@article {pmid40316599,
year = {2025},
author = {Vázquez-González, L and Regueira-Iglesias, A and Balsa-Castro, C and Tomás, I and Carreira, MJ},
title = {A curated bacterial and archaeal 16S rRNA Gene Oral Sequences dataset.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {729},
pmid = {40316599},
issn = {2052-4463},
support = {PI24/00222//Ministry of Economy and Competitiveness | Instituto de Salud Carlos III (Institute of Health Carlos III)/ ; ED481A-2021//Consellería de Cultura, Educación e Ordenación Universitaria, Xunta de Galicia (Ministry of Culture, Education and University Planning, Government of Galicia)/ ; IN606B-2023/005//Consellería de Cultura, Educación e Ordenación Universitaria, Xunta de Galicia (Ministry of Culture, Education and University Planning, Government of Galicia)/ ; },
abstract = {In a given species, genomes and 16S rRNA gene sequences, along with their intragenomic copy numbers, can vary greatly across environments. The gene copy numbers are crucial for technologies which estimate microbial abundances based on gene counts, such as polymerase chain reaction and high-throughput sequencing. In these, taxa with fewer genes may be underestimated, while those with more genes might be overestimated. Therefore, it is essential to have accurate gene copy number databases specific to the niche under study. The 16S rRNA Gene Oral Sequences dataset (16SGOSeq) contains the number of 16S rRNA genes and their variants in the complete genomes of the bacterial and archaeal species present in the human oral cavity. It includes 3,192 complete genomes of oral bacteria and 191 complete genomes of oral archaea, from which the 16S rRNA gene sequences were extracted, and the sequence variants were identified. This oral-specific dataset of prokaryotic organisms and the pipeline followed for its construction can be applied by clinical microbiologists, bioinformaticians, or microbial ecologists in future microbiome research.},
}

@article {pmid40316575,
year = {2025},
author = {Uengwetwanit, T and Uawisetwathana, U and Angthong, P and Phanthura, M and Phromson, M and Tala, S and Thepsuwan, T and Chaiyapechara, S and Prathumpai, W and Rungrassamee, W},
title = {Investigating a novel β-glucan source to enhance disease resistance in Pacific white shrimp (Penaeus vannamei).},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {15377},
pmid = {40316575},
issn = {2045-2322},
support = {P1652214//National Center for Genetic Engineering and Biotechnology/ ; B05F640108//NSRF via the Program Management Unit for Human Resources & Institutional Development, Research and Innovation/ ; },
abstract = {β-glucans supplements are known for enhancing disease resistance and performance in shrimp aquaculture, but their effectiveness depends on their source and structure. This study investigated a novel β-glucan derived from the insect fungus Ophiocordyceps dipterigena BCC 2073 as a potential feed additive for Pacific white shrimp (Penaeus vannamei). To determine its feasibility, juvenile shrimps were fed diets supplemented with 0%, 0.1%, and 0.4% β-glucan oligosaccharide for 30 days prior to their performance evaluation. The groups with β-glucan supplementation showed improved immune levels and significantly higher survival rates (p-value < 0.05) when exposed to the pathogen Vibrio harveyi. Transcriptome, microbiome, and metabolome were employed to understand mechanisms of β-glucan supplement. The feed additive altered the expression of host genes linked to immunity, inflammation, and intestinal barrier function. Moreover, Vibrio spp. and Pseudoalteromonas spp. abundances were significantly modulated (p-value < 0.05) with specific Vibrio clades responding differently depending on the β-glucan concentration. Metabolomic analysis revealed immune-supporting metabolites such as hydroquinone and nicotinic acid, potentially promoting homeostasis, consistent with the observed gene expression profiles. This study highlights the potential of O. dipterigena BCC 2073 β-glucan as a novel feed additive to improve disease resistance and shrimp health.},
}

@article {pmid40316568,
year = {2025},
author = {Joshi, P and Bhattacharjee, R and Sahu, M and Gajjar, D},
title = {Insights into urinary catheter colonisation and polymicrobial biofilms of Candida- bacteria under flow condition.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {15375},
pmid = {40316568},
issn = {2045-2322},
abstract = {Most hospital-acquired urinary tract infections are the result of implanted urinary catheter, with majority of studies focused on a single species colonisation, but recently polymicrobial colonisations are being reported. In this study, indwelling urinary catheters were collected from ICU patients and the colonising microbiome was isolated and identified by the traditional; culturing method and metagenomics. It was observed that majority of catheters were colonised by polymicrobial biofilms, containing both bacterial and fungal isolates making them diverse and complex. However, the metagenomics results were quite surprising showing the presence of multiple organisms of which only 1or 2 showed growth when cultured. Later, in vitro assays were performed by selecting 6 combinations, with each combination containing one Candida spp. - C. albicans or C. tropicalis with one bacteria K. pneumoniae, P. aeruginosa or E. coli. It was observed that polymicrobial biofilms were stronger than mono-microbial biofilms, suggesting their increased surface adhesion. Furthermore, to simulate the dynamic environment in which cells are exposed to a certain level of fluid movement, a flow system was established to imitate the flow generated in colonized urinary catheter. We have observed changes in biofilm architecture, adhesion and thickness under flow conditions compared with static conditions, with a uniformly adhered biofilm with increased thickness of polymicrobial biofilms as compared to mono-species biofilms. The biofilm formed under flow was more viable than the static biofilm with higher number of live cells in flow condition.},
}

@article {pmid40316518,
year = {2025},
author = {Zhang, S and Clasen, F and Cai, H and Do, T and Shoaie, S and Carpenter, GH},
title = {Nitrate supplementation affects taste by changing the oral metabolome and microbiome.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {69},
pmid = {40316518},
issn = {2055-5008},
abstract = {Nitrate, an inorganic anion found in various foods is also present in saliva and has emerged as a potential prebiotic for the oral microbiome. Salivary glands concentrate nitrate from the bloodstream and release it into the oral cavity via the anion transporter sialin SLC17A5. In previous studies dietary nitrate supplementation altered oral bacteria composition, favouring genera like Rothia and Neisseria while reducing Streptococcus, Veillonella, Prevotella, and Actinomyces. The present study hypothesized that taste intensity might adapt to changes in the oral microbiome caused by nitrate supplementation. Participants underwent taste tests before, during, and after supplementation. All subjects showed greater levels of salivary nitrate during supplementation and had higher levels of Neisseria compared to before. Subjects were then grouped according to taste tests (before vs. during) as responders (ANOVA p < 0.05, n = 7), and non-responders (ANOVA p > 0.05, n = 6) and their salivary metabolome and oral microbiome further analysed. Responders had significantly less 5-amino pentanoate, formate, propionate and butyrate in saliva while non-responders showed no metabolite changes between before and during supplementation. In contrast, non-responders had increased Capnocytophaga gingivalis and altered lysosomal degradation pathways. Overall, nitrate supplementation shifted the oral microbiome composition in all subjects and when taste intensity was altered this correlated to bacteria-derived short-chain fatty acid production. This suggests taste perception is affected by the oral microbiome.},
}

@article {pmid40316483,
year = {2025},
author = {Zeng, S and Wang, S and Mu, D},
title = {Seeding microbes in defined early-life windows to fight diabetes.},
journal = {Trends in endocrinology and metabolism: TEM},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tem.2025.04.005},
pmid = {40316483},
issn = {1879-3061},
abstract = {Establishment of the early-life gut microbiome, coinciding with the host development, predisposes to long-term disease risk if disrupted. Recently, Hill et al. precisely delineated a critical early-life window in humans and mice during which specific fungi and bacteria play indispensable roles in β-cell development, thereby regulating lifelong metabolic homeostasis.},
}

@article {pmid40316371,
year = {2025},
author = {Werner, M and Vigani, A},
title = {The Microbiome in Critical Illness.},
journal = {The Veterinary clinics of North America. Small animal practice},
volume = {55},
number = {3},
pages = {443-458},
doi = {10.1016/j.cvsm.2025.01.008},
pmid = {40316371},
issn = {1878-1306},
abstract = {Evidence suggests that the intestinal microbiome may play an important role in the pathogenesis and progression of acute critical illness in humans and other mammals, although evidence in small animal medicine is sparse. Moreover, the intestinal microbiota plays many important metabolic roles (production of short-chain fatty acids, trimethylamine-N-oxide, and normal bile acid metabolism) and is crucial for immunity as well as defense against enteropathogens. The use of probiotics and fecal microbiota transplantation as instruments to modulate the intestinal microbiota seems to be safe and effective in studies on critically ill dogs with acute gastrointestinal diseases.},
}

@article {pmid40316177,
year = {2025},
author = {Yin, Y and Guan, M and Wu, S and Cui, C and Wang, R and Zhao, X and Yang, X and Qiao, L and Li, Y and Zhang, C},
title = {Young fecal microbiota transplantation improves working memory in aged recipient rats by increasing interleukin-4 and interleukin-17 levels.},
journal = {Neuroscience research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.neures.2025.04.005},
pmid = {40316177},
issn = {1872-8111},
abstract = {While transplanting the fecal microbiota from young to aged rodents has been extensively studied (that is, young FMT [yFMT]), its mechanism of alleviating working memory decline has not been fully elucidated. In this report, we aimed to investigate the effect of yFMT on the working memory of aged recipient rats performing delayed match-to-position (DMTP) tasks and the associated cellular and molecular mechanisms. The results revealed that yFMT mitigated the decline in DMTP task performance of aged recipients. This improvement was associated with a reshaped gut microbiota and increased levels of brain-derived neurotrophic factor, N-methyl-D-aspartate receptor subunit 1, and synaptophysin, enhancing synaptic formation and transmission. The remodeling of the gut microbiome influenced peripheral circulation and the hippocampus and medial prefrontal cortex by regulating the Th17/Treg ratio and microglial polarization. Ultimately, interleukin-4 and interleukin-17 emerged as potential key molecules driving the beneficial effects of FMT. These observations provide new insights into the gutbrain axis, emphasizing the connection between the gut and brain through the circulation system, and suggest an immunological mechanism that may help reverse age-related declines in the gut microbiota.},
}

@article {pmid40316065,
year = {2025},
author = {Hembrom, PS and Deepthi, M and Kannoth, S and Reeja, N and Antony, G and Grace, T},
title = {Amplicon Sequencing Reveals Growth-Associated Microbial Communities in Black Tiger Shrimp (Penaeus monodon).},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {107636},
doi = {10.1016/j.micpath.2025.107636},
pmid = {40316065},
issn = {1096-1208},
abstract = {Recent evidence has underscored the significance of intestinal microbes in host growth performance, shedding light on the complex relationship between gut microbiota and host physiology. Even though Penaeus monodon exhibits notable size variations attributed to rapid growth and larger body mass, the specific association of the microbial community with body size remains unexplored. In this study, we employed a 16S rRNA amplicon sequencing approach to investigate the composition, diversity, and functional potential of gut microbiota in two populations of adult P. monodon (fast-growing and slow-growing). Significant variations in microbial architecture were found between the study groups based on alpha and beta diversity analyses. Differential abundance analysis identified the enrichment of specific genera, including Desulfovibrio, Ferrimonas, and Fusibacter, in the fast-growing P. monodon. These genera have been previously implicated in female shrimp growth. Functional prediction of the observed microbiota composition highlighted the predominance of growth-associated pathways, such as iron and sulfur metabolism, in the fast-growing population. Overall, our comprehensive analysis revealed discernible differences in gut microbiota between fast-growing and slow-growing populations of P. monodon, possibly indicating dynamic changes associated with host growth and development. The variations observed in the abundance of growth-related microbial taxa between these populations may provide insights into the underlying mechanisms influencing shrimp growth and development.},
}

@article {pmid40315964,
year = {2025},
author = {Gupta, MK and Gouda, G and Moazzam-Jazi, M and Vadde, R and Nagaraju, GP and El-Rayes, BF},
title = {CRISPR/Cas9-directed epigenetic editing in colorectal cancer.},
journal = {Biochimica et biophysica acta. Reviews on cancer},
volume = {},
number = {},
pages = {189338},
doi = {10.1016/j.bbcan.2025.189338},
pmid = {40315964},
issn = {1879-2561},
abstract = {Colorectal cancer (CRC) remains a leading cause of cancer-related illness and death worldwide, arising from a complex interplay of genetic predisposition, environmental influences, and epigenetic dysregulation. Among these factors, epigenetic modifications-reversible and heritable changes in gene expression-serve as crucial regulators of CRC progression. Understanding these modifications is essential for identifying potential biomarkers for early diagnosis and developing targeted therapeutic strategies. Epigenetic drugs (epidrugs) such as DNA methyltransferase inhibitors (e.g., decitabine) and bromodomain inhibitors (e.g., JQ1) have shown promise in modulating aberrant epigenetic changes in CRC. However, challenges such as drug specificity, delivery, and safety concerns limit their clinical application. Advances in CRISPR-Cas9-based epigenetic editing offer a more precise approach to modifying specific epigenetic markers, presenting a potential breakthrough in CRC treatment. Despite its promise, CRISPR-based epigenome editing may result in unintended genetic modifications, necessitating stringent regulations and safety assessments. Beyond pharmacological interventions, lifestyle factors-including diet and gut microbiome composition-play a significant role in shaping the epigenetic landscape of CRC. Nutritional and microbiome-based interventions have shown potential in preventing CRC development by maintaining intestinal homeostasis and reducing tumor-promoting epigenetic changes. This review provides a comprehensive overview of epigenetic alterations in CRC, exploring their implications for diagnosis, prevention, and treatment. By integrating multi-omics approaches, single-cell technologies, and model organism studies, future research can enhance the specificity and efficacy of epigenetic-based therapies. Shortly, a combination of advanced gene-editing technologies, targeted epidrugs, and lifestyle interventions may pave the way for more effective and personalized CRC treatment strategies.},
}

@article {pmid40315838,
year = {2025},
author = {Yu, KB and Chandra, F and Coley-O'Rourke, EJ and Paulson, ET and Novoselov, A and Zhang, D and Finnigan, D and Paramo, J and Lopez-Romero, A and Dong, TS and Schartup, AT and Hsiao, EY},
title = {An engineered gut bacterium protects against dietary methylmercury exposure in pregnant mice.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2025.04.009},
pmid = {40315838},
issn = {1934-6069},
abstract = {Despite efforts to decrease mercury emissions, chronic exposure to the neurotoxicant methylmercury (MeHg) continues to be a global problem that contributes to disparities in risk for neurological and metabolic diseases. Herein we engineer a human commensal gut bacterium, Bacteroides thetaiotaomicron (Bt), to detoxify MeHg by heterologous expression of organomercury lyase (MerB) and mercuric reductase (MerA) genes derived from a resistant bacterium isolated from Hg-polluted mines. We demonstrate that Bt[merA/B] demethylates MeHg both in vitro and within the intestines of mice orally exposed to MeHg or diets containing MeHg-rich fish. In pregnant mice exposed to dietary MeHg, Bt[merA/B] decreases MeHg accumulation in the maternal liver, brain, placenta, and fetal brain, and attenuates the expression of cellular stress genes in the fetal brain. Overall, this work provides foundational proof-of-principle supporting the ability of an engineered gut bacterium to limit MeHg bioaccumulation and reduce adverse effects of chronic MeHg exposure.},
}

@article {pmid40315837,
year = {2025},
author = {Baker, JS and Qu, E and Mancuso, CP and Tripp, AD and Conwill, A and Lieberman, TD},
title = {Intraspecies dynamics underlie the apparent stability of two important skin microbiome species.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2025.04.010},
pmid = {40315837},
issn = {1934-6069},
abstract = {Adult human facial skin microbiomes are remarkably similar at the species level, dominated by Cutibacterium acnes and Staphylococcus epidermidis, yet each person harbors a unique community of strains. Understanding how person-specific communities assemble is critical for designing microbiome-based therapies. Here, using 4,055 isolate genomes and 356 metagenomes, we reconstruct on-person evolutionary history to reveal on- and between-person strain dynamics. We find that multiple cells are typically involved in transmission, indicating ample opportunity for migration. Despite this accessibility, family members share only some of their strains. S. epidermidis communities are dynamic, with each strain persisting for an average of only 2 years. C. acnes strains are more stable and have a higher colonization rate during the transition to an adult facial skin microbiome, suggesting this window could facilitate engraftment of therapeutic strains. These previously undetectable dynamics may influence the design of microbiome therapeutics and motivate the study of their effects on hosts.},
}

@article {pmid40315582,
year = {2025},
author = {Jadhav, VV and Fasina, YO and Harrison, SH},
title = {Dietary polyunsaturated fatty acids effect on cecal microbiome profile of maturing broiler chicken.},
journal = {Poultry science},
volume = {104},
number = {7},
pages = {105167},
doi = {10.1016/j.psj.2025.105167},
pmid = {40315582},
issn = {1525-3171},
abstract = {Diet has been reported to impact the diversity and function of gut microbiota. Our study investigated the effect of dietary fat types on cecal microbial composition and predicted function in broiler chickens at days 41 and 55 of age. Four dietary fat sources were evaluated and compared to a control dietary fat source of poultry fat. These were for two diets rich in omega-3 polyunsaturated fatty acids (PUFA) - fish oil and flaxseed oil, a diet rich in long-chain saturated fatty acid (SFA) - lard, and a diet rich in medium-chain saturated fatty acid - coconut oil. At day 55, broiler chickens fed a PUFA-rich diet maintained cecal microbial diversity while broiler chickens fed a SFA-rich diet exhibited a significant reduction in diversity compared to the control diet-fed chickens. More specifically, PUFA intake was associated with elevated levels of microbial carbohydrate metabolizing capability, contributing to efficient energy utilization and enhanced short-chain fatty acid production capability. In contrast, SFA-rich diets lowered abundances for key microbial families like Lachnospiraceae and Bifidobacteriaceae hampering nutrient digestibility and pathogen resistance. The microbiomes for chickens fed lard and coconut oil diets showed a significant reduction in SCFA-producing microbial taxa abundance while the microbial functional profile indicated reduced carbohydrate metabolism. Our findings underscore the contrasting effects of SFA-rich fat and PUFA-rich fat on the cecal microbiota of broiler chickens. The results suggest that incorporating PUFA-rich dietary fats into broiler feed may offer potential benefits by modulating the cecal gut microbiota toward outcomes associated with elevated carbohydrate utilization without hampering nutrient digestibility and pathogen resistance.},
}

@article {pmid40315481,
year = {2025},
author = {Ottenbrite, M and Yilmaz, G and Chan, M and Devenish, J and Kang, M and Dan, H and Lau, C and Capitani, S and Carrillo, CD and Bessonov, K and Nash, J and Topp, E and Guan, J},
title = {Food-borne Microbes Influence Conjugative Transfer of Antimicrobial Resistance Plasmids in Pre-disturbed Gut Microbiome.},
journal = {Canadian journal of microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1139/cjm-2024-0168},
pmid = {40315481},
issn = {1480-3275},
abstract = {Ingestion of antibiotic-resistant bacteria following antibiotic treatments may lead to the transfer of antimicrobial resistance genes (ARGs) within a disturbed gut microbiota. However, it remains unclear if and how microbes present in food matrices influence ARG transfer. Thus, a previously established mouse model, which demonstrated the conjugative transfer of a multi-drug resistance plasmid (pIncA/C) from Salmonella Heidelberg (donor) to S. Typhimurium (recipient), was used to assess the effects of food-borne microbes derived from fresh carrots on pIncA/C transfer. Mice were pre-treated with ampicillin, streptomycin, sulfamethazine, or left untreated as a control to facilitate bacterial colonization. Contrary to previous findings where high-density colonization of the donor and recipient bacteria occurred in the absence of food-borne microbes, the presence of these microbes resulted in a low abundance of S. Typhimurium and no detection of S. Typhimurium transconjugants in the fecal samples from any of the mice. However, in mice pre-treated with streptomycin, a significant reduction in microbial species richness allowed for the significant enrichment of Enterobacteriaceae and pIncA/C transfer to bacteria from the genera Escherichia, Enterobacter, Citrobacter, and Proteus. These findings suggest that food-borne microbes may enhance ARG dissemination by influencing the population dynamics of bacterial hosts within a pre-disturbed gut microbiome.},
}

@article {pmid40315344,
year = {2025},
author = {Zhang, B and Zhang, Y and Zhang, X and Qu, J and Ruan, C and Liao, J and Alvarez, PJJ and Yu, P},
title = {Enhanced Phytopathogen Biofilm Control in the Soybean Phyllosphere by the Phoresy of Bacteriophages Hitchhiking on Biocontrol Bacteria.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c09851},
pmid = {40315344},
issn = {1520-5851},
abstract = {Phage-based biocontrol has shown notable advantages in protecting plants against pathogenic bacteria in agricultural settings compared to chemical-based bactericides. However, the efficiency and scope of phage biocontrol of pathogenic bacteria are limited by the intrinsic properties of phages. Here, we investigated pathogen biofilm eradication in the phyllosphere using the phoresy system of hitchhiking phages onto carrier biocontrol bacteria. The phoresy system efficiently removed the pathogen biofilm in the soybean phyllosphere, reducing the total biomass by 58% and phytopathogens by 82% compared to the untreated control. Biofilm eradication tests demonstrated a significant combined beneficial effect (Bliss independence model, CI < 1) as phages improved carrier bacteria colonization by 1.2-fold and carrier bacteria facilitated phage infection by 1.4-fold. Transcriptomic analysis showed that phoresy significantly enhanced motility (e.g., fliC and pilD genes) and energy metabolism (e.g., pgm and pgk genes) of carrier bacteria and suppressed the defense system (e.g., MSH3 and FLS2 genes) and energy metabolism (e.g., petB and petC genes) of pathogens. Metabolomics analysis revealed that the phoresy system stimulated the secretion of beneficial metabolites (e.g., flavonoid and tropane alkaloid) that could enhance stress response and phyllosphere protection in soybeans. Overall, the phoresy of phages hitchhiking on biocontrol bacteria offers a novel and effective strategy for phyllosphere microbiome manipulation and bacterial disease control.},
}

@article {pmid40314762,
year = {2025},
author = {Wu, Q and Ning, Z and Zhang, A and Zhang, X and Sun, Z and Figeys, D},
title = {Operational Taxon-Function Framework in MetaX: Unveiling Taxonomic and Functional Associations in Metaproteomics.},
journal = {Analytical chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.analchem.4c06645},
pmid = {40314762},
issn = {1520-6882},
abstract = {Metaproteomics analyzes the functional dynamics of microbial communities by identifying peptides and mapping them to the most likely proteins and taxa. One challenge in this field lies in seamlessly integrating taxonomic and functional annotations to accurately represent the contributions of individual microbial taxa to functional diversity. We introduce MetaX, a comprehensive tool for analyzing taxon-function relationships in metaproteomics by mapping peptides to their lowest common ancestors and assigning functions based on proportional thresholds, ensuring accurate peptide-level mappings. Importantly, MetaX introduces the Operational Taxon-Function (OTF), a new conceptual unit for exploring microbial roles and interactions within ecosystems. Additionally, MetaX includes extensive statistical and visualization tools, establishing it as a robust platform for metaproteomics analysis. We validated MetaX by reanalyzing ex vivo gut microbiome metaproteomic data exposed to various sweeteners, yielding more detailed results than traditional protein analysis. Furthermore, using the peptide-centric approach and OTF, we observed that Parabacteroides distasonis significantly responds to certain sweeteners, highlighting its role in modifying specific metabolic functions. With its intuitive, user-friendly interface, MetaX facilitates a detailed study of the complex interactions between microbial taxa and their functions in metaproteomics. It enhances our understanding of microbial roles in ecosystems and health.},
}

@article {pmid40314735,
year = {2025},
author = {Rohde, C},
title = {[Basic knowledge of phages and their therapeutic application].},
journal = {Bundesgesundheitsblatt, Gesundheitsforschung, Gesundheitsschutz},
volume = {},
number = {},
pages = {},
pmid = {40314735},
issn = {1437-1588},
abstract = {Phages (bacteriophages) are viruses that specifically infect and kill bacteria. They are very abundant in nature, playing a highly relevant role in microbial ecosystems. In medicine, they are investigated as a potential alternative or supplement to antibiotics and can be used to treat wound, urinary tract and lung infections, for example. Single phages or so-called "phage cocktails" are applied.This overview article on basic knowledge of phages sheds light on well-known keywords from classical knowledge of phage biology and on state-of-the-art research focuses. Mechanisms of phage activity are presented as a basis for therapeutic application. Particularly, the phage-host interaction, lysis mechanisms, phage morphologies and specific methods for visualisation are discussed. Being part of the human microbiome, phages contribute to immune defence, especially in the mucosa. Temperate phages that are able to reside in bacterial genomes as prophages and therefore not suitable for therapy use as well as the CrAss phages (Crassvirales) and Lak megaphages discovered in recent years are also introduced. Further topics are bacterial phage defence, phage resistance and phage-antibiotic synergies. An outlook on future research is given, emphasising the importance of a coordinated collection of scientific results.Phages should not replace antibiotics, but they can even improve their efficiency. Currently, the licensing processes for phage therapy are still challenging. However, trust in phage preparations must be based on quality, which has to be guaranteed by harmonised standards.},
}

@article {pmid40314721,
year = {2025},
author = {Tang, J and Ruan, P and Wei, Z},
title = {Untargeted Metabolomics Revealed Metabolomic Profile in Patients with Primary Systemic Sclerosis.},
journal = {Applied biochemistry and biotechnology},
volume = {},
number = {},
pages = {},
pmid = {40314721},
issn = {1559-0291},
abstract = {Systemic sclerosis (SSc) is a systemic autoimmune disease characterized by increased morbidity and mortality. The intestinal microbiome and serum metabolites had been implicated in SSc, but the connection between the gut microbiome and serum metabolites remains poorly understood. In this study, we aimed to investigate the relationship between the gut microbiome and serum metabolome in SSc patients. Untargeted metabolomics was employed to examine the metabolic profiles of SSc patients. The results revealed significant alterations in metabolic pathways, particularly beta-alanine metabolism and pyrimidine metabolism in SSc patients. Specifically, reductions in spermine and beta-alanine were observed within beta-alanine metabolism, while uridylic acid decreased in pyrimidine metabolism. Furthermore, fecal microbiome analysis showed an increased relative abundance of Firmicutes, Verrucomicrobia, and Proteobacteria in SSc patients, whereas the abundance of Bacteroidetes and Actinobacteria was reduced at the phylum level. KEGG pathway analysis, combined with transcriptomic analysis of peripheral blood from SSc patients, identified upregulation of Toll-like receptor signaling, TNF signaling, lipid and atherosclerosis pathways, IL-17 signaling, and AMPK signaling. In summary, we performed a comprehensive analysis of the metabolic profile, which may provide insights for understanding the mechanisms of SSc.},
}

@article {pmid40314699,
year = {2025},
author = {Ramzy, A and Abdelmoneim, TK and Arafat, M and Mokhtar, M and Bakkar, A and Mokhtar, A and Anwar, W and Magdeldin, S and Enany, S},
title = {Metabolomic analysis reveals key changes in amino acid metabolism in colorectal cancer patients.},
journal = {Amino acids},
volume = {57},
number = {1},
pages = {22},
pmid = {40314699},
issn = {1438-2199},
support = {(AI 42547)//The work presented here is funded by the Armed Force College of Medicine, Cairo, Egypt, and it is partially supported by Science, Technology & Innovation Funding Authority (STDF) under grant (AI 42547)./ ; (AI 42547)//The work presented here is funded by the Armed Force College of Medicine, Cairo, Egypt, and it is partially supported by Science, Technology & Innovation Funding Authority (STDF) under grant (AI 42547)./ ; },
mesh = {Humans ; *Colorectal Neoplasms/metabolism/microbiology/pathology ; *Metabolomics/methods ; Male ; Female ; Middle Aged ; Gastrointestinal Microbiome ; Aged ; *Amino Acids/metabolism ; Feces/microbiology/chemistry ; Tandem Mass Spectrometry ; Biomarkers, Tumor/metabolism ; Metabolome ; Chromatography, High Pressure Liquid ; Metabolic Networks and Pathways ; Case-Control Studies ; },
abstract = {The number of colorectal cancer (CRC) patients is steadily growing worldwide, particularly in developing nations. Nonetheless, recent advances in early detection studies and therapy alternatives have reduced CRC mortality in affluent countries, despite rising incidence. Gut microbiota and their metabolites may contribute to tumor growth and reduced therapeutic efficacy. This preliminary study sought to uncover metabolic fingerprints in colorectal cancer patients. It also emphasizes the correlation between the gut microbiome, microbial metabolism, and altered metabolites in CRC. In this study, stool samples from 20 CRC patients and matched healthy controls were enrolled. Untargeted metabolomics approach based on an ultra-high-performance liquid chromatography high-resolution mass spectrometry (UHPLC-MS/MS) were applied. Statistical approaches, pathway enrichment analysis, and network analysis were employed to unleash CRC perturbed metabolic pathways and putative biomarkers. The study identified a distinct manually curated metabolite profile that is substantially linked to CRC. The steroidogenesis, aspartate, tryptophan (Trp), and urea cycle were the most significant pathways that concurrently contributed to CRC.Prominently, among other pathways, Trp metabolism was identified as a critical pathway, indicating a possible connection between the development of CRC and gut microbiota. In a nutshell the notable resulted metabolites reveal auspicious biomarkers for the initial diagnosis as well as surveilling of CRC progression. This preliminary study highlights the potential involvement that gut bacteria may contribute in CRC patients. Further investigation into the composition of the gut microbiome associated with this metabolic profile may lead to the identification of novel biomarkers for early detection and possible targets for treatment.},
}

Humans
*Colorectal Neoplasms/metabolism/microbiology/pathology
*Metabolomics/methods
Male
Female
Middle Aged
Gastrointestinal Microbiome
Aged
*Amino Acids/metabolism
Feces/microbiology/chemistry
Tandem Mass Spectrometry
Biomarkers, Tumor/metabolism
Metabolome
Chromatography, High Pressure Liquid
Metabolic Networks and Pathways
Case-Control Studies

@article {pmid40314614,
year = {2025},
author = {Lee, WM and Ahn, SY and Lee, GS and Park, I and Kim, J and Lee, SH and Lee, S and Kim, CS},
title = {Discovery and Biosynthesis of Indole-Functionalized Metabolites from the Human Blood Bacterium, Paracoccus sanguinis, and Their Anti-Skin Aging Activity.},
journal = {Journal of natural products},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jnatprod.4c01354},
pmid = {40314614},
issn = {1520-6025},
abstract = {The human microbiome plays a crucial role in health and disease, with microbial metabolites acting as key mediators of physiological processes. While extensive research has focused on gut-derived microbes, the metabolic contributions of blood-derived bacteria remain underexplored. Here, we investigate the facultative anaerobe Paracoccus sanguinis, a Gram-negative bacterium isolated from human blood, and its metabolome, revealing insights into its potential impacts on health and disease. Using advanced analytical methods, we characterized 12 metabolites (1-12), including six novel compounds (1-3, 9, 10, and 12). Biosynthetic studies demonstrated that these metabolites are derived through enzymatic and nonenzymatic pathways. Functional evaluations revealed significant antiaging activities for 1, 6, and 11 in TNF-α-stimulated normal human dermal fibroblasts (NHDFs), including suppression of reactive oxygen species (ROS), inhibition of matrix metalloproteinase-1 (MMP-1) secretion, and reduction of inflammatory cytokines interleukin (IL)-6 and IL-8. Among the tested compounds, 11 exhibited the highest antiaging efficacy, highlighting its potential as a candidate for therapeutic applications targeting skin aging. This study elucidates the biosynthetic pathways of P. sanguinis metabolites and their antiskin aging activity, underscoring their potential in modulating skin health and offering novel insights into the functional roles of blood-derived microbiota in human health.},
}

@article {pmid40314468,
year = {2025},
author = {Nguyen, RD and Nortey, J and Gebreegziabher, E and Hinterwirth, A and Zhong, L and Chen, C and Doan, T and Lietman, TM and Gonzales, JA},
title = {A Distinguishable Peripheral Blood and Conjunctival Transcriptome and Gut Microbiome in Sjögren's Disease: A Pilot Study.},
journal = {Eye & contact lens},
volume = {},
number = {},
pages = {},
doi = {10.1097/ICL.0000000000001186},
pmid = {40314468},
issn = {1542-233X},
support = {K23 Award EY026998//Foundation for the National Institutes of Health/ ; },
abstract = {OBJECTIVE: To create a comprehensive multi-tissue molecular atlas of Sjögren's disease by using unbiased RNA sequencing to identify differentially expressed genes (DEGs) in peripheral blood and conjunctival transcriptomes, and to characterize the ocular surface and gut microbiome profiles in participants classified as Sjögren's versus non-Sjögren's disease.

METHODS: This exploratory study used high-throughput RNA sequencing to analyze peripheral blood, conjunctival swabs, and rectal swabs from participants (11 classified as Sjögren's disease and four classified as non-Sjögren's) to identify DEGs and microbial profiles that could distinguish these groups.

RESULTS: Differential gene expression analysis revealed upregulated type I interferon (IFI44L, OASL, USP18) and complement pathways (SERPING1) in peripheral blood, alongside activation of several novel pathways in the conjunctiva including intracellular vesicle trafficking (HIP1, GOLIM4, FIG4), immunometabolism (CERS5, HPRT1, ULK2), and cytoskeletal remodeling (MARK1, IQCB1) in Sjögren's disease. In addition, distinct gut microbiome compositions were observed in Sjögren's disease participants, characterized by an increased presence of Lactobacillus reuteri species.

CONCLUSIONS: Using unbiased RNA sequencing, we confirmed the role of type I interferon and complement pathways in the peripheral blood and identified novel molecular signatures in the conjunctiva of Sjögren's disease participants. These newly identified pathways-involved in intracellular vesicle trafficking, immunometabolism, and cytoskeletal remodeling-expand our understanding of disease mechanisms beyond traditional immune pathways. In addition, we found distinct gut microbial profiles in Sjögren's disease participants, although ocular surface microbiome showed no significant differences. Such findings may suggest possible new therapeutic targets and allow for Sjögren's disease patient stratification. However, validation in larger cohorts is needed to establish clinical significance and potential applications in Sjögren's disease.},
}

@article {pmid40314439,
year = {2025},
author = {Austin, GI and Korem, T},
title = {Compositional transformations can reasonably introduce phenotype-associated values into sparse features.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0002125},
doi = {10.1128/msystems.00021-25},
pmid = {40314439},
issn = {2379-5077},
abstract = {UNLABELLED: Gihawi et al. (mBio 14:e01607-23, 2023, https://doi.org/10.1128/mbio.01607-23) argued that the analysis of tumor-associated microbiome data by Poore et al. (Nature 579:567-574, 2020, https://doi.org/10.1038/s41586-020-2095-1) is invalid because features that were originally very sparse (genera with mostly zero read counts) became associated with the phenotype following batch correction. Here, we examine whether such an observation should necessarily indicate issues with processing or machine learning pipelines. We show counterexamples using the centered log ratio (CLR) transformation, which is often used for analysis of compositional microbiome data. The CLR transformation has similarities to voom-SNM, the batch-correction method brought into question by Gihawi et al., and yet is a sample-wise operation that cannot, in itself, "leak" information or invalidate downstream analyses. We show that because the CLR transformation divides each value by the geometric mean of its sample, common imputation strategies for missing or zero values result in transformed features that are associated with the geometric mean. Through analyses of both synthetic and vaginal microbiome data sets, we demonstrate that when the geometric mean is associated with a phenotype, sparse and CLR-transformed features will also become associated with it. We re-analyze features highlighted by Gihawi et al. and demonstrate that the phenomenon of sparse features becoming phenotype-associated can also be observed after a CLR transformation, which serves as a counterexample to the claim that such an observation necessarily means information leakage. While we do not intend to address other concerns regarding tumor microbiome analyses, validate Poore et al.'s results, or evaluate batch-correction pipelines, we conclude that because phenotype-associated features that were initially sparse can be created by a sample-wise transformation that cannot artifactually inflate machine learning performance, their detection is not independently sufficient to demonstrate information leakage in machine learning pipelines. Microbiome data are multivariate, and as such, a value of 0 carries a different meaning for each sample. Many transformations, including CLR and other batch-correction methods, are likewise multivariate, and, as these issues demonstrate, each individual feature should be interpreted with caution.

IMPORTANCE: Gihawi et al. claim that finding that a transformation turned highly sparse (mostly zero) features into features that are associated with a phenotype is sufficient to conclude that there is information leakage and to invalidate an analysis. This claim has critical implications for both the debate regarding The Cancer Genome Atlas (TCGA) cancer microbiome analysis and for interpretation and evaluation of analyses in the microbiome field at large. We show by counterexamples and by reanalysis that such transformations can be valid.},
}

@article {pmid40313608,
year = {2025},
author = {Luo, J and Wang, Y},
title = {Precision Dietary Intervention: Gut Microbiome and Meta-metabolome as Functional Readouts.},
journal = {Phenomics (Cham, Switzerland)},
volume = {5},
number = {1},
pages = {23-50},
pmid = {40313608},
issn = {2730-5848},
abstract = {Gut microbiome, the group of commensals residing within the intestinal tract, is closely associated with dietary patterns by interacting with food components. The gut microbiome is modifiable by the diet, and in turn, it utilizes the undigested food components as substrates and generates a group of small molecule-metabolites that addressed as "meta-metabolome" in this review. Profiling and mapping of meta-metabolome could yield insightful information at higher resolution and serve as functional readouts for precision nutrition and formation of personalized dietary strategies. For assessing the meta-metabolome, sample preparation is important, and it should aim for retrieval of gut microbial metabolites as intact as possible. The meta-metabolome can be investigated via untargeted and targeted meta-metabolomics with analytical platforms such as nuclear magnetic resonance spectroscopy and mass spectrometry. Employing flux analysis with meta-metabolomics using available database could further elucidate metabolic pathways that lead to biomarker discovery. In conclusion, integration of gut microbiome and meta-metabolomics is a promising supplementary approach to tailor precision dietary intervention. In this review, relationships among diet, gut microbiome, and meta-metabolome are elucidated, with an emphasis on recent advances in alternative analysis techniques proposed for nutritional research. We hope that this review will provide information for establishing pipelines complementary to traditional approaches for achieving precision dietary intervention.},
}

@article {pmid40313607,
year = {2025},
author = {Kriti, M and Ojha, R and Singh, S and Sarma, DK and Verma, V and Yadav, AK and Nagpal, R and Kumar, M},
title = {Implication of Gut Mycobiome and Virome in Type-2 Diabetes Mellitus: Uncovering the Hidden Players.},
journal = {Phenomics (Cham, Switzerland)},
volume = {5},
number = {1},
pages = {51-64},
pmid = {40313607},
issn = {2730-5848},
abstract = {Type-2 diabetes mellitus (T2DM) is a global epidemic with significant societal costs. The gut microbiota, including its metabolites, plays a pivotal role in maintaining health, while gut dysbiosis is implicated in several metabolic disorders, including T2DM. Although data exists on the relationship between the gut bacteriome and metabolic disorders, further attention is needed for the mycobiome and virome. Recent advancements have begun to shed light on these connections, offering potential avenues for preventive measures. However, more comprehensive investigations are required to untangle the interrelations between different microbial kingdoms and their role in T2DM development or mitigation. This review presents a simplified overview of the alterations in the gut bacteriome in T2DM and delves into the current understanding of the mycobiome and virome's role in T2DM, along with their interactions with the cohabiting bacteriome. Subsequently, it explores into the age-related dynamics of the gut microbiome and the changes observed in the microbiome composition with the onset of T2DM. Further, we explore the basic workflow utilized in gut microbiome studies. Lastly, we discuss potential therapeutic interventions in gut microbiome research, which could contribute to the amelioration of the condition, serve as preventive measures, or pave the way towards personalized medicine.},
}

@article {pmid40313605,
year = {2025},
author = {Zhou, X and Chen, X and Davis, MM and Snyder, MP},
title = {Embracing Interpersonal Variability of Microbiome in Precision Medicine.},
journal = {Phenomics (Cham, Switzerland)},
volume = {5},
number = {1},
pages = {8-13},
pmid = {40313605},
issn = {2730-5848},
}

@article {pmid40313603,
year = {2025},
author = {Pu, Y and Zhou, X and Cai, H and Lou, T and Liu, C and Kong, M and Sun, Z and Wang, Y and Zhang, R and Zhu, Y and Ye, L and Zheng, Y and Zhu, B and Quan, Z and Zhao, G and Zheng, Y},
title = {Impact of DNA Extraction Methods on Gut Microbiome Profiles: A Comparative Metagenomic Study.},
journal = {Phenomics (Cham, Switzerland)},
volume = {5},
number = {1},
pages = {76-90},
pmid = {40313603},
issn = {2730-5848},
abstract = {UNLABELLED: In gut microbial research, DNA extraction remarkably influences study outcomes and biological interpretations. Rapid advancements in the research scale and technological upgrades necessitate evaluating new methods to ensure reliability and precision in microbial community profiling. We systematically evaluated the performance of eight recent and commonly used extraction methods using a microbial mock community (MMC) and fecal samples from two healthy volunteers, incorporating bacterial, archaeal, and fungal constituents. Performance metrics included nucleic acid assessment, microbial profile assessment, and scalability for large-scale studies, leveraging shotgun metagenomics for in-depth analysis. Despite variations in DNA quantity and quality, all methods yielded sufficient DNA for shotgun metagenomic sequencing. In the MMC microbial profile assessment, the QIAamp PowerFecal pro Kit (PF) and DNeasy PowerSoil HTP kit (PS) methods exhibited higher similarity with the theoretical composition and lower variability across technical replicates compared to other methods. For fecal samples, the extraction method accounted for 21.4% of the overall microbiome variation and significantly affected the abundances of 32% of detected microbial species. Methods using mechanical lysis with small beads, such as PF and PS, demonstrated better efficiency, indicated by increased microbial diversity in extracting DNA from Gram-positive bacteria. Furthermore, the PF and PS methods are notably simple to execute and automation-friendly, though relatively costly. Our study underscores the importance of maintaining consistency in DNA extraction methods for reliable comparative metagenomic analyses. We recommend PF and PS methods as optimal for expansive gut metagenomic research, emphasizing the critical role of mechanical lysis in DNA extraction.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s43657-025-00232-x.},
}

@article {pmid40313601,
year = {2025},
author = {Zhao, L},
title = {Relational Stability: A New Strategy for Defining the Human Core Microbiome.},
journal = {Phenomics (Cham, Switzerland)},
volume = {5},
number = {1},
pages = {14-17},
pmid = {40313601},
issn = {2730-5848},
}

@article {pmid40313461,
year = {2025},
author = {Bessa, LJ and Egas, C and Pires, C and Proença, L and Mascarenhas, P and Pais, RJ and Barroso, H and Machado, V and Botelho, J and Alcoforado, G and Mendes, JJ and Alves, R},
title = {Linking peri-implantitis to microbiome changes in affected implants, healthy implants, and saliva: a cross-sectional pilot study.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1543100},
pmid = {40313461},
issn = {2235-2988},
mesh = {Humans ; *Peri-Implantitis/microbiology ; *Saliva/microbiology ; Pilot Projects ; Cross-Sectional Studies ; *Microbiota ; *Dental Implants/microbiology ; Male ; Female ; Biofilms/growth & development ; Middle Aged ; *Bacteria/classification/genetics/isolation & purification ; Aged ; Metagenomics ; Adult ; },
abstract = {INTRODUCTION: The rising use of dental implants is accompanied by an expected increase in peri-implant diseases, particularly peri-implantitis (PI), which poses a significant threat to implant success and necessitates a thorough understanding of its pathogenesis for effective management.

METHODS: To gain deeper insights into the role and impact of the peri-implant microbiome in the pathogenesis and progression of PI, we analyzed 100 samples of saliva and subgingival biofilm from 40 participants with healthy implants (HI group) or with co-occurrence of diagnosed PI-affected implants and healthy implants (PI group) using shotgun metagenomic sequencing. We identified the most discriminative species distinguishing healthy from diseased study groups through log ratios and differential ranking analyses.

RESULTS AND DISCUSSION: Mogibacterium timidum, Schaalia cardiffensis, Parvimonas micra, Filifactor alocis, Porphyromonas endodontalis, Porphyromonas gingivalis and Olsenella uli were associated with the subgingival peri-implant biofilm. In contrast, Neisseria sp oral taxon 014, Haemophilus parainfluenzae, Actinomyces naeslundii, Rothia mucilaginosa and Rothia aeria were more prevalent in the healthy peri-implant biofilm. Functional pathways such as arginine and polyamine biosynthesis, including putrescine and citrulline biosynthesis, showed stronger correlations with PI-affected implants. In contrast, peri-implant health was characterized by the predominance of pathways involved in purine and pyrimidine deoxyribonucleotide de novo biosynthesis, glucose and glucose-1-phosphate degradation, and tetrapyrrole biosynthesis. Our findings reveal that healthy implants in PI-free oral cavities differ significantly in microbial composition and functional pathways compared to healthy implants co-occurring with PI-affected implants, which more closely resemble PI-associated profiles. This pattern extended to salivary samples, where microbial and functional biomarkers follow similar trends.},
}

Humans
*Peri-Implantitis/microbiology
*Saliva/microbiology
Pilot Projects
Cross-Sectional Studies
*Microbiota
*Dental Implants/microbiology
Male
Female
Biofilms/growth & development
Middle Aged
*Bacteria/classification/genetics/isolation & purification
Aged
Metagenomics
Adult

@article {pmid40313460,
year = {2025},
author = {Wang, Y and Liu, Y and Liu, X and Xu, P and Luo, M and Huang, A and Su, Z},
title = {Comprehensive analysis of transcriptome and microbiome in colorectal cancer with synchronous polyp patients.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1547057},
pmid = {40313460},
issn = {2235-2988},
mesh = {Humans ; *Colorectal Neoplasms/microbiology/genetics ; *Gastrointestinal Microbiome/genetics ; Male ; Female ; RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/isolation & purification ; Middle Aged ; Feces/microbiology ; *Transcriptome ; Aged ; Gene Expression Profiling ; },
abstract = {BACKGROUND: Colorectal cancer (CRC) is a prevalent and lethal malignancy, with the role of gut microbiota in its development still unclear. This study examines differences in gut microbiota between CRC patients and healthy controls and explores their association with host gene expression to identify potential diagnostic and therapeutic targets.

METHODS: Fecal samples from 10 CRC patients and 13 healthy controls were subjected to 16S rRNA sequencing. Transcriptome sequencing of tumor tissues, normal mucosa, and colorectal polyps from same 10 CRC patients was performed to identify differentially expressed genes (DEGs). Pearson correlation analysis was employed to associate operational taxonomic units (OTUs) with host gene expression.

RESULTS: β-diversity analysis showed significant differences in microbiota between CRC patients and controls (P < 0.01). LEfSe identified 38 distinct bacterial taxa, with genera such as Bacteroides, Peptostreptococcus, and Parabacteroides being enriched in CRC patients. Transcriptome analysis uncovered 1,026 DEGs. Notably, TIMP1 and BCAT1 were positively correlated (r > 0.76, P < 0.01) with pathogenic bacteria like Fusobacterium nucleatum and Peptostreptococcus stomatis. Tumor-related genes TRPM4, MYBL2, and CDKN2A were significantly upregulated and correlated with specific bacterial taxa.

CONCLUSION: This study underscores the significant alterations in gut microbiota associated with CRC and reveals novel correlations between specific microbes and host gene expression, offering potential diagnostic markers and therapeutic targets for CRC.},
}

Humans
*Colorectal Neoplasms/microbiology/genetics
*Gastrointestinal Microbiome/genetics
Male
Female
RNA, Ribosomal, 16S/genetics
*Bacteria/classification/genetics/isolation & purification
Middle Aged
Feces/microbiology
*Transcriptome
Aged
Gene Expression Profiling

@article {pmid40313408,
year = {2025},
author = {Wang, M and Liu, W and Zheng, L and Ma, S and Jin, L and Zhao, D and Li, D},
title = {Broadening horizons: microbiota as a novel biomarker and potential treatment for endometriosis.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1521216},
pmid = {40313408},
issn = {1664-302X},
abstract = {As a heterogeneous disease, endometriosis is associated with diagnostic delay. Delayed diagnosis, physical discomfort, hormone therapy, and inconvenience in daily life and work all contribute to a decreased quality of life for endometriosis patients. Early clinical diagnosis is highly important for the intervention and treatment of endometriosis. Currently, reliable non-invasive diagnostic methods are lacking, and laparoscopic examination combined with pathological diagnosis is considered the "gold standard" for definitively diagnosing endometriosis. An increasing number of studies have confirmed the correlation between endometriosis and microbial ecological changes. Microbial dysbiosis is an important factor in the development and progression of endometriosis. Certain key microbial species and their metabolites can induce functional alterations in endometrial cells through various mechanisms, often preceding the emergence of clinical symptoms. Endometriosis are chronic inflammatory diseases, with an immunoinflammatory response as the pathological foundation. The microbiome may participate in the pathological mechanisms of endometriosis through multiple pathways, including mediating inflammatory responses, regulating immune responses, participating in estrogen regulation, interfering with metabolic activities, and modulating the gut-brain axis. Therefore, the microbiome holds potential as an early non-invasive diagnostic and therapeutic target for endometriosis patients. This study summarizes and analyses the correlations between microorganisms and their metabolites and the onset of endometriosis, aiming to provide novel insights into the etiology, diagnosis, and treatment of endometriosis.},
}

@article {pmid40313288,
year = {2025},
author = {Katsuhara, Y and Khan, U and Miller, ZA and Allen, IE and Oskotsky, TT and Sirota, M and Tang, AS},
title = {Decoding subphenotypes in electronic medical records within late-onset Alzheimer's disease reveals heterogeneity and sex-specific differences.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.04.24.25326306},
pmid = {40313288},
abstract = {BACKGROUND: Alzheimer's disease is a progressive neurodegenerative disorder with no curative treatment. Identifying distinct subphenotypes and understanding potential personalized modifications remain critical unmet needs.

METHODS: We applied unsupervised learning techniques to electronic medical records from UCSF to identify distinct Alzheimer's disease subphenotypes based on comorbidity profiles. We conducted enrichment analyses to determine cluster-specific comorbidities. Based on the observed sex-based differences, we subsequently conducted sex-stratified analyses to assess differences in disease manifestations between males and females. Findings were validated using an independent UC-Wide dataset.

RESULTS: Among 8,363 patients, we identified five Alzheimer's disease subphenotypes, characterized by comorbidities related to cardiovascular conditions, gastrointestinal disorders, and frailty-related conditions such as pneumonia and pressure ulcers. Sex-stratified analyses revealed significant differences in comorbidity distributions across clusters. Notably, in Cluster 2, circulatory diseases were more prevalent among males, whereas in Cluster 3, bladder stones were more common among females. Key results were consistent across the UCSF and UC-Wide datasets.

CONCLUSIONS: Our study identifies clinically meaningful Alzheimer's disease subphenotypes and highlights sex-specific variations, suggesting potential underlying biological factors such as Apolipoprotein E and gut microbiome alterations contributing to Alzheimer's disease heterogeneity. These findings underscore the need for further research into the biological mechanisms driving these differences and may inform the development of individualized therapeutic regimens.

FUNDING: This study was supported by grants from the National Institute on Aging (R01AG060393 and R01AG057683).},
}

@article {pmid40313234,
year = {2025},
author = {Leibovitzh, H and Fliss Isakov, N and Werner, L and Thurm, T and Hirsch, A and Cohen, NA and Maharshak, N},
title = {A Mushroom Based Prebiotic Supplement Pilot Study Among Patients with Crohn's Disease.},
journal = {Journal of dietary supplements},
volume = {},
number = {},
pages = {1-14},
doi = {10.1080/19390211.2025.2498127},
pmid = {40313234},
issn = {1939-022X},
abstract = {Data on a mushroom based prebiotic supplementation in patients with Crohn's disease (CD) in western population is scarce. In this pilot trial, we aimed to assess the clinical efficacy and fecal microbial compositional and functional alterations associated with 'Mycodigest,' a commercial prebiotic supplement composed of three mushroom extracts. Patients with mild to moderate CD were recruited to a single center, randomized, double-blind, placebo-controlled pilot induction trial. Clinical efficacy using the Harvey-Bradshaw index and biochemical response using C-reactive protein and fecal calprotectin were assessed at week 8 post-intervention. Fecal samples were assessed by DNA shotgun metagenomic sequencing. A multivariable linear mixed effects model was used to assess alteration in fecal microbiome composition and function pre- and post-'Mycodigest' intervention. Clinical response was higher in the 'Mycodigest' intervention (N = 10) compared to the placebo (N = 6) group (80 vs. 16.7%, respectively, p = 0.035). There were no differences in terms of biochemical response within each group pre- and post-intervention. Post-'Mycodigest' intervention, 25 species were found to be differentially abundant compared to baseline, including increase in short chain fatty acid producing bacteria, such as Parabacteroides distasonis (Beta coefficient 0.92, 95% Confidence interval [CI] 0.36-1.47) and Faecalimonas umbilicata (Beta coefficient 0.57, 95% CI 0.23-0.90). Two microbial pathways related to the metabolism of isoprenoid compounds were increased post-'Mycodigest' intervention. Mushroom based prebiotic supplementation in subjects with CD resulted in clinical improvement which may be related to post-intervention favorable compositional and functional microbial alterations.},
}

@article {pmid40313185,
year = {2025},
author = {Li, X and Huang, R and Li, P and Tang, FK and He, J and Sun, H and Wang, X and Wang, M and Lan, X and Wang, X and Wong, SSW and Jin, L and Leung, KC and Wong, HM and Wang, S and Guo, L and Ding, PH and Yu, X},
title = {Berberine-Functionalized Bismuth-Doped Carbon Dots in a Pathogen-Responsive Hydrogel System: A Multifaceted Approach to Combating Periodontal Diseases.},
journal = {ACS nano},
volume = {},
number = {},
pages = {},
doi = {10.1021/acsnano.5c00561},
pmid = {40313185},
issn = {1936-086X},
abstract = {Periodontal disease, a global health burden linked to dysbiotic oral polymicrobial communities and disrupted immune-inflammatory responses, is critically mediated byPorphyromonas gingivalis(Pg)─the keystone pathogen that sabotages host immunity, triggers tissue inflammation and destruction, and disrupts microbiota balance. Effective therapies should combine antimicrobial action, immune modulation, virulence suppression, and microbiome restoration. Bismuth ions and berberine, which exhibit antimicrobial and epithelial barrier-protecting effects, show potential effectiveness in treating periodontal diseases but face practical limitations due to poor water solubility and bioavailability. To address this, we developed bismuth-doped carbon dots functionalized with structure-modified berberine (BiCD-Ber) as a multifunctional nanomedicine. BiCD-Ber eradicated Pg in various forms, restored Pg-perturbed immune responses in gingival fibroblasts, and preserved epithelial barrier integrity. The doped bismuth ions neutralized Pg virulence factors by blocking the catalytic sites of gingipains. To facilitate in vivo delivery, BiCD-Ber was encapsulated in a disulfide-modified hyaluronic acid hydrogel that degrades in response to Pg metabolites. This BiCD-Ber hydrogel system modulated subgingival microbiota, alleviated inflammation in gingiva, and thereby prevented alveolar bone loss. This approach to concurrently eliminating Pg, modulating inflammatory responses , suppressing virulence factors, and restoring microbiota showcases great potential in managing periodontitis effectively.},
}

@article {pmid40312907,
year = {2025},
author = {Zheng, CM and Kang, HW and Moon, S and Byun, YJ and Kim, WT and Choi, YH and Moon, SK and Piao, XM and Yun, SJ},
title = {Optimizing extraction of microbial DNA from urine: Advancing urinary microbiome research in bladder cancer.},
journal = {Investigative and clinical urology},
volume = {66},
number = {3},
pages = {272-280},
doi = {10.4111/icu.20240454},
pmid = {40312907},
issn = {2466-054X},
support = {2020R1I1A3062508/NRF/National Research Foundation of Korea/Korea ; RS-2023-00245919/NRF/National Research Foundation of Korea/Korea ; RS-2024-00342111/NRF/National Research Foundation of Korea/Korea ; 5199990614277/NRF/National Research Foundation of Korea/Korea ; /KHIDI/Korea Health Industry Development Institute/Korea ; },
mesh = {Humans ; *Microbiota/genetics ; *Urinary Bladder Neoplasms/microbiology/urine ; *DNA, Bacterial/isolation & purification/urine ; Male ; Female ; Middle Aged ; *Urine/microbiology ; Aged ; RNA, Ribosomal, 16S ; Reproducibility of Results ; },
abstract = {PURPOSE: This study aimed to evaluate and optimize microbial DNA extraction methods from urine, a non-invasive sample source, to enhance DNA quality, purity, and reliability for urinary microbiome research and biomarker discovery in bladder cancer.

MATERIALS AND METHODS: A total of 302 individuals (258 with genitourinary cancers and 44 with benign urologic diseases) participated in this study. Urine samples were collected via sterile catheterization, resulting in 445 vials for microbial analysis. DNA extraction was performed using three protocols: the standard protocol (SP), water dilution protocol (WDP), and chelation-assisted protocol (CAP). DNA quality (concentration, purity, and contamination levels) was assessed using NanoDrop spectrophotometry. Microbial analysis was conducted on 138 samples (108 cancerous and 30 benign) using 16S rRNA sequencing. Prior to sequencing on the Illumina MiSeq platform, Victor 3 fluorometry was used for validation.

RESULTS: WDP outperformed other methods, achieving significantly higher 260/280 and 260/230 ratios, indicating superior DNA purity and reduced contamination, while maintaining reliable DNA yields. CAP was excluded due to poor performance across all metrics. Microbial abundance was significantly higher in WDP-extracted samples (p<0.0001), whereas SP demonstrated higher alpha diversity indices (p<0.01), likely due to improved detection of low-abundance taxa. Beta diversity analysis showed no significant compositional differences between SP and WDP (p=1.0), supporting the reliability of WDP for microbiome research.

CONCLUSIONS: WDP is a highly effective and reliable method for microbial DNA extraction from urine, ensuring high-quality and reproducible results. Future research should address sample variability and crystal precipitation to further refine microbiome-based diagnostics and therapeutics.},
}

Humans
*Microbiota/genetics
*Urinary Bladder Neoplasms/microbiology/urine
*DNA, Bacterial/isolation & purification/urine
Male
Female
Middle Aged
*Urine/microbiology
Aged
RNA, Ribosomal, 16S
Reproducibility of Results

@article {pmid40312795,
year = {2025},
author = {Emoto, S and Inoue, R and Murai, S and Inagaki, Y and Nozawa, H and Sasaki, K and Murono, K and Kaneko, K and Yokoyama, Y and Abe, S and Nagai, Y and Shinagawa, T and Tachikawa, Y and Okada, S and Tsukahara, T and Ohashi, K and Ohno, M and Andoh, A and Ishihara, S},
title = {A pilot study of gut mucosal and faecal microbiota in rectal cancer: associations with histological response and adverse events following preoperative chemoradiotherapy.},
journal = {Colorectal disease : the official journal of the Association of Coloproctology of Great Britain and Ireland},
volume = {27},
number = {5},
pages = {e70106},
doi = {10.1111/codi.70106},
pmid = {40312795},
issn = {1463-1318},
support = {//Japan Society for the Promotion of Science/ ; },
mesh = {Humans ; *Rectal Neoplasms/therapy/microbiology/pathology ; *Gastrointestinal Microbiome/genetics ; Male ; Female ; Pilot Projects ; Middle Aged ; *Feces/microbiology ; Prospective Studies ; Aged ; *Intestinal Mucosa/microbiology/pathology ; *Chemoradiotherapy/adverse effects ; Treatment Outcome ; Neoadjuvant Therapy/adverse effects/methods ; Diarrhea/etiology/microbiology ; RNA, Ribosomal, 16S ; },
abstract = {AIM: Preoperative chemoradiotherapy (CRT) is administered for locally advanced rectal cancer (LARC); however, its efficacy and toxicity vary among patients. This study aimed to elucidate the relationship between the gut microbiota and the effectiveness and adverse events of CRT.

METHODS: This prospective study included 21 patients with LARC with no history of antibiotic or probiotic administration for 6 months. Tumour mucosa, non-tumour mucosa and faecal samples were collected before and after CRT, and bacterial DNA was extracted. Metataxonomic analysis targeting the V3 and V4 regions of the 16S rRNA gene was conducted to determine the diversity and composition of the microbiota. Linear discriminant analysis effect size (LEfSe) was used to explore potential bacterial taxa predicting pathological complete response (pCR) and treatment-associated diarrhoea, which are major adverse events of CRT.

RESULTS: Among the 21 patients, five achieved pCR and seven experienced severe treatment-associated diarrhoea. There were no significant differences in α-diversity and β-diversity of the microbiota between the groups at any sampling sites before or after CRT. Exploratory analysis using LEfSe identified Peptostreptococcus, Coprococcus and Phoceaicola in the tumour mucosa before CRT as significant indicators for achieving pCR. Additionally, Collinsella, Haemophilus and Desulfovibrionaceae are associated with treatment-associated diarrhoea. Microbiome composition changed before and after CRT, with a notable decrease in the genus Fusobacterium_C and other taxa. β-diversity in the tumour area also changed significantly (P = 0.03).

CONCLUSIONS: This study suggests an association between the gut microbiota, the therapeutic effectiveness of CRT and the occurrence of treatment-associated diarrhoea in rectal cancer. These results indicate the potential for predicting treatment efficacy and adverse events based on the microbiota composition.},
}

Humans
*Rectal Neoplasms/therapy/microbiology/pathology
*Gastrointestinal Microbiome/genetics
Male
Female
Pilot Projects
Middle Aged
*Feces/microbiology
Prospective Studies
Aged
*Intestinal Mucosa/microbiology/pathology
*Chemoradiotherapy/adverse effects
Treatment Outcome
Neoadjuvant Therapy/adverse effects/methods
Diarrhea/etiology/microbiology
RNA, Ribosomal, 16S

@article {pmid40312781,
year = {2025},
author = {Shibata, T and Ohno, A and Murakami, I and Takakura, M and Sasagawa, T and Imanishi, T and Mikami, M},
title = {Effect of chemical peeling therapy for treatment of cervical intraepithelial neoplasia on cervicovaginal microbio.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxaf080},
pmid = {40312781},
issn = {1365-2672},
abstract = {AIM: The cervicovaginal microbiome is associated with progression and regression of cervical intraepithelial neoplasia (CIN). Chemical peeling, an investigational treatment that shows promise as a non-invasive treatment for CIN, exfoliates the human papillomavirus (HPV)-infected cervical epithelium; subsequent alterations to the cervicovaginal microbiome may be a key mechanism of its effect.

METHODS AND RESULTS: Using a retrospective paired-sample analysis, we investigated the cervicovaginal microbiota of 28 CIN patients, comparing pre- and post-treatment samples from the same individuals who achieved high-risk HPV clearance. We used 16S ribosomal RNA gene sequencing to detect microbial markers in liquid-based cytology solution from cervical scrapings. Enrichment of Lactobacillus hominis was significantly observed after chemical peeling by differential abundance analysis. Alterations in cervicovaginal bacteria after chemical peeling predicted multiple biochemical changes such as increased selenocompound and thiamine metabolism.

CONCLUSIONS: Chemical peeling may modulate microbiota and bacteria-derived metabolites, thereby contributing to an additional therapeutic mechanism against CIN.},
}

@article {pmid40312483,
year = {2025},
author = {Aksenfeld, R},
title = {Fungus from the human gut slows liver disease in mice.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {40312483},
issn = {1476-4687},
}

@article {pmid40312439,
year = {2025},
author = {He, F and Zheng, Y and Elsabagh, M and Fan, K and Zha, X and Zhang, B and Wang, M and Zhang, H},
title = {Gut microbiota modulate intestinal inflammation by endoplasmic reticulum stress-autophagy-cell death signaling axis.},
journal = {Journal of animal science and biotechnology},
volume = {16},
number = {1},
pages = {63},
pmid = {40312439},
issn = {1674-9782},
abstract = {The intestinal tract, a complex organ responsible for nutrient absorption and digestion, relies heavily on a balanced gut microbiome to maintain its integrity. Disruptions to this delicate microbial ecosystem can lead to intestinal inflammation, a hallmark of inflammatory bowel disease (IBD). While the role of the gut microbiome in IBD is increasingly recognized, the underlying mechanisms, particularly those involving endoplasmic reticulum (ER) stress, autophagy, and cell death, remain incompletely understood. ER stress, a cellular response to various stressors, can trigger inflammation and cell death. Autophagy, a cellular degradation process, can either alleviate or exacerbate ER stress-induced inflammation, depending on the specific context. The gut microbiome can influence both ER stress and autophagy pathways, further complicating the interplay between these processes. This review delves into the intricate relationship between ER stress, autophagy, and the gut microbiome in the context of intestinal inflammation. By exploring the molecular mechanisms underlying these interactions, we aim to provide a comprehensive theoretical framework for developing novel therapeutic strategies for IBD. A deeper understanding of the ER stress-autophagy axis, the gut microbial-ER stress axis, and the gut microbial-autophagy axis may pave the way for targeted interventions to restore intestinal health and mitigate the impact of IBD.},
}

@article {pmid40312370,
year = {2025},
author = {BharathwajChetty, B and Kumar, A and Deevi, P and Abbas, M and Alqahtani, A and Liang, L and Sethi, G and Liu, L and Kunnumakkara, AB},
title = {Gut microbiota and their influence in brain cancer milieu.},
journal = {Journal of neuroinflammation},
volume = {22},
number = {1},
pages = {129},
pmid = {40312370},
issn = {1742-2094},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Brain Neoplasms/microbiology/metabolism/pathology ; *Dysbiosis/metabolism/microbiology ; Animals ; },
abstract = {Microbial communities are not simply remnants of the past but dynamic entities that continuously evolve under the selective pressures of nature, reflecting the intricate and adaptive processes of evolution. The microbiota residing in the various regions of the human body has numerous roles in different physiological processes such as nutrition, metabolism, immune regulation, etc. In the zeal of achieving empirical insights into the ambit of the gut microbiome, the research over the years led to the revelation of reciprocal interaction between the gut microbiome and the cognitive functioning of the human body. Dysbiosis in the gut microbial composition disturbs the homeostatic cognitive functioning of the human body. This dysbiosis has been associated with various chronic diseases, including brain cancer, such as glioma, glioblastoma, etc. This review explores the mechanistic role of dysbiosis-mediated progression of brain cancers and their subtypes. Moreover, it demonstrates the regulatory role of microbial metabolites produced by the gut microbiota, such as short-chain fatty acids, amino acids, lipids, etc., in the tumour progression. Further, we also provide valuable insights into the microbiota mediating the efficiency of therapeutic regimens, thereby leveraging gut microbiota as potential biomarkers and targets for improved treatment outcomes.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Brain Neoplasms/microbiology/metabolism/pathology
*Dysbiosis/metabolism/microbiology
Animals

@article {pmid40312144,
year = {2025},
author = {Liu, H and Wang, Q and Zeng, L and Liu, Y and Zhang, Y and Sun, Z and Guo, Q and Cui, SW},
title = {Structural Dynamics, Gut Microbiota Modulation, and Immunological Impacts of Shiitake Mushroom β-Glucan during In Vitro Intestinal Fermentation.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c01611},
pmid = {40312144},
issn = {1520-5118},
abstract = {This study investigated the structure-function relationship of shiitake β-glucan (SBG) through simulated digestion and colonic fermentation. SBG, composed of β-(1 → 3)-linked glucan backbones with β-(1 → 6)-linked side chains, exhibited notable resistance to enzymatic and acidic degradation in the upper gastrointestinal tract. During in vitro colonic fermentation, 59% of carbohydrates were consumed within 48 h, with a significant pH reduction and a 1.5-fold increase in short-chain fatty acid production. Microbiome analysis demonstrated that SBG enhanced Bacteroides and Lactobacillus populations, while suppressing Escherichia-Shigella. Within the first 12 h, SBG maintained a rigid triple-helix structure, with a slight decrease in branching from 48.02 to 44.26%. After 24 h, the triple helix unwound, and extensive depolymerization of the backbone occurred by 48 h. Immunomodulatory activity was preserved early in fermentation but decreased as the triple-helix structure broke down. These findings emphasize the critical role of molecular rigidity and conformational integrity in β-glucan's functionality for food and therapeutic applications.},
}

@article {pmid40312036,
year = {2025},
author = {Patangia, DV and Grimaud, G and Lyons, K and Dempsey, E and Ryan, CA and O'Shea, CA and Ross, RP and Stanton, C},
title = {Influence of feeding habit and duration on infant gut microbiome - a 6 month pilot study.},
journal = {Beneficial microbes},
volume = {},
number = {},
pages = {1-15},
doi = {10.1163/18762891-bja00075},
pmid = {40312036},
issn = {1876-2891},
abstract = {While the importance of breastfeeding on the developing infant gut microbiota has been established, few studies have compared the effect of breastfeeding duration on infant gut microbiota development. In this pilot study, we included 23 infants, divided into 4 groups to compare the effect of breastfeeding duration for first 4 (BreastFed_4) or 8 weeks (BreastFed_8) compared to exclusive breast (Exc Breast Fed) or formula feeding (Formula Fed) for 6 months. We used metagenomics shotgun sequencing of 88 infant stool samples and 64 corresponding maternal milk samples to examine the microbial composition. Breast milk samples showed the presence of previously defined core bacteria including spp. belonging to Staphylococcus, Streptococcus, Corynebacterium, Cutibacterium, Rothia and Pseudomonas. We report that the Exc Breast Fed infant group had the lowest alpha diversity and a distinct microbial composition compared to the Formula Fed group. BreastFed_4 clustered distinctly from all other groups, indicating the impact of duration and time of feeding on infant microbiota. Certain Bifidobacterium spp. were more associated to certain groups, in particular, B. infantis was more associated to Exc Breast Fed while Bacteroides/Phocaeicola with BreastFed_8. Exc Breast Fed showed the highest frequency of persisters with B. infantis being the dominant persister, while B. bifidum was the dominant persister in Formula Fed group. Persisters showed significantly higher abundance of several glycoside hydrolases (GH) important in early life across all groups compared to non-persisters. This study highlights infant gut microbiota changes associated with breastfeeding duration, warranting more detailed studies on the impact of breastfeeding duration on long-term health outcomes.},
}

@article {pmid40312035,
year = {2025},
author = {Choi, Y and Choi, JG and Huh, E and Eo, H and Shin, YJ and Park, MG and Kim, DH and Oh, MS},
title = {Lactobacillus taiwanensis BCRC17755 alleviates motor dysfunction and dopaminergic neuronal loss in mouse models of Parkinson's disease.},
journal = {Beneficial microbes},
volume = {},
number = {},
pages = {1-11},
doi = {10.1163/18762891-bja00066},
pmid = {40312035},
issn = {1876-2891},
abstract = {Parkinson's disease (PD) is a complex progressive neurodegenerative disease characterized by both motor and nonmotor symptoms such as constipation and dyspepsia. Recently, growing evidence has suggested that a specific gut microbiome is associated with the pathophysiology of PD through the microbiota-gut-brain axis. We previously discovered that Proteus mirabilis induced motor impairment and brain dopaminergic neurodegeneration in normal mice. In this context, exploring beneficial microbe would be reasonable strategy to treat PD fundamentally. With that the current study aimed to evaluate whether Lactobacillus taiwanensis BCRC17755 (BCRC17755) could ameliorate PD pathologies induced by 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) and P. mirabilis in mice. To demonstrate this, we measured motor function by performing pole test and the rotarod test and conducted histological analysis to assess the changes of factors in both brain and the gut. As a result, BCRC17755 decreased faecal abundance of P. mirabilis, which was higher in both the MPTP and P. mirabilis-treated mice. Additionally, BCRC17755 improved the motor deficits and alleviated damage to nigrostriatal dopaminergic neurons observed in both MPTP and P. mirabilis-induced PD mice. Furthermore, BCRC17755 mitigated microglial hyperactivation triggered by MPTP and P. mirabilis in the substantia nigra pars compacta and striatum of mice. Similarly, the release of inflammatory cytokines, including interleukin-1 beta and tumor necrosis factor alpha, was suppressed following the administration of BCRC17755 in the colon. Taken together, all the results suggest that BCRC17755 is a beneficial microbe for the treatment of PD by inhibiting the P. mirabilis growth.},
}

@article {pmid40312034,
year = {2025},
author = {Das, DJ and Jaikumar, VS and Suryaletha, K and Paul, M and Shankar, A and Nath, SR and Thomas, S},
title = {Probiotic Lacticaseibacillus paracasei from human gut microbiome against colistin-resistant Klebsiella pneumoniae: in vitro, in vivo and probiogenomic approaches.},
journal = {Beneficial microbes},
volume = {},
number = {},
pages = {1-21},
doi = {10.1163/18762891-bja00065},
pmid = {40312034},
issn = {1876-2891},
abstract = {Antibiotic treatment regimens fail to address Klebsiella pneumoniae exhibiting resistance to multiple drugs, including the last resort antibiotic, colistin. The use of probiotics as candidates for alternative antimicrobial therapy or as a source of new antibiotics is considered as an emerging trend in therapeutics. Rejuvenating the human gut with probiotics offers an intriguing therapeutic approach in various enteric diseases. However, the precise role of probiotics in non-enteric infections, particularly those caused by colistin-resistant Klebsiella pneumoniae remains unresolved, prompting further comprehensive research. Therefore, we propose an innovative prophylactic approach using Lacticaseibacilli of human gut origin against this pathogen. Probiotic characterisation like tolerance to acid, bile and sodium chloride were performed to evaluate its gastric survival. In vitro experiments revealed that non-neutralised cell-free supernatant (CFS) of Lacticaseibacillus has the potential to inhibit pathogenic K. pneumoniae. The observed growth reduction is suggestive of the cumulative effect of organic acids and other antimicrobial substances in CFS. The two Lacticaseibacillus paracasei isolates exhibited promising activity (with suspected proteinaceous heat labile molecules) against K. pneumoniae and those with better adhesion to CaCo-2 cell lines were selected for downstream studies. Scanning electron microscopic analysis of CFS treated pathogen cells revealed cell surface distortions and pore formations. The prophylactic potential of Lacticaseibacillus (live and heat-inactivated forms) in Balb/c mice model showed a reduction in histopathological and microbiological alterations caused by K. pneumoniae, when compared with untreated pathogen control. Whole genome analysis of the potential probiotic isolate revealed the genome is devoid of any antibiotic resistance genes and other virulence markers indicating its safety in vivo. Furthermore, the in vitro pathogen inhibition results were reinforced by antiSMASH and BAGEL analysis, which predicted the presence of putative bacteriocin genes. Hence, this multiapproach research study has revealed a promising prophylactic probiotic from human gut microbiome against multi-drug resistant K. pneumoniae.},
}

@article {pmid40313604,
year = {2025},
author = {Wu, H and Forslund, S and Wang, Z and Zhao, G},
title = {Human Gut Microbiome Researches Over the Last Decade: Current Challenges and Future Directions.},
journal = {Phenomics (Cham, Switzerland)},
volume = {5},
number = {1},
pages = {1-7},
pmid = {40313604},
issn = {2730-5848},
}

@article {pmid40312033,
year = {2025},
author = {Sahran, NF and Chong, CW and Ismail, IH and Taib, F and Hoo, PS and Palanisamy, UD and Sundralingam, U and Teh, CSJ and Kong, ZX and Ayub, Q and Yoke Ling, F and Hazlan, SNH and Azlan, M and Abdul Razak, S and Tengku Din, TADA and Abdullah, N and Tagiling, N and Tee, V and Ehab Ayad, M and Zheng, FM and El-Omar, E and Lee, YY},
title = {Effects of Traditional Asian Diet on dietary fibre requirement, gut microbiome composition, and faecal and urine metabolomes in healthy Asian women: a pilot study.},
journal = {Beneficial microbes},
volume = {},
number = {},
pages = {1-14},
doi = {10.1163/18762891-bja00074},
pmid = {40312033},
issn = {1876-2891},
abstract = {The Traditional Asian Diet (TAD) is characterised by high dietary fibre and functional foods. This study investigated TAD's effects on meeting fibre requirements, gut microbiome, and faecal and urine metabolomes. A four-week randomised controlled trial was conducted among healthy Asian women allocated into the TAD group (n = 11) following a newly developed TAD program and the control group (n = 11). Assessments included dietary intake, gut health (symptoms, faecal form, frequency), serum fatty acids binding protein-2 (FABP-2) levels, faecal microbiome via 16s rRNA sequencing, and faecal and urine metabolites which were analysed using gas chromatography-mass spectrometry (GC-MS) and nuclear magnetic resonance (NMR), respectively. The TAD group showed significant increases in dietary fibre (P < 0.001), reduced fat (P < 0.05), and improved faecal form (P = 0.009) compared to the control group. The TAD group was enriched with Parabacteroides merdae, while Bacteroides uniformis was more abundant in the control group. Individuals with baseline Prevotella copri showed its enrichment following TAD and higher butyrate levels, unlike the control group. The TAD led to lower urine levels of creatinine, dimethylamine, and phenethylamine compared to the control diet. In conclusion, the TAD program has proven beneficial effects in achieving dietary fibre, enriching the beneficial microbiota and metabolites, reducing harmful metabolites, and improving faecal form compared to a control diet. Clinical trial registration: NCT04885959, clinicaltrials.gov.},
}

@article {pmid40311922,
year = {2025},
author = {Wach, AA and Storman, D and Wieckowski, K and Wojtaszek-Główka, M and Żabicka, W and Krupka, K and Abadi, AK and Celinska-Lowenhoff, M and Bala, MM},
title = {The efficacy of probiotics, synbiotics or prebiotics in scleroderma: a systematic review.},
journal = {Clinical nutrition ESPEN},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.clnesp.2025.04.004},
pmid = {40311922},
issn = {2405-4577},
abstract = {INTRODUCTION: Pathogenesis of systemic scleroderma is a complex subject. Previous research has emphasized a possible contribution of the intestinal microbiome in developing symptoms. The use of probiotic formulas brings benefit in treatment of various autoimmune diseases, but the evidence for scleroderma is still not exhaustive. No official recommendations have been formulated on this topic, nor has the existing evidence been evaluated.

OBJECTIVE: We aimed to assess the efficacy of probiotics, prebiotics, or synbiotics in patients with scleroderma with a focus on the improvement of symptoms and change in the quality of life (QoL) both measured using validated scales, small intestinal bacterial overgrowth (SIBO) eradication, as well as change in the intensity of interstitial lung disease and occurrence of pulmonary hypertension.

METHODS: We performed a systematic search for randomised trials that assessed the beneficial and harmful effects of pro-, syn-, and prebiotics in patients with scleroderma. Pairs of authors independently selected studies for inclusion, extracted data, and assessed the risk of bias (RoB) of the included studies. We examined the certainty of evidence in accordance with the GRADE approach.

RESULTS: We screened 1,801 references (after the removal of duplicates), and assessed 16 citations in full text. We identified four randomised controlled trials (RCTs) with 103 participants in intervention and 87 in control groups. The evidence suggests that probiotic intake may not affect gastrointestinal symptoms measured with Visual Analogue Scale for Gastrointestinal Tract (VAS-GIT) (change in the VAS-GIT: MD 0.04, 95% CI -0.31 to 0.40, low certainty, n=56 probiotic group, n=57 placebo group) and the evidence is very uncertain about the effect on gastrointestinal symptoms measured with The University of California Los Angeles Scleroderma Clinical Trial Consortium GIT 2.0 instrument (UCLA GIT 2.0) (change in the UCLA GIT 2.0 - total score: MD -0.18 95% CI -0.44, 0.07, very low certainty, n=76 probiotic group, n=74 placebo group). Meta-analysis showed that probiotic intake may slightly improve the social functioning measured with UCLA GIT 2.0 compared to placebo (MD -0.21, 95% CI -0.32 to -0.10, low certainty, n=57 probiotic group, n=53 placebo group), yet may result in little to no difference in physical functioning measured with HAQ-DI (MD 0.08, 95% CI -0.15 to 0.32, low certainty, n=56 probiotic group, n=57 placebo group) and frequency of adverse events, change in QoL and SIBO eradication. We did not find any studies addressing the effect of pro-, pre-, synbiotics on interstitial lung disease or pulmonary hypertension. The certainty of evidence was low to very low mainly due to high RoB (lack of blinding, incomplete reporting) and imprecision.

CONCLUSIONS: We were unable to definitively prove a positive or negative effect of probiotic intake in patients with systemic sclerosis. The results should be interpreted with caution due to low or very low certainty of evidence and would need more confirmation from strain and dose specific RCTs at a lower RoB.},
}

@article {pmid40311903,
year = {2025},
author = {Morgan, S and Raza Shah, SH and Comstock, SS and Goodrich, JM and Liang, D and Tan, Y and McKee, K and Ruden, D and Sitarik, AR and Cassidy-Bushrow, AE and Dunlop, AL and Petriello, MC and , and , and Smith, PB and Newby, LK and Jacobson, LP and Catellier, DJ and Gershon, R and Cella, D and Parsons, P and Kurunthachalam, K and Fennell, TR and Sumner, SJ and Du, X and , },
title = {Prenatal PFAS exposure and outcomes related to maternal gut microbiome composition in later pregnancy.},
journal = {Environmental research},
volume = {},
number = {},
pages = {121709},
doi = {10.1016/j.envres.2025.121709},
pmid = {40311903},
issn = {1096-0953},
abstract = {The composition of the gut microbiome is dependent on factors including diet, lifestyle, and exposure to environmental chemicals, and has implications for human health. Per- and polyfluoroalkyl substances (PFAS), a class of man-made chemicals that have nonstick and flame-retardant properties may impact on gut microbiome composition. Our objective was to elucidate links between PFAS and maternal gut microbiome composition in two geographically diverse sites of the Environmental Influences on Child Health Outcomes program. The present analysis includes participants in the Atlanta African American Maternal Child Cohort;ATL AA and a predominately non-Hispanic White subsample of the Michigan Archive for Research on Child Health Cohort;MARCH with serum or plasma PFAS concentrations measured in early or late pregnancy and 16s rRNA sequencing from maternal gut microbiome samples available primarily in later pregnancy (2[nd]-3[rd] trimester). Linear regression models tested associations between prenatal PFAS levels (separately for the 1[st]/3[rd] trimesters) and measures of alpha diversity, bacterial composition differences, and differential taxonomic abundance. Bayesian Kernel Machine Regression and Elastic net regression mixture modeling were also incorporated. In both cohorts, multiple PFAS were significantly associated with the relative abundance of specific microbiome taxa even after adjustment for covariates including maternal diet, age, race, BMI, and smoking; A total of 16 significant family-level associations were identified for ATL AA (e.g., PFOA with Clostridiaceae; natural log fold change=0.94) and 13 significant family-level associations identified for MARCH e.g., PFOS with Desulfovibrionaceae; natural log fold change=-1.53 (pFDR<0.05), but similarities between cohorts were lacking. Mixture analyses did not identify interactive or combined effects but did provide modest evidence of inclusion of individual PFAS in beta diversity models in both cohorts. In 2 distinct cohorts, there were significant associations between prenatal PFAS and the relative abundance of several bacterial taxa, but these differences were cohort-specific. This work suggests that PFAS may modulate the gut microbiome during pregnancy.},
}

@article {pmid40311787,
year = {2025},
author = {Riechelman-Casarin, L and Valente, LC and Otton, R and Barbisan, LF and Romualdo, GR},
title = {Are glyphosate or glyphosate-based herbicides linked to Metabolic dysfunction-associated steatotic liver disease (MASLD)? The weight of current evidence.},
journal = {Environmental toxicology and pharmacology},
volume = {},
number = {},
pages = {104705},
doi = {10.1016/j.etap.2025.104705},
pmid = {40311787},
issn = {1872-7077},
abstract = {Metabolic dysfunction-associated steatotic liver disease (MASLD) affects around 30% of the world's population, increasing its prevalence by 50% in the last three decades. MASLD pathogenesis is considered multiaxial, involving disturbances in the liver, adipose tissue (AT) and gut microbiome. In parallel with MASLD increasing trends, the total herbicide use has nearly tripled over the last three decades. Glyphosate (GLY) is the most used herbicide worldwide (825mikg/year). The intensive use of GLY-based herbicides (GBH) - largely driven by the adoption of glyphosate-tolerant genetically modified crops over the past two decades - has led to environmental (soil and water) and food contamination, resulting in continuous human exposure. Emerging (pre)clinical data highlights the significant implications of this herbicide on MASLD, marking a critical area of research. Thus, this narrative review paper aimed at gathering and evaluating all epidemiological and (pre)clinical data on the implications of GLY or GBH on MASLD outcomes. Our work encompassed literature published within 2008 - 2025. Human urinary GLY levels are associated with different MASLD outcomes (steatosis risk, advanced fibrosis, increased transaminases) and comorbidities (higher risk for metabolic syndrome, diabetes, obesity and cardiovascular diseases) (6 studies). In vitro data indicate that GBH/GLY cause oxidative stress, genomic instability, apoptosis and membrane disruption in hepatocytes, while promoting apoptosis and lipid peroxidation in (pre)adipocytes and cytokine production in monocytes (15 studies). In rodent studies (21 studies), GLY/GBH - in doses based on human exposure/toxicological limits - induces inflammatory and oxidative responses in the liver and AT, while causing dysbiosis and metabolic alterations in gut microbiome axis. In the light of populational-, cell- and animal-based evidence, GLY/GBH disturbs key axis of MASLD pathogenesis and is hypothesized to be associated with its clinical outcomes.},
}

@article {pmid40311681,
year = {2025},
author = {Bhowmick, K and Yang, X and Mohammad, T and Xiang, X and Molmenti, CL and Mishra, B and Dasarathy, S and Krainer, AR and Hassan, MI and Crandall, KA and Mishra, L},
title = {Microbial metabolite ammonia disrupts TGF-β signaling to promote colon cancer.},
journal = {The Journal of biological chemistry},
volume = {},
number = {},
pages = {108559},
doi = {10.1016/j.jbc.2025.108559},
pmid = {40311681},
issn = {1083-351X},
abstract = {Colorectal cancer (CRC) is rising alarmingly in younger populations, potentially arising from factors such as obesity, pro-inflammatory gut microbiome and the accumulation of toxic metabolites. However, how metabolites such as ammonia impact key signaling pathways to promote CRC remains unclear. Our study investigates a critical link between gut microbiome alterations, ammonia, and their toxic effects on the TGF-β signaling pathway, driving CRC progression. We observe altered microbial populations in an obesity-induced mouse model of cancer, where ammonia promotes caspase-3-mediated cleavage of the SMAD3 adaptor βII-spectrin (SPTBN1). Cleaved SPTBN1 fragments form adducts with ammonia that induce pro-inflammatory cytokine expression and disrupt TGF-β signaling. Extending from AlphaFold docking simulations, we identified that ammonia interacts with N-terminal SPTBN1 potentially through residues D81, Y556, S663, Y666, N986, and D1177 to form hydrogen bonds that disrupt downstream SMAD3 signaling, altering TGF-β signaling to a protumorigenic phenotype. Blocking SPTBN1, through an SPTBN1-specific siRNA blocks ammonia toxicity and restores normal SMAD3/TGF-β signaling by reducing the abundance of SPTBN1 cleaved fragments in SW480 and Caco-2 (CRC) cell lines. In addition, our research establishes crosstalk between TGF-β signaling and a microbial sensor, carcinoembryonic antigen-related cell adhesion molecule 1 (CEACAM1), which is significantly overexpressed in CRC patients. We identified CEACAM1-SPTBN1 interactions at specific residues (E517 and Y520) within the immunoreceptor tyrosine-based inhibitory motif (ITIM) of CEACAM1 cytoplasmic domain, identifying distinguishing a potential axis that is harnessed by the altered microbiome. Our study identifies mechanistic insights into how microbial metabolites target TGF-β as a major signaling pathway to promote CRC.},
}

@article {pmid40311618,
year = {2025},
author = {Andreu-Sánchez, S and Blanco-Míguez, A and Wang, D and Golzato, D and Manghi, P and Heidrich, V and Fackelmann, G and Zhernakova, DV and Kurilshikov, A and Valles-Colomer, M and Weersma, RK and Zhernakova, A and Fu, J and Segata, N},
title = {Global genetic structure of human gut microbiome species is related to geographic location and host health.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2025.04.014},
pmid = {40311618},
issn = {1097-4172},
abstract = {The human gut harbors thousands of microbial species, each exhibiting significant inter-individual genetic variability. Although many studies have associated microbial relative abundances with human-health-related phenotypes, the substantial intraspecies genetic variability of gut microbes has not yet been comprehensively considered, limiting the potential of linking such genetic traits with host conditions. Here, we analyzed 32,152 metagenomes from 94 microbiome studies across the globe to investigate the human microbiome intraspecies genetic diversity. We reconstructed 583 species-specific phylogenies and linked them to geographic information and species' horizontal transmissibility. We identified 484 microbial-strain-level associations with 241 host phenotypes, encompassing human anthropometric factors, biochemical measurements, diseases, and lifestyle. We observed a higher prevalence of a Ruminococcus gnavus clade in nonagenarians correlated with distinct plasma bile acid profiles and a melanoma and prostate-cancer-associated Collinsella clade. Our large-scale intraspecies genetic analysis highlights the relevance of strain diversity as it relates to human health.},
}

@article {pmid40311592,
year = {2025},
author = {Qi, F and Shen, Z and Zhou, S and Zhang, Y and Zhang, Y and Wang, H and Du, Y and Xie, Z and Li, D and Ge, H},
title = {Tea residue protein-derived oligopeptides attenuate DSS-induced acute colitis complicated with hepatic injury in C57BL/6J mice by regulating the gut-microbiome-liver axis.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {142},
number = {},
pages = {156792},
doi = {10.1016/j.phymed.2025.156792},
pmid = {40311592},
issn = {1618-095X},
abstract = {BACKGROUND: Impairment of the intestinal mucosal barrier is a prevalent feature of acute colitis, and untreated acute colitis can lead to extra-intestinal manifestations, including hepatic injury. Previous research has demonstrated that large-leaf yellow tea residue protein-derived oligopeptides (TPP) can alleviate ulcerative colitis symptoms and hepatic injury in mice. However, the underlying regulatory mechanisms by which TPP improves colitis complicated with liver injury are unknown.

PURPOSE: To explore the potential mechanism by which TPP alleviates acute colitis complicated with hepatic injury.

METHODS: Acute colitis with hepatic injury was induced in mice using 3.5 % dextran sodium sulfate. Both 16S rRNA sequencing and transcriptomic analyses were utilized to investigate the impact of TPP on mitigating symptoms in mice.

RESULTS: It indicated that TPP administration effectively reduced inflammatory symptoms in the colon and liver, enhanced the secretion of mucin occluding, claudin-1, ZO-1, and MUC-2, decreased intestinal mucosal permeability, and restored homeostasis within the gut microbiome of mice. Moreover, transcriptomic analysis has evidenced the effectiveness of TPP in mitigating liver-related effects. RNA-seq KEGG enrichment and RT-qPCR analyses validated TPP could modulate the "gut-microbiome-liver" axis, and participate in signaling pathways related to inflammatory regulation, as well as bile acid metabolism and synthesis.

CONCLUSION: These findings suggest that TPP administration is a promising novel approach for preventing and treating acute colitis complicated with hepatic injury.},
}

@article {pmid40311534,
year = {2025},
author = {Shahzad, M and Arshad, M and Ahmad, HA and Iddrissu, I and Bailey, EH and Dru, N and Khan, S and Khan, H and Andrews, SC},
title = {Nutritional status reshapes gut microbiota composition in adolescent Afghan refugees in Peshawar, Pakistan.},
journal = {Nutrition research (New York, N.Y.)},
volume = {138},
number = {},
pages = {55-67},
doi = {10.1016/j.nutres.2025.04.004},
pmid = {40311534},
issn = {1879-0739},
abstract = {Although the human gut microbiome, and its role in health and disease, have been extensively studied in different populations, a comprehensive assessment of gut microbiome composition has not been performed in vulnerable refugee populations. In this study, we hypothesized that overall nutritional status, as indicated by serum micronutrients concentrations, is an important driver of variations in gut microbiome composition. Therefore, gut-microbiome diversity and associated demographic, health and nutritional factors were assessed in adolescent Afghan refugees (n=206). Blood and faecal samples were collected and analysed for nutrition status markers and 16S rRNA gene amplicon-based community profiling, respectively. Bioinformatics and statistical analysis were performed using SPSS, QIIME and R. Overall, 56 distinct phyla, 117 families and 252 genera were identified in the faecal samples. Bacterial diversity (alpha and beta diversity) and the Firmicutes:Bacteroidetes (F/B) ratio were significantly higher in the 15 to 19 year old age group (cf. the 10-14 age group) but were lower in the underweight and vitamin D deficient groups. Furthermore, LEfSe analysis identified significant differences in the relative abundance of bacterial genera based on age, BMI and micronutrient (vitamins and minerals) status. These results were further scrutinised by correlation analysis which confirmed that age, BMI and micronutrient status show significant correlations with F/B ratio and the relative abundance of specific bacterial taxa. Collectively, our study provides the first indication of how the gut-microbiota profile of adolescent Afghan refugees is associated with a range of nutrition-status factors. These findings can thus provide a basis for translational microbiota research aimed at improving the health of such understudied and vulnerable populations.},
}

@article {pmid40310598,
year = {2025},
author = {Luangphiphat, W and Jamjuree, P and Chantarangkul, C and Amornariyakool, O and Taweechotipatr, M},
title = {Protective Effects of Limosilactobacillus reuteri MSMC64 in Hyperlipidemia Rats Induced by a High-Cholesterol Diet.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {40310598},
issn = {1867-1314},
support = {324/2565//Center of Excellence in Probiotics at Srinakharinwirot University/ ; },
abstract = {Hyperlipidemia, characterized by abnormally elevated levels of lipids such as cholesterol, is a significant risk factor for cardiovascular diseases (CVD), contributing to increased oxidative stress, inflammation, and disruption of gut immunity. Dysbiosis, or imbalance in the gut microbiome, plays a critical role in the pathogenesis of hyperlipidemia. Probiotics, as key components of the gut microbiome, have been shown to positively impact health. This study aimed to evaluate the effects of Limosilactobacillus reuteri MSMC64 on lipid profiles, blood glucose levels, hepatic steatosis, antioxidant capacity, inflammatory biomarkers, and colon barrier immunity in hyperlipidemic rats induced by a high-cholesterol diet. The results demonstrated that the administration of L. reuteri MSMC64 may improve lipid profiles and blood glucose levels, reduce hepatic steatosis and oxidative stress, and lower inflammatory biomarkers while maintaining colon barrier integrity. These findings suggest that L. reuteri MSMC64 has the potential to be developed as a probiotic supplement for mitigating risk factors associated with hyperlipidemia and CVD.},
}

@article {pmid40310548,
year = {2025},
author = {Hochuli, N and Kadyan, S and Park, G and Patoine, C and Nagpal, R},
title = {A Gut Microbial Metabolite Alleviates Stress-Induced Neurobehavioral Dysfunction in an Alzheimer's Disease Model.},
journal = {Molecular neurobiology},
volume = {},
number = {},
pages = {},
pmid = {40310548},
issn = {1559-1182},
abstract = {Chronic psychological stress is a known risk factor for neurodegenerative disorders like Alzheimer's disease (AD), but its role in AD neuropathology remains unclear. Using the water-avoidance stress model in the APP/PS1 preclinical mouse model of AD, we investigate how chronic stress exacerbates neurobehavioral dysfunction and cognitive impairment and explore the neuroprotective potential of indole-3-propionate (IPA), a microbiome-derived metabolite, in mitigating these effects. Our findings show that psychological stress leads to depression- and anxiety-like behaviors, as indicated by reduced grooming and exploration behaviors; however, these effects are ameliorated by IPA supplementation. Stress also disrupts the gut microbiome and promotes intestinal inflammation. While IPA does not significantly alter microbiome composition, it mitigates inflammation by normalizing IL-17a and TGF-β gene expression and reducing TNF-⍺ and IL-6 protein levels. Although stress has a limited effect on hippocampal inflammation, IPA suppresses low-grade neuroinflammation by downregulating IL-1β, TNF-⍺, IL-6, and MCP-1 protein levels. Additionally, IPA treatment tends to reduce hippocampal amyloid-β plaques. These findings highlight the detrimental effects of chronic psychosocial stress on AD pathology and suggest that IPA may confer neuroprotection through the gut-immune-brain axis, supporting the therapeutic potential of microbial metabolites in mitigating cognitive decline.},
}

@article {pmid40310467,
year = {2025},
author = {Mukherjee, SD and Batagello, C and Adler, A and Agudelo, J and Zampini, A and Suryavanshi, M and Nguyen, A and Orr, T and Dearing, D and Monga, M and Miller, AW},
title = {Complex system modeling reveals oxalate homeostasis is driven by diverse oxalate-degrading bacteria.},
journal = {eLife},
volume = {14},
number = {},
pages = {},
pmid = {40310467},
issn = {2050-084X},
support = {DK121689-01A1/NH/NIH HHS/United States ; },
mesh = {*Oxalates/metabolism ; *Homeostasis ; Animals ; *Oxalobacter formigenes/metabolism ; Mice ; *Bacteria/metabolism ; *Gastrointestinal Microbiome ; Host Microbial Interactions ; },
abstract = {Decades of research have made clear that host-associated microbiomes touch all facets of health. However, effective therapies that target the microbiome have been elusive given its inherent complexity. Here, we experimentally examined diet-microbe-host interactions through a complex systems framework, centered on dietary oxalate. Using multiple, independent molecular, rodent, and in vitro experimental models, we found that microbiome composition influenced multiple oxalate-microbe-host interfaces. Importantly, the administration of the oxalate-degrading specialist, Oxalobacter formigenes, was only effective against a poor oxalate-degrading microbiota background and gives critical new insights into why clinical intervention trials with this species exhibit variable outcomes. Data suggest that, while heterogeneity in the microbiome impacts multiple diet-host-microbe interfaces, metabolic redundancy among diverse microorganisms in specific diet-microbe axes is a critical variable that may impact the efficacy of bacteriotherapies, which can help guide patient and probiotic selection criteria in probiotic clinical trials.},
}

*Oxalates/metabolism
*Homeostasis
Animals
*Oxalobacter formigenes/metabolism
Mice
*Bacteria/metabolism
*Gastrointestinal Microbiome
Host Microbial Interactions

@article {pmid40310312,
year = {2025},
author = {Popovici, IA and Orasanu, CI and Cozaru, GC and Ionescu, AC and Kajanto, L and Cimpineanu, B and Chisoi, A and Mitroi, AN and Poinareanu, I and Voda, RI and Ursica, OA and Pundiche, MB},
title = {An Overview of the Etiopathogenic Mechanisms Involved in the Expression of the Oral Microbiota.},
journal = {Clinics and practice},
volume = {15},
number = {4},
pages = {},
doi = {10.3390/clinpract15040080},
pmid = {40310312},
issn = {2039-7275},
abstract = {Background/Objectives: The diversity of the oral microbiota exerts its effects in maintaining dental and overall health. The unique genetic profile of each individual influences the composition of the oral microbiota, determining susceptibility to certain diseases. The aim is to observe its role by highlighting the pathogenic mechanisms involved in oral dysbiosis and identify genetic determinism's influence in maintaining balance. Methods: This study was designed as a narrative review of the oral microbiota, utilizing some of the principles and guidelines of systematic review to increase methodological rigor. We examined 121 articles such as reviews, meta-analyses, editorials, and observational studies, which met the inclusion and exclusion criteria. The inclusion criteria for studies were as follows: (1) studies that evaluated the impact of the microbiota in oral or/and systemic diseases; (2) studies that observed pathogenic mechanisms in the oral microbiota; (3) studies that evaluated the interaction of the microbiota with the immune system (4); studies that evaluated genetic implications in the microbiota. Results: Host genes regulate inflammatory and immunological reactions that play a role in microbiological balance. This explains the increased resistance of some to diseases, including gingivitis or periodontitis. Also, the implications of oral dysbiosis are reflected not only locally, but also generally, being associated with various systemic conditions. Conclusions: Understanding the pathogenic mechanisms and genetic determinants involved in oral dysbiosis may help create individualized therapies for preventing and managing oral and systemic disorders. A healthy lifestyle and adequate oral hygiene can facilitate a diverse and balanced microbiome, crucial for overall health.},
}

@article {pmid40310091,
year = {2025},
author = {Turon, M and Koutsouveli, V and Conejero, M and Taboada, S and Verdes, A and Lorente-Sorolla, JM and Díez-Vives, C and Riesgo, A},
title = {The archaeal class Nitrososphaeria is a key component of the reproductive microbiome in sponges during gametogenesis.},
journal = {mBio},
volume = {},
number = {},
pages = {e0201924},
doi = {10.1128/mbio.02019-24},
pmid = {40310091},
issn = {2150-7511},
abstract = {UNLABELLED: Sponge-associated microbes play fundamental roles in regulating their hosts' physiology, yet their contribution to sexual reproduction has been largely overlooked. Most studies have concentrated on the proportion of the microbiome transmitted from parents to offspring, providing little evidence of the putative microbial role during gametogenesis in sponges. Here, we use 16S rRNA gene analysis to assess whether the microbial composition of five gonochoristic sponge species differs between reproductive and non-reproductive individuals and correlate these changes with their gametogenic stages. In sponges with mature oocytes, reproductive status did not influence either beta or alpha microbial diversity. However, in two of the studied species, Geodia macandrewii and Petrosia ficiformis, which presented oocytes at the previtellogenic stage, significant microbial composition changes were detected between reproductive and non-reproductive individuals. These disparities were primarily driven by differentially abundant taxa affiliated with the Nitrososphaeria archaeal class in both species. We speculate that the previtellogenic stages are more energetically demanding, leading to microbial changes due to the phagocytosis of microbes to meet nutritional demands during this period. Supporting our hypothesis, we observed significant transcriptomic differences in G. macandrewii, mainly associated with the immune system, indicating potential changes in the sponge's recognition system. Overall, we provide new insights into the possible roles of sponge microbiomes during reproductive periods, potentially uncovering critical interactions that support reproductive success.

IMPORTANCE: Our research explores the fascinating relationship between sponges and their resident microbes, focusing specifically on how these microbes might influence sponge reproduction. Sponges are marine animals known for their complex and beneficial partnerships with various microbes. While previous studies have mainly looked at how these microbes are passed from parent sponges to their offspring, our study is among the first to examine how microbial communities change during the different stages of sponge reproduction. By analyzing the microbial composition in five sponge species, we discovered that significant changes occur in species with premature oocytes, suggesting that microbes may play a crucial role in providing the necessary nutrients during early egg development. This work not only enhances our understanding of sponge biology but also opens up new avenues for studying how microbes support the reproductive success of their hosts in marine environments.},
}

@article {pmid40309975,
year = {2025},
author = {Rasoul, KB and Nielsen, HV and Thorsteinsson, AL and Porskrog, A},
title = {[Diagnosing visceral Leishmaniasis using the microbiome 16S/18S test].},
journal = {Ugeskrift for laeger},
volume = {187},
number = {16},
pages = {},
doi = {10.61409/V08240552},
pmid = {40309975},
issn = {1603-6824},
mesh = {Humans ; *Leishmaniasis, Visceral/diagnosis/drug therapy/microbiology ; Male ; Aged, 80 and over ; RNA, Ribosomal, 16S/genetics ; Denmark ; High-Throughput Nucleotide Sequencing ; Immunocompromised Host ; Microbiota ; },
abstract = {Visceral leishmaniasis in northern parts of Europe is rare and can be difficult to diagnose. The microbiome 16S/18S-test is based on next-generation sequencing (NGS)-technology and a software program able to species annotate most types of bacteria, fungi, and parasites. We present a case of an 86-year-old male born in Denmark with multiple myeloma diagnosed with visceral leishmaniasis via the 16S/18S metabarcode test. This case highlights the potential of the test and the importance of obtaining a thorough travel anamnesis, as immunocompromised patients are susceptible to opportunistic infections.},
}

Humans
*Leishmaniasis, Visceral/diagnosis/drug therapy/microbiology
Male
Aged, 80 and over
RNA, Ribosomal, 16S/genetics
Denmark
High-Throughput Nucleotide Sequencing
Immunocompromised Host
Microbiota

@article {pmid40309850,
year = {2025},
author = {Chapela, S and Alvarez-Córdova, L and Martinuzzi, A and Suarez, R and Gonzalez, V and Manrique, E and Castaño, J and Rossetti, G and Cobellis, L and Pilone, V and Frias-Toral, E and Schiavo, L},
title = {Neurobiological and Microbiota Alterations After Bariatric Surgery: Implications for Hunger, Appetite, Taste, and Long-Term Metabolic Health.},
journal = {Brain sciences},
volume = {15},
number = {4},
pages = {},
doi = {10.3390/brainsci15040363},
pmid = {40309850},
issn = {2076-3425},
abstract = {Bariatric surgery (BS) is an effective intervention for obesity, inducing significant neurobiological and gut microbiota changes that influence hunger, appetite, taste perception, and long-term metabolic health. This narrative review examines these alterations by analyzing recent findings from clinical and preclinical studies, including neuroimaging, microbiome sequencing, and hormonal assessments. BS modulates appetite-regulating hormones, reducing ghrelin while increasing glucagon-like peptide-1 (GLP-1) and peptide tyrosine-tyrosine (PYY), leading to enhanced satiety and decreased caloric intake. Neuroimaging studies reveal structural and functional changes in brain regions involved in reward processing and cognitive control, contributing to reduced cravings and altered food choices. Additionally, BS reshapes the gut microbiota, increasing beneficial species such as Akkermansia muciniphila, which influence metabolic pathways through short-chain fatty acid production and bile acid metabolism. These findings highlight the complex interplay between the gut and the brain in post-surgical metabolic regulation. Understanding these mechanisms is essential for optimizing post-operative care, including nutritional strategies and behavioral interventions. Future research should explore how these changes impact long-term outcomes, guiding the development of targeted therapies to enhance the recovery and quality of life for BS patients.},
}

@article {pmid40309529,
year = {2025},
author = {Goel, R and Gupta, B and Satodiya, VN and Vala, AU and Dabhi, H and Mittal, A},
title = {Association of Gut-Microbiome and mental health and effects of probiotics on psychiatric disorders: A Meta-analysis and systematic review.},
journal = {Nigerian medical journal : journal of the Nigeria Medical Association},
volume = {66},
number = {1},
pages = {13-25},
pmid = {40309529},
issn = {0300-1652},
abstract = {BACKGROUND: A correlation between gut microbiome and mental health has drawn significant attention lately. The effects of microbiome microorganisms and their byproducts on disease states represent a complex and dynamic field of study. The objective of this article is to review the association of gut microbes and mental health and the effects of probiotics on psychiatric disorders, if any.

METHODOLOGY: This meta-analysis was conducted using the PRISMA standards. We have compiled the most recent advancements in the field according to human research published in this Systematic review and meta-analysis.

RESULTS: The forest plot analysis revealed that probiotics or probiotics combined with other intervention modalities did significantly reduce some extent of mental disorders in comparison to the control group (Standardized mean difference) SMD = 0.95, 95% Confidence Interval (CI): -6.52 to 8.42, P value< 0.01.

CONCLUSION: Overall, the reviewed literature supports the importance of gut microbiota-brain interaction in human mental illnesses, including the impact of probiotics on mental health outcomes and brain connection.},
}

@article {pmid40309355,
year = {2025},
author = {Hand, E and Hood-Pishchany, I and Darville, T and O'Connell, CM},
title = {Influence of cervicovaginal microbiota on Chlamydia trachomatis infection dynamics.},
journal = {Microbial cell (Graz, Austria)},
volume = {12},
number = {},
pages = {93-108},
pmid = {40309355},
issn = {2311-2638},
abstract = {The cervicovaginal microbiome (CVM) is increasingly being considered as an important aspect of women's health, particularly in relation to the risk and progression of sexually transmitted infections (STIs). CVM composition varies significantly between individuals and is shaped by factors including diet, age, environmental exposures, and lifestyle. Understanding these influences may shed light on how microbial imbalances contribute to infection susceptibility and the development of reproductive health disorders. Five distinct community state types (CSTs) classify common CVM compositions. Most CSTs (I, II, III, V) are characterized by a dominant Lactobacillus species and are associated with better or neutral reproductive health, including reduced coincident detection of STIs such as Chlamydia trachomatis. In contrast, CST IV is composed of diverse, predominantly anaerobic, microbial species and is associated with CVM dysbiosis, bacterial vaginosis, and a heightened risk of STI acquisition. This review examines the complex interplay between the CVM, C. trachomatis infection, and host immune responses, highlighting the role of metabolites such as short-chain and long-chain fatty acids, indole, and iron in modulating pathogen survival and host defenses. Additionally, the impacts of CVM composition on C. trachomatis persistence, ascension, and clearance are discussed, alongside co-infection dynamics with pathogens like Neisseria gonorrhoeae and Mycoplasma genitalium.},
}

@article {pmid40309115,
year = {2025},
author = {Wang, X and Chen, H and Yang, M and Huang, M and Zhang, D and Li, M and Wang, H and Zhou, Q and Lu, L and Li, Y and Yu, J and Ma, L},
title = {Influence of gut microbiota and immune markers in different stages of colorectal adenomas.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1556056},
pmid = {40309115},
issn = {1664-302X},
abstract = {OBJECTIVE: Colorectal adenomas (CRA) are the primary precancerous lesions leading to colorectal cancer (CRC). Early detection and intervention of CRA can significantly reduce the incidence of CRC. We investigated the relationships between the gut microbiome and the expression levels of PD-L1, IL-6, and IFN-γ at different CRA stages.

METHODS: Participants were divided into normal, non-advanced adenoma (NAA), and advanced adenoma (AA) groups. PD-L1 expression in collected tissues was analyzed via immunohistochemistry (IHC) and Western blotting. Serum IL-6 and IFN-γ levels were measured using Enzyme-Linked Immunosorbent Assay (ELISA). 16S rRNA gene sequencing was used to examine gut microbiota changes, with correlation analysis to assess microbial influences on CRA progression.

RESULTS: The main differences in bacterial composition among the three groups were found within the Firmicutes and Bacteroidetes phyla. In the normal vs. NAA comparison, Clostridium sensu stricto, Faecalimonas, Gemmiger, and Ruminococcus were more abundant in the normal group, while Solobacterium was enriched in the NAA group. For the normal vs. AA comparison, the normal group was enriched with Anaerostipes, Blautia, Clostridium sensu stricto, Intestinibacter, Phocaeicola, and Turicibacter, whereas Solobacterium was more abundant in the AA group. In the NAA vs. AA comparison, the NAA group exhibited higher levels of Blautia, Faecalimonas, and Turicibacter relative to the AA group. Anaerostipes and Blautia are positively correlated with taurine and hypotaurine metabolism, propanoate metabolism, and zeatin biosynthesis. PD-L1 protein levels progressively increase with CRA advancement. Additionally, Faecalimonas, and Solobacterium were negatively associated with IFN-γ, while Gemmiger, and Anaerostipes were positively associated with IL-6.

CONCLUSION: This study highlights the dynamic alterations in gut microbiota composition and their potential influence on the regulation of inflammatory cytokines and PD-L1 expression during CRA progression. The enrichment of protective taxa, such as Anaerostipes and Blautia, in the normal group emphasizes their potential role in mitigating adenoma progression. Dietary modulation to promote the proliferation of these beneficial bacteria could serve as a promising strategy to improve colorectal health. Future research should further explore the specific relationships between dietary components, gut microbiota, and metabolic pathways, and assess the effects of dietary interventions on gut health.},
}

@article {pmid40308898,
year = {2025},
author = {Palmer, B and Karačić, S and Bierbaum, G and Gee, CT},
title = {Microbial methods matter: Identifying discrepancies between microbiome denoising pipelines using a leaf biofilm taphonomic dataset.},
journal = {Applications in plant sciences},
volume = {13},
number = {2},
pages = {e11628},
pmid = {40308898},
issn = {2168-0450},
abstract = {PREMISE: The occurrence of different microorganisms on aquatic macrophyte fossils suggests that biofilm microbes may facilitate leaf preservation. Understanding the impact of microorganisms on leaf preservation requires studies on living plants coupled with microbial amplicon sequencing. Choosing the most suitable bioinformatic pipeline is pivotal to accurate data interpretation, as it can lead to considerably different estimations of microbial community composition.

METHODS: We analyze biofilms from floating and submerged leaves of Nymphaea alba and Nuphar lutea and mock communities using primers for the 16S ribosomal RNA (rRNA), 18S rRNA, and ITS amplicon regions and compare the microbial community compositions derived from three bioinformatic pipelines: DADA2, Deblur, and UNOISE.

RESULTS: The choice of denoiser alters the total number of sequences identified and differs in the identified taxa. Results from all three denoising pipelines show that the leaf microbial communities differed between depths and that the effect of the environment varied depending on the amplicon region.

DISCUSSION: Considering the performance of denoising algorithms and the identification of amplicon sequence variants (ASVs), we recommend DADA2 for analyzing 16S rRNA and 18S rRNA. For the ITS region, the choice is more nuanced, as Deblur identified the most ASVs and was compositionally similar to DADA2.},
}

@article {pmid40308807,
year = {2025},
author = {Zhu, Y and Geng, SY and Chen, Y and Ru, QJ and Zheng, Y and Jiang, N and Zhu, FY and Zhang, YS},
title = {Machine learning algorithms reveal gut microbiota signatures associated with chronic hepatitis B-related hepatic fibrosis.},
journal = {World journal of gastroenterology},
volume = {31},
number = {16},
pages = {105985},
pmid = {40308807},
issn = {2219-2840},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Liver Cirrhosis/microbiology/virology/diagnosis/pathology/etiology ; *Machine Learning ; *Hepatitis B, Chronic/complications/microbiology ; Male ; Female ; Middle Aged ; Disease Progression ; Adult ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; Liver/pathology/diagnostic imaging ; Algorithms ; },
abstract = {BACKGROUND: Hepatic fibrosis (HF) represents a pivotal stage in the progression and potential reversal of cirrhosis, underscoring the importance of early identification and therapeutic intervention to modulate disease trajectory.

AIM: To explore the complex relationship between chronic hepatitis B (CHB)-related HF and gut microbiota to identify microbiota signatures significantly associated with HF progression in CHB patients using advanced machine learning algorithms.

METHODS: This study included patients diagnosed with CHB and classified them into HF and non-HF groups based on liver stiffness measurements. The HF group was further subdivided into four subgroups: F1, F2, F3, and F4. Data on clinical indicators were collected. Stool samples were collected for 16S rRNA sequencing to assess the gut microbiome. Microbiota diversity, relative abundance, and linear discriminant analysis effect size (LEfSe) were analyzed in different groups. Correlation analysis between clinical indicators and the relative abundance of gut microbiota was performed. The random forest and eXtreme gradient boosting algorithms were used to identify key differential gut microbiota. The Shapley additive explanations were used to evaluate microbiota importance.

RESULTS: Integrating the results from univariate analysis, LEfSe, and machine learning, we identified that the presence of Dorea in gut microbiota may be a key feature associated with CHB-related HF. Dorea possibly serves as a core differential feature of the gut microbiota that distinguishes HF from non-HF patients, and the presence of Dorea shows significant variations across different stages of HF (P < 0.05). The relative abundance of Dorea significantly decreases with increasing HF severity (P = 0.041). Moreover, the gut microbiota composition in patients with different stages of HF was found to correlate with several liver function indicators, such as γ-glutamyl transferase, alkaline phosphatase, total bilirubin, and the aspartate aminotransferase/alanine transaminase ratio (P < 0.05). The associated pathways were predominantly enriched in biosynthesis, degradation/utilization/assimilation, generation of precursors, metabolites, and energy, among other categories.

CONCLUSION: HF affects the composition of the gut microbiota, indicating that the gut microbiota plays a crucial role in its pathophysiological processes. The abundance of Dorea varies significantly across various stages of HF, making it a potential microbial marker for identifying HF onset and progression.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Liver Cirrhosis/microbiology/virology/diagnosis/pathology/etiology
*Machine Learning
*Hepatitis B, Chronic/complications/microbiology
Male
Female
Middle Aged
Disease Progression
Adult
RNA, Ribosomal, 16S/genetics
Feces/microbiology
Liver/pathology/diagnostic imaging
Algorithms

@article {pmid40308573,
year = {2025},
author = {Lu, J and Wang, Y and Wu, J and Duan, Y and Zhang, H and Du, H},
title = {Linking microbial communities to rheumatoid arthritis: focus on gut, oral microbiome and their extracellular vesicles.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1503474},
pmid = {40308573},
issn = {1664-3224},
mesh = {Humans ; *Arthritis, Rheumatoid/microbiology/immunology/etiology ; *Extracellular Vesicles/immunology/metabolism ; *Mouth/microbiology/immunology ; *Gastrointestinal Microbiome/immunology ; Animals ; *Microbiota/immunology ; Bacteria/immunology ; },
abstract = {Rheumatoid arthritis (RA) is a severe, chronic autoimmune disease affecting approximately 1% of the global population. Research has demonstrated that microorganisms play a crucial role in the onset and progression of RA. This indicates that the disruption of immune homeostasis may originate from mucosal sites, such as the gut and oral cavity. In the intestines of patients in the preclinical stage of RA, an increased abundance of Prevotella species with a strong association to the disease was observed. In the oral cavity, infections by Porphyromonas gingivalis and Aggregatibacter actinomycetemcomitans can mediate the production of anti-citrullinated protein antibodies (ACPAs), potentially contributing to RA pathogenesis. Nevertheless, no single bacterial species has been consistently identified as the primary driver of RA. This review will discuss the connection between gut and oral bacteria in the development of arthritis. Additionally, it explores the role of bacterial extracellular vesicles (bEVs) in inducing inflammation and their potential pathogenic roles in RA.},
}

Humans
*Arthritis, Rheumatoid/microbiology/immunology/etiology
*Extracellular Vesicles/immunology/metabolism
*Mouth/microbiology/immunology
*Gastrointestinal Microbiome/immunology
Animals
*Microbiota/immunology
Bacteria/immunology

@article {pmid40307949,
year = {2025},
author = {Lee, JY and Jo, S and Lee, J and Choi, M and Kim, K and Lee, S and Kim, HS and Bae, JW and Chung, SJ},
title = {Distinct gut microbiome characteristics and dynamics in patients with Parkinson's disease based on the presence of premotor rapid-eye movement sleep behavior disorders.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {108},
pmid = {40307949},
issn = {2049-2618},
support = {RS-2024-00353952//Ministry of Science and ICT, South Korea/ ; RS-2023-00265588//the Ministry of Health and Welfare, Republic of Korea/ ; },
mesh = {Humans ; *Parkinson Disease/microbiology/complications ; *Gastrointestinal Microbiome/genetics ; Male ; *REM Sleep Behavior Disorder/microbiology ; Female ; Aged ; Middle Aged ; Disease Progression ; *Bacteria/classification/genetics/isolation & purification ; Feces/microbiology ; RNA, Ribosomal, 16S/genetics ; },
abstract = {BACKGROUND: Alpha-synuclein aggregation, a hallmark of Parkinson's disease (PD), is hypothesized to often begin in the enteric or peripheral nervous system in "body-first" PD and progresses through the vagus nerve to the brain, therefore REM sleep behavior disorder (RBD) precedes the PD diagnosis. In contrast, "brain-first" PD begins in the central nervous system. Evidence that gut microbiome imbalances observed in PD and idiopathic RBD exhibit similar trends supports body-first and brain-first hypothesis and highlights the role of microbiota in PD pathogenesis. However, further investigation is needed to understand distinct microbiome changes in body-first versus brain-first PD over the disease progression.

RESULTS: Our investigation involved 104 patients with PD and 85 of their spouses as healthy controls (HC), with 57 patients (54.8%) categorized as PD-RBD(+) and 47 patients (45.2%) as PD-RBD(-) based on RBD presence before the PD diagnosis. We evaluated the microbiome differences between these groups over the disease progression through taxonomic and functional differential abundance analyses and carbohydrate-active enzyme (CAZyme) profiles based on metagenome-assembled genomes. The PD-RBD(+) gut microbiome showed a relatively stable microbiome composition irrespective of disease stage. In contrast, PD-RBD(-) microbiome exhibited a relatively dynamic microbiome change as the disease progressed. In early-stage PD-RBD(+), Escherichia and Akkermansia, associated with pathogenic biofilm formation and host mucin degradation, respectively, were enriched, which was supported by functional analysis. We discovered that genes of the UDP-GlcNAc synthesis/recycling pathway negatively correlated with biofilm formation; this finding was further validated in a separate cohort. Furthermore, fiber intake-associated taxa were decreased in early-stage PD-RBD(+) and the biased mucin-degrading capacity of CAZyme compared to fiber degradation.

CONCLUSION: We determined that the gut microbiome dynamics in patients with PD according to the disease progression depend on the presence of premotor RBD. Notably, early-stage PD-RBD(+) demonstrated distinct gut microbial characteristics, potentially contributing to exacerbation of PD pathophysiology. This outcome may contribute to the development of new therapeutic strategies targeting the gut microbiome in PD. Video Abstract.},
}

Humans
*Parkinson Disease/microbiology/complications
*Gastrointestinal Microbiome/genetics
Male
*REM Sleep Behavior Disorder/microbiology
Female
Aged
Middle Aged
Disease Progression
*Bacteria/classification/genetics/isolation & purification
Feces/microbiology
RNA, Ribosomal, 16S/genetics

@article {pmid40307838,
year = {2025},
author = {Huang, L and Li, K and Peng, C and Gu, S and Huang, X and Gao, C and Ren, X and Cheng, M and He, G and Xu, Y and Jiang, Y and Wang, H and Wang, M and Shen, P and Wang, Q and He, X and Zhong, L and Wang, S and Wang, N and Zhang, G and Cai, H and Jiang, C},
title = {Elevated antibiotic resistance gene abundance of ICU healthcare workers, a multicentre, cross-sectional study.},
journal = {Critical care (London, England)},
volume = {29},
number = {1},
pages = {170},
pmid = {40307838},
issn = {1466-609X},
support = {LTGY24H190001//Zhejiang Provincial Natural Science Fund/ ; 82202356, 82341109, and 82173645//National Natural Science Foundation of China/ ; 82202356, 82341109, and 82173645//National Natural Science Foundation of China/ ; 2021YFA1301001//National Key Research and Development Program/ ; 2025C02090//"Pioneer" and "Leading Goose" R&D Program of Zhejiang/ ; WKJ-ZJ-2526//National Health Commission Scientific Research Fund - Zhejiang Provincial Health Major Science and Technology Plan Project/ ; },
mesh = {Humans ; Cross-Sectional Studies ; Male ; Female ; Intensive Care Units/organization & administration/statistics & numerical data ; Prospective Studies ; *Health Personnel/statistics & numerical data ; China ; Adult ; Middle Aged ; *Drug Resistance, Microbial/genetics ; Gastrointestinal Microbiome/genetics ; Feces/microbiology ; },
abstract = {OBJECTIVE: Studies suggest that the colonization of multidrug-resistant organism in the gut of healthcare workers is similar to that of healthy individuals. However, due to exposure to medical environments, is the abundance of antibiotic resistance genes (ARG) in the gut of ICU healthcare workers higher than that of healthy individuals?

DESIGN: Prospective, multicentre, cross-sectional study.

SETTING: Eight medical centers in China, recruiting from January 2024 to February 2024.

PARTICIPANTS: 303 Healthy people (201 ICU healthcare workers and 103 healthy controls) were screened and 290 Healthy people (191 ICU healthcare workers and 99 healthy controls) were included in analysis.

MAIN OUTCOME MEASURES: Fecal samples were collected and subjected to metagenomic sequencing. We compared the total ARG abundance, ARG diversity, and gut microbiome composition between the two groups.

RESULTS: After adjusting for age, sex, and body mass index, ICU healthcare workers exhibited a significantly higher total ARG abundance compared to healthy controls (fold change = 1.22, 95% CI: 1.12-1.34, p < 0.001). The β-diversity of ARG between the two groups differed significantly (p = 0.001). No significant linear or nonlinear relationship was observed between the duration of ICU occupational exposure and ARG abundance (p for overall = 0.96, p for nonlinear = 0.84).

CONCLUSION: In this prospective, multicenter study, we found that ICU healthcare workers exhibit significantly higher gut ARGs abundance compared to healthy controls. Meanwhile, ICU healthcare workers, including physicians, nurses, and nursing assistants, have a different composition of gut ARGs compared to healthy individuals.

TRIAL REGISTRATION: NCT06228248.},
}

Humans
Cross-Sectional Studies
Male
Female
Intensive Care Units/organization & administration/statistics & numerical data
Prospective Studies
*Health Personnel/statistics & numerical data
China
Adult
Middle Aged
*Drug Resistance, Microbial/genetics
Gastrointestinal Microbiome/genetics
Feces/microbiology

@article {pmid40307670,
year = {2025},
author = {Daniel, SL and Ridlon, JM},
title = {Clostridium scindens: History and current outlook for a keystone species in the mammalian gut involved in bile acid and steroid metabolism.},
journal = {FEMS microbiology reviews},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsre/fuaf016},
pmid = {40307670},
issn = {1574-6976},
abstract = {Clostridium scindens is a keystone bacterial species in the mammalian gut that, while low in abundance, has a significant impact on bile acid and steroid metabolism. Numerous studies indicate that the two most studied strains of C. scindens (i.e. ATCC 35704 and VPI 12708) are important for a myriad of physiological processes in the host. We focus on both historical and current microbiological and molecular biology work on the Hylemon-Björkhem pathway and the steroid-17,20-desmolase pathway that were first discovered in C. scindens. Our most recent analysis now calls into question whether strains currently defined as C. scindens represent two separate taxonomic groups. Future directions include developing genetic tools to further explore the physiological role of bile acid and steroid metabolism by strains of C. scindens, and the causal role of these pathways in host physiology and disease.},
}

@article {pmid40307658,
year = {2025},
author = {Damianos, JA and Matar, A and Halawi, H},
title = {Gas-tly Interpretations: A Case-Based Approach to the Nuances of SIBO Breath Testing.},
journal = {Current gastroenterology reports},
volume = {27},
number = {1},
pages = {30},
pmid = {40307658},
issn = {1534-312X},
mesh = {Humans ; Breath Tests/methods ; Female ; Male ; *Blind Loop Syndrome/diagnosis ; Middle Aged ; Methane/analysis ; *Gastrointestinal Microbiome ; Hydrogen/analysis ; },
abstract = {PURPOSE OF REVIEW: Breath testing to diagnose intestinal microbial overgrowth (MO) is being increasingly utilized, in part due to direct-to-consumer testing modalities. However, the concept of breath testing in the diagnosis of MO is controversial due to numerous limitations regarding optimal substrate, diagnostic thresholds, and confounding variables. We provide seven real-world cases which comprehensively illustrate the principles and nuances of the interpretation of breath testing.

RECENT FINDINGS: We highlight recent studies which examine the optimal substrate for breath testing (glucose versus lactulose), the subtypes and clinical significance of breath test patterns including hydrogen, methane, and hydrogen-sulfide, elevated baseline gas levels, and confounders to breath test interpretation including transit time and diet. Reviewing the latest evidence, we provide recommendations for a personalized interpretation of breath tests utilizing unique patient factors. We conclude with an algorithm to assist clinicians in providing more accurate diagnoses.},
}

Humans
Breath Tests/methods
Female
Male
*Blind Loop Syndrome/diagnosis
Middle Aged
Methane/analysis
*Gastrointestinal Microbiome
Hydrogen/analysis

@article {pmid40307618,
year = {2025},
author = {Huysentruyt, J and Steels, W and Ruiz Pérez, M and Verstraeten, B and Divert, T and Flies, K and Lemeire, K and Takahashi, N and De Bruyn, E and Joossens, M and Brown, AS and Lambrecht, BN and Declercq, W and Vanden Berghe, T and Maelfait, J and Vandenabeele, P and Tougaard, P},
title = {RIPK1 ablation in T cells results in spontaneous enteropathy and TNF-driven villus atrophy.},
journal = {EMBO reports},
volume = {},
number = {},
pages = {},
pmid = {40307618},
issn = {1469-3178},
support = {G.0E04.16N//Fonds Wetenschappelijk Onderzoek (FWO)/ ; G.0C76.18N//Fonds Wetenschappelijk Onderzoek (FWO)/ ; G.0B71.18N//Fonds Wetenschappelijk Onderzoek (FWO)/ ; G.0B96.20N//Fonds Wetenschappelijk Onderzoek (FWO)/ ; G.0A93.22N//Fonds Wetenschappelijk Onderzoek (FWO)/ ; 30826052//Fonds Wetenschappelijk Onderzoek (FWO)/ ; 40007512//Fonds Wetenschappelijk Onderzoek (FWO)/ ; 1S44919N//Fonds Wetenschappelijk Onderzoek (FWO)/ ; 12U8318N//Fonds Wetenschappelijk Onderzoek (FWO)/ ; BOF16/MET_V/007//Universiteit Gent (UGent)/ ; BOF22/MET_V/007//Universiteit Gent (UGent)/ ; 20/IBF/039//Universiteit Gent (UGent)/ ; BOF20/PDO/027//Universiteit Gent (UGent)/ ; F/2016/865//Union for International Cancer Control (UICC)/ ; F/2020/1505//Union for International Cancer Control (UICC)/ ; },
abstract = {RIPK1 is a crucial regulator of cell survival, inflammation and cell death. Human RIPK1 deficiency leads to early-onset intestinal inflammation and peripheral T cell imbalance, though its role in αβT cell-mediated intestinal homeostasis remains unclear. In this study, we demonstrate that mice with RIPK1 ablation in conventional αβT cells (Ripk1[ΔCD4]) developed a severe small intestinal pathology characterized by small intestinal elongation, crypt hyperplasia, and duodenum-specific villus atrophy. Using mixed bone marrow chimeras reveals a survival disadvantage of αβT cells compared to γδT cells in the small intestine. Broad-spectrum antibiotic treatment ameliorates crypt hyperplasia and prevents intestinal elongation, though villus atrophy persists. Conversely, crossing Ripk1[ΔCD4] with TNF receptor 1 Tnfr1[-/-] knockout mice rescues villus atrophy but not intestinal elongation. Finally, combined ablation of Ripk1[∆CD4] and Casp8[∆CD4] fully rescues intestinal pathology, revealing that αβT cell apoptosis in Ripk1[∆CD4] drives the enteropathy. These findings demonstrate that RIPK1-mediated survival of αβT cells is essential for proximal small intestinal homeostasis. In Ripk1[∆CD4] mice, the imbalanced T cell compartment drives microbiome-mediated intestinal elongation and TNF-driven villus atrophy.},
}

@article {pmid40307565,
year = {2025},
author = {Setshedi, M and Ianiro, G},
title = {Developing microbiome research in Africa: the essential role of clinician scientists.},
journal = {Nature reviews. Gastroenterology & hepatology},
volume = {},
number = {},
pages = {},
pmid = {40307565},
issn = {1759-5053},
}

@article {pmid40307551,
year = {2025},
author = {Kennedy, MS and Freiburger, A and Cooper, M and Beilsmith, K and St George, ML and Kalski, M and Cham, C and Guzzetta, A and Ng, SC and Chan, FK and DeLeon, O and Rubin, D and Henry, CS and Bergelson, J and Chang, EB},
title = {Diet outperforms microbial transplant to drive microbiome recovery in mice.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {40307551},
issn = {1476-4687},
abstract = {A high-fat, low-fibre Western-style diet (WD) induces microbiome dysbiosis characterized by reduced taxonomic diversity and metabolic breadth[1,2], which in turn increases risk for a wide array of metabolic[3-5], immune[6] and systemic pathologies. Recent work has established that WD can impair microbiome resilience to acute perturbations such as antibiotic treatment[7,8], although little is known about the mechanism of impairment and the specific consequences for the host of prolonged post-antibiotic dysbiosis. Here we characterize the trajectory by which the gut microbiome recovers its taxonomic and functional profile after antibiotic treatment in mice on regular chow (RC) or WD, and find that only mice on RC undergo a rapid successional process of recovery. Metabolic modelling indicates that a RC diet promotes the development of syntrophic cross-feeding interactions, whereas in mice on WD, a dominant taxon monopolizes readily available resources without releasing syntrophic byproducts. Intervention experiments reveal that an appropriate dietary resource environment is both necessary and sufficient for rapid and robust microbiome recovery, whereas microbial transplant is neither. Furthermore, prolonged post-antibiotic dysbiosis in mice on WD renders them susceptible to infection by the intestinal pathogen Salmonella enterica serovar Typhimurium. Our data challenge widespread enthusiasm for faecal microbiota transplant (FMT) as a strategy to address dysbiosis, and demonstrate that specific dietary interventions are, at a minimum, an essential prerequisite for effective FMT, and may afford a safer, more natural and less invasive alternative.},
}

@article {pmid40307498,
year = {2025},
author = {Bui, TNY and Paul, A and Guleria, S and O'Sullivan, JM and Toldi, G},
title = {Short-chain fatty acids-a key link between the gut microbiome and T-lymphocytes in neonates?.},
journal = {Pediatric research},
volume = {},
number = {},
pages = {},
pmid = {40307498},
issn = {1530-0447},
abstract = {Infancy is a vulnerable and critical phase in the acquisition of the gut microbiome and the establishment of immune function. Short-chain fatty acids (SCFAs), such as acetate, propionate and butyrate, are compounds mostly produced by the microbiome through various metabolic pathways and play an indispensable role in connecting the microbiome and the adaptive immune system. This review aims to summarise recent findings regarding the intricate relationship between SCFAs, the gut microbiome, and T lymphocytes with a focus on early life interactions. The paper discusses factors affecting the establishment of the neonatal microbiome, especially human milk versus formula milk, and how these influence SCFA concentrations in feces, which in turn directly impact T cell development and function. Despite recent advances in understanding the role of gut microbiome derived SCFAs in adults, a significant knowledge gap remains in translating these findings to neonates and exploring the utility of SCFAs as a potential therapeutic intervention in inflammatory complications of preterm and term neonates. IMPACT: This review highlights potential therapeutic applications of short-chain fatty acids (SCFAs) in neonatal care, particularly in preventing and treating inflammatory conditions. This could lead to new treatment strategies for conditions like NEC and other immune-mediated disorders in neonates. By identifying significant knowledge gaps in neonatal SCFA research, this review helps future investigations toward understanding SCFA mechanisms specifically in neonates, potentially leading to age-appropriate therapeutic interventions. Understanding the relationship between early-life factors (such as feeding methods and microbiome development) and immune system development through SCFAs could inform public health policies and recommendations for infant nutrition and care practices.},
}

@article {pmid40307492,
year = {2025},
author = {Li, Z and Kim, E and Ko, K and Liu, A and Lee, Y and Zhang, G},
title = {Integrating microbiome and metabolome analyses to unravel the role of inulin in enhancing the meat quality and bone health of ducks.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {15194},
pmid = {40307492},
issn = {2045-2322},
support = {2019YFE0107700, NRF-2019K1A3A1A20081146//the National Key R&D program of China-Korea cooperative project/ ; 2019YFE0107700, NRF-2019K1A3A1A20081146//the National Key R&D program of China-Korea cooperative project/ ; WRS2023075//the key project for foreign experts of Shandong Province/ ; WRS2023075//the key project for foreign experts of Shandong Province/ ; NRF-2020R1A2C2004144//the National Research Foundation Grant of Korea/ ; 2023RIS-009//the Regional Innovation Strategy (RIS) through the NRF funded by the Ministry of Education/ ; SDAIT-23-05//the Forage Industrial Innovation Team Project/ ; 2022TZXD0018//the Key R&D program of Shandong Province/ ; },
abstract = {Inulin, a natural dietary fiber, has various health-promoting bioactivities. However, the impacts of dietary inulin on duck productivity and overall health remain unclear. This study investigated the effects of inulin supplementation on systemic health and its underlying mechanisms by integrating the microbiota and metabolome analyses. One hundred twenty 16-day-old male Cherry Valley ducks with similar initial body weight (BW) were randomly assigned to 20 cages, with two treatments (6 ducks/cage and 10 cages/treatment): a basal diet (CON group) or a basal diet supplemented with 25 g inulin/kg (INU group). The 18-d feeding trials demonstrated that ducks fed the inulin-supplemented diet presented significantly improved growth performance, bone health, and meat quality compared with those in the control group (P < 0.05). Additionally, inulin supplementation reshaped the intestinal microbiota, increasing diversity and the abundance of Alistipes, Ligilactobacillus, and Streptococcus (P < 0.05). Metabolome analysis revealed that inulin feeding significantly modulated 13 metabolites (P < 0.05), which were enriched primarily in health-related metabolic pathways such as taurine and hypotaurine metabolism, steroid hormone biosynthesis, and histidine metabolism. Correlation analysis revealed a positive relationship among the modulated microbes and metabolites and improved healthy parameters. Overall, inulin supplementation improved the bone and muscle health of ducks by specifically modulating key gut microbes, metabolites, and associated metabolic pathways. These findings suggest that inulin supplementation represents a feasible nutritional strategy for improving the meat quality and bone health of intensively raised ducks.},
}

@article {pmid40307477,
year = {2025},
author = {Iyengar, A and Ramadass, B and Venkatesh, S and Mak, RH},
title = {Gut microbiota-targeted therapies in pediatric chronic kidney disease: gaps and opportunities.},
journal = {Pediatric nephrology (Berlin, Germany)},
volume = {},
number = {},
pages = {},
pmid = {40307477},
issn = {1432-198X},
abstract = {Given the complex relationship between the gut microbiome and chronic kidney disease (CKD), exploring the potential role and scope of microbiota-targeted therapies in pediatric CKD is highly relevant. We aim to provide an overview of gut-targeted therapeutic strategies, including nutritional interventions (fiber, phytochemicals, fermented foods, and traditional Chinese medicines), probiotics, synbiotics, oral absorbents, and fecal microbial transplantation. Enhancing physical activity and preventing constipation are additional strategies that may promote gut microbiome health. In a uremic environment, gut microbiota-targeted therapies could potentially rebalance the gut microbiota, improve gut barrier function, decrease uremic toxin concentrations, enhance the production of short-chain fatty acids (SCFA), and reduce inflammation. While research in adult CKD patients has provided insights into these approaches, there are limited data in children with CKD. This review aims to summarize potential targeted therapies for restoring a balanced gut microbiota, emphasizing the need for studies that evaluate their effects on clinical outcomes in pediatric CKD.},
}

@article {pmid40307400,
year = {2025},
author = {Ledford, H},
title = {How to fix a gut microbiome ravaged by antibiotics.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {40307400},
issn = {1476-4687},
}

@article {pmid40307287,
year = {2025},
author = {Wu, J and He, D and Wang, Y and Liu, S and Du, Y and Wang, H and Tan, S and Zhang, D and Xie, J},
title = {An integrated transcriptome, metabolome, and microbiome dataset of Populus under nutrient-poor conditions.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {717},
pmid = {40307287},
issn = {2052-4463},
abstract = {The rhizosphere microbiota recruited by plants contributes significantly to maintaining host productivity and resisting stress. However, the genetic mechanisms by which plants regulate this recruitment process remain largely unclear. Here, we generated a comprehensive dataset, including 27 root transcriptomes, 27 root metabolomes, and 54 bulk or rhizosphere soil 16S rRNA amplicons across nine poplar species from four sections grown in nutrient-poor natural soil, along with eleven growth phenotype data. We provided a thorough description of this dataset, followed by a comprehensive co-expression network analysis example that broke down the wall of the four-way relationship between plant gene-metabolite-microbe-phenotype, thus identifying the links between plant gene expression, metabolite accumulation, growth behavior, and rhizosphere microbiome variation under nutrient-poor conditions. Overall, this dataset enhances our understanding of plant and microbe interactions, offering valuable strategies and novel insights for resolving how plants regulate rhizosphere microbial compositions and functions, thereby improving host fitness, which will benefit future research.},
}

@article {pmid40307209,
year = {2025},
author = {Song, X and Wang, Y and Wang, Y and Zhao, K and Tong, D and Gao, R and Lv, X and Kong, D and Ruan, Y and Wang, M and Tang, X and Li, F and Luo, Y and Zhu, Y and Xu, J and Ma, B},
title = {Rhizosphere-triggered viral lysogeny mediates microbial metabolic reprogramming to enhance arsenic oxidation.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {4048},
pmid = {40307209},
issn = {2041-1723},
support = {42277283//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42090060//National Natural Science Foundation of China (National Science Foundation of China)/ ; 41991334//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {The rhizosphere is a critical hotspot for metabolic activities involving arsenic (As). While recent studies indicate many functions for soil viruses, much remains overlooked regarding their quantitative impact on rhizosphere processes. Here, we analyze time-series metagenomes of rice (Oryza sativa L.)rhizosphere and bulk soil to explore how viruses mediate rhizosphere As biogeochemistry. We observe the rhizosphere favors lysogeny in viruses associated with As-oxidizing microbes, with a positive correlation between As oxidation and the prevalence of these microbial hosts. Moreover, results demonstrate these lysogenic viruses enrich both As oxidation and phosphorus co-metabolism genes and mediated horizontal gene transfers (HGTs) of As oxidases. In silico simulation with genome-scale metabolic models (GEMs) and in vitro validation with experiments estimate that rhizosphere lysogenic viruses contribute up to 25% of microbial As oxidation. These findings enhance our comprehension of the plant-microbiome-virome interplay and highlight the potential of rhizosphere viruses for improving soil health in sustainable agriculture.},
}

@article {pmid40307181,
year = {2025},
author = {Rathbun, KP and Sole, ML and Yooseph, S and Xie, R and Bourgault, AM and Talbert, S},
title = {Oral Microbiome Changes During Hospitalization in Older Adults Not Receiving Mechanical Ventilation.},
journal = {American journal of critical care : an official publication, American Association of Critical-Care Nurses},
volume = {34},
number = {3},
pages = {208-217},
doi = {10.4037/ajcc2025470},
pmid = {40307181},
issn = {1937-710X},
abstract = {BACKGROUND: Oral bacteria can be pathogenic and may change during hospitalization, potentially increasing risk for complications for older adults, including residents of skilled nursing facilities (SNFs).

OBJECTIVES: To compare the oral microbiome at hospital admission by prehospital residence (SNF vs home) in older adults not receiving mechanical ventilation and to assess changes in their oral microbiome during hospitalization.

METHODS: This prospective, observational study included 46 hospitalized adults (≥65 years old) not receiving mechanical ventilation, enrolled within 72 hours of hospitalization (15 admitted from SNF, 31 from home). Oral health was assessed with the Oral Health Assessment Tool at baseline and days 3, 5, and 7. Genomic DNA was extracted from unstimulated oral saliva specimens for microbiome profiling using 16S ribosomal RNA sequencing. Taxonomic composition, relative abundance, α-diversity (Shannon Index), and β-diversity (Bray-Curtis dissimilarity) of bacterial communities were determined.

RESULTS: Most patients were female (70%) and White (74%) or Hispanic (11%). Mean age was 78.7 years. More patients admitted from SNFs than from home had cognitive impairment (P < .001), delirium (P = .01), frailty (P < .001), and comorbidities (P = .04). Patients from SNFs had more oral bacteria associated with oral disease, lower α-diversity (P < .001), and higher β-diversity (P = .01). In the 28 study completers, α-diversity altered over time (P < .001). A significant interaction was found between groups after adjusting for covariates (P < .001).

CONCLUSIONS: Hospitalized older adults admitted from SNFs experience oral microbial and oral health disparities.},
}

@article {pmid40307095,
year = {2025},
author = {Zhang, D and Gao, JT and Zhou, SG},
title = {Microbial electrotaxis: rewiring environmental microbiomes.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2025.04.005},
pmid = {40307095},
issn = {1878-4380},
abstract = {Electric fields in sediments and soils are critical yet overlooked drivers of microbial ecology. This review examines the importance of electrotaxis in shaping microbial community dynamics and ecology models, surpassing traditional frameworks centered on chemotaxis. We analyze evidence that electric field gradients influence microbial community structure, function, and biogeochemical cycles in natural environments. Current mechanistic models, primarily based on eukaryotic systems, insufficiently explain bacterial electrotactic responses, necessitating new conceptual frameworks that integrate electrochemical and biological perspectives. We also evaluate its applications in environmental and microbiome engineering, with future research recommendations and methodologies in electrotaxis research. This synthesis aims to establish electrotaxis as an essential consideration in microbial ecology, presenting both challenges and opportunities for advancing our understanding of microbial ecosystems.},
}

@article {pmid40306604,
year = {2025},
author = {Lee, SH and Han, C and Shin, C},
title = {IUPHAR Review: Microbiota-Gut-Brain Axis and its role in Neuropsychiatric Disorders.},
journal = {Pharmacological research},
volume = {},
number = {},
pages = {107749},
doi = {10.1016/j.phrs.2025.107749},
pmid = {40306604},
issn = {1096-1186},
abstract = {The human gut microbiome, composed of a vast array of microorganisms that have co-evolved with humans, is crucial for the development and function of brain systems. Research has consistently shown bidirectional communication between the gut and the brain through neuronal, endocrine, and immunological, and chemical pathways. Recent neuroscience studies have linked changes in the microbiome and microbial metabolites to various neuropsychiatric disorders such as autism, depression, anxiety, schizophrenia, eating disorders, and neurocognitive disorders. Novel metagenome-wide association studies have confirmed these microbiome variations in large samples and expanded our understanding of the interactions between human genes and the gut microbiome. The causal relationship between gut microbiota and neuropsychiatric disorders is being elucidated through the establishment of large cohort studies incorporating microbiome data and advanced statistical techniques. Ongoing animal and human studies focused on the microbiota-gut-brain axis are promising for developing new prevention and treatment strategies for neuropsychiatric conditions. The scope of these studies has broadened from microbiome-modulating therapies including prebiotics, probiotics, synbiotics and postbiotics to more extensive approaches such as fecal microbiota transplantation. Recent systematic reviews and meta-analyses have strengthened the evidence base for these innovative treatments. Despite extensive research over the past decade, many intriguing aspects still need to be elucidated regarding the role and therapeutic interventions of the microbiota-gut-brain axis in neuropsychiatric disorders.},
}

@article {pmid40306591,
year = {2025},
author = {Syahmi Sam-On, MF and Mustafa, S and Hashim, AM and Abdul Malek, AZ},
title = {Probiogenomic insights into Bacillus velezensis MFSS1 for controlling aquaculture pathogens.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {107645},
doi = {10.1016/j.micpath.2025.107645},
pmid = {40306591},
issn = {1096-1208},
abstract = {Bacillus velezensis MFSS1 (previously known as B. subtilis FS6) was reported to have good probiotic criteria and antibacterial activity against Vibrio spp. and Aeromonas spp., through phenotypic analysis. However, whole genome sequencing is required for commercialising a new probiotic, especially due to reports on probiotics that can cause horizontal gene transfer towards the host microbiome. Therefore, this study aims to investigate the comprehensive genomic characteristics of B. velezensis MFSS1, focusing on its antimicrobial genes against aquaculture pathogens, its probiotic traits, and safety assessment. The bacterial genome was sequenced using Oxford Nanopore sequencing, resulting in 7 contigs with a total length of 3,914,361 base pairs and an average G+C content of 46.58%. The analysis using ContEst16S and average nucleotide identity revealed that the bacterium previously reported as B. subtilis is actually B. velezensis. Additionally, secondary metabolites against pathogens were predicted using the antiSMASH website, which identified eight secondary metabolites: Bacillibactin, Bacilysin, Surfactin, Difficidin, Fengycin, Bacillaene, Macrolactin H, and Plantazolicin. Furthermore, several probiotic markers were detected, functioning in acid tolerance, bile salt tolerance, adhesion, osmotic stress, and intestinal persistence during the delivery of the bacteria to the host. Interestingly, the in silico safety assessment of the bacterium revealed a lack of 96 antibiotic resistance genes and confirmed it as non-pathogenic to humans, compared with genomic bacteria from ATCC. The study indicates that B. velezensis MFSS1 is a good probiotic through genomic analysis and can be commercialised to control aquaculture pathogens and reduce reliance on antibiotics.},
}

@article {pmid40306553,
year = {2025},
author = {Ladas, EJ and Collier, W and Park, H and Auletta, JJ and Dvorak, CC and August, A and Esbenshade, AJ and Bhatia, M and Fisher, BT and Levine, JE and Pollock, BH and Uhlemann, AC and Verneris, MR and Walters, M and Yu, L and Nieder, M},
title = {A randomized clinical trial evaluating Lactiplantibacillus plantarum for the prevention of GI aGvHD: A Report from the Children's Oncology Group (ACCL1633).},
journal = {Transplantation and cellular therapy},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jtct.2025.04.009},
pmid = {40306553},
issn = {2666-6367},
abstract = {Gastrointestinal (GI) acute graft-versus-host disease (aGvHD) is a leading cause of non-relapse mortality following allogeneic hematopoietic cell transplant (alloHCT). Previous studies have suggested that the intestinal microbiome may influence the risk of GI aGvHD. We performed a Phase 3, randomized, placebo-controlled clinical trial to examine the effect of L. plantarum 299v (LBP 299v) in preventing GI aGvHD. Participants (N=161 evaluable participants) received LBP 299v or placebo from the start of conditioning therapy to 56 days post alloHCT (D56). Blood, stool, and clinical data were collected until 120 days post-transplant (D120). The D120 cumulative incidences of stages 1-4 GI aGvHD were 16% and 15% (P=0.54), and overall grades 2-4 aGvHD were 26% and 29% (P=0.95), LBP 299v and placebo groups, respectively. No patients developed L. plantarum bacteremia and no difference in serious adverse events was reported (P=1.00). Administration of LBP 299v was associated with increased microbial diversity at D0 (P=0.02) and reduced mucosal barrier injury at D7 (P =0.02). Microbial signatures significantly differed between the groups; however, this was not associated with the investigated clinical outcomes. We conclude that administration of LBP 299v is safe among children and adolescents undergoing alloHCT but ineffective at preventing GI aGvHD.},
}

@article {pmid40306360,
year = {2025},
author = {Raza, MF and Li, W},
title = {Biogenic amines in honey bee cognition: Neurochemical pathways and stress impacts.},
journal = {Current opinion in insect science},
volume = {},
number = {},
pages = {101376},
doi = {10.1016/j.cois.2025.101376},
pmid = {40306360},
issn = {2214-5753},
abstract = {Honey bees, as indispensable pollinators, rely on sophisticated neuromodulatory networks to regulate learning, memory, and social behaviours, all essential for colony function, ecosystem stability and global agricultural systems. Biogenic amines octopamine, dopamine, serotonin, and tyramine are key modulators of these cognitive and behavioural processes, regulating foraging efficiency, navigational precision, and division of labour. However, we argue that anthropogenic stressors, including pesticides, pollutants, heavy metals and microbiome dysbiosis disrupt aminergic pathways by impairing neurotransmitter synthesis and neuronal signaling, leading to maladaptive behaviors and colony collapse. Recent discoveries expand this paradigm, revealing those biogenic amines in floral nectar act as exogenous neurochemicals, potentially altering pollinator behavior; however, their interaction with agrochemicals remains underexplored. While most studies focus on Apis mellifera, we caution that cautious extrapolation to wild and solitary bees is critical, given the evolutionary conservation of aminergic signaling across insect taxa. Cognitive deficits observed in managed honeybees likely extend to wild pollinators, threatening pollination network resilience and food security. To address these gaps, we advocate for CRISPR-based neurogenetic tools and multi-omics approaches to dissect stress susceptibility and BA regulation. Integrating neurobiology, ecotoxicology, and conservation science is imperative to develop precision strategies that mitigate anthropogenic threats, safeguard biodiversity, and stabilize global agriculture.},
}

@article {pmid40306274,
year = {2025},
author = {Kim, SH and White, Z and Gainullina, A and Kang, S and Kim, J and Dominguez, JR and Choi, Y and Cabrera, I and Plaster, M and Takahama, M and Czepielewski, RS and Yeom, J and Gunzer, M and Hay, N and David, O and Chevrier, N and Sano, T and Kim, KW},
title = {IL-10 sensing by lung interstitial macrophages prevents bacterial dysbiosis-driven pulmonary inflammation and maintains immune homeostasis.},
journal = {Immunity},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.immuni.2025.04.004},
pmid = {40306274},
issn = {1097-4180},
abstract = {Crosstalk between the immune system and the microbiome is critical for maintaining immune homeostasis. Here, we examined this communication and the impact of immune-suppressive IL-10 signaling on pulmonary homeostasis. We found that IL-10 sensing by interstitial macrophages (IMs) is required to prevent spontaneous lung inflammation. Loss of IL-10 signaling in IMs initiated an inflammatory cascade through the activation of classical monocytes and CD4[+] T cell subsets, leading to chronic lung inflammation with age. Analyses of antibiotic-treated and germ-free mice established that lung inflammation in the animals lacking IL-10 signaling was triggered by commensal bacteria. 16S rRNA sequencing revealed Delftia acidovorans and Rhodococcus erythropolis as potential drivers of lung inflammation. Intranasal administration of these bacteria or transplantation of human fecal microbiota elicited lung inflammation in gnotobiotic Il10-deficient mice. These findings highlight that IL-10 sensing by IMs contributes to pulmonary homeostasis by preventing lung inflammation caused by commensal dysbiosis.},
}

@article {pmid40306271,
year = {2025},
author = {Pan, X and Yue, Y and Zhao, F and Song, T and Xu, B and Li, Z and Qi, Z and Yu, J and Cao, H and Yu, M and Shen, Q and Xu, J and Xiong, W and Liu, Y},
title = {Rhizosphere microbes facilitate the break of chlamydospore dormancy and root colonization of rice false smut fungi.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2025.04.005},
pmid = {40306271},
issn = {1934-6069},
abstract = {Dormant chlamydospore germination of fungal pathogens directly affects disease occurrence and severity. The rice false smut (RFS) fungus Ustilaginoidea virens produces abundant chlamydospores, but their germination process and roles in plant infection remain unclear. Here, we found that soil-borne chlamydospores are a major source of U. virens inoculum and impact RFS development. Rhizosphere microbiome analysis of high-susceptibility (HS) and low-susceptibility (LS) rice varieties revealed that HS varieties recruited bacteria from the Sphingomonadaceae family, thereby facilitating the breakdown of chlamydospore dormancy through secreted exopolysaccharides. Hyphae formed by germinating chlamydospores grew on the root surfaces, invaded the root cortex, and grew intercellularly, potentially spreading further to aboveground plant parts. Furthermore, field experiments confirmed that treating the root with 30% prothioconazole and 20% zinc thiazole effectively reduced RFS incidence. Overall, these findings enhance our understanding of chlamydospore germination in natural environments and inform strategies for disease control.},
}

@article {pmid40306093,
year = {2025},
author = {Pires, PGDS and Cardinal, KM and Elnesr, SS and Peripolli, V and Santos, BRCD and Moraes, PO},
title = {Non-invasive biomarkers for monitoring intestinal health in broilers - A systematic review.},
journal = {Research in veterinary science},
volume = {190},
number = {},
pages = {105669},
doi = {10.1016/j.rvsc.2025.105669},
pmid = {40306093},
issn = {1532-2661},
abstract = {This systematic review aimed to identify and evaluate non-invasive biomarkers for assessing gut health in broilers, following PRISMA guidelines and using the PICO strategy. A comprehensive search was conducted in Web of Science, Scopus, and PubMed for papers written in English, Portuguese, and Spanish. After screening 1196 papers, 21 studies met the inclusion criteria and were included in the review. The studies, primarily conducted in Europe, Oceania, and North America, were published between 2003 and 2024. The review highlighted the intestinal microbiota as the most studied non-invasive biomarker, using excreta, cloacal swabs, poultry litter, and poultry dust as sample sources. Poultry litter and dust were identified as promising non-invasive alternatives for assessing gut microbiota, with excreta being the most commonly used sample type. Biomarkers like ovotransferrin, lipocalin-2, and calprotectin are under investigation for broiler gut health assessment. Cecal samples were frequently used as a gold standard for comparison. The choice of reference databases, such as SILVA and Greengenes, varied among studies, which may have influenced taxonomic classification and microbial group abundance. Methodological quality varied across studies, with a mix of observational and experimental designs. Many studies involved comparative analyses related to dietary and sanitary challenges, though inconsistencies in reporting diet composition and performance data were observed. In conclusion, many non-invasive biomarkers are under investigation for broiler gut health assessment, but challenges remain in validating these markers due to the complexity of the gut ecosystem. These challenges emphasize the need for rigorous study design, thorough data collection, and standardized protocols.},
}

@article {pmid40306083,
year = {2025},
author = {Urbaniak, M and Mierzejewska-Sinner, E and Wyrwicka-Drewniak, A and Tsuzuki, H and Yoshida, M and Chitose, N and Chujo, M and Azuma, S and Kawahara, S and Inui, H},
title = {Fungicide-mediated modulation of dieldrin uptake in zucchini: effects on pollutant reduction, plant physiology, and endophytic microbiome.},
journal = {The Science of the total environment},
volume = {980},
number = {},
pages = {179498},
doi = {10.1016/j.scitotenv.2025.179498},
pmid = {40306083},
issn = {1879-1026},
abstract = {The contamination of agricultural soils with organochlorine pesticides (OCPs), such as dieldrin, poses significant risks to consumer health worldwide. This issue is particularly significant in crops like zucchini (Cucurbita pepo), which effectively accumulate hydrophobic organic pollutants. There is hence a pressing need to develop strategies to reduce OCP uptake in cucurbits. This study evaluated the efficacy of two fungicides, Benomyl (Be) and Daconil (Da), in reducing dieldrin (Di) accumulation in Cucurbita pepo cv. Atena Polka. Di concentrations were measured in soil and plant tissues, and bioconcentration factors (BCFs) were calculated to assess soil to plant pollutant transfer. It also assessed the effects of Di, and Di with Be or Da on plant health and endomicrobiome functional diversity. The applied fungicides significantly lowering pollutant levels in the crop. Initial soil Di level was 12.5 μg/kg, decreasing to 7.88 μg/kg after incubation. However, fungicide treatments resulted in higher residual Di levels in soil: 10.65 μg/kg for Di + Be and 8.68 μg/kg for Di + Da. Conversely, Di accumulation fell in the aboveground plant tissues, with Be reducing accumulation by 31 % and Da by 13 %. The role of major latex-like proteins (MLPs) in dieldrin binding and transport was also examined. Recombinant CpMLP-AP1 from Atena Polka showed strong dieldrin-binding affinity, confirming the important role of MLPs in OCP uptake. The fungicide treatments were found to improve physiological parameters, insofar that they reduced lipid peroxidation and oxidative stress markers, and increased chlorophyll content and biomass. They also influenced the functional diversity of endophytic microbiota, indicating a broader impact on plant-microbe interactions. This study proposes promising strategies for reducing OCP contamination in cucurbits, improving food safety and crop production, while advancing our understanding of molecular and ecological mechanisms in pollutant management.},
}

@article {pmid40305979,
year = {2025},
author = {Yi, K and Huang, Y and Jiang, Y and Zhou, L},
title = {Causal relationship between gut microbiota and laryngeal cancer: a mendelian randomization analysis.},
journal = {Brazilian journal of otorhinolaryngology},
volume = {91},
number = {4},
pages = {101634},
doi = {10.1016/j.bjorl.2025.101634},
pmid = {40305979},
issn = {1808-8686},
abstract = {OBJECTIVE: Laryngeal cancer incidence is rising globally; the role of gut microbiota remains underexplored. This study aimed to establish a causal link between gut microbiota and laryngeal cancer to inform preventive and therapeutic strategies.

METHODS: Gut microbiota data from GWAS conducted by the MiBioGen consortium served as the exposure variable, with laryngeal cancer as the outcome variable. the exposure variable and the outcome variable were analyzed using Mendelian Randomization. The primary method was Inverse Variance Weighted analysis, with heterogeneity and pleiotropy assessed through Cochran's Q test, MR-Egger regression, and MR-PRESSO.

RESULTS: In the study, we identified five bacterial taxa with potential causal relationships with laryngeal cancer risk: Higher levels of Clostridiaceae1 (OR = 0.9993, 95% CI 0.9986-0.9999, p = 0.0463) and Turicibacter (OR = 0.9995, 95% CI 0.9989-0.9999, p = 0.0384) were linked to reduced cancer risk, while Mollicutes RF9 (OR = 1.0010, 95% CI 1.0003-1.0016, p = 0.0027), Euryarchaeota (OR = 1.0004, 95% CI 1.0001-1.0007, p = 0.0234), and Cyanobacteria (OR = 1.0005, 95% CI 1.0000-1.0009, p = 0.0464) were associated with increased risk.

CONCLUSION: Our findings suggest a causal relationship between gut microbiota composition and laryngeal cancer risk. Clostridiaceae1 and Turicibacter may play a protective role, while Mollicutes RF9, Euryarchaeota, and Cyanobacteria could contribute to increased cancer susceptibility. These insights highlight potential microbiome-based strategies for early detection, prevention, and therapeutic intervention in laryngeal cancer.

LEVEL OF EVIDENCE: Level 5.},
}

@article {pmid40305906,
year = {2025},
author = {Xie, X and Niyongabo Turatsinze, A and Liu, Y and Chen, G and Yue, L and Ye, A and Zhou, Q and Zhang, Z and Wang, Y and Zhang, Y and Jin, W and Li, Z and Sessitsch, A and Brader, G and Wang, R},
title = {Bioinoculant substitution enhances rhizosphere soil quality and maize growth by modulating microbial communities and host gene expression in alkaline soils.},
journal = {Microbiological research},
volume = {297},
number = {},
pages = {128194},
doi = {10.1016/j.micres.2025.128194},
pmid = {40305906},
issn = {1618-0623},
abstract = {The application of plant growth-promoting bacteria (PGPB) as bioinoculants is widely recognized for improving crop yields and soil fertility. However, the precise mechanisms underlying their impact on rhizosphere soil quality and crop productivity remain insufficiently understood. This study elucidates how a solid bioinoculant, comprising Bacillus velezensis FZB42 and attapulgite clay, enhances rhizosphere soil quality and maize (Zea mays) growth in nutrient-deficient alkaline calcareous soils. Pot experiments reveal that bioinoculant application promotes extensive root colonization under nitrogen-deficient conditions, with significantly higher colonization rates observed in the half-nitrogen (HN) and zero-nitrogen (ZN) treatments compared to full-nitrogen conditions. Notably, bioinoculant application in ZN and HN significantly increases phosphorus availability and soil quality in the rhizosphere. Furthermore, maize growth parameters, including plant height, stem diameter, and kernel yield, are markedly enhanced, with optimal biomass accumulation achieved under HN conditions. High-throughput sequencing of rhizosphere microbiomes uncovers significant shifts in microbial community composition, with enrichment of key taxa involved in nutrient cycling and plant-microbe interactions. Transcriptomic analysis of maize tissues demonstrates the upregulation of genes associated with nutrient transport, photosynthesis, fatty acid biosynthesis, and kernel development, with a pronounced enrichment in metabolic pathways linked to growth and productivity. Structural equation modeling indicates that increased microbial diversity and gene expression collectively account for 69 % of the variance in the soil quality index and 45 % of the variance in maize yield. These findings provide critical mechanistic insights into the role of solid bioinoculant in enhancing soil fertility and crop performance, highlighting their potential as a sustainable agricultural strategy for improving productivity in low-fertility alkaline soils.},
}

@article {pmid40305679,
year = {2025},
author = {Morel-Journel, T and Lehtinen, S and Cotto, O and Amia, R and Dion, S and Figueroa, C and Martinson, JNV and Ralaimazava, P and Clermont, O and Duval, X and Nowrouzian, FL and Walk, ST and Denamur, E and Blanquart, F},
title = {Residence-colonization trade-off and niche differentiation enable coexistence of Escherichia coli phylogroups in healthy humans.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf089},
pmid = {40305679},
issn = {1751-7370},
abstract = {Despite abundant literature on pathogenicity and virulence of the opportunistic pathogen Escherichia coli, much less is known about its ecological and evolutionary dynamics as a commensal. Based on two detailed longitudinal datasets on the gut microbiota of healthy adults followed for months to years in France and the USA, we identified a robust trade-off between the ability to establish in a new host (colonization) and to remain in the host (residence). Major E. coli lineages (phylogroups or subgroups) exhibited similar fitness but diverse strategies, from strong colonisers residing few days in the gut to poor colonisers residing for years. Strains with the largest number of extra-intestinal virulence associated genes and highest pathogenicity also resided for longest in hosts. Furthermore, the residence of a strain was more strongly reduced when it competed with other strains from the same phylogroup than from another phylogroup, suggesting niche differentiation between phylogroups. Based on a discrete-state Markov model developed to describe E. coli dynamics in a host population, we found that the trade-off and niche differentiation acted together as equalizing and stabilizing mechanisms allowing phylogroups to coexist over long periods of time. Our model also predicted that external disturbances may disproportionately affect resident strains, such as the extraintestinal pathogenic ones of subgroup B2.3. Our results call for further studies outside high-income countries, where the prevalence of this phylogroup is much lower. More generally, the trade-off between colonization and persistence could play a role in the diversification of other bacterial species of the microbiome.},
}

@article {pmid40305669,
year = {2025},
author = {Snyder, ME and Haidar, G and Li, K and Kitsios, GD and Fitch, A and Zemke, A and Iasella, C and Musgrove, C and Bukhari, M and Methé, BA and McDyer, JF and Morris, A},
title = {Donor Lung Prevotella Predicts Favorable Early FEV1 Trajectory Following Lung Transplantation.},
journal = {American journal of respiratory cell and molecular biology},
volume = {},
number = {},
pages = {},
doi = {10.1165/rcmb.2024-0441LE},
pmid = {40305669},
issn = {1535-4989},
}

@article {pmid40305456,
year = {2025},
author = {Hoogendijk, R and Geurts, M and van der Lugt, J},
title = {Correlative Studies In Central Nervous System Tumors Clinical Trials: The Emerging Role Of Microbiome Research.},
journal = {Neuro-oncology},
volume = {},
number = {},
pages = {},
doi = {10.1093/neuonc/noaf111},
pmid = {40305456},
issn = {1523-5866},
}

@article {pmid40305442,
year = {2025},
author = {Cayrou, C and Silver, K and Owen, L and Dunlop, J and Laird, K},
title = {Domestic laundering of healthcare textiles: Disinfection efficacy and risks of antibiotic resistance transmission.},
journal = {PloS one},
volume = {20},
number = {4},
pages = {e0321467},
doi = {10.1371/journal.pone.0321467},
pmid = {40305442},
issn = {1932-6203},
mesh = {*Disinfection/methods ; *Textiles/microbiology ; Humans ; *Laundering/methods ; Microbial Sensitivity Tests ; Detergents/pharmacology ; *Cross Infection/prevention & control/microbiology ; *Drug Resistance, Microbial ; Staphylococcus aureus/drug effects/genetics ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial ; United Kingdom ; Microbiota/drug effects ; Decontamination/methods ; Klebsiella pneumoniae/drug effects ; Pseudomonas aeruginosa/drug effects ; Enterococcus faecium/drug effects ; },
abstract = {Hospital-acquired infections (HAIs) and antimicrobial resistance (AMR) are a major public health concern, with the evidence base for the potential role of textiles as fomites in microbial transmission growing. In the UK, domestic laundering machines (DLMs) are commonly used to clean healthcare worker uniforms, raising concerns about their effectiveness in microbial decontamination and role in AMR development. This study aimed to evaluate DLMs' ability to decontaminate microorganisms and their potential impact on AMR. The performance of six DLMs was assessed using Enterococcus faecium bioindicators under various wash cycles and detergent conditions. Shotgun metagenomics was used to analyse the microbiome and resistome of DLMs. The minimum inhibitory concentrations of domestic detergents were determined for Staphylococcus aureus, Klebsiella pneumoniae, and Pseudomonas aeruginosa, and detergent tolerance and antibiotic cross-resistance were assessed. Results showed only 50% (3/6) of DLMs achieved sufficient decontamination (≥5 log10 CFU reduction) at 60°C during full-length cycles, with rapid cycles performing inconsistently. Microbiome analysis revealed the presence of potentially pathogenic bacteria (e.g., Mycobacterium sp. Pseudomonas sp. and Acinetobacter sp.) and antibiotic resistance genes, including efflux pumps and target modification genes. Detergent tolerance assays showed increased bacterial tolerance to detergents, with cross-resistance to antibiotics observed in S. aureus and K. pneumoniae, including carbapenem and β-lactam groups. Whole genome sequencing identified mutations in genes encoding efflux pumps in S. aureus (MrgA) and K. pneumoniae (AcrB) after detergent exposure, which could impact efflux pump function. Findings suggest domestic laundering of healthcare uniforms may be insufficient for decontamination, posing risks for HAI transmission and AMR. Revising laundering guidelines to ensure effective DLM performance, detergent efficacy, and considering alternatives like onsite/industrial laundering are crucial to enhancing patient safety and controlling AMR in healthcare settings.},
}

*Disinfection/methods
*Textiles/microbiology
Humans
*Laundering/methods
Microbial Sensitivity Tests
Detergents/pharmacology
*Cross Infection/prevention & control/microbiology
*Drug Resistance, Microbial
Staphylococcus aureus/drug effects/genetics
Anti-Bacterial Agents/pharmacology
*Drug Resistance, Bacterial
United Kingdom
Microbiota/drug effects
Decontamination/methods
Klebsiella pneumoniae/drug effects
Pseudomonas aeruginosa/drug effects
Enterococcus faecium/drug effects

@article {pmid40305392,
year = {2025},
author = {Niu, HY and Zhang, J and Huang, HJ and Sun, XW and Chen, HY and Wang, XM and Liu, C and Bi, MX and Liu, SJ},
title = {Flavonifractor porci sp. nov. and Flintibacter porci sp. nov., two novel butyrate-producing bacteria of the family Oscillospiraceae.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {75},
number = {4},
pages = {},
doi = {10.1099/ijsem.0.006767},
pmid = {40305392},
issn = {1466-5034},
mesh = {RNA, Ribosomal, 16S/genetics ; Fatty Acids/chemistry/analysis ; *Phylogeny ; Animals ; DNA, Bacterial/genetics ; Bacterial Typing Techniques ; Swine ; Base Composition ; Sequence Analysis, DNA ; *Butyrates/metabolism ; *Manure/microbiology ; *Clostridiales/classification/isolation & purification/genetics/metabolism ; Nucleic Acid Hybridization ; Fermentation ; },
abstract = {Two Gram-stain-negative, strictly anaerobic, non-motile, non--spore-forming and rod-shaped bacterial strains, namely, P01024[T] and P01025[T], were isolated from piglet manure. The strains P01024[T] and P01025[T] fermented glucose to acetate and butyrate. The major cellular fatty acids (>10.0%) of strain P01024[T] were C14 : 0, C16 : 0 and summed feature 9 (iso-C17:1 ω9c and/or 10-Methyl-C16:0) and of strain P01025[T] were C14 : 0, C16 : 0 and summed feature 3 (C16 : 1 ω6c and/or C16 : 1 ω7c). Analysis of 16S rRNA gene sequences indicated that strains P01024[T] and P01025[T] belonged to the family Oscillospiraceae. The strain P01024[T] showed high identities of 16S rRNA genes to type species Flavonifractor plautii ATCC 29863[T] (96.64%). The highest percentages of conserved protein (POCP) value between strain P01024[T] and Flavonifractor plautii ATCC 29863[T] was 59.84%. The average nt identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain P01024[T] and Flavonifractor plautii ATCC 29863[T] were 79.51% and 23.80%, respectively, supporting that strain P01024[T] represented a novel species of the genus Flavonifractor. Strain P01025[T] showed high identities of 16S rRNA genes to the type species Flintibacter butyricus BLS21[T] (95.87%). The highest POCP and AAI (average aa identity) values of strains P01025[T] to Flintibacter hominis New-19[T] were 53.02% and 73.11%, respectively. The ANI and dDDH values between strains P01025[T] and Flintibacter hominis New-19[T] were 75.44% and 23.40%, respectively, supporting that strain P01025[T] represented a novel species in the genus Flintibacter. The calculated G+C molar contents for strains P01024[T] and P01025[T] were 58.43 and 56.44 mol%, respectively. Together with phenotypic features, we concluded that strains P01024[T] and P01025[T] represented novel species in the genera Flavonifractor and Flintibacter of the family Oscillospiraceae, respectively, for which the names Flavonifractor porci sp. nov. (type strain P01024[T]=CGMCC 1.18055[T]=KCTC 25793[T]) and Flintibacter porci sp. nov. (type strain P01025[T]=CGMCC 1.18060[T]=KCTC 25794[T]) are proposed.},
}

RNA, Ribosomal, 16S/genetics
Fatty Acids/chemistry/analysis
*Phylogeny
Animals
DNA, Bacterial/genetics
Bacterial Typing Techniques
Swine
Base Composition
Sequence Analysis, DNA
*Butyrates/metabolism
*Manure/microbiology
*Clostridiales/classification/isolation & purification/genetics/metabolism
Nucleic Acid Hybridization
Fermentation

@article {pmid40305369,
year = {2025},
author = {Zhai, D and Lu, H and Liu, S and Liu, J and Zhang, W and Wu, J and Li, J and Bai, R and Yan, F and Zhao, C},
title = {Fungal Warriors: Effects of Beauveria bassiana and Purpureocillium lilacinum on CCYV-Carrying Whiteflies.},
journal = {Biomolecules},
volume = {15},
number = {4},
pages = {},
doi = {10.3390/biom15040593},
pmid = {40305369},
issn = {2218-273X},
support = {30501338//Young Talents in Henan Agricultural University/ ; },
mesh = {Animals ; *Beauveria/physiology/pathogenicity ; *Hemiptera/virology/microbiology ; *Hypocreales/physiology/pathogenicity ; Pest Control, Biological/methods ; *Crinivirus/pathogenicity ; Plant Diseases/virology ; Biological Control Agents/pharmacology ; },
abstract = {Bemisia tabaci is a major agricultural pest that affects both greenhouse and field crops by feeding on plant sap, which impairs plant growth, and by secreting honeydew, promotes sooty mold growth that further reduces photosynthesis. Additionally, these insects are vectors for viruses such as the cucurbit chlorotic yellows virus (CCYV), which causes significant damage to cucurbit crops. Traditional chemical pesticide treatments have limitations, including the development of resistance, harm to non-target organisms, and environmental contamination. Traditional chemical pesticides have limitations when it comes to controlling plants infested by CCYV and whitefly. However, the underlying reasons for these limitations remain unclear, as does the impact of entomopathogenic fungi on whitefly responses. This study explores the potential of using biological control agents, specifically Beauveria bassiana and Purpureocillium lilacinum, to manage whitefly populations and control CCYV transmission. Laboratory experiments were conducted to evaluate the pathogenicity of these fungi on non/viruliferous whitefly. The results indicated that both fungi effectively reduced whitefly populations, with B. bassiana showing particularly strong adverse effects. Whiteflies infected with CCYV exhibited a higher LC50 to B. bassiana and P. lilacinum. Furthermore, bio-pesticides significantly altered the bacterial microbiome dynamics of the whitefly. Interestingly, CCYV increased the susceptibility of whiteflies to entomopathogenic fungus. The findings suggest that these biocontrol agents offer a sustainable alternative to chemical pesticides. Our study unraveled a new horizon for the multiple interaction theories among bio-pesticides-insects-symbionts-viruses.},
}

Animals
*Beauveria/physiology/pathogenicity
*Hemiptera/virology/microbiology
*Hypocreales/physiology/pathogenicity
Pest Control, Biological/methods
*Crinivirus/pathogenicity
Plant Diseases/virology
Biological Control Agents/pharmacology

@article {pmid40305310,
year = {2025},
author = {Wróblewska, J and Złocińska, H and Wróblewski, M and Nuszkiewicz, J and Woźniak, A},
title = {The Role of Vitamins in Pediatric Urinary Tract Infection: Mechanisms and Integrative Strategies.},
journal = {Biomolecules},
volume = {15},
number = {4},
pages = {},
doi = {10.3390/biom15040566},
pmid = {40305310},
issn = {2218-273X},
mesh = {Humans ; *Urinary Tract Infections/drug therapy/prevention & control/microbiology ; Child ; *Vitamins/therapeutic use/pharmacology ; Antioxidants/therapeutic use/pharmacology ; Vitamin D/therapeutic use ; Anti-Bacterial Agents/therapeutic use ; Ascorbic Acid/therapeutic use ; Vitamin A/therapeutic use ; Vitamin E/therapeutic use ; },
abstract = {Urinary tract infections (UTI) are among the most frequent bacterial infections in children, representing a significant cause of morbidity with potential long-term complications, including renal scarring and chronic kidney disease. This review explores the multifaceted roles of vitamins A, D, E, and C in the prevention and management of pediatric UTI. Vitamin A supports mucosal barrier integrity and immune modulation, reducing pathogen adhesion and colonization. Vitamin C exhibits antioxidant and antimicrobial properties, acidifying urine to inhibit bacterial growth and enhancing the efficacy of antibiotics. Vitamin D strengthens innate immunity by promoting antimicrobial peptide production, such as cathelicidins, and improves epithelial barrier function, while vitamin E mitigates oxidative stress, reducing renal inflammation and tissue damage. The interplay between oxidative stress, immune response, and nutritional factors is emphasized, highlighting the potential of these vitamins to restore antioxidant balance and prevent renal injury. Complementary strategies, including probiotics and phytotherapeutic agents, further enhance therapeutic outcomes by addressing microbiome diversity and providing additional antimicrobial effects. While these approaches show promise in mitigating UTI recurrence and reducing dependence on antibiotics, evidence gaps remain regarding optimal dosing, long-term outcomes, and their integration into pediatric care. By adopting a holistic approach incorporating vitamin supplementation and conventional therapies, clinicians can achieve improved clinical outcomes, support antibiotic stewardship, and reduce the risk of renal complications in children with UTI.},
}

Humans
*Urinary Tract Infections/drug therapy/prevention & control/microbiology
Child
*Vitamins/therapeutic use/pharmacology
Antioxidants/therapeutic use/pharmacology
Vitamin D/therapeutic use
Anti-Bacterial Agents/therapeutic use
Ascorbic Acid/therapeutic use
Vitamin A/therapeutic use
Vitamin E/therapeutic use

@article {pmid40305219,
year = {2025},
author = {Alves Costa Silva, C and Almonte, AA and Zitvogel, L},
title = {Oncobiomics: Leveraging Microbiome Translational Research in Immuno-Oncology for Clinical-Practice Changes.},
journal = {Biomolecules},
volume = {15},
number = {4},
pages = {},
doi = {10.3390/biom15040504},
pmid = {40305219},
issn = {2218-273X},
mesh = {Humans ; *Neoplasms/immunology/microbiology/therapy/metabolism ; *Translational Research, Biomedical ; *Microbiota ; *Gastrointestinal Microbiome/immunology ; Dysbiosis/microbiology/immunology ; },
abstract = {Growing evidence suggests that cancer should not be viewed solely as a genetic disease but also as the result of functional defects in the metaorganism, including disturbances in the gut microbiota (i.e., gut dysbiosis). The human microbiota plays a critical role in regulating epithelial barrier function in the gut, airways, and skin, along with host metabolism and systemic immune responses against microbes and cancer. Collaborative international networks, such as ONCOBIOME, are essential in advancing research equity and building microbiome resources to identify and validate microbiota-related biomarkers and therapies. In this review, we explore the intricate relationship between the microbiome, metabolism, and cancer immunity, and we propose microbiota-based strategies to improve outcomes for individuals at risk of developing cancer or living with the disease.},
}

Humans
*Neoplasms/immunology/microbiology/therapy/metabolism
*Translational Research, Biomedical
*Microbiota
*Gastrointestinal Microbiome/immunology
Dysbiosis/microbiology/immunology

@article {pmid40305008,
year = {2025},
author = {Kratschmer, C and Curiel, DT and Ciorba, MA},
title = {Gut-directed therapeutics in inflammatory bowel disease.},
journal = {Current opinion in gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1097/MOG.0000000000001099},
pmid = {40305008},
issn = {1531-7056},
abstract = {PURPOSE OF REVIEW: Tissue-directed therapies (TDTs) provide potential advantages, including improved tolerance, safety, and efficacy. This review provides a conceptual framework for understanding intestinal TDT and summarizes the current landscape of TDT in inflammatory bowel disease (IBD).

RECENT FINDINGS: Vedolizumab, a mAb targeting the gut homing α4β7 integrin, served as revolutionary proof-of-principle for the power of advanced TDT in IBD. The development of other monoclonal antibodies targeting cell adhesion molecules followed including abrilumab (α4β7), etrolizumab (β7), and ontamalimab (MAdCAM-1). MORF-057, an oral small molecule inhibitor of α4β7, is now in development for ulcerative colitis. Efforts have also been made toward gut specific JAK inhibitors. Microbiome-based therapies, including engineered probiotics, bacteriophages, and postbiotics, are gaining interest. There are also a number of innovative drug delivery methods, including engineered yeast, hydrogels, and nanoparticles, and viral-based gene therapy.

SUMMARY: Gut-targeted therapies range from novel variations on traditional drugs (i.e., mAbs and small molecules) to microbiome-based therapeutics and engineered delivery systems. They can be used alone or in combination with currently available therapies. Future directions should focus on the development of tried-and-true modalities (mAbs, small molecules) as well as the microbiome and more innovative delivery systems.},
}

@article {pmid40304791,
year = {2025},
author = {Bu, Y and Zhang, X and Xiong, Z and Li, K and Zhang, S and Lin, M and Zhao, G and Zheng, N and Wang, J and Zhao, S},
title = {Effect of red clover isoflavones on ruminal microbial composition and fermentation in dairy cows.},
journal = {Applied microbiology and biotechnology},
volume = {109},
number = {1},
pages = {107},
pmid = {40304791},
issn = {1432-0614},
support = {2022YFD1301000//National Key R&D Program of China/ ; CAAS-ZDRW202308//the Agricultural Science and Technology Innovation Program/ ; 2004DA125184G2108//State Key Laboratory of Animal Nutrition and Feeding/ ; },
mesh = {Animals ; Cattle ; *Rumen/microbiology ; *Fermentation/drug effects ; *Isoflavones/pharmacology/administration & dosage/metabolism ; *Trifolium/chemistry ; Genistein/pharmacology/administration & dosage ; *Bacteria/classification/genetics/drug effects/metabolism/isolation & purification ; Female ; Ammonia/metabolism ; Urease/metabolism ; Urea/metabolism ; *Gastrointestinal Microbiome/drug effects ; Animal Feed/analysis ; Metagenomics ; },
abstract = {Red clover isoflavones, particularly biochanin A and formononetin, are known for their benefits in enhancing feed efficiency and nitrogen utilization in ruminants. However, their specific effects on rumen fermentation and microbial diversity remain insufficiently explored. This study investigated the impacts of red clover isoflavones on rumen function and bacterial diversity in dairy cows, utilizing both in vivo and in vitro methodologies. In the in vivo study, 40 Holstein dairy cows were allocated to four groups, each receiving red clover isoflavones at doses of 0, 0.4, 0.8, and 1.6 g/kg. Rumen fluid was collected for analysis of fermentation parameters, enzyme activity, and microbial composition through shotgun metagenomic sequencing. Concurrently, an in vitro rumen fermentation trial was conducted to evaluate the effects of biochanin A and formononetin on urea hydrolysis. Results from the in vivo experiments showed that red clover isoflavones significantly decreased ammonia nitrogen (NH3-N) concentrations and urease activity in the rumen (P < 0.05). Species level metagenomic analysis indicated a reduced abundance of proteolytic and ureolytic bacteria, such as Prevotella sp002317355 and Treponema_D bryantii_C, with a corresponding increase in cellulolytic bacteria, including Ruminococcus_D sp900319075 and Ruminococcus_C sp000433635 (P < 0.05). The in vitro trial further demonstrated that biochanin A and formononetin significantly reduced urea decomposition rates (P < 0.05), with biochanin A exerting a more pronounced effect. These findings align with the observed reduction in ureolytic and proteolytic bacteria, along with an increase in cellulolytic bacteria across both trials. In conclusion, biochanin A emerged as the primary active component of red clover isoflavones, modulating urea nitrogen hydrolysis and rumen fermentation. This study substantiates previous findings and highlights the potential of red clover isoflavones for enhancing rumen microbial fermentation, offering a promising strategy for future dairy industry applications. KEY POINTS: • Red clover isoflavones inhibit urease activity to decrease the abundance of urealytic bacteria. • Biochanin A reduces ammonia nitrogen and urease activity, promoting protein efficiency. • Red clover isoflavones may improve dairy cow rumen health and nitrogen utilization.},
}

Animals
Cattle
*Rumen/microbiology
*Fermentation/drug effects
*Isoflavones/pharmacology/administration & dosage/metabolism
*Trifolium/chemistry
Genistein/pharmacology/administration & dosage
*Bacteria/classification/genetics/drug effects/metabolism/isolation & purification
Female
Ammonia/metabolism
Urease/metabolism
Urea/metabolism
*Gastrointestinal Microbiome/drug effects
Animal Feed/analysis
Metagenomics

@article {pmid40304704,
year = {2025},
author = {Burnside, M and Tang, J and Baker, JL and Merritt, J and Kreth, J},
title = {Shining Light on Oral Biofilm Fluorescence In Situ Hybridization (FISH): Probing the Accuracy of In Situ Biogeography Studies.},
journal = {Molecular oral microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/omi.12494},
pmid = {40304704},
issn = {2041-1014},
support = {DE029612//NIH-NIDCR/ ; DE029492//NIH-NIDCR/ ; DE029228//NIH-NIDCR/ ; DE028252//NIH-NIDCR/ ; },
abstract = {The oral biofilm has been instrumental in advancing microbial research and enhancing our understanding of oral health and disease. Recent developments in next-generation sequencing have provided detailed insights into the microbial composition of the oral microbiome, enabling species-level analyses of biofilm interactions. Fluorescence in situ hybridization (FISH) has been especially valuable for studying the spatial organization of these microbes, revealing intricate arrangements such as "corncob" structures that highlight close bacterial interactions. As more genetic sequence data become available, the specificity and accuracy of existing FISH probes used in biogeographical studies require reevaluation. This study examines the performance of commonly used species-specific FISH probes, designed to differentiate oral microbes within in situ oral biofilms, when applied in vitro to an expanded set of bacterial strains. Our findings reveal that the specificity of several FISH probes is compromised, with cross-species hybridization being more common than previously assumed. Notably, we demonstrate that biogeographical associations within in situ oral biofilms, particularly involving Streptococcus and Corynebacterium, may need to be reassessed to align with the latest metagenomic data.},
}