structure and induced inflammation and immune dysregulation in clams. Immunofluorescence staining showed that BPA disrupted the distribution of occludin and ZO-1 proteins in the intestine and significantly reduced their expression. Mucus secretion and tight junction genes were downregulated, which may be attributed to BPA-induced oxidative stress and the dysregulation of antioxidant homeostasis in the intestine. Besides, 16S rRNA sequencing revealed BPA not only influenced the beta diversity of intestinal bacteria but also the overall composition of the intestinal microbiome, with potential effects on metabolism predicted by PICRUSt2. Taken together, our results indicated that higher concentrations of BPA may pose safety concerns and enhanced our comprehension of the toxicological processes responsible for BPA-related intestinal toxicity in marine bivalves.},
}
@article {pmid40403991,
year = {2025},
author = {Esfandiari, Z and Vakili, B and Shoaei, P},
title = {Probiotic effects of Lactobacillus strains on enterohaemorrhagic E. coli infection in mice.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {107713},
doi = {10.1016/j.micpath.2025.107713},
pmid = {40403991},
issn = {1096-1208},
abstract = {Enterohemorrhagic Escherichia coli (EHEC) O157:H7 is a prevalent cause of intestinal infections that destroy epithelial transport and barrier function.This study aimed to determine the intestinal colonization of probiotics Lacticaseibacillus rhamnosus and Limosilactobacillus fermentum to alleviate the lethal toxicity of EHEC on the gut microbiome of BALB/c mice. Quantitative real-time PCR was performed to measure the levels of L. rhamnosus, L. fermentum and E. coli O157:H7. The feces of the mice were periodically analyzed every two days to count E.coli O157:H7 and Lactobacillus strains. In uninfected treated mice, the mean fecal counts of L. rhamnosus and L. fermentum were 7.95 log and 4.81 log CFU/g, respectively. The highest count of L. rhamnosus was 8.26 log on day -3. A significant reduction in E. coli O157: H7 counts was observed in groups given probiotics one week before infection (approximately 5 log CFU/g, P < 0.001). E. coli O157: H7 counts decreased on day 7 after infection in groups pre-treated with L. rhamnosus and L. fermentum. Shiga toxin (stx) was not detected in the tissues or fecal contents of pre-infected mice, showing a difference from the infected group (P<0.05).Pretreatment with L. rhamnosus and L. fermentum disrupts the E. coli O157: H7 infectious processes and promotes potential targets for renal and intestinal protection against Shiga toxin- induced damage.},
}
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