@article {pmid41106704,
year = {2025},
author = {Heckmann, ND and Culler, M and Atallah, LM and Mont, MA and Lieberman, JR and Parvizi, J},
title = {Emerging Concepts in Periprosthetic Joint Infection Research: Infection Recurrence and Microbe Persistence.},
journal = {The Journal of arthroplasty},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.arth.2025.10.033},
pmid = {41106704},
issn = {1532-8406},
abstract = {Recurrent periprosthetic joint infection (PJI) is a highly morbid complication following total joint arthroplasty (TJA). Despite appropriate medical and surgical management with targeted antimicrobial therapies, many patients who suffer from a PJI experience clinically relevant episodes of recurrence. Though the majority of these recurrent infections are due to microbes that are different from the species initially isolated at the index infection, approximately 15 to 50% of subsequent PJIs are attributed to recurrence with the same causative organism. Treatment resistance, contamination during revision surgery, hematogenous spread of bacteria from a distant source, and the presence of resilient biofilms have long been implicated in these recurrent infections. However, recent preclinical and clinical evidence has demonstrated that certain organisms that commonly cause PJI, namely staphylococcal species, can undergo phenotypic transformation into viable, but non-culturable (VBNC) and quasi-dormant small colony variant (SCV) forms that may persist intracellularly and lead to recurrent infection. Moreover, some organisms are known to infiltrate the osteocyte lacuno-canalicular network (OLCN) and invade eukaryotic cells to avoid targeting by the host immune system and antimicrobial agents. In doing so, they create microbial reservoirs that may be capable of reactivating to cause symptomatic infection locally or after being transported to the joint by circulating phagocytic cells. Commensal species present in the human microbiome may also become pathogenic and lead to recurrent PJI. Evidence suggests dysbiosis, a pathological imbalance in the composition and function of the microbiome, may induce the translocation of resident organisms from the gut into the bloodstream. Recent studies have also identified joint microbiota signatures that vary in accordance with the presence or absence of certain pathologies, including PJI.},
}

@article {pmid41106636,
year = {2025},
author = {Chen, T and Tang, Q and Yu, B and Tang, L and Lin, J and Zhang, L and Shan, W and Yu, H},
title = {Investigation of the mechanism involved in high-fat diet-induced depressive behavior based on energy metabolism.},
journal = {Journal of affective disorders},
volume = {},
number = {},
pages = {120505},
doi = {10.1016/j.jad.2025.120505},
pmid = {41106636},
issn = {1573-2517},
abstract = {BACKGROUND: The specific mechanisms underlying high-fat diet (HFD) and depressive behaviors remain elusive. Meanwhile, the impact of calorie restriction (CR) on the development of depression has not been explored in-depth. Thus, we aimed to examine the pathways underlying how long-term HFD intake leads to depression, focusing on energy metabolism.

METHODS: C57BL/6J mice were randomly divided into four groups-control (CK) group, CR group, HFD group, and chronic unpredictable mild stress (CUMS) group. Enzyme-linked immunosorbent assay, western blot, metabolomics and 16s rRNA gene sequencing analysis were undertaken to investigate the 5-hydroxytryptamine system, glucolipid metabolism, brain energy metabolism and gut microbiome.

RESULTS: Mice with HFD- and CUMS-induced depressive-like symptoms exhibited a significant decrease in serotonergic activity in the hippocampus. The behaviors of CR mice did not differ significantly from CK mice. Fasting blood glucose levels, fatty acid contents, and reactive oxygen species (ROS) levels were all negatively affected in unrestricted HFD and CUMS mice, suggestive of energy metabolism disruption. Metabolomic analysis revealed that tricarboxylic acid cycle activity was inhibited in the HFD and CUMS groups but not in the CR group. Additionally, analysis of the gut microbiome revealed that [Ruminococcus] gnavus exhibited higher predictive potential for HFD-induced depression, while Allobaculum showed greater predictive potential for stress-induced depression.

LIMITATIONS: Causal relationship between brain energy metabolism and gut microbiome unclear.

CONCLUSION: An unrestricted HFD promotes dysbiosis of the gut microbiota, impairs energy metabolism in the brain, affects the serotonergic system, and ultimately induces depressive-like behaviors.},
}

@article {pmid41106616,
year = {2025},
author = {Israel, A and Weizman, A and Israel, S and Stokar, J and Ashkenazi, S and Vinker, S and Magen, E and Merzon, E},
title = {Systematic screening Identifies medication and disease factors associated with Schizophrenia risk.},
journal = {Brain, behavior, and immunity},
volume = {},
number = {},
pages = {106135},
doi = {10.1016/j.bbi.2025.106135},
pmid = {41106616},
issn = {1090-2139},
abstract = {Schizophrenia (SCZ) is a severe psychiatric disorder with a complex and poorly understood etiology. Previous studies have linked Toxoplasma gondii infection to SCZ, though its clinical relevance remains uncertain. To identify factors associated with SCZ risk, we analyzed electronic health records from a national Israeli health provider, retrospectively comparing 3,273 individuals with SCZ to 32,730 matched controls. We systematically screened all medication purchases and medical diagnoses recorded from 10 years to 30 days before SCZ onset. Significant associations, adjusted for residual confounding, were further evaluated in the TriNetX network, where large propensity score-matched cohorts were compared for incident SCZ following medication exposure. Among all medication classes screened, strong protective associations were detected for specific antimicrobials, notably atovaquone/proguanil, clindamycin, and ophthalmic fluoroquinolones. Nonsteroidal anti-inflammatory drugs, particularly COX-2 inhibitors, were also linked to reduced SCZ risk, whereas neomycin, tramadol, and desmopressin were associated with increased risk. Key associations were confirmed within TriNetX with high statistical significance. These observational findings, reproduced across two national cohorts, are hypothesis-generating and may reflect multiple, non-exclusive mechanisms, including antimicrobial, anti-inflammatory, and microbiome-related pathways, with T. gondii elimination through antiprotozoal activity representing one compelling explanatory hypothesis that warrants further investigation.},
}

@article {pmid41106336,
year = {2025},
author = {Pereira, G and Wise, CM and Pagenkopp Lohan, KM and Noyce, GL and Lopes, ML and Magalhães, L},
title = {Trait-mediated effects of Macoma balthica (L.) on nitrogen and carbon biogeochemistry in estuarine ecosystems.},
journal = {Marine environmental research},
volume = {213},
number = {},
pages = {107621},
doi = {10.1016/j.marenvres.2025.107621},
pmid = {41106336},
issn = {1879-0291},
abstract = {Coastal ecosystems rely on microbially mediated biogeochemical processes for ecosystem functioning, particularly carbon (C) and nitrogen (N) cycling across the water-sediment interface, supported by bivalves through bioturbation activity. Here, we conducted an 8-week coastal microcosm experiment using Macoma balthica sampled from the Rhode River (Chesapeake Bay) to assess how bivalve presence and individual traits (burial position and shell length) influence the N cycle (NH3 and NOX) and C cycle (CDOM, measured as aCDOM 250 m[-1]) in the water column and interstitial water. Our results show that bivalve presence significantly affected N cycling: NH3 initially rose in the water column before declining, followed by exponential increases in NOx in both water and interstitial water. Burial position influenced NH3 and NOx concentrations throughout the experiment, and larger individuals were associated with higher NOx levels. Additionally, aCDOM 250 m[-1] increased over time regardless of bivalve presence, likely due to daily feeding with artificial algae, suggesting that future studies should include additional C parameters such as dissolved and particulate forms of organic and inorganic C. Overall, our findings show that M. balthica's influence on N cycling is shaped by individual traits and temporal dynamics, creating functional heterogeneity with implications for Rhode River nutrient fluxes and ecosystem functioning. While microbiomes might contribute to the nitrification processes observed, future research should clarify the pathways of bivalve-microbiome interactions in M. balthica.},
}

@article {pmid41106321,
year = {2025},
author = {Wang, X and Wang, Y and Guo, C and Guo, R and Zuo, W and Liu, C and Wang, J and Gao, C and Zhang, L and Yuan, W and Ma, J},
title = {Targeted depletion of intratumoral bacteria using PEGylated metronidazole to augment cancer treatment efficacy.},
journal = {Biomaterials},
volume = {327},
number = {},
pages = {123772},
doi = {10.1016/j.biomaterials.2025.123772},
pmid = {41106321},
issn = {1878-5905},
abstract = {Since the infiltration of intratumoral microbiota is associated with aggressive phenotypes of cancer, eliminating bacteria within tumors has become an attractive approach to cancer treatment. By self-assembly of PEGylated metronidazole (MTI-PEG), we developed a nanosized antibiotic that effectively eliminates intratumoral bacteria without causing gut microbiome dysbiosis. In Fusobacterium nucleatum spp (Fn) colonized tumor models, we observed significant adjuvant effects of MTI-PEG on chemotherapy, immunotherapy and targeted therapy through reversing drug resistance through the modulation of autophagy, the human T-cell immunoglobulin and ITIM domain (TIGIT) and the phosphatidylinositol-3-kinase/protein kinase B (PI3K-AKT) signaling pathway, respectively, while reshaping immune landscape of tumor microenvironment. The encouraging results indicate a promising future for MTI-PEG in microbiome-infiltrated tumors, with potential to improve the overall therapeutic efficacy of current cancer treatments.},
}

@article {pmid41106256,
year = {2025},
author = {Wang, S and Song, F and Yang, Y and Liu, B and Zhou, C and Wang, C and Wang, Y and Luo, H},
title = {Exploring the forensic skin and 'touched' bacterial community through full-length and variable region sequencing of the 16S rRNA gene.},
journal = {Forensic science international. Genetics},
volume = {81},
number = {},
pages = {103374},
doi = {10.1016/j.fsigen.2025.103374},
pmid = {41106256},
issn = {1878-0326},
abstract = {The human skin microbiome is unique to each individual, and the microbial exchange between human skin and their touched objects could aid in tracing individuals. However, the microbial transfer and deposition on transiently touched items, and their forensic potential application remain insufficiently understood. Therefore, we simulate a scenario where a suspect holds a knife for a brief time to investigate the transfer of skin-associated microbiota from the hand to the touched object's surface using sequencing of the 16S rRNA gene full length and variable region. The results showed the full-length 16S rRNA gene sequencing (V1-V9) achieved significantly higher taxonomic resolution (species-level) and enriched α-diversity in both skin and contact-objects microbiomes compared to the variable region (V3-V4) sequencing approach. The skin bacterial community exhibited greater biodiversity than the "touched" bacterial communities, and there was no significant similarity between the skin and "touched" bacterial communities for each individual. The intra-individual β diversity of "touched" bacterial communities was close to 1, while the β diversity within individuals (ranging from 0.7 to 0.9) was significantly lower than that observed between individuals in the skin bacterial community. Skin bacterial communities were individual-specific, and the efficacy in discriminating individuals through individual-specific amplicon sequence variants was 100 % using the support vector machine model, in both of the two sequencing datasets. Individual-specific amplicon sequence variants were observed within high relative abundance bacterial taxa (e.g., Staphylococcus epidermidis, Streptococcus mitis, and Streptococcus parasanguinis), but the number of skin individual-specific amplicon sequence variants detectable in "touched" bacterial communities was low. Only a small fraction of skin-derived taxa was detectable on objects and detectability couldn't be explained by robust individual-specific signatures. The dominant bacterial genera and species identified in the shared amplicon sequence variants between skin and "touched" bacterial communities were among the relatively high-abundance taxa within the skin microbiome, like Streptococcus, Staphylococcus, Corynebacterium, Staphylococcus epidermidis, Streptococcus mitis, Corynebacterium bovis, Streptococcus parasanguinis, etc. Such high relative abundance bacterial species showed both individual-specific, easy-to-transfer, and easy-to-deposit in touch events, which may be new marks in forensic identification.},
}

@article {pmid41106100,
year = {2025},
author = {Wang, H and Nie, Y and Luo, Y and Sun, Z and He, Y and Yang, J},
title = {Daidzein alleviates chronic restraint stress-induced depression-like behavior by regulating neuroinflammation and synaptic plasticity via microbiota-gut-brain axis.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {148},
number = {},
pages = {157394},
doi = {10.1016/j.phymed.2025.157394},
pmid = {41106100},
issn = {1618-095X},
abstract = {BACKGROUND: Depression is one of the most serious psychological disorders worldwide. Growing evidence suggests that the gut-brain axis plays a pivotal role in its pathophysiology. Daidzein, a naturally occurring isoflavone compound, exhibits neuroprotective properties and can be metabolized by gut microbiota into highly bioactive secondary metabolites.

PURPOSE: This study aims to evaluate the antidepressant effects of daidzein and to investigate its underlying mechanisms, particularly mediated by the gut microbiome.

STUDY DESIGN AND METHODS: We employed the chronic restraint stress (CRS) mice models and classic behavioral tests to investigate the therapeutic effect of daidzein. Furthermore, we used 16S rRNA sequencing and metabolomics methods to explore the regulatory effects of daidzein on key functional bacteria and metabolites after CRS exposure. Intestinal barrier function was evaluated by histopathology and FITC-dextran detection. Neuroinflammatory responses, neuronal morphology, and plasticity were also evaluated using immunofluorescence staining, western blotting, and Nissl staining. Finally, we employed an antibiotic intervention experiment to validate the pivotal role of gut microbiota in the antidepressant effect of daidzein.

RESULTS: Our data demonstrate that daidzein administration mitigated the depression-like behaviors in CRS mice, with gut microbiota composition playing a potentially critical mediating role. Specifically, daidzein induced significant modulations in gut microbial communities (Rikenella, Enterococcus, Akkermansia, and Ruminococcus) and associated metabolic profiles, particularly affecting short-chain fatty acid biosynthesis (valeric acid and acetic acid) and bile acid metabolism (cholic acid/allocholic acid, taurine-deoxycholic acid, and 3-dehydrocholic acid). Mechanistic investigations revealed that daidzein exerted protective effects on intestinal barrier integrity while concurrently reducing pro-inflammatory cytokine levels in both serum and hippocampus. At the neurobiological level, daidzein exhibited multifaceted regulatory effects, including attenuation of glial cell activation (microglia and astrocytes), normalization of FXR/NF-κB/NLRP3 inflammasome signaling, and enhancement of BDNF/TrkB neurotrophic pathways. These molecular changes were further associated with improved neuronal morphological complexity and upregulated expression of synaptic plasticity markers (SYP and PSD95) in the hippocampus.

CONCLUSION: These data propose a gut-brain axis-mediated mode of action for daidzein's antidepressant-like effects, highlighting its promise as a potential candidate for depression, while further investigations are required to elucidate the specific microbial and metabolic drivers of these effects.},
}

@article {pmid41105996,
year = {2025},
author = {Chen, ZY and Gao, FZ and Bai, H and He, LY and Liu, YS and Ying, GG},
title = {Airborne free DNA in chicken farms: The overlooked traits in microbial diversity, viral composition, and antimicrobial resistance risk.},
journal = {Journal of hazardous materials},
volume = {499},
number = {},
pages = {140144},
doi = {10.1016/j.jhazmat.2025.140144},
pmid = {41105996},
issn = {1873-3336},
abstract = {The enrichment of DNA from total suspended particulates (TSP) onto 0.22 µm pore size filters (intracellular DNA, iDNA) is a critical step in characterizing the airborne microbiome. However, free DNA (< 0.22 µm, fDNA) may harbor unrecognized microbial and genetic components. In this study, metagenomic analysis was employed to compare airborne fDNA and iDNA from eight chicken houses. Overall, the average concentration of fDNA was 5.6-fold higher than that of iDNA. A total of 587 genera spanning 28 phyla were identified in fDNA, including 162 genera absent from iDNA. Notably, 39.7 % of open reading frames were unique to fDNA, involving key metabolic and regulatory pathways. A total of 50.2 % viral contigs were only detected in fDNA, carrying mobile genetic elements, virulence factor genes, and resistance genes against antibiotics, biocides, and metals. The total absolute abundance of the antibiotic resistome was higher in fDNA, with 79.2 % of significantly varied genes enriched therein, including 16 high-risk genes. Metagenomic binning further supported that fDNA harbors broader microbial diversity and functional traits. These findings underscore airborne fDNA as an underexplored reservoir of microbial and genetic diversity, meriting further investigation for its ecological and public health implications.},
}

@article {pmid41105994,
year = {2025},
author = {Diambra, L},
title = {Network-based community analysis of microbial composition: Insights into dysbiosis and assembly.},
journal = {Computers in biology and medicine},
volume = {198},
number = {Pt A},
pages = {111190},
doi = {10.1016/j.compbiomed.2025.111190},
pmid = {41105994},
issn = {1879-0534},
abstract = {Traditional analyses of the human gut microbiome, often relying on differential abundance of individual taxa, face significant challenges due to the inherent complexity of microbial communities and frequently yield inconsistent findings. This study introduces a novel network-based approach to overcome these limitations by reducing data dimensionality and facilitating the identification of biologically relevant patterns. Our method constructs microbial association networks, applies community detection algorithms to identify robust groups of co-occurring species, and defines 'community strength variables' as the aggregated abundance of these communities, serving as a reduced-dimension framework for downstream analysis. We applied this approach to two distinct publicly available human gut microbiome datasets: a longitudinal study of infant gut microbiome assembly in Bangladeshi children and an obesity-control study in Danish adults. In the infant cohort, our analysis revealed key community transitions linked to developmental stages, highlighting the dynamic interplay between host growth and microbial colonization. For instance, Community 1 showed a strong positive correlation with age, while the Bifidobacterium-dominated Community 4 declined with age. In the Danish obesity study, our method identified distinct community profiles associated with obesity, effectively circumventing the inconsistencies observed in traditional differential abundance comparisons. Notably, Communities C1 and C19 showed significantly higher fractional abundances in lean participants compared to obese individuals. These findings underscore the context-specificity of microbial associations and demonstrate the power of community-level analysis. Despite limitations such as reliance on correlation-based networks, our framework offers a valuable tool for investigating microbiome structure and function, providing a promising avenue for developing robust microbiome-based biomarkers and therapeutic interventions through the quantification of key microbial consortia.},
}

@article {pmid41105671,
year = {2025},
author = {Thompson, RN and Blumenthal, A and Morrison, M and Thomson, RM},
title = {The microbiome and gut-lung axis in nontuberculous mycobacterial pulmonary disease.},
journal = {PLoS pathogens},
volume = {21},
number = {10},
pages = {e1013603},
doi = {10.1371/journal.ppat.1013603},
pmid = {41105671},
issn = {1553-7374},
mesh = {Humans ; *Mycobacterium Infections, Nontuberculous/microbiology/immunology ; *Gastrointestinal Microbiome/physiology ; *Lung/microbiology/immunology ; *Lung Diseases/microbiology/immunology ; Animals ; Nontuberculous Mycobacteria ; },
abstract = {Nontuberculous mycobacterial pulmonary disease (NTM-PD) is increasingly recognised as a significant global health concern. It is characterised by a highly heterogenous clinical course and remains poorly understood, from host susceptibility to disease pathophysiology, and is notoriously difficult to treat. Recent advances highlight the microbiome as a critical modulator of host physiology, with site-specific 'microbiota' influencing the delicate balance between health, infection and disease. While microbial populations vary across discrete anatomical sites, there is a growing recognition that they are interconnected. For example, gut microbes can influence immune cell functions in the lung via the gut-lung axis (GLA). Drawing parallels with other related chronic respiratory diseases, it is hypothesised that microbiota-host-interactions shape susceptibility and manifestation of NTM-PD. This review synthesises current knowledge of some key host susceptibility factors in NTM-PD, and their potential interactions with host microbiota. With only recently emerging studies, we explore the potential role of the GLA in NTM-PD, given its promising links to microbial communities and immunological and metabolic pathways. We assess the limited, but growing body of research on the lung microbiota in NTM-PD and evaluate the small number of studies on faecal microbiota in NTM-PD. By considering insights across anatomical sites, this review aims to contextualise the microbiome within multiple dimensions of NTM-PD, including host susceptibility, disease progression, treatment responsiveness, and the effects of antibiotic therapy. A better understanding of the microbiome in NTM-PD could hold promise in uncovering the complex and multifactorial mechanisms that contribute to the heterogenous clinical course and challenging management of NTM-PD.},
}

Humans
*Mycobacterium Infections, Nontuberculous/microbiology/immunology
*Gastrointestinal Microbiome/physiology
*Lung/microbiology/immunology
*Lung Diseases/microbiology/immunology
Animals
Nontuberculous Mycobacteria

@article {pmid41105587,
year = {2025},
author = {Nikam, B and Jha, SN and Thakare, Y and Coshic, P and Gupta, N},
title = {Short-Chain Fatty Acid Sodium Butyrate Suppresses Protective Humoral Immunity by Inhibiting Follicular T Helper Cell Differentiation.},
journal = {European journal of immunology},
volume = {55},
number = {10},
pages = {e70076},
doi = {10.1002/eji.70076},
pmid = {41105587},
issn = {1521-4141},
support = {//National Institute of Immunology/ ; },
mesh = {Animals ; Mice ; *Butyric Acid/pharmacology ; *Cell Differentiation/drug effects/immunology ; *Immunity, Humoral/drug effects ; *T Follicular Helper Cells/immunology/drug effects ; Germinal Center/immunology ; *Orthomyxoviridae Infections/immunology ; *Fatty Acids, Volatile ; Mice, Inbred C57BL ; B-Lymphocytes/immunology ; Gastrointestinal Microbiome/immunology ; *T-Lymphocytes, Helper-Inducer/immunology ; Lymphocyte Activation/drug effects/immunology ; },
abstract = {The gut microbiome and its metabolites are critical regulators of intestinal homeostasis, with emerging evidence highlighting their influence on humoral immune responses and vaccine efficacy. The development of effective humoral immunity depends on the magnitude and quality of germinal centers (GCs), which are driven by follicular T helper (Tfh) cells. Here, we investigate the role of short-chain fatty acids (SCFAs) in shaping humoral immunity, with a particular focus on Tfh cells. In ex vivo assays, we found that sodium butyrate, not sodium acetate or sodium propionate, directly suppresses Tfh cells differentiation and helper functions. Using antigen-specific and influenza virus infection models, we further demonstrate that sodium butyrate impairs Tfh cell differentiation, leading to diminished GC B cell responses and compromised humoral immunity during systemic infection. Notably, mice treated with sodium butyrate succumbed to virus infection, underscoring its effect on impairing protective immunity. Mechanistically, our findings reveal that sodium butyrate mediates these suppressive effects on Tfh cells via histone deacetylase (HDAC) inhibition. Together, our findings establish sodium butyrate as a negative regulator of humoral immunity by directly suppressing the Tfh-cell differentiation and Tfh-derived GC responses. These insights provide a mechanistic link between gut microbiome-derived metabolites and humoral immunity, with potential implications for vaccine efficacy and therapeutic interventions.},
}

Animals
Mice
*Butyric Acid/pharmacology
*Cell Differentiation/drug effects/immunology
*Immunity, Humoral/drug effects
*T Follicular Helper Cells/immunology/drug effects
Germinal Center/immunology
*Orthomyxoviridae Infections/immunology
*Fatty Acids, Volatile
Mice, Inbred C57BL
B-Lymphocytes/immunology
Gastrointestinal Microbiome/immunology
*T-Lymphocytes, Helper-Inducer/immunology
Lymphocyte Activation/drug effects/immunology

@article {pmid41105342,
year = {2025},
author = {Lu, L and Li, Z and Qiang, P and Shao, Y},
title = {Gut microbiota and risk of cervical cancer: a Mendelian multivariable randomization study.},
journal = {Discover oncology},
volume = {16},
number = {1},
pages = {1912},
pmid = {41105342},
issn = {2730-6011},
abstract = {BACKGROUND AND HYPOTHESIS: Epidemiological evidence demonstrates associations between gut microbial dysbiosis and cervical cancer, though causal inference remains limited by potential confounding.

STUDY DESIGN: A meta-analysis of the largest available genome-wide association study (GWAS) meta-analysis using the MiBioGen consortium (n = 14,306 individuals; 8,107,040 SNPs analyzed) was conducted for the summary statistics of the gut microbiome. A two-sample Mendelian randomization study was performed using the statistics of cervical cancer from BioBank Japan (BBJ) and the European Bioinformatics Institute (EBI) GWAS Catalog. The causal relationship between the gut microbiome and cervical cancer was examined using inverse variance weighting, maximum likelihood, MR-Egger, weighted median, weighted model, and MR-PRESSO methods. The Cochran Q statistic was used to quantify the heterogeneity of the instrumental variables.

STUDY RESULTS: The odds ratio (OR) values obtained by the IVW method indicate that the consistent microbial communities in the validation results from two different cervical cancer datasets are: Actinomyces (BBJ OR = 0.52, 95% CI: 0.29-0.92, P < 0.05), (EBI OR = 0.55, 95% CI: 0.29-0.87, P < 0.05) It has a protective effect on the occurrence of cervical cancer, Lachnospiraceae UCG001 (BBJ OR = 2.00, 95% CI: 1.11-3.58, P < 0.05), (EBI OR = 1.91, 95% CI: 1.16-3.13, P < 0.05) It has a promoting risk effect on the occurrence of cervical cancer, and there is no significant heterogeneity or horizontal pleiotropy.

CONCLUSIONS: Both datasets consistently showed that Actinomyces was protective against cervical cancer (BBJ OR = 0.52; EBI OR = 0.55), while Lachnospiraceae UCG001 increased risk (BBJ OR = 2.00; EBI OR = 1.91), with no evidence of heterogeneity or pleiotropy in these robust MR analyses.},
}

@article {pmid41105100,
year = {2025},
author = {Arellano, AA and Prack, JL and Coon, KL},
title = {Host-mediated niche construction of bacterial communities in an aquatic microecosystem.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf233},
pmid = {41105100},
issn = {1751-7370},
abstract = {Microbes coordinate homeostasis in host-associated and environmental ecosystems alike, but the connectivity of these biomes is seldom considered. Hosts exert controls on the composition and function of their internally associated symbionts, but an underappreciated modality of microbiome curation is external to the host through changes to the environmental species pool from which they recruit microbial symbionts. Niche construction theory describes how organisms alter their environment and the selective landscape of their offspring and conspecifics. We hypothesize that host-driven manipulation of environmental microbial communities is an underexplored form of this concept. Using the pitcher plant mosquito (Wyeomyia smithii) as a model, we tested how hosts shape microbial communities across developmental stages and gradients of pre-existing community complexity. We report three lines of evidence supporting host-mediated niche construction, leveraging amplicon sequencing and microbiota manipulation experiments with germ-free (axenic) and selectively recolonized (gnotobiotic) mosquitoes. First, single female egg-laying assays showed repeatable adult inoculation of sterile water with beneficial bacteria capable of sustaining robust larval development. Second, increasing larval density in assays inoculated with complex, field-derived microbial communities selected for environmental and host-associated bacteria that correlated with increased larval fitness. Finally, exposing axenic larvae to mixtures of parentally and environmentally derived microbiota demonstrated that prior conditioning by conspecifics enhanced offspring fitness. Although the bacterial taxa associated with mosquito structuring varied, members of the Actinobacteriota and Acetobacteraceae were consistently associated with increased fitness. Overall, our results provide an example of host-mediated niche construction to favor environmental microbial communities that positively impact host fitness.},
}

@article {pmid41104927,
year = {2025},
author = {Anwar, S and Lamaudiere, M and Hassall, J and Dehinsilu, J and Bhuller, RK and Hold, GL and Vázquez-Campos, X and Mahnert, A and Moissl-Eichinger, C and Gallé, B and Kainz, G and Pjevac, P and Hausmann, B and Schwarz, J and Kohl, G and Berry, D and Vancuren, SJ and Allen-Vercoe, E and Nielsen, N and Sørensen, N and Eklund, A and Nielsen, HB and Riedel, R and Krause, JL and Chang, H-D and Park, S and Song, H-Y and Seo, H and Ul-Haq, A and Kim, S and Kwon, Y and Park, S and Soberon, X and Silva-Herzog, E and Verlouw, JAM and Arp, P and Jhamai, M and Kraaij, R and Geelen, AR and Ducarmon, QR and Smits, WK and Kuijper, EJ and Zwittink, RD and van Best, N and Penders, J and Le, G and Driessen, C and Kool, J and Shetty, SA and Fuentes, S and Demirci, M and Yigin, A and Whalley, C and Beggs, AD and Quince, C and James, R and Raguideau, S and Gordon, M and Mate, R and Fritzsche, M and Danckert, NP and Blanco, JM and Marchesi, JR and Rauch, M and Williamson, RA and Van't Wout, AB and Kritz, A and Rosecker, S and Stevens, R and Laws, L and Sayavedra, L and Romano, S and Telatin, A and Baker, D and Narbad, A and Servetas, SL and Kralj, JG and Forry, SP and Hunter, ME and Dootz, JN and Jackson, SA and Mason, CE and Butler, DJ and Mozsary, C and Foox, J and Damle, N and Resh, A and Busswitz, A and Lenz, P and Sontag, S and Cross, A and Sanchez, C and Guo, M and Olson, K and Smith, EA and La Reau, AJ and Ward, T and Kuersten, S and Hyde, F and Khrebtukova, I and Schroth, G and Rijpkema, S and Amos, GCA and Sergaki, C},
title = {DNA reference reagents isolate biases in microbiome profiling: a global multi-lab study.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0046625},
doi = {10.1128/msystems.00466-25},
pmid = {41104927},
issn = {2379-5077},
abstract = {When profiling the human gut microbiome, technical biases introduced by analytical approaches impede translational research, reducing data reliability and study comparability. Here, through a global study involving 23 labs, we analyzed a wide range of sequencing and bioinformatic approaches for the taxonomic profiling of two well-defined DNA reference reagents (RRs) comprised of 20 common gut bacteria. Through both shotgun and 16S rRNA gene amplicon sequencing, we aimed to isolate sources of bias and understand their impact on microbiome profiling accuracy. Importantly, minimum quality criteria (MQC) were established and are used to evaluate profiling performance. We found that the variability of shotgun sequencing data sets was greater than that of 16S rRNA gene amplicon sequencing and isolated sources of bias in wet and dry lab steps, such as sequencing depth, primer and database choices, rarefaction, and 16S copy number adjustment. This study presents well-defined RRs and MQC to combat technical bias, paving the way for reliable and comparable microbiome research.IMPORTANCEThis benchmark paper highlights the true level of variability in microbiome data across the world and across sectors, underscoring the critical need for the use of WHO International DNA Gut Reference Reagents (RRs) to elevate the quality of data in microbiome research. This global study is the first of its kind, revealing the reality of the bias in the field, comprehensively testing methodologies used by leading laboratories across the world, but also providing avenues for workflow optimization, to accelerate innovation and translational research and move the field forward.},
}

@article {pmid41104769,
year = {2025},
author = {Chapman, PA and Day, RC and Hudson, DT and Ward, JM and Morgan, XC and Beck, CW},
title = {Commensal skin bacteria interact with the innate immune system to promote tail regeneration in Xenopus laevis tadpoles.},
journal = {Developmental dynamics : an official publication of the American Association of Anatomists},
volume = {},
number = {},
pages = {},
doi = {10.1002/dvdy.70088},
pmid = {41104769},
issn = {1097-0177},
support = {MFP-UOO1910//Royal Society Te Apārangi/ ; },
abstract = {BACKGROUND: Tadpoles of the clawed frog Xenopus laevis can regenerate their tails following partial amputation, replacing the missing spinal cord, muscles, and fin. However, for a brief period of development this response becomes unstable, leading to a proportion of tadpoles that undergo wound healing rather than regenerative programme. Inspired by a growing number of links between the microbiome and human inflammatory disease, we asked how the tadpole skin microbiome and innate immunity influence the regeneration of a complex appendage. We previously showed that tadpoles raised in antibiotics such as gentamicin or penicillin/streptomycin or with reduced Toll-like receptor 4 signaling regenerated tails poorly, while adding exogenous lipopolysaccharide promoted or rescued tail regeneration.

RESULTS: Here, we show that CRISPR/Cas9 knockdown of Toll-like receptor 2 also reduces tadpole tail regeneration. Conversely, addition of the pathogen-associated molecular pattern peptidoglycan to the medium at the time of amputation increases the likelihood of regeneration. While we have previously shown that tadpoles acquire most of their early skin microbiome from their mothers, analysis of mitochondrial haplotypes did not support a genetic maternal explanation of regenerative bias. Levels of endogenous lipopolysaccharides on tail tips were also not predictive of regenerative success, and shotgun sequencing indicated that there was no difference in bacterial loads. To see if the composition of native microbiome was associated with regenerative success, we sequenced the 16S rRNA genes of 503 tadpole tail tips from 12 sibships and mapped these to the regenerative outcome of each tadpole. While no one taxon was found to be associated with regenerative success, higher proportions of Gram-positive genera overall correlated with improved regeneration outcomes. Supporting this finding, when tadpoles were raised with the antibiotic vancomycin, to select against Gram-positive bacteria, the number of individuals undergoing tail regeneration was significantly decreased.

CONCLUSIONS: Taken together, our results suggest a previously undocumented role for Tlr2, possibly activated by peptidoglycan from Gram-positive commensal skin bacteria, in tipping the balance from wound repair to regenerative programmes in Xenopus laevis refractory stage tadpoles.},
}

@article {pmid41104650,
year = {2025},
author = {Yasinzai, AQK and Jalali, P and Syaj, S and Sahin, IH and Nassour, I and George, TJ and Saeed, A},
title = {Trends and Projected Burden of Early-Onset Gastrointestinal Malignancies in the United States: A Population-Based Analysis (2001-2021).},
journal = {Journal of the National Cancer Institute},
volume = {},
number = {},
pages = {},
doi = {10.1093/jnci/djaf304},
pmid = {41104650},
issn = {1460-2105},
abstract = {BACKGROUND: Early-onset colorectal cancer (eoCRC) has become a serious public health concern in recent years. This study aims to contribute to the growing body of evidence on the rise in early onset gastrointestinal cancers (eoGIC), anatomical sub-sites of eoCRC, and explore racial and gender disparities in these trends.

METHODS: We analyzed data from the NPCR-SEER database (2001-2021) for people aged 20 to 49 with gastrointestinal (GI) cancers. The dataset covers cancer incidence rates for about 98% of United States population. Joinpoint regression was used to calculate average annual percent change (AAPC), and polynomial regression was applied to forecast rates from 2021 to 2031.

RESULTS: A total of 527,411 cases were analyzed. Colorectal comprised of the highest cases (n = 313,513) followed by pancreatic (n = 50,448). Intrahepatic bile duct had the highest AAPC (+6.24%, 95% CI +5.20 to + 7.45) followed by small intestine (+3.19%, 95% CI: +2.69 to + 3.72), eoCRC (+1.65%, 95% CI: +1.45 to + 1.92), pancreatic (+1.52, 95% CI: +1.37 to + 1.66), and stomach (+1.20, 95% CI: +0.89 to + 1.53). In colorectum, rectum had the highest AAPC (+2.09%). Females (+1.81%) experienced disproportionate rise when compared to males (+0.83%). Projection suggests a demographic shift with female surpassing males in the overall age adjusted rate of eoGIC.

CONCLUSION: The study highlights that eoCRC is not an isolated phenomenon but part of a broader epidemiologic shift across gastrointestinal malignancies. The parallel rise in other sites suggests shared upstream risk factors or exposures and supports investigations into potential environmental, dietary, microbiome, or hormonal risk factors.},
}

@article {pmid41104481,
year = {2025},
author = {},
title = {Laila P. Partida-Martínez.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.70665},
pmid = {41104481},
issn = {1469-8137},
abstract = {Laila P. Partida-Martínez, Cinvestav-Irapuato (Mexico).},
}

@article {pmid41104474,
year = {2025},
author = {Piekiełko-Witkowska, A and Elisei, R and Leger, J and Bendlová, B and Pekova, BB and Caron, P and Durante, C and Fassnacht, M and Feldt-Rasmussen, U and Nyström, HF and Jansen, H and Köhrle, J and Kuś, A and Ludgate, M and Mertens, J and Oczko-Wojciechowska, M and Peters, C and Schoenmakers, N and Stoupa, A and van Santen, H and Trimboli, P and van Trotsenburg, P and Edward Visser, W},
title = {EndoCompass project: research roadmap for thyroid endocrinology.},
journal = {European journal of endocrinology},
volume = {193},
number = {Supplement_2},
pages = {ii117-ii127},
doi = {10.1093/ejendo/lvaf010},
pmid = {41104474},
issn = {1479-683X},
mesh = {Humans ; *Endocrinology/trends/organization & administration/methods ; *Thyroid Diseases/therapy/diagnosis/epidemiology ; *Biomedical Research/trends ; European Union ; Databases, Factual ; },
abstract = {BACKGROUND: Endocrine science remains underrepresented in European Union research programs despite the fundamental role of hormone health in human well-being. Analysis of the CORDIS database reveals a persistent gap between the societal impact of endocrine disorders and their research prioritization. At national funding level, endocrine societies report limited or little attention of national research funding toward endocrinology. The EndoCompass project-a joint initiative between the European Society of Endocrinology and the European Society of Paediatric Endocrinology, aimed to identify and promote strategic research priorities in endocrine science to address critical hormone-related health challenges.

METHODS: Research priorities were established through comprehensive analysis of the EU CORDIS database covering the Horizon 2020 framework period (2014-2020). Expert consultation in thyroid endocrinology was conducted to identify key research priorities, followed by broader stakeholder engagement including society members and patient advocacy groups.

RESULTS: For thyroid disorders, research priorities encompass neoplastic and nonneoplastic conditions, focusing on disease mechanisms, improved diagnostics and treatments, and the impact of environmental and metabolic factors. Key areas include personalized medicine approaches, artificial intelligence applications, and the establishment of pan-European registries to advance understanding of rare thyroid conditions.

CONCLUSIONS: The thyroid component of the EndoCompass project provides an evidence-based roadmap for strategic research investment. This framework identifies crucial investigation areas into thyroid disease pathophysiology, prevention, and treatment strategies, ultimately aimed at reducing the burden of thyroid disorders on individuals and society. The findings support the broader EndoCompass objective of aligning research funding with areas of highest potential impact in endocrine health.},
}

Humans
*Endocrinology/trends/organization & administration/methods
*Thyroid Diseases/therapy/diagnosis/epidemiology
*Biomedical Research/trends
European Union
Databases, Factual

@article {pmid41104472,
year = {2025},
author = {Mathieu, C and Meireles, M and Pagotto, U and Wabitsch, M and Banerjee, I and Bartolomé, A and Battelino, T and Beck, J and Chiarelli, F and De Leon, DD and Dovč, K and El Ghoch, M and Galderisi, A and Gevers, E and Gillard, P and Haliloglu, B and Hoermann, H and Mankovsky, B and Mertens, J and Mohnike, K and Oram, R and Pasquini, T and Pearson, E and Pieber, TR and Polovina, S and Raskin, J and Roeper, M and Ruck, L and Salomon Estebanez, M and Tankova, T and Thornton, P and van Rossum, EFC and Vukovic, R and Worth, C and Zachurzok, A},
title = {EndoCompass project: research roadmap for diabetes, obesity, and metabolism.},
journal = {European journal of endocrinology},
volume = {193},
number = {Supplement_2},
pages = {ii47-ii71},
doi = {10.1093/ejendo/lvaf065},
pmid = {41104472},
issn = {1479-683X},
mesh = {Humans ; *Obesity/therapy/metabolism/epidemiology ; *Endocrinology ; *Biomedical Research/trends ; *Diabetes Mellitus/therapy ; European Union ; *Metabolic Diseases/therapy ; },
abstract = {BACKGROUND: Endocrine science remains underrepresented in European Union research programmes despite the fundamental role of hormone health in human well-being. Analysis of the CORDIS database reveals a persistent gap between the societal impact of endocrine disorders and their research prioritization. At national funding level, endocrine societies report limited or little attention of national research funding towards endocrinology. The EndoCompass project-a joint initiative between the European Society of Endocrinology and the European Society of Paediatric Endocrinology, aimed to identify and promote strategic research priorities in endocrine science to address critical hormone-related health challenges.

METHODS: Research priorities were established through comprehensive analysis of the EU CORDIS database covering the Horizon 2020 framework period (2014-2020). Expert consultation was conducted to identify key research priorities, followed by broader stakeholder engagement including society members and patient advocacy groups.

RESULTS: Research priorities include: genetic/epigenetic factors, brain-periphery communication, and environmental influences. Key therapeutic areas include innovative approaches for monogenic disorders, incretin mimetics, dual receptor agonists, microbiome analysis, and improved behavioural interventions. For type 1 diabetes, priorities focus on early detection, insulin delivery systems, and disease-modifying therapies.

CONCLUSIONS: This component of the EndoCompass project provides an evidence-based roadmap for strategic research investment. This framework identifies crucial investigation areas into diabetes and obesity pathophysiology, prevention, and treatment strategies, ultimately aimed at reducing the burden of metabolic disorders on individuals and society. The findings support the broader EndoCompass objective of aligning research funding with areas of highest potential impact in endocrine health.},
}

Humans
*Obesity/therapy/metabolism/epidemiology
*Endocrinology
*Biomedical Research/trends
*Diabetes Mellitus/therapy
European Union
*Metabolic Diseases/therapy

@article {pmid41104433,
year = {2025},
author = {Pandey, AK and Vurukonda, SSKP and Giovanardi, D},
title = {Editorial: Unraveling pathogen-plant-microbiome interactions in horticultural crops through omics approaches.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1696789},
pmid = {41104433},
issn = {1664-462X},
}

@article {pmid41104285,
year = {2025},
author = {Ji, K and Lei, S and Wang, L and Tian, L and Wen, Z and Shi, R and Liu, L and Liu, J and Shi, B and Wang, J},
title = {Synergistic effects of multi-strain probiotics and Chinese herbal medicine on growth performance and gut health in weaned piglets.},
journal = {Frontiers in veterinary science},
volume = {12},
number = {},
pages = {1677127},
pmid = {41104285},
issn = {2297-1769},
abstract = {BACKGROUND: Weaning stress represents a considerable challenge in global swine production. While probiotics and Chinese herbal medicine have been extensively studied as individual interventions, their combined application as alternative feed additives in swine production requires further investigation.

METHODS: Forty-five weaned piglets (35 ± 3 days old) were randomly allocated to five treatment groups (n = 9 per group) for a 28-day feeding trial: control (CON), antibiotic (A), probiotic (PRO), Chinese herbal medicine (CHM), and probiotic plus Chinese herbal medicine (PROC). Growth performance, serum antioxidant levels, and immune parameters were assessed alongside 16S rRNA microbiome sequencing and liquid chromatography-mass spectrometry metabolomics analysis.

RESULTS: The PROC group significantly improved growth performance compared to controls (p < 0.05), showing 8.91% higher final body weight, significantly increased average daily gain, and the most efficient feed conversion ratio (1.55) among treatments. Serum analysis indicated a significant increase in total antioxidant capacity (T-AOC) in the PROC group relative to the other groups. The probiotic (PRO) and PROC groups enhanced superoxide dismutase (SOD) and glutathione peroxidase (GSH-Px) activities, while reducing malondialdehyde (MDA) levels (p < 0.05). Pro-inflammatory cytokines IL-2 and IL-6 were significantly reduced in the PRO and PROC groups, while immunoglobulins IgA and IgG levels were increased (p < 0.05). Microbiota analysis revealed increased α-diversity (Shannon and Chao1 indices) and altered community structure in the PROC group. Metabolomic profiling identified 5,090 metabolites with distinct profiles between groups based on OPLS-DA. KEGG pathway analysis indicated that the PRO group exhibited enrichment in nucleotide and purine metabolism, whereas the PROC group activated supplementary pathways, including purine and lipid metabolism.

CONCLUSION: These findings suggest that combined probiotic and Chinese herbal medicine supplementation may serve as an effective feed strategy for promoting intestinal health and alleviating weaning stress, providing valuable insights for developing antibiotic alternatives in swine production.},
}

@article {pmid41104042,
year = {2025},
author = {Yassin, LK and Skrabulyte-Barbulescu, J and Alshamsi, SH and Saeed, S and Alkuwaiti, SH and Almazrouei, S and Alnuaimi, A and BaniYas, S and Aldhaheri, D and Alderei, M and Shehab, S and Hamad, MIK},
title = {The microbiota-gut-brain axis in mental and neurodegenerative disorders: opportunities for prevention and intervention.},
journal = {Frontiers in aging neuroscience},
volume = {17},
number = {},
pages = {1667448},
pmid = {41104042},
issn = {1663-4365},
abstract = {The microbiota-gut-brain axis (MGBA) is increasingly recognized as a critical regulator of brain health, influencing both neurodevelopment and age-related neurological decline. Disruptions in this axis, driven by gut dysbiosis, have been implicated in the pathogenesis of a wide range of neurodegenerative and neuropsychiatric disorders. This review synthesizes current evidence linking microbiota alterations to Alzheimer's disease (AD), Parkinson's disease (PD), amyotrophic lateral sclerosis (ALS), multiple sclerosis (MS), and stroke-including post-stroke cognitive impairment (PSCI), as well as major depressive disorder (MDD), bipolar disorder (BD), anxiety disorders, post-traumatic stress disorder (PTSD), and chronic fatigue syndrome (CFS). Common findings include reduced microbial diversity, depletion of short-chain fatty acid (SCFA)-producing genera, and enrichment of pro-inflammatory taxa. These changes contribute to neuroinflammation, blood-brain barrier (BBB) dysfunction, microglial activation, and neurotransmitter imbalances. The review further explores the neurotoxic effects of external factors such as radiation and xenobiotics on the MGBA. Despite disorder-specific variations, shared microbial and immunological mechanisms emerge across the spectrum of conditions. Importantly, we present current and emerging strategies aimed at restoring gut-brain communication, including dietary interventions such as fiber-rich and Mediterranean diets, SCFA supplementation, probiotics, and fecal microbiota transplantation (FMT). These approaches show promise in alleviating cognitive and emotional symptoms, modulating immune responses, and potentially slowing disease progression. By integrating mechanistic insights with therapeutic perspectives, this review underscores the gut microbiota as a modifiable factor in neuropsychiatric and neurodegenerative disease. Targeting the MGBA offers a novel, translational approach to intervention that may ultimately contribute to healthier brain aging and improved outcomes across the lifespan.},
}

@article {pmid41103946,
year = {2025},
author = {Zhou, L and Li, B and Ren, J and Wang, S and Wang, J},
title = {Microbiome-mediated regulation of chemoradiotherapy response.},
journal = {Frontiers in oncology},
volume = {15},
number = {},
pages = {1659467},
pmid = {41103946},
issn = {2234-943X},
abstract = {The gut microbiota critically influences patient responses to chemoradiotherapy through bidirectional interactions with host physiology, modulating both therapeutic efficacy and toxicity. Radiotherapy and chemotherapy disrupt microbial homeostasis, exacerbating intestinal damage, systemic inflammation, and immune dysfunction, while specific commensals and metabolites enhance treatment response via metabolic reprogramming, DNA repair regulation, and immune activation. Key mechanisms include microbiota-mediated TLR/NF-κB signaling, SCFA-dependent epigenetic modifications, and microbial enhancement of immune checkpoint inhibitors. Clinical interventions such as probiotics, fecal microbiota transplantation, and targeted antibiotics demonstrate potential to mitigate toxicity and overcome resistance. This review summarizes emerging evidence on how microbial dysbiosis induced by radiotherapy and chemotherapy exacerbates intestinal damage, systemic inflammation, and immune dysfunction, while specific commensals and metabolites enhance chemoradiotherapy response via metabolic reprogramming, DNA repair modulation, and immune activation. These findings underscore the gut microbiota as a critical determinant of chemoradiotherapy precision, offering actionable targets for microbiome-guided therapeutic optimization.},
}

@article {pmid41103764,
year = {2025},
author = {Jiang, T and Yang, X and Wu, B and Tao, R and Chen, R and Jin, L and Sun, D and Weng, H},
title = {Gut microbiota in hypothyroidism: pathogenic mechanisms and opportunities for precision microbiome interventions.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1661211},
pmid = {41103764},
issn = {1664-302X},
abstract = {Hypothyroidism is a common endocrine disorder characterized by insufficient thyroid hormone synthesis or secretion, most frequently caused by Hashimoto's thyroiditis, an autoimmune condition that leads to chronic thyroid gland damage. Despite the widespread use of levothyroxine replacement therapy, a substantial proportion of patients continue to experience persistent symptoms and metabolic dysregulation even after achieving biochemical euthyroidism. These observations have prompted growing interest in non-hormonal contributors to hypothyroidism, particularly the role of the gut microbiota. Recent studies indicate that gut microbial dysbiosis may influence the onset and progression of hypothyroidism through mechanisms involving immune dysregulation, increased intestinal permeability, chronic low-grade inflammation, and impaired nutrient absorption. Additionally, microbial metabolites such as short-chain fatty acids and bile acids are increasingly recognized as modulators of thyroid hormone metabolism, tissue sensitivity, and enterohepatic circulation. The bidirectional interactions between thyroid function and the gut microbiota constitute the emerging concept of the gut-thyroid axis, providing a novel framework for understanding the disease. Microbiota-targeted interventions, including probiotics, prebiotics, synbiotics, and dietary modulation, have demonstrated potential to improve microbial composition, alleviate systemic inflammation, enhance thyroid hormone utilization, and reduce autoantibody levels. This review systematically explores the mechanistic links between gut microbiota and hypothyroidism, critically evaluates current microbiota-based therapeutic strategies, and highlights future opportunities for personalized, microbiome-driven interventions to optimize the management of hypothyroidism.},
}

@article {pmid41103759,
year = {2025},
author = {Khelfaoui, I and Wang, W and Meskher, H and Shehata, AI and El Basuini, MF and Abouelenein, MF and Degha, HE and Alhoshy, M and Teiba, II and Mahmoud, SS},
title = {Beyond just correlation: causal machine learning for the microbiome, from prediction to health policy with econometric tools.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1691503},
pmid = {41103759},
issn = {1664-302X},
abstract = {The human microbiome is increasingly recognized as a key mediator of health and disease, yet translating microbial associations into actionable interventions remains challenging. This review synthesizes advances in machine learning (ML) and causal inference applied to human microbiome research, emphasizing policy-relevant applications. Explainable ML approaches, have identified microbial drivers, guiding targeted strategies. Econometric tools, including instrumental variables, difference-in-differences, and panel data models, provide robust frameworks for validating causal relationships, while hybrid methods like Double Machine Learning (Double ML) and Deep Instrumental Variables (Deep IV) address high-dimensional and non-linear effects, enabling precise evaluation of microbiome-mediated interventions. Policy translation is further enhanced by federated learning, standardized analytical pipelines, and model visualization frameworks, which collectively improve reproducibility, scalability, and data privacy compliance. By integrating predictive power with causal rigor, microbiome research can move beyond observational associations to generate interventions that are biologically grounded, clinically actionable, and policy-ready. This roadmap provides a blueprint for translating mechanistic microbial insights into real-world health solutions, emphasizing interdisciplinary collaboration, standardized reporting, and evidence-based policymaking.},
}

@article {pmid41103722,
year = {2025},
author = {Menozzi, E and Geiger, M and Meslier, V and Fierli, F and Gilles, M and Chau, KY and David, A and Shahar Golan, R and Famechon, A and Koletsi, S and Morabito, C and Quinquis, B and Pons, N and Ehrlich, SD and Macnaughtan, J and Almeida, M and Schapira, AH},
title = {Exploring the relationship between GBA1 host genotype and gut microbiome in the GBA1 [L444P/WT] mouse model: implications for Parkinson's disease pathogenesis.},
journal = {Frontiers in neuroscience},
volume = {19},
number = {},
pages = {1546203},
pmid = {41103722},
issn = {1662-4548},
abstract = {BACKGROUND: Heterozygous variants in GBA1 are the commonest genetic risk factor for Parkinson's disease (PD), but penetrance is incomplete. GBA1 dysfunction can cause gastrointestinal disturbances and microbiome changes in preclinical models. Mounting evidence suggests that the microbiota-gut-brain axis is potentially implicated in PD pathogenesis. Whether the gut microbiome composition is influenced by host GBA1 genetics in heterozygosis has never been explored.

OBJECTIVES: This study aimed to evaluate whether heterozygosity for the GBA1 pathogenic L444P variant can cause perturbations in gut microbiome composition.

METHODS: Faecal samples collected from GBA1 [L444P/WT] and GBA1 [WT/WT] mice at 3 and 6 months of age were analysed through shotgun metagenomic sequencing.

RESULTS: No differences in α- and β-diversities were detected between genotyped groups, at either time point. Overall, we found a little variation in the gut microbiome composition and functional potential between GBA1 [L444P/WT] and GBA1 [WT/WT] mice over time.

CONCLUSION: Host GBA1 genotype does not impact gut microbiome structure and composition in the presented GBA1 [L444P/WT] mouse model. Studies investigating the effect of a second hit on gut physiology and microbiome composition could explain the partial penetrance of GBA1 variants in PD.},
}

@article {pmid41103434,
year = {2025},
author = {Yang, L and Chen, H and Zeng, M and Lu, Y and Xu, C and Cao, Z and Zhong, F and Yang, X and Shen, A and Su, Y and Deng, C and Cao, H},
title = {Prenatal Poly I:C exposure affects tryptophan-kynurenine metabolism associated with intestinal microbiome in female juvenile rats.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1669845},
pmid = {41103434},
issn = {1664-3224},
mesh = {Animals ; Female ; *Poly I-C ; *Tryptophan/metabolism ; *Gastrointestinal Microbiome/drug effects ; Pregnancy ; Rats ; *Prenatal Exposure Delayed Effects/metabolism ; *Kynurenine/metabolism ; Prefrontal Cortex/metabolism ; Behavior, Animal ; Male ; Anxiety ; },
abstract = {BACKGROUND: Emerging evidence suggests that disrupted tryptophan (TRP) metabolism may contribute to an increased risk of neurodevelopmental disorders (NDDs) in the context of maternal inflammation, with gut microbiota playing a pivotal role in regulating TRP metabolic pathways.

METHODS: Juvenile female rats prenatally exposed to polyriboinosinic-polyribocytidylic acid (Poly I:C) were used to investigate the association between TRP metabolite disturbance and neuropathological/behavioral abnormalities. Behavioral tests assessed anxiety-like behavior, social interaction, and spatial memory. Immunohistochemical and gene expression analyses were performed on the prefrontal cortex (PFC) to evaluate microglial activation and neuroinflammation. TRP-kynurenine (KYN) pathway activity was measured in both PFC and peripheral circulation, along with intestinal TRP metabolism. Gut microbial composition was analyzed through diversity metrics and specific taxa identification.

RESULTS: Prenatal Poly I:C exposure induced anxiety-like behavior, impaired social interaction, and spatial memory deficits in offspring. The PFC showed sustained microglial activation and chronic neuroinflammation. TRP-KYN pathway activation was observed in both central and peripheral systems, accompanied by significant disruptions in intestinal TRP metabolism. Gut microbial analysis revealed reduced diversity and specific alterations in TRP-related taxa (Ruminococcus gauvreauii_group and Candidatus Saccharimonas). These microbial changes correlated with both intestinal TRP metabolic levels and behavioral abnormalities.

CONCLUSION: Our findings demonstrate that aberrant TRP metabolism associated with gut microbiota dysbiosis contributes to neuroinflammation and behavioral deficits in offspring following prenatal immune activation, highlighting the gut-microbiota-TRP axis as a key mechanism in neurodevelopmental impairments.},
}

Animals
Female
*Poly I-C
*Tryptophan/metabolism
*Gastrointestinal Microbiome/drug effects
Pregnancy
Rats
*Prenatal Exposure Delayed Effects/metabolism
*Kynurenine/metabolism
Prefrontal Cortex/metabolism
Behavior, Animal
Male
Anxiety

@article {pmid41103267,
year = {2025},
author = {Du, C and Kang, Y and Zeng, Q and Zhao, X and Qi, G},
title = {Metabolic changes in root exudates of plants with different disease severity affect plant resistance by regulating the rhizosphere microbiome.},
journal = {Pest management science},
volume = {},
number = {},
pages = {},
doi = {10.1002/ps.70306},
pmid = {41103267},
issn = {1526-4998},
support = {//Hubei Tobacco Company/ ; },
abstract = {BACKGROUND: Root exudates play a critical role in plant-microorganism interactions. However, information on the metabolic change in root exudates of plants with different disease severities of bacterial wilt is limited. Here, we investigate the differential metabolic pathway and metabolites among root exudates secreted by the low-grade, moderately, and severely Ralstonia solanacearum-infected tobacco plants and healthy plants.

RESULTS: Comparative analysis reveals a large divergence among metabolic profiles and rhizosphere microbial communities of the healthy plants and R. solanacearum-infected plants in terms of metabolic spectrum, community composition and diversity. The intensities of efetaal, 6-methylnicotinamide, proline, sinapinic acid, and syringic acid increase with increasing disease severity, which are chemoattractants of R. solanacearum and pathogen helpers Sphingobacterium and Stenotrophomonas, suggesting a potential role of metabolites in pathogen infection. Metabolites upregulated in R. solanacearum-infected plants inhibit the biofilm formation of antagonistic Bacillus amyloliquefaciens WH1. Metabolites elevated in healthy plants including N-acetyl-L-leucine, 3,3-dimethylglutaric acid, 4-ethylphenol, protocatechuic acid, pyridoxine, salicylic acid, trans-cinnamic acid, and tropine are chemoattractants of WH1, support cell growth and enhance biofilm formation and colonization of WH1. McpB and McpC3 are the major methyl-accepting chemotaxis proteins for salicylic acid and trans-cinnamic acid. Nutritional competition is present between WH1 and R. solanacearum.

CONCLUSION: Root exudates regulate the rhizosphere microbiome and affect plant resistance. Metabolites upregulated in healthy plants recruit antagonistic bacteria to defend the plant from pathogen invasion. Metabolites upregulated in R. solanacearum-infected plants attract pathogens and their helpers, thus aggravating the disease. © 2025 Society of Chemical Industry.},
}

@article {pmid41103006,
year = {2025},
author = {Erdem Eralp, E and Karadag, B},
title = {Insights into sinonasal disease in patients with primary ciliary dyskinesia.},
journal = {Expert review of respiratory medicine},
volume = {},
number = {},
pages = {},
doi = {10.1080/17476348.2025.2577483},
pmid = {41103006},
issn = {1747-6356},
abstract = {INTRODUCTION: Primary ciliary dyskinesia (PCD) is a rare genetic disorder characterized by impaired motile ciliary function, resulting in defective mucociliary clearance and chronic sinopulmonary disease. Although lower airway manifestations are well known, sinonasal disease is often underrecognized or undertreated outside specialist centers, particularly in adults and in settings without routine Ear-Nose-Throat evaluation.

AREAS COVERED: Despite its clinical burden, standardized diagnostic and therapeutic protocols for sinonasal disease in PCD are limited. This review synthesizes current knowledge on the pathophysiology, clinical presentation, diagnostic approaches, and management strategies for sinonasal involvement in PCD based on recent publications. Additionally, the review highlights the burden of disease and its impact on quality of life, role of genotype-phenotype correlations, and the emerging need for disease-specific outcome measures.

EXPERT OPINION: Despite growing evidence, diagnosis and management remain inconsistent due to a lack of standardized tools and guidelines. Multidisciplinary care and implementation of validated outcome measures are essential to optimize clinical follow-up and improve quality of life in this population. Future advances in imaging, microbiome profiling, and personalized interventions are needed. Furthermore, defining a standardized criteria for sinonasal exacerbations and integrating upper airway outcomes into clinical studies will be critical for advancing both research and patient care.},
}

@article {pmid41102935,
year = {2025},
author = {Rosier, BT and Hajishengallis, G and Wink, DA and Mira, A},
title = {Nitrate metabolism and periodontal health: The roles of nitric oxide in microbial killing and immunoregulation.},
journal = {Periodontology 2000},
volume = {},
number = {},
pages = {},
doi = {10.1111/prd.70006},
pmid = {41102935},
issn = {1600-0757},
support = {PID2022-143332OB-I00//European Regional Development Fund and Spanish Ministry of Science, Innovation and Universities/ ; 1ZIABC009283-36//National Cancer Institute (NCI), Cancer Innovation Laboratory (CIL)/ ; },
abstract = {BACKGROUND: Dietary nitrate, primarily sourced from vegetables, is reduced by oral bacteria to nitrite and subsequently to nitric oxide (NO), a molecule with antimicrobial and immunoregulatory properties, as well as vasodilatory and other cardiometabolic effects. Studies have shown that nitrate supplementation can lower blood pressure, reduce gingival inflammation, and lead to a shift toward microbial eubiosis in the periodontium. However, a paradox arises: nitrate and nitrite-when produced via NO synthase (NOS) activity during chronic inflammation-can serve as biomarkers of periodontitis.

AIM: This narrative review aims to (1) examine the molecular mechanisms underlying the health benefits of NO, particularly those stimulated by nitrate-rich vegetable intake; and (2) explore how chronic inflammation can alter the local environment leading to nitrate and nitrite accumulation.

MATERIALS AND METHODS: A targeted literature search was conducted in PubMed and Google Scholar to identify articles related to NO, nitrate metabolism, inflammation, and/or periodontitis.

RESULTS: Under homeostatic conditions, NO can react with bacterial iron-sulfur clusters, promoting the elimination of sensitive species, and with host soluble guanylyl cyclase (sGC), activating cGMP signaling pathways that suppress inflammation. In contrast, the inflammatory milieu of periodontitis is characterized by elevated levels of reactive oxygen species (ROS) and free heme, both of which act as NO scavengers, thereby diminishing its bioavailability. Importantly, the reaction of NO with ROS generates various reactive nitrogen species (RNS), which differ functionally from NO. These RNS can be converted into nitrate and/or nitrite (e.g., peroxynitrite, ONOO[-], decomposes into nitrate), contributing to their accumulation. Additionally, oxidative stress promotes NOS uncoupling, converting NOS from a NO-producing to a ROS-producing enzyme. Furthermore, periodontitis is associated with an impaired nitrate-reduction capacity of the oral microbiota, further decreasing NO levels.

CLINICAL RELEVANCE: Oxidative stress and reduced NO availability may drive periodontal dysbiosis and contribute to the systemic impact of periodontitis. These disease-related conditions could be mitigated through dietary interventions with nitrate-rich vegetables and adjunctive use of nitrate-reducing probiotics, which warrants further investigation.},
}

@article {pmid41102925,
year = {2025},
author = {Quigley, EMM and Kashyap, P and Moayyedi, P and Simren, M and Vanner, S},
title = {Response to Maximilian and Gasche.},
journal = {Neurogastroenterology and motility},
volume = {},
number = {},
pages = {e70182},
doi = {10.1111/nmo.70182},
pmid = {41102925},
issn = {1365-2982},
}

@article {pmid41102818,
year = {2025},
author = {Ahmed, F and Alhodieb, FS and Alsanie, SA and Rasheed, M and Ndagire, CT},
title = {Relationship between stress, diet, and gut microbiota: a cross-sectional study.},
journal = {Nutrition & metabolism},
volume = {22},
number = {1},
pages = {122},
pmid = {41102818},
issn = {1743-7075},
abstract = {BACKGROUND: The complex interaction of food habits, stress levels, and gut microbiota is instrumental in shaping global human well-being. Lifestyle indicators like diet, stress, and exercise have immense potential to drive gut health but are usually plagued by the divide between knowledge and action.

METHODLOGY: This research compared lifestyle variables and awareness of gut health in 51 participants on a standardized questionnaire. It analyzed variables such as frequency of meals, intake of processed foods, intake of dietary fiber and probiotics, history of digestive diseases, perceived influence of stress, and knowledge of the gut-brain axis.

RESULTS: Results indicated that 69.05% of the participants ate only 1-2 meals a day, and 71.43% had moderate consumption (1-2 times per week) of fast or processed foods. A concerning fact is that only 7.14% ate probiotic foods daily, and only 28.57% had high-fiber foods in their daily diet. Gastrointestinal problems were prevalent, with 56.41% having issues and 51.28% having occasional problems (1-2 times per week). In addition, 66.67% thought that stress influences their digestion, and 74.36% experienced changes in diet influencing their gut. Just 13.16% were physically active daily, and 44.74% slept for less than six hours daily, both are known to influence the gut microbiome. While 76.32% understood the diet-stress-microbiota connection, just 57.89% were of the view that dietary modifications can help manage stress.

CONCLUSION: The research points to an important gap between knowledge and practical behaviors concerning gut health and stress management. There is a need for public health programs to enhance sustainable lifestyle and dietary changes to improve microbial diversity, digestive well-being, and mental health.},
}

@article {pmid41102770,
year = {2025},
author = {Tanes, C and Hu, W and Friedman, E and Hecht, A and Daniel, S and Clish, C and Lewis, JD and Wu, GD and Bittinger, K},
title = {Distinguishing diet- and microbe-derived metabolites in the human gut.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {206},
pmid = {41102770},
issn = {2049-2618},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/physiology ; Adult ; *Diet ; Dysbiosis/microbiology/metabolism ; *Bacteria/metabolism/classification/genetics/isolation & purification ; Anti-Bacterial Agents/pharmacology ; Male ; *Metabolome ; Female ; Inflammatory Bowel Diseases/microbiology/metabolism ; Metabolomics/methods ; Feces/microbiology ; Enteral Nutrition ; Polyethylene Glycols ; },
abstract = {BACKGROUND: Human gut microbes metabolize food and host secretions, consuming and producing small molecules that are important to health and homeostasis. Here, we present an atlas of diet- and microbiome-derived metabolites in the human gut, constructed from a controlled feeding experiment of adults on omnivore and enteral nutrition diets.

RESULTS: By comparing metabolite concentration before and after microbiome depletion with antibiotics and polyethylene glycol, we identified 2856 microbial products decreasing and 1057 microbial substrates increasing in concentration after depletion. We also identified 2496 diet-derived metabolites by comparing diet groups when the microbiome was depleted. Seven days after antibiotics, 98% of gut metabolites recovered to pre-antibiotic levels in the omnivore group. In plasma samples, only 93 microbiome-derived metabolites varied with gut microbiome depletion, indicating a limited impact on circulating metabolites. To demonstrate our metabolite atlas, we annotated metabolites associated with inflammatory bowel disease and identified the microbiome-derived metabolites altered in gut dysbiosis.

CONCLUSIONS: We identified metabolites associated with the metabolism of the human gut microbiome, mapping its overall metabolic potential. Furthermore, we measured the rate at which metabolites were recovered following gut microbiome disruption.},
}

Humans
*Gastrointestinal Microbiome/drug effects/physiology
Adult
*Diet
Dysbiosis/microbiology/metabolism
*Bacteria/metabolism/classification/genetics/isolation & purification
Anti-Bacterial Agents/pharmacology
Male
*Metabolome
Female
Inflammatory Bowel Diseases/microbiology/metabolism
Metabolomics/methods
Feces/microbiology
Enteral Nutrition
Polyethylene Glycols

@article {pmid41102553,
year = {2025},
author = {Winer, DA and Du, H and Kim, J and Chang, V and Burke, M and Winer, S and Costes, SV and Frippiat, JP and Sams, C and Paul, AM and Wu, H and Ullrich, O and Baatout, S and Beheshti, A and Mason, CE and Choukér, A and Crucian, BE},
title = {Astroimmunology: the effects of spaceflight and its associated stressors on the immune system.},
journal = {Nature reviews. Immunology},
volume = {},
number = {},
pages = {},
pmid = {41102553},
issn = {1474-1741},
abstract = {As humans embark on longer and deeper missions into space, it is crucial to understand how spaceflight impacts the immune system. Decades of discoveries, bolstered by recent multiomic analyses, have identified key immune processes that are affected by the spaceflight environment. These findings form the foundations of the emerging field of 'astroimmunology'. Spaceflight stressors - such as microgravity and galactic cosmic radiation - and other mission-associated variables, including psychological stress and abnormal circadian rhythms, can disrupt or adversely affect immune cell biology. In addition, spaceflight alters host-microbiome interactions, which can increase susceptibility to opportunistic pathogens and viral reactivation. Although ground-based analogues for human spaceflight have provided insights into these stressors individually, their combined effects during spaceflight remain less understood. This Review explores our current knowledge of the effects of spaceflight stressors on the immune system and the clinical implications for human space exploration. It also highlights current and developing countermeasures, including machine-learning approaches, advanced monitoring technologies and standardized biobanking, that can facilitate research into the impact of spaceflight on the immune system. Looking ahead, progressing from low Earth orbit missions to long-term missions to the Moon, Mars and beyond will introduce new challenges, including increased radiation, variable gravity and regolith exposure. We discuss these prospective challenges and outline potential preventive and mitigative strategies for sustaining immune health to enable safe and effective space exploration and habitation of distant worlds.},
}

@article {pmid41102509,
year = {2025},
author = {Oh, JY and Ko, YK and Jeon, MH and Doo, HM and Roh, S and Gim, JA},
title = {Distinguishing tuberculosis from non-tuberculous mycobacteria and other respiratory conditions by microbiome patterns.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {36129},
pmid = {41102509},
issn = {2045-2322},
support = {2022R1C1C1009250//National Research Foundation of Korea/ ; 2022R1C1C1009250//National Research Foundation of Korea/ ; 2022R1C1C1009250//National Research Foundation of Korea/ ; 2022R1C1C1009250//National Research Foundation of Korea/ ; 2022R1C1C1009250//National Research Foundation of Korea/ ; 2022R1C1C1009250//National Research Foundation of Korea/ ; },
mesh = {Humans ; *Nontuberculous Mycobacteria/genetics/isolation & purification ; *Microbiota/genetics ; *Mycobacterium Infections, Nontuberculous/diagnosis/microbiology ; Female ; Male ; RNA, Ribosomal, 16S/genetics ; Middle Aged ; Adult ; Aged ; *Tuberculosis/diagnosis/microbiology ; Diagnosis, Differential ; },
abstract = {Tuberculosis (TB) and non-tuberculous mycobacterial (NTM) infections, both caused by acid-fast bacteria, exhibit overlapping clinical presentations and radiological findings, making accurate and swift differentiation imperative for appropriate patient management. The ability to promptly distinguish between TB and NTM is pivotal, particularly in healthcare settings where TB patients require isolation. So, there is a pressing need to identify reliable biomarkers capable of delineating these conditions. In this study, we carefully analyzed a group of 108 patients, including 38 with TB, 29 with NTM, and 41 with other respiratory diseases. We used bacterial 16 S rRNA sequencing to examine the relative amounts of different microbial species in each patient group. We also used advanced methods like co-occurrence analysis, mutually exclusive analysis, and decision tree analysis to explore the complex patterns within the microbial communities. Our investigation revealed intriguing associations between microbial taxa and disease entities. In TB patients, prominent species were Enterococcus faecalis, Streptococcus mutans, and Snodgrassella alvi, while in NTM, prominent species were Cariobacterium hominis and Prevotella nigrescens. The absence of Mobiluncus curtisii indicated a higher probability of NTM, especially if Olsenella phocaeensis was also absent. This comprehensive analysis unveiled distinct microbial signatures that serve as discerning markers for discriminating TB, NTM infections, and other respiratory ailments. By elucidating microbial patterns unique to each condition, our findings offer valuable insights into the development of diagnostic strategies and therapeutic interventions tailored to specific respiratory infections.},
}

Humans
*Nontuberculous Mycobacteria/genetics/isolation & purification
*Microbiota/genetics
*Mycobacterium Infections, Nontuberculous/diagnosis/microbiology
Female
Male
RNA, Ribosomal, 16S/genetics
Middle Aged
Adult
Aged
*Tuberculosis/diagnosis/microbiology
Diagnosis, Differential

@article {pmid41102501,
year = {2025},
author = {Lin, YY and Ding, JL and Shen, HT and Lin, YM and Adhidjaja, EC and Chang, SC},
title = {PD-1/PD-L1 Cancer Immunotherapeutics Reshape Tumor Microenvironment - Clinical Evidence and Molecular Mechanisms for AI-based Precision Medicine.},
journal = {Clinical reviews in allergy & immunology},
volume = {68},
number = {1},
pages = {91},
pmid = {41102501},
issn = {1559-0267},
support = {H-154-00-000019//National University of Singapore/ ; A-0001574//Taipei Medical University, Taiwan/ ; NSTC 112-2314-B-038-134//National Science and Technology Council, Taiwan/ ; NSTC 114-2314-B-038-107-MY3//National Science and Technology Council/ ; },
mesh = {Humans ; *Tumor Microenvironment/immunology/drug effects ; *B7-H1 Antigen/metabolism/antagonists & inhibitors/immunology ; *Neoplasms/therapy/immunology/metabolism/etiology ; *Precision Medicine/methods ; *Programmed Cell Death 1 Receptor/metabolism/antagonists & inhibitors ; *Immunotherapy/methods ; *Immune Checkpoint Inhibitors/therapeutic use ; Animals ; Gastrointestinal Microbiome ; Protein Processing, Post-Translational ; },
abstract = {PD-1 (Programmed cell death protein 1) located on T cells, binds to PD-L1 (Programmed cell death ligand 1) on cancer cells, to suppress T cell activation and enable immune evasion. Hitherto, reviews have mainly highlighted the role of PD-1/PD-L1 in anti-cancer immunomodulation, anti-cancer therapy resistance, and immune-related adverse events. However, there are critical modes of enhancement of therapeutic efficacy, which remain underappreciated. This review provides a holistic perspective on: (a) a comprehensive analysis of recent clinical trials targeting PD-1/PD-L1, specifically on the use of immune checkpoint inhibitors (ICIs); (b) the underlying molecular mechanisms of immune surveillance; (c) the role of ubiquitin-mediated post-translational modifications (PTMs, viz the ubiquitin machinery); and (d) the gut microbiome crosstalk with the PD-1/PD-L1 axis, which influences the tumor microenvironment (TME). Clarity gained from opinions exerted from these four factors, in this review, will provide insights on improving cancer prevention, diagnosis, and treatment, thus bridging translational research to the clinic. These standpoints will be presented with a view to advocating the integration of precision medicine with AI, to accelerate the discovery of more effective ICIs and enhance mono-/combinatorial drug strategies for PD-1/PD-L1-targeted therapy. Altogether, this review opines that AI-driven analytics will provoke an innovative impact on promoting clinical outcomes beneficial for cancer patients.},
}

Humans
*Tumor Microenvironment/immunology/drug effects
*B7-H1 Antigen/metabolism/antagonists & inhibitors/immunology
*Neoplasms/therapy/immunology/metabolism/etiology
*Precision Medicine/methods
*Programmed Cell Death 1 Receptor/metabolism/antagonists & inhibitors
*Immunotherapy/methods
*Immune Checkpoint Inhibitors/therapeutic use
Animals
Gastrointestinal Microbiome
Protein Processing, Post-Translational

@article {pmid41102477,
year = {2025},
author = {Zaparte, A and Lammons, JW and Taylor, CM and Luo, M and Lin, HY and Siggins, RW and Molina, PE and Welsh, DA},
title = {Sex specific gut bacterial community structure: implications for frailty risk in people with HIV.},
journal = {GeroScience},
volume = {},
number = {},
pages = {},
pmid = {41102477},
issn = {2509-2723},
support = {P60 AA009803/AA/NIAAA NIH HHS/United States ; T32AA007577/AA/NIAAA NIH HHS/United States ; },
abstract = {Frailty is a major health concern associated with aging and has been linked to gut microbiome composition, especially in elderly individuals needing care. People with HIV (PWH) present high risk of early-onset frailty. This study examines the relationship between frailty and the gut microbiome, with an emphasis on sex-based differences in PWH. Data were drawn from 268 participants in the New Orleans Alcohol Use in HIV (NOAH) Study, including 16S microbiome sequencing from stool samples, cytokine levels, viral load, and T cell counts. Frailty was assessed using phenotypic frailty index (PFI) and a 58-item deficit index (DI-58). Fourteen taxa were significantly linked to both PFI and DI-58. Among females, butyrate-producing genera (e.g., Eubacterium ventriosum and Butyricimonas) were inversely associated with frailty, while genera such as Paraprevotella and Romboutsia showed positive associations. In males, Prevotella and Erysipelotrichaceae UCG-003 were inversely associated, whereas Christensenellaceae R-7, Clostridium sensu stricto, and others were positively associated with frailty. Fifteen genera were also linked to circulating cytokine levels (IL-1β, IL-17A, IL-2, IFN-γ). We identified three community state types (CSTs) with unique bacterial structures. Community state analysis identified CST 2, characterized by lower diversity and more pathobionts, to be highly predictive of increased frailty. These findings underscore the relevance of sex-specific differences in the gut microbiota relations with frailty, supporting tailored interventions for frailty in PWH.},
}

@article {pmid41102233,
year = {2025},
author = {Kwak, MJ and Park, J and Park, H and Yoon, J and Lee, J and Hahnke, RL and Lee, SW and Kwon, SK and Song, JY and Kim, JF},
title = {Polyphasic and comparative genomic characterization of a novel Mariniflexile species in the rhizosphere microbiome of tomato resistant to bacterial wilt.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {36158},
pmid = {41102233},
issn = {2045-2322},
support = {918011-4//Ministry of Agriculture, Food and Rural Affairs/ ; NRF-2023R1A2C3004496//Ministry of Science and ICT, South Korea/ ; NRF-2018R1A6A1A03025607//Ministry of Education, South Korea/ ; },
mesh = {*Solanum lycopersicum/microbiology ; *Rhizosphere ; Phylogeny ; *Plant Diseases/microbiology ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Genome, Bacterial ; Ralstonia solanacearum ; Soil Microbiology ; Genomics ; Disease Resistance ; },
abstract = {A plethora of microbes resides in the plant rhizosphere, and some play roles in host health and disease. We previously isolated a Gram-negative, aerobic, rod-shaped rhizobacterium, TRM1-10, that contributes to bacterial wilt resistance of tomato caused by Ralstonia solanacearum. In this study, we characterized TRM1-10 through physiological and biochemical analyses, complemented by whole genome sequencing and comparative genomic analyses. Phylogenetic analysis using the 16S rRNA gene and genome sequences revealed that TRM1-10 belongs to the genus Mariniflexile and represents a new lineage. TRM1-10 also exhibits noticeable differences in physiological and biochemical characteristics compared to other Mariniflexile species. Thus, based on phylogenetic affiliation and chemotaxonomic characteristics, we propose this bacterium as a novel species in the genus, Mariniflexile rhizosphaerae sp. nov. (type strain TRM1-10[T] = KCTC 18646P[T] = DSM 33122[T]). Comparative genome analyses revealed that TRM1-10 harbors more genes linked to soil adaptation compared to other phylogenetically related Mariniflexile species, most of which are associated with marine habitats. The genomic features of TRM1-10 and other strains in the species may allow the taxon to adapt to the soil and rhizosphere, compete effectively with the resident soil microbiota, and contribute to plant health.},
}

*Solanum lycopersicum/microbiology
*Rhizosphere
Phylogeny
*Plant Diseases/microbiology
RNA, Ribosomal, 16S/genetics
*Microbiota/genetics
Genome, Bacterial
Ralstonia solanacearum
Soil Microbiology
Genomics
Disease Resistance

@article {pmid41102214,
year = {2025},
author = {Hara, T and Meng, S and Motooka, D and Arao, Y and Saito, Y and Rennie, S and Uchida, S and Ofusa, K and Arai, T and Konno, M and Satoh, T and Ishii, H},
title = {Deficiencies in methionine, tryptophan, and niacin remodels intestinal transcriptome and gut microbiota in female mice.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {36155},
pmid = {41102214},
issn = {2045-2322},
support = {JP23ym0126809 and JP24ym0126809//Japan Agency for Medical Research and Development/ ; 19K22658, 20H00541, 21K19526, 22H03146, 22K19559, 23K19505, 23K18313, 23KK0153, 24K22144, and 16H06279 (PAGS)//Ministry of Education, Culture, Sports, Science and Technology/ ; },
mesh = {Animals ; Female ; *Gastrointestinal Microbiome/genetics ; *Niacin/deficiency ; Mice ; *Tryptophan/deficiency ; *Methionine/deficiency ; *Transcriptome ; Mice, Inbred C57BL ; Caloric Restriction ; *Intestines/microbiology ; },
abstract = {Caloric restriction is well-established as a robust intervention that may extend lifespan and improve metabolic health across species with effects that are increasingly attributed to both host metabolic remodeling and alterations in the gut microbiota. Recent studies suggest that restricting specific dietary components can replicate these benefits. While methionine and branched-chain amino acid restriction improve metabolism and modulate the gut microbiome, the effects of other nutrients remain unclear. Here, we explore the effects of methionine, tryptophan and niacin deprivation on host intestinal gene expression and gut microbiota using female murine models. Through transcriptomic analysis of the intestinal tissue, we found that transient dietary restriction of methionine, tryptophan, and niacin induced significant changes in intestinal gene expression, particularly in genes involved in oxidative phosphorylation and ATP production. Single-cell analysis revealed that dietary restriction of those nutrients led to an increase in intestinal immune cell populations. Gut microbiota profiling also revealed that transient deprivation of those nutrients resulted in changes in microbial composition, with an increased relative abundance of Lactobacillus species observed in some cases. Our findings highlight the potential of targeted nutrient restriction as a strategy to reprogram host-microbiome interactions.},
}

Animals
Female
*Gastrointestinal Microbiome/genetics
*Niacin/deficiency
Mice
*Tryptophan/deficiency
*Methionine/deficiency
*Transcriptome
Mice, Inbred C57BL
Caloric Restriction
*Intestines/microbiology

@article {pmid41102028,
year = {2025},
author = {Schmitt, C and Goedicke-Fritz, S and Fortmann, I and Zemlin, M},
title = {Vaccinations in preterm infants: Which and when?.},
journal = {Seminars in fetal & neonatal medicine},
volume = {},
number = {},
pages = {101670},
doi = {10.1016/j.siny.2025.101670},
pmid = {41102028},
issn = {1878-0946},
abstract = {Preterm infants, who represent around 10 % of births worldwide, are at markedly increased risk of infections due to their immunological immaturity and reduced maternal antibody transfer. Although international guidelines recommend immunization based on chronological age, vaccination in this population is frequently delayed or incomplete. This review summarizes the current evidence on vaccine safety, efficacy, and timing in preterm infants, with particular emphasis on primary immunizations and vaccines administered during the first year of life. Distinct immunological characteristics-including impaired T- and B-cell responses as well as altered microbiome development-contribute to reduced vaccine responsiveness. Emerging approaches such as mRNA vaccine technologies, novel adjuvants, maternal immunization, and microbiome modulation hold promise for enhancing vaccine efficacy. Ensuring timely immunization and adherence to vaccination recommendations in preterm infants is essential to reduce preventable morbidity and mortality in this highly vulnerable group.},
}

@article {pmid41101759,
year = {2025},
author = {Thomas, MC and Fisher, R and Waugh, G and Vanwonterghem, I and Webster, NS and Negri, AP and Luter, HM},
title = {Defining Site-Specific Water Quality Guidelines for Marine Microbiomes under Contaminant Stress.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c04124},
pmid = {41101759},
issn = {1520-5851},
abstract = {Marine ecosystem resilience is closely linked to microbiome health, yet prokaryotes are typically overlooked in conservation management due to challenges in quantitatively defining microbial sensitivity thresholds. This study introduces a novel approach that combines 16S rRNA gene amplicon sequencing with ecotoxicological concentration-response modeling to assess marine microbial responses to contamination stress at both community and taxon levels. By applying propidium monoazide to differentiate intact from membrane-compromised cells combined with normalization of relative to absolute abundances via flow cytometry, no-significant-effect concentration values can be derived from individual taxon-specific stress-response curves. These thresholds inform prokaryotic sensitivity distributions, enabling the derivation of microbiome hazard concentrations that estimate the contaminant concentrations affecting x% of the microbial community─a metric fully compatible with existing eukaryotic datasets and regulatory frameworks. Applied to seawater microbiomes exposed to copper along a disturbance gradient, higher copper sensitivities were observed in microbiomes from ecologically valuable sites, such as coral reefs, compared to disturbed areas. The site-specific microbiome hazard concentrations for copper affecting 5% of community taxa ranged from 0.10 to 0.94 μg L[-1], highlighting the need for stricter environmental protection of ecologically valuable sites. This quantitative approach provides a robust pathway for direct integration of site-specific microbiome sensitivity data into environmental risk assessments.},
}

@article {pmid41101348,
year = {2025},
author = {Koehlen, S and Harks, I and Matern, J and Prior, K and Eickholz, P and Lorenz, K and Kim, TS and Kocher, T and Meyle, J and Kaner, D and Jockel-Schneider, Y and Harmsen, D and Ehmke, B and Kleine Bardenhorst, S and Hagenfeld, D},
title = {Exhaled Carbon Monoxide Indicates Persistent Subgingival Dysbiosis After Periodontal Therapy.},
journal = {Journal of clinical periodontology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jcpe.70053},
pmid = {41101348},
issn = {1600-051X},
support = {468857272//Deutsche Forschungsgemeinschaft/ ; },
abstract = {AIM: To investigate whether exhaled carbon monoxide (CO) is dose-dependently associated with subgingival polymicrobial clusters before and after non-surgical periodontal therapy.

MATERIAL AND METHODS: We followed 163 adults with periodontitis, measuring CO before and at 2, 14 and 26 months after therapy. Subgingival plaque samples were analysed using 16S rRNA gene sequencing. We applied topic models and regression analysis, adjusted for age, sex, treatment group, pocket probing depth and plaque levels.

RESULTS: Smokers had generally higher mean CO levels at every visit and showed significant declines at 14 and 26 months after therapy (p < 0.01). Before therapy, CO was not associated with dysbiosis; after therapy, higher levels were positively associated. In sensitivity analyses, self-reported smoking status explained more variance in dysbiosis than CO alone, with only marginal gains when both were combined. Among smokers, a distinct polymicrobial cluster dominated by Fusobacterium and Prevotella increased with higher exhaled CO. Every 10 parts per million increase in CO was associated with an estimated 16% increase in cluster abundance (95% confidence interval: 8%-26%).

CONCLUSION: Exhaled CO may help monitor persistent dysbiosis and select an anaerobe-dominated subgingival community after periodontal therapy among smokers.},
}

@article {pmid40622976,
year = {2025},
author = {Kehila, D and Tafreshi, AG and Tokuriki, N},
title = {Stability of multi-species consortia during microbial metabolic evolution.},
journal = {Evolution; international journal of organic evolution},
volume = {79},
number = {10},
pages = {2156-2166},
doi = {10.1093/evolut/qpaf141},
pmid = {40622976},
issn = {1558-5646},
support = {RGPIN 2017-04909//Natural Sciences and Engineering Research Council of Canada/ ; },
mesh = {*Biological Evolution ; *Microbial Consortia ; Xenobiotics/metabolism ; *Metabolic Networks and Pathways ; *Bacteria/metabolism/genetics ; *Evolution, Molecular ; },
abstract = {Explaining multi-genic adaptations is a major objective of evolutionary theory. Metabolic pathways require multiple functional enzymes to generate a phenotype, and their evolution in microbes remains underexplored. In particular, sites polluted with manmade chemicals or "xenobiotics", like plastic or pesticides, provide evidence for the rapid adaptation of novel metabolic pathways in microbes, which degrade these xenobiotics into utilizable nutrients. Decades of microbiological studies revealed that these pathways often are not consolidated within a single microbial species but are rather distributed across several different species cooperatively degrading xenobiotics. These diverse consortia are remarkably stable in the laboratory, but the determinants of this stability have not been hereto addressed. In this study, we predict barriers to stable co-existence arising from the metabolic roles each species plays in the novel metabolic pathway. Then, we show that ecological variation in microbial life history overcomes these barriers and explains stable co-existence in mathematical models of exemplary consortia growing on a xenobiotic as the sole source of a limiting nutrient. Stability hinges on an "ecological matching" between a species' metabolic role and its nutrient utilization strategy, which, if satisfied, can greatly accelerate the evolution of metabolic pathways in both field and laboratory.},
}

*Biological Evolution
*Microbial Consortia
Xenobiotics/metabolism
*Metabolic Networks and Pathways
*Bacteria/metabolism/genetics
*Evolution, Molecular

@article {pmid41101342,
year = {2025},
author = {Niu, C and Zhang, J and Singh, H and Mostafa, MAO and Zhu, K and Farooq, U and Okolo, PI and Mushtaq, A and Daglilar, E and Alweis, R},
title = {Impact of Concomitant Proton Pump Inhibitor Use on the Efficacy of Immune Checkpoint Inhibitors Across Multiple Cancer Types.},
journal = {Journal of the National Comprehensive Cancer Network : JNCCN},
volume = {},
number = {},
pages = {1-7},
doi = {10.6004/jnccn.2025.7070},
pmid = {41101342},
issn = {1540-1413},
abstract = {BACKGROUND: Proton pump inhibitors (PPIs) are commonly prescribed medications that may influence the gut microbiome and impact the efficacy of immune checkpoint inhibitors (ICIs) in cancer treatment.

PATIENTS AND METHODS: We conducted a large retrospective cohort study using the TriNetX database, encompassing >35,621 patients with cancer treated with ICIs between January 2015 and June 2021. Patients were stratified into 2 cohorts: those receiving ICIs with concurrent PPI use and those without PPI use.

RESULTS: Concomitant PPI use was associated with significantly higher mortality rates in patients treated with PD-1 inhibitors across multiple cancer types, including melanoma (hazard ratio [HR], 1.889; 95% CI, 1.752-2.037); breast cancer (HR, 1.512; 95% CI, 1.345-1.701); urothelial carcinoma (HR, 1.406; 95% CI, 1.276-1.551); colorectal cancer (HR, 1.310; 95% CI, 1.187-1.445); hepatocellular carcinoma (HR, 1.413; 95% CI, 1.238-1.614); renal cancer (HR, 1.490; 95% CI, 1.375-1.614); Hodgkin lymphoma (HR, 1.646; 95% CI, 1.212-2.236); head and neck cancers (HR, 1.402; 95% CI, 1.259-1.561); and lung cancer (HR, 1.308; 95% CI, 1.184-1.445). Similar trends were observed with PD-L1 inhibitors, where PPI use correlated with increased mortality in melanoma (HR, 1.657; 95% CI, 1.049-2.617); breast cancer (HR, 1.584; 95% CI, 1.297-1.934); renal cancer (HR, 1.380; 95% CI, 1.059-1.799); and urothelial carcinoma. ICU admissions were more frequent among PPI users across different cancer types and ICI treatments.

CONCLUSIONS: This study underscores the potential risks associated with the concomitant use of PPIs and ICIs in cancer treatment. The findings suggest that careful consideration is necessary when prescribing PPIs to patients undergoing ICI therapy.},
}

@article {pmid41101029,
year = {2025},
author = {Ma, L and Liu, F and Zhou, M and Zhang, M and Zheng, J and Wang, Z and He, Z and Yan, Q and Wu, B and Wang, C and Shu, L},
title = {Amoebae contribute to the diversity and fate of antibiotic resistance genes in drinking water system.},
journal = {Environment international},
volume = {204},
number = {},
pages = {109867},
doi = {10.1016/j.envint.2025.109867},
pmid = {41101029},
issn = {1873-6750},
abstract = {Free-living amoebae represent a significant eukaryotic group that thrives in drinking water systems, posing considerable risks to water quality due to their inherent pathogenicity and associations with various microorganisms. However, the symbiotic microbial profiles of different amoeba species and the impact of amoeba-bacteria interactions on the antibiotic resistome within drinking water systems remain poorly understood. In this study, we obtained 24 amoeba isolates from tap water, encompassing diverse phyla within the amoeba lineage. Through metagenome sequencing, we uncovered variations in symbiotic microbiome composition across different amoeba species and strains. Notably, amoebae acted as vectors for human pathogens, including bacteria and viruses. The majority of symbionts carried multiple antibiotic-resistance genes and virulence factors. Furthermore, dominant symbiotic species could be cultured independently, underscoring the critical role of amoebae in preserving and transmitting antibiotic-resistant opportunistic pathogens in drinking water systems. Disinfection experiments demonstrated highly diverse viability of amoebae and their protective capabilities for symbionts against chlorine disinfection. Our findings expand the germplasm bank for amoebae and symbiotic bacteria derived from tap water and emphasize the necessity for further research on amoeba-bacteria symbiosis to ensure drinking water quality and public health safety.},
}

@article {pmid41100899,
year = {2025},
author = {Gélinas, V and Paquet, VE and Paquet, MF and Vincent, AT and Charette, SJ},
title = {Phylogenetic and Genomic Insights of Flavobacterium Diversity in Quebec's Fish Farms.},
journal = {Canadian journal of microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1139/cjm-2025-0076},
pmid = {41100899},
issn = {1480-3275},
abstract = {The genus Flavobacterium constitutes a vast pool of microorganisms living in multiple environmental niches including fish pathogens and species in the fish microbiome. Veterinary reports have identified flavobacteria in fish from Quebec's fish farms, confirming their association with infections. However, these reports have not conducted in-depth characterization, and the diversity of non-pathogenic flavobacteria in Quebec remains unknown. This study is the first step in assessing the diversity of Flavobacterium in Quebec's fish farms, without focusing solely on pathogenic strains. Seventeen isolates were collected from different fish farms, from either the water or fish. Microbial species identification was performed using PCR genotyping of the gyrB gene, whole-genome sequencing, and phylogenetic analysis. Antimicrobial susceptibility tests for tetracycline and florfenicol, the two most commonly used antibiotics in Quebec aquaculture, along with predictive tools, were employed to assess resistance. This study revealed potential new species among the isolates. No known pathogenic species were detected, and all 17 isolates clustered within CIIIb or CIIIc, recently described phylogenetic clades of Flavobacterium found in various environments, and the majority showed resistance to antibiotics. This study highlights the expanding diversity of Flavobacterium, particularly among species associated with fish, and underscores the need for further research in Quebec.},
}

@article {pmid41100723,
year = {2025},
author = {Guan, WJ and Pan, CX and Martinez-Garcia, MA},
title = {The Upper Airway Microbiome in Bronchiectasis: Expanding the Landscape of Airway Dysbiosis.},
journal = {American journal of respiratory and critical care medicine},
volume = {},
number = {},
pages = {},
doi = {10.1164/rccm.202508-2095ED},
pmid = {41100723},
issn = {1535-4970},
}

@article {pmid41100528,
year = {2025},
author = {Deschner, D and Hill, JE},
title = {Identification of genes that differentiate Mannheimia haemolytica genotypes 1 and 2 using a pangenome approach.},
journal = {PloS one},
volume = {20},
number = {10},
pages = {e0325338},
doi = {10.1371/journal.pone.0325338},
pmid = {41100528},
issn = {1932-6203},
mesh = {*Mannheimia haemolytica/genetics/pathogenicity/classification ; Genotype ; *Genome, Bacterial ; Animals ; Cattle ; *Genes, Bacterial ; Bacterial Proteins/genetics ; },
abstract = {Mannheimia haemolytica is an opportunistic bacterial pathogen associated with the economically costly bovine respiratory disease. Two genotypes have been described, of which genotype 2 is more strongly associated with disease. Several previous studies have investigated the genomic differences between the genotypes and/or the major serotypes (1, 2 and 6) of M. haemolytica, however we still lack a clear basis for the greater disease association of genotype 2 (serotypes 1 and 6) and demonstrations of phenotypic differences are scarce. This work builds upon previous investigations to identify genes that differentiate the two genotypes with a particular focus on genes that may play a role in virulence and fitness in the respiratory tract microbiome. We identified 422 genotype differentiating genes in a collection of 206 unique M. haemolytica genomes (61 genotype 1, 145 genotype 2). Genotype differentiating genes included genotype-associated variants of a TonB-dependent siderophore receptor homolog, transferrin binding protein B, leukotoxin A, and IgA1 proteases. We also identified a genotype 1 associated lytic transglycosylase, and a genotype 2 specific highly immunogenic outer membrane lipoprotein. Genotype 2 genomes were significantly larger in size and contained more predicted protein coding genes than genotype 1 genomes. These results expand our knowledge of what differentiates the genotypes 1 and 2 of M. haemolytica and provides information that can be used as the basis for laboratory investigations of corresponding phenotypic differences.},
}

*Mannheimia haemolytica/genetics/pathogenicity/classification
Genotype
*Genome, Bacterial
Animals
Cattle
*Genes, Bacterial
Bacterial Proteins/genetics

@article {pmid41100520,
year = {2025},
author = {Stirnemann, EM and Sasse, J},
title = {How to harness the effects of exudates and microbes that support beneficial plant-plant interactions for sustainable agriculture.},
journal = {PLoS biology},
volume = {23},
number = {10},
pages = {e3003416},
doi = {10.1371/journal.pbio.3003416},
pmid = {41100520},
issn = {1545-7885},
mesh = {*Crops, Agricultural/microbiology/growth & development/metabolism ; *Agriculture/methods ; Plant Roots/microbiology/metabolism ; Rhizosphere ; *Plant Exudates/metabolism ; Microbiota/physiology ; Soil Microbiology ; *Plants/microbiology/metabolism ; },
abstract = {Root exudates, species-specific metabolites released by plants into the rhizosphere, shape plant nutrient uptake, plant-plant and plant-microbiome interactions. When optimized, such interactions boost the productivity of sustainable agricultural systems such as intercropping and crop rotation. However, why certain combinations of crops are beneficial and others are not, remains unclear. This Essay outlines how optimal crop combinations could be determined, focusing on the molecular interplay of crops and their microbial partners. With an advanced understanding of root exudation and its effects on microbes, new strategies for sustainable farming could be unlocked, reducing reliance on fertilizers and pesticides, and tackling challenges raised by a changing climate.},
}

*Crops, Agricultural/microbiology/growth & development/metabolism
*Agriculture/methods
Plant Roots/microbiology/metabolism
Rhizosphere
*Plant Exudates/metabolism
Microbiota/physiology
Soil Microbiology
*Plants/microbiology/metabolism

@article {pmid41100345,
year = {2025},
author = {Meunier, D and Corona-Torres, R and Boulton, K and Wu, Z and Ballantyne, M and Glendinning, L and Ahmad, AA and Borowska, D and Taylor, L and Vervelde, L and Del Pozo, J and Vasilogianni, M and Jaramillo-Ortiz, J and Sanchez-Arsuaga, G and Psifidi, A and Tomley, F and Watson, KA and McGrew, MJ and Stevens, MP and Blake, DP and Hume, DA},
title = {Interleukin 10 controls the balance between tolerance, pathogen elimination, and immunopathology in birds.},
journal = {eLife},
volume = {14},
number = {},
pages = {},
doi = {10.7554/eLife.106252},
pmid = {41100345},
issn = {2050-084X},
support = {BB/P022049/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/P021638/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 13393976//Cobb-Vantress/ ; 13302777//Roslin Institute/ ; BBS/E/D/20002174/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/RL/230002B/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Animals ; *Interleukin-10/genetics/metabolism/immunology ; *Chickens/immunology ; Salmonella typhimurium/immunology ; *Immune Tolerance ; Campylobacter jejuni/immunology ; Macrophages/immunology ; *Immunity, Mucosal ; Cecum/microbiology ; *Poultry Diseases/immunology/microbiology ; Campylobacter Infections/immunology/veterinary ; Gastrointestinal Microbiome ; },
abstract = {Effective mucosal immunity in the intestine involves a fine balance between tolerance of the microbiome, recognition, and elimination of pathogens, and inflammatory tissue injury. The anti-inflammatory cytokine IL10 regulates these processes in the intestines of mice and humans; the anti-inflammatory activity of IL10 is also conserved in birds. To determine the function of IL10 in avian mucosal immunity, we generated germ line modifications of the chicken IL10 locus to abolish or reduce IL10 expression. In vitro analysis of macrophage response to lipopolysaccharide confirmed the loss of IL10 protein expression, the lack of dosage compensation in heterozygotes, and prevention of autocrine inhibition of nitric oxide production in homozygous IL10 knockout macrophages. IL10-deficiency significantly altered the composition of the caecal microbiome, but unlike IL10-deficient mice and humans, IL10-deficient chickens did not exhibit spontaneous colitis. Following experimental challenge with Salmonella enterica serovar Typhimurium or Campylobacter jejuni in IL10-deficient chickens, enhanced clearance of the pathogens was associated with elevated transcription of pro-inflammatory genes and increased infiltration of inflammatory cells into gut mucosa. In IL10-deficient chickens challenged with the parasite Eimeria tenella, pathogen clearance was accelerated but caecal lesions were more severe and weight gain was compromised. Neither the heterozygous IL10 knockout nor a homozygous IL10 enhancer mutation had a major effect on pathogen clearance or inflammation in any of the challenge models. Our findings highlight the intrinsic compromise in mucosal immune response and have important implications for the development of strategies to combat avian and zoonotic pathogens in poultry.},
}

Animals
*Interleukin-10/genetics/metabolism/immunology
*Chickens/immunology
Salmonella typhimurium/immunology
*Immune Tolerance
Campylobacter jejuni/immunology
Macrophages/immunology
*Immunity, Mucosal
Cecum/microbiology
*Poultry Diseases/immunology/microbiology
Campylobacter Infections/immunology/veterinary
Gastrointestinal Microbiome

@article {pmid41100191,
year = {2025},
author = {Fernandes, ILB and Cantor, MC and Fonseca, A and Ganda, E and Felix, TL},
title = {The association of lung consolidation in beef × dairy cattle at weaning with feedlot growth performance, carcass characteristics, liver health, and liver microbiome diversity.},
journal = {Journal of animal science},
volume = {},
number = {},
pages = {},
doi = {10.1093/jas/skaf358},
pmid = {41100191},
issn = {1525-3163},
abstract = {Bovine respiratory disease (BRD) is the costliest disease in the cattle industry and often compromises the immune system. The objective of this observational cohort study was to evaluate the impact of lung consolidation (LC) diagnosed at weaning (8 ± 2 wk of age) on feedlot growth performance, carcass characteristics, and liver health and microbiome in beef × dairy cattle. At 4 d post-weaning, LC was assessed by thoracic ultrasonography. The cattle (n = 139) either had ≥ 1 cm2 LC in at least one lung lobe and were BRD positive (35 calves; BRD) or did not (< 1 cm2) and were negative (104 calves; CONTROL). Cattle were moved to the feedlot at 353 ± 53 d of age where individual feed intake and body weights (BW) were recorded. Cattle were sent to slaughter when they reached a target final BW (steers = 680 kg and heifers = 635 kg). Liver scores and carcass data were collected. A subset (n = 29; 18 BRD cattle vs. 11 CONTROL cattle) had healthy liver tissue analyzed to investigate the association of LC at weaning with the liver microbiome diversity at slaughter. Only cattle with edible livers and no lung lesions were included in the microbiome analysis subset. Liver tissue samples were collected at slaughter and subsequently sequenced for microbiome analysis using an Illumina platform through targeted sequencing of the V4 region of the 16S rRNA gene. Mixed linear models were used to assess the effects of LC on growth performance and carcass characteristics with calf ranch, sex, and breed as fixed effects in the model. Generalized linear mixed models were used to assess the distributions of lung scores, liver scores, and quality grade at slaughter between LC and CONTROL cattle. To assess the effect of LC at weaning on the liver microbial communities at slaughter, the beta diversity (ADONIS) test was run, and the relative abundance of taxa is presented. There were no differences between BRD and CONTROL cattle for growth performance or most carcass traits (P > 0.05). However, the marbling score was greater (P = 0.05) in carcasses from CONTROL cattle (495 ± 7.82; LSM ± SEM) when compared with carcasses from BRD cattle (462 ± 13.84at 8 ± 2 wk of age. The beta diversity in the liver did not differ (P > 0.05) between BRD and CONTROL cattle. Staphylococcus was the most abundant genus among the liver samples, regardless of health status at weaning. A diagnosis of BRD by LC in beef × dairy cattle at weaning (57 ± 14 d of age) reduced marbling and impacted quality grade.},
}

@article {pmid41100183,
year = {2025},
author = {Miller, HE and Sasser, CN and Hernandez, MS and Legako, JF and Anderson, CJ and Schmitz-Esser, S and Ericsson, AC and Broadway, PR and Sanchez, NCB and Carroll, JA and Penn, MJC and Petry, AL},
title = {Fiber deprivation and insoluble corn-based fibrous co-products modulate gastrointestinal mucosa-associated microbiota, extracellular matrix remodeling, and intestinal morphology in growing pigs.},
journal = {Journal of animal science},
volume = {},
number = {},
pages = {},
doi = {10.1093/jas/skaf360},
pmid = {41100183},
issn = {1525-3163},
abstract = {This study examined how insoluble corn-based fibrous coproducts (ICBF) affect gastrointestinal (GI) mucosal microbiota, gene expression, and intestinal morphology in growing pigs compared to fiber deprivation. Fifty-six gilts (26.7±2.5 kg BW), were randomly assigned to one of 7 semi-synthetic diets. Treatments included a fiber-deprived control [CTL;<1% insoluble dietary fiber (IDF)], and 6 diets where an ICBF replaced 30% of corn starch: dehulled degermed corn (DHDG; IDF=1.7%), ground corn (COR; IDF=4.7%), corn gluten meal (CGM; IDF=5.2%), dried distillers grains (DDGS; IDF=8.6%), high protein dried distillers grains (HP; IDF=13.5%), and corn bran (BRN; IDF=17.5%). Pigs were individually housed and limit-fed 2.4 times maintenance. On day 31, duodenum, jejunum, ileum, and colon tissues were collected. Microbial 16S rRNA sequencing of mucosal material, tissue transcriptomics, and histological analyses were conducted in various intestinal regions. Data were analyzed using mixed models with diet as a fixed effect and linear and quadratic contrasts to assess response IDF. A negative binomial model with FDR correction were used for operational taxonomic unit (OTU) analysis, and transcriptomics were evaluated with DESeq2 comparing ICBF sources to CTL (Q ≤ 0.05, |log2FC| ≥ 2). In the ileal mucosa, Shannon and Simpson diversity indices linearly increased with IDF%, while in the colon mucosa Chao1 and Shannon diversity responded quadratically (P<0.05). Among the top 100 most abundant OTUs, 60 and 86 differed in ileal and colonic mucosa, respectively (Q<0.05). In the ileum and colon pigs fed low-ICBF diets (CTL, DHDG) had increased abundance of OTUs containing opportunistic or potentially pathogenic species (e.g., Enterobacteriaceae, Campylobacter, Streptococcus). However, moderate-to-high ICBF diets, CGM, DDGS, and BRN, enriched mucosal-associated Lactobacillus, Bifidobacterium, and Akkermansia. In the duodenum and ileum, villous height had a positive quadratic relationship to increasing IDF, while the jejunum villous height linearly decreased (P<0.05). Gene expression profiles revealed that moderate-to-high ICBF (DDGS, HP, and BRN) upregulated genes associated with cell structure and extracellular matrix (ECM) remodeling (TPPP3, MUC5AC, SERPINA1). Fiber-deprivation upregulated genes associated with ECM degradation (MMP9, MMP12), and collagen formation (COL26A1). Thus, both fiber deprivation and excessive ICBF can disrupt mucosal microbial and host homeostasis.},
}

@article {pmid41099894,
year = {2025},
author = {Khumalo, NN and Obi, LU and Yusuf, AA and Adeleke, RA},
title = {Dietary modulation of gut microbiota and functional enzymes in savannah honey bees (Apis mellifera scutellata Lepeletier).},
journal = {Applied microbiology and biotechnology},
volume = {109},
number = {1},
pages = {226},
pmid = {41099894},
issn = {1432-0614},
support = {PR_DAAD210907637972//National Research Foundation/ ; SRUG220326856//National Research Foundation/ ; },
mesh = {Animals ; Bees/microbiology/enzymology ; *Gastrointestinal Microbiome ; *Diet ; Pollen ; *Bacteria/classification/genetics/isolation & purification/enzymology ; Biodiversity ; Animal Feed/analysis ; },
abstract = {Honey bees gather pollen from flowering plants, using it as a vital protein source and, in turn, acquire pollen-associated microbes that interact with their existing gut microbiota. Despite their ecological importance, limited information exists regarding the gut microbiota of African savannah honey bees (Apis mellifera scutellata Lepeletier) and how diet and its associated microbial community influence this crucial internal ecosystem. This study aimed to investigate the differences in gut microbiota between wild honey bees collected during the flowering season and microbially depleted honey bees reared under semi-sterile conditions and fed various protein diets. To achieve this, freshly hatched worker bees were maintained in hoarding cages and assigned one of four protein diets: fresh sunflower pollen, casein, sterilised casein, or sterilised pollen. High-throughput DNA metabarcoding was then employed to compare the microbial composition of the honey bee gut across these groups. Our findings revealed that the gut of microbially depleted honey bees exhibited higher species diversity and richness. Conversely, the non-core gut microbial community predominated in wild bees and those fed the different protein diets. Specifically, Commensalibacter, Bartonella, and Bifidobacterium were the most dominant bacterial genera across all treatments. Interestingly, Gilliamella, a common core gut bacterium, was undetected, while Apibacter was exclusively found in wild honey bees. Furthermore, pollen-associated microbes such as Devosia and Pedobacter were identified solely in the gut of honey bees fed a pollen diet. Functional predictions of the gut microbial community also indicated the presence of key enzymes such as β-glucosidase, β-galactosidase, pyruvate dehydrogenase and phosphoglycerate mutase, which are crucial for enhancing nutrient absorption, digestion, and carbohydrate metabolism. These results underscore the intricate relationship between honey bees, microbes, and plants, offering valuable insights into how diet and its associated microbial communities could shape the gut microbiota of African honey bees. KEY POINTS: • The non-core gut microbiota dominates the African savannah honey bee • The type of diet influenced the microbial diversity and community abundance in the honey bee gut • Key enzymes involved in digestion, nutrition absorption, and carbohydrate metabolism were enhanced in the gut • Pollen-associated microbes found in the diet present potential avenues for probiotic development to improve honey bee health.},
}

Animals
Bees/microbiology/enzymology
*Gastrointestinal Microbiome
*Diet
Pollen
*Bacteria/classification/genetics/isolation & purification/enzymology
Biodiversity
Animal Feed/analysis

@article {pmid41099815,
year = {2025},
author = {Price, A and Mog, SYA and Dubach, J and Billington, C and Larsen, P},
title = {Microbiomes of 2024's Periodical Cicada Brood XIII Vary By Species and Location.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {105},
pmid = {41099815},
issn = {1432-184X},
support = {2216567 & 1912104//National Science Foundation (NSF)/ ; },
mesh = {Animals ; *Microbiota ; *Hemiptera/microbiology ; *Bacteria/classification/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Symbiosis ; Illinois ; Male ; Female ; },
abstract = {The 17-year Periodical cicadas (Magicicada spp.) are long-lived insects that emerge in mass synchronized events after 17 years underground. Their survival and ecological success depend heavily on their microbiomes, which include obligate bacterial symbionts essential for nutrient acquisition, as well as occasional pathogens such as the behavior-altering fungus Massospora cicadina. While the periodical cicada lifecycle is well studied, little is known about how cicada microbiomes vary across species and environments during a single emergence event. During the 2024 emergence of Brood XIII in northern Illinois, 17-year cicadas were sampled from four ecologically distinct forest preserves. Cicadas were identified by species and sex; their microbiomes were assayed using 16S rRNA gene sequencing and tested for the presence of the fungal pathogen M. cicadina DNA in asymptomatic individuals. Sampling sites were characterized by plant community composition, historical disturbance, and potential presence of the antifungal compound juglone. Microbiome composition differed significantly by cicada species and site, but not by sex. The obligate symbionts Hodgkinia cicadicola and Sulcia muelleri dominated microbiome profiles, though other bacteria-including Pantoea agglomerans, a potential pheromone producer-were variably abundant. Cicada species distributions were non-random across sites and correlated with local plant diversity. M. cicadina DNA was detected in 23% of otherwise asymptomatic cicadas, with infection rates varying by location and negatively correlated with microbiome diversity. This study highlights complex interactions between cicada species, their microbial communities, and environmental variables such as plant diversity, soil chemistry, and land use history.},
}

Animals
*Microbiota
*Hemiptera/microbiology
*Bacteria/classification/genetics/isolation & purification
RNA, Ribosomal, 16S/genetics
Symbiosis
Illinois
Male
Female

@article {pmid41099795,
year = {2025},
author = {Baars, IM and Mrázek, J and Kreisinger, J and Mikšík, I and Dietz, MW and Falcao Salles, J and Tieleman, BI and Gvoždíková Javůrková, V},
title = {Exploring the associations between preen oil bacterial, chemical and proteomic profiles of passerines.},
journal = {Antonie van Leeuwenhoek},
volume = {118},
number = {11},
pages = {173},
pmid = {41099795},
issn = {1572-9699},
support = {OCENW.KLEIN.541//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; 14-16861P//Grantová Agentura České Republiky/ ; RVO: 68081766//Institutional Research Support of the Czech Academy of Sciences/ ; },
mesh = {Animals ; Proteomics ; Volatile Organic Compounds/metabolism/analysis ; *Bacteria/classification/metabolism/isolation & purification/genetics ; *Passeriformes/microbiology/metabolism ; *Proteome/analysis ; Bacteriocins/metabolism ; },
abstract = {Preen gland bacteria are thought to be the key producers of preen oil components such as chemosignalling molecules including volatile organic compounds (VOCs) and antimicrobial compounds including peptides and antimicrobial VOCs. However, data on the preen oil bacteriome and chemical composition are limited to a small subset of bird species, and the presence of antimicrobial peptides is largely unexplored. Here, we performed an exploratory study to characterize, for the first time, the preen oil chemical and proteomic profiles and to explore the possible contribution of the bacteriome to the production of preen oil VOCs and antimicrobial peptides (bacteriocins) in eight passerine species, each represented by a single individual. Preen oil bacteriome, chemical and proteomic profiles varied among birds. The bacterial profiles were dominated by the genera Streptococcus, Lactococcus, Corynebacterium and Cutibacterium. The chemical profiles mainly consisted of alcohols, ketones and carboxylic acids. The biological functions primarily associated with the proteomic profiles were proteolysis and response to oxidative stress. Although we were unable to explore a direct association between the bacteriome and chemical profiles, the preen oil contained bacteriocin- and VOC-producing bacterial genera capable of producing detected microbially-derived VOCs (mVOCs), the relative abundance of which varied between birds. Riparian species showed the highest chemical diversity and high abundances of putative preen oil mVOC-producing bacteria, which could suggest habitat-specific adaptations. This exploratory study may significantly contribute to the formulation of hypotheses on the potential role of host ecological factors in the variation of preen oil bacterial, chemical and proteomic profiles in passerines.},
}

Animals
Proteomics
Volatile Organic Compounds/metabolism/analysis
*Bacteria/classification/metabolism/isolation & purification/genetics
*Passeriformes/microbiology/metabolism
*Proteome/analysis
Bacteriocins/metabolism

@article {pmid41099783,
year = {2025},
author = {Alavian, F and Hajimohammadi, A},
title = {Interplay between gut Microbiome and glymphatic system in cognitive function and memory regulation.},
journal = {Molecular biology reports},
volume = {52},
number = {1},
pages = {1038},
pmid = {41099783},
issn = {1573-4978},
mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; *Cognition/physiology ; *Glymphatic System/metabolism/physiology ; *Memory/physiology ; Animals ; Brain/metabolism ; Neurodegenerative Diseases/metabolism ; Dysbiosis ; Aquaporin 4/metabolism ; },
abstract = {The glymphatic system, a network of perivascular channels in the brain, clears toxins and metabolic products such as amyloid-β (Aβ), supporting cognitive function and preventing neurodegenerative diseases. The gut microbiome also affects brain health and cognitive functions by producing anti-inflammatory metabolites and neurotransmitters. In this narrative review study, recently published articles from reputable scientific databases were collected and analyzed. Characteristics related to the gut microbiome, its metabolites, and their impact on the glymphatic system and ultimately cognitive function were examined. These findings indicate that microbial metabolites such as short-chain fatty acids (SCFAs) and neurotransmitters such as serotonin and melatonin reduce brain inflammation and improve sleep quality and synaptic plasticity, which are essential for memory stabilization. Disruption of the gut microbiome (dysbiosis) leads to increased inflammation and dysfunction of the glymphatic system, resulting in the accumulation of toxic proteins and decreased cognitive function. Proper polarization of aquaporin-4 (AQP4), a water channel protein critical for fluid homeostasis in the brain, in astrocytes is essential for the effective functioning of this system, and its disruption is associated with diseases such as Alzheimer's disease (AD) and Parkinson's disease (PD). Understanding the interaction between the gut microbiome and the glymphatic system presents a new pathway for regulating memory and cognitive health, which could be an important target for the prevention and treatment of neurodegenerative diseases. Enhancing the gut microbiome through probiotics and a healthy diet may improve glymphatic system function and brain health, thereby preventing cognitive disorders.},
}

*Gastrointestinal Microbiome/physiology
Humans
*Cognition/physiology
*Glymphatic System/metabolism/physiology
*Memory/physiology
Animals
Brain/metabolism
Neurodegenerative Diseases/metabolism
Dysbiosis
Aquaporin 4/metabolism

@article {pmid41099660,
year = {2025},
author = {Yang, X and Luo, H and Li, Q and Zhu, W and Fu, L and Chen, L and Li, X and Su, H and Zhang, L and Huang, Y},
title = {Gut Microbiota and SCFAs Mediate the Therapeutic Effects of Canagliflozin in PCOS by Promoting White Fat Browning.},
journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology},
volume = {39},
number = {20},
pages = {e71138},
doi = {10.1096/fj.202502661R},
pmid = {41099660},
issn = {1530-6860},
support = {2024NSFSC1730//National Science Foundation project of Sichuan Province/ ; 2024LZXNYDJ101//Science and Technology Strategic Coopration Project of Luzhou-Southwest Medical University/ ; 2024SYF169//Science and Technology Strategic Cooperation Project of Luzhou Government - Southwest Medical University/ ; CYZZD24-12//Chengdu Medical College Technology Program/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Polycystic Ovary Syndrome/drug therapy/metabolism/microbiology ; Female ; Mice ; *Canagliflozin/pharmacology/therapeutic use ; *Fatty Acids, Volatile/metabolism ; *Adipose Tissue, White/metabolism/drug effects ; *Adipose Tissue, Brown/metabolism/drug effects ; Sodium-Glucose Transporter 2 Inhibitors/pharmacology ; Insulin Resistance ; Mice, Inbred C57BL ; },
abstract = {Polycystic ovary syndrome (PCOS) is a common endocrine disorder in women, characterized by hyperandrogenism and frequently accompanied by insulin resistance. Canagliflozin (Cana), a sodium-dependent glucose transporter 2 (SGLT2) inhibitor used to treat diabetes, significantly inhibits renal SGLT2 activity. Clinical studies indicate that SGLT2 inhibitors improve endocrine and reproductive disorders in PCOS patients; however, whether these benefits involve the gut microbiota remains unknown. A PCOS mouse model was established by subcutaneous administration of dehydroepiandrosterone (DHEA). Serum samples were collected for the quantification of sex hormones, insulin, and lipid profiles. Ovarian, adipose tissue, and intestinal samples were harvested for analyses including hematoxylin-eosin staining, immunohistochemistry, reverse transcription polymerase chain reaction, and Western blotting. Gut microbiota composition was assessed via 16S rDNA sequencing, and short-chain fatty acid (SCFA) concentrations in intestinal contents were measured by gas chromatography. Cana improves ovarian function in PCOS mice, addressing disrupted estrous cycles, abnormal ovarian morphology, and hormonal imbalances. Meanwhile, Cana also demonstrated positive effects on glucose tolerance, insulin sensitivity, and gut barrier function. These changes were accompanied by enhanced white fat browning and increased mitochondrial biogenesis. Mechanistically, these beneficial effects were associated with modulation of the gut microbiota and its metabolites SCFAs, and butyric acid add-on treatment could significantly ameliorate insulin resistance and reproductive dysfunction in a PCOS mouse. This study reveals that Cana contributes to WAT browning and gut microbiota homeostasis, indicating that its therapeutic effects on PCOS-related metabolic and reproductive dysfunction are partially driven by modulation of the gut microbiome.},
}

Animals
*Gastrointestinal Microbiome/drug effects
*Polycystic Ovary Syndrome/drug therapy/metabolism/microbiology
Female
Mice
*Canagliflozin/pharmacology/therapeutic use
*Fatty Acids, Volatile/metabolism
*Adipose Tissue, White/metabolism/drug effects
*Adipose Tissue, Brown/metabolism/drug effects
Sodium-Glucose Transporter 2 Inhibitors/pharmacology
Insulin Resistance
Mice, Inbred C57BL

@article {pmid41099535,
year = {2025},
author = {Rusanova, A and Mamontov, V and Ri, M and Meleshko, D and Trofimova, A and Fedorchuk, V and Ezhova, M and Finoshin, A and Lyupina, Y and Isaev, A and Sutormin, D},
title = {Taxonomically different symbiotic communities of sympatric Arctic sponge species show functional similarity with specialization at species level.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0114725},
doi = {10.1128/msystems.01147-25},
pmid = {41099535},
issn = {2379-5077},
abstract = {UNLABELLED: Marine sponges harbor diverse communities of associated organisms, including eukaryotes, viruses, and bacteria. Sponge-associated microbiomes contribute to the health of host organisms by defending them against invading bacteria and providing them with essential metabolites. Here, we describe the microbiomes of three sympatric species of cold-water marine sponges-Halichondria panicea, Halichondria sitiens, and Isodictya palmata-sampled at three time points over a period of 6 years in the White Sea. We identified the sponges as low microbial abundance species and detected stably associated bacteria that represent new taxa of sponge symbionts within Alpha- and Gammaproteobacteria. The sponges carried unique sets of unrelated species of symbiotic bacteria, illustrating the varying complexity of their microbiomes. At the community level, sponge-associated microbiomes shared common symbiotic features: they encoded multiple eukaryotic-like proteins, biosynthetic pathways and transporters of amino acids and vitamins essential for sponges. At the species level, however, different classes of eukaryotic-like proteins and pathways were distributed between dominant and minor symbionts, indicating specialization within microbiomes. Particularly, the taurine and sulfoacetate import and degradation pathways were associated exclusively with dominant symbionts in all three sponge species, suggesting that these pathways may represent symbiotic features. Our study indicates convergent evolution in the microbiomes of sympatric cold-water sponge species, as reflected by strong functional similarity despite the presence of distinct, taxonomically unrelated symbiotic communities.

IMPORTANCE: Sponges are regarded among the earliest multicellular organisms and the most ancient examples of animal-bacterial symbiosis. The study of host-microbe interactions in sponges has advanced rapidly due to the application of next-generation sequencing (NGS) technologies that help overcome the challenges of investigating their communities. However, many sponge species, particularly those from polar ecosystems, remain poorly characterized. Here, we demonstrate that three sympatric cold-water sponge species, including two analyzed for the first time, harbor distinct sets of bacterial symbionts, stably associated over 6 years. Using CORe contigs ITerative Expansion and Scaffolding, an algorithm developed in this study, we reconstructed high-quality symbiont genomes and revealed shared features indicative of convergent evolution toward symbiosis. Notably, we identified a potentially novel symbiotic feature-a gene cluster likely involved in sulfoacetate uptake and dissimilation. We also observed shifts in microbiome composition, associated with increasing water temperatures, raising concerns about the impact of global warming on cold-water ecosystems.},
}

@article {pmid41099524,
year = {2025},
author = {Day, AW and Hayes, E and Perez-Lozada, J and DiLeo, A and Blandino, K and Maguire, J and Kumamoto, CA},
title = {Candida albicans colonization modulates murine ethanol consumption and behavioral responses through elevation of serum prostaglandin E2 and impact on the striatal dopamine system.},
journal = {mBio},
volume = {},
number = {},
pages = {e0223925},
doi = {10.1128/mbio.02239-25},
pmid = {41099524},
issn = {2150-7511},
abstract = {UNLABELLED: Candida albicans is a commensal yeast that is a common component of the gastrointestinal (GI) microbiome of humans. C. albicans has been shown to bloom in the GI tract of individuals with alcohol use disorder (AUD) and can promote and increase the severity of alcoholic liver disease. However, the effects of C. albicans blooms on the host in the context of AUD or AUD-related phenotypes, such as ethanol preference, have been unstudied. In this work, we report a reduction in ethanol consumption and preference in mice colonized with C. albicans. C. albicans-colonized mice exhibited elevated levels of serum prostaglandin E2 (PGE2), and the reduced ethanol preference was reversed by injection with antagonists of PGE2 receptors. Furthermore, injection of mice with a PGE2 derivative decreased their ethanol preference. These results show that PGE2 acting on its receptors prostaglandin E receptor 1 (EP1) and prostaglandin E receptor 2 (EP2) drives reduced ethanol preference in C. albicans-colonized mice. We also showed altered transcription of dopamine receptors in the dorsal striatum of C. albicans-colonized mice and more rapid acquisition of ethanol-conditioned taste aversion, suggesting alterations to reinforcement or aversion learning. Finally, C. albicans-colonized mice were more susceptible to ethanol-induced motor coordination impairment, showing significant alterations to the behavioral effects of ethanol. This study identifies a member of the fungal microbiome that alters ethanol preference and demonstrates a role for PGE2 signaling in these phenotypes.

IMPORTANCE: Candida albicans is a commensal yeast that is found in the gut of most individuals. C. albicans has been shown to contribute to alcoholic liver disease. Outside of this, the impact of intestinal fungi on alcohol use disorder (AUD) had been unstudied. As AUD is a complex disorder characterized by high relapse rates and there are only three FDA-approved therapies for the maintenance of abstinence, it is important to study novel AUD contributors to find new therapeutic targets. Here, we show that an intestinal fungus, C. albicans, can alter mammalian ethanol consumption through an immune modulator, prostaglandin E2. The results highlight novel contributors to AUD-related phenotypes and further implicate the gut-brain axis in AUD. Future studies could lead to new therapeutic avenues for the treatment of AUD.},
}

@article {pmid41099510,
year = {2025},
author = {Wallace, BA and Varona, NS and Stiffler, AK and Vermeij, MJA and Silveira, C},
title = {High microbial diversity, functional redundancy, and prophage enrichment support the success of the yellow pencil coral, Madracis mirabilis, in Curaçao's coral reefs.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0120825},
doi = {10.1128/msystems.01208-25},
pmid = {41099510},
issn = {2379-5077},
abstract = {UNLABELLED: Coral reefs have undergone extensive coral loss and shifts in community composition worldwide. Despite this, some coral species appear naturally more resistant, such as Madracis mirabilis (herein Madracis). Madracis has emerged as the dominant hard coral in Curaçao, comprising 26% of coral cover in reefs that declined by 78% between 1973 and 2015. Although life history traits and competitive mechanisms contribute to Madracis's success, these factors alone may not fully explain it, as other species with similar traits have not shown comparable success. Here, we investigated the potential role of microbial communities in the success of Madracis on Curaçao reefs by leveraging a low-bias bacterial and viral enrichment method for metagenomic sequencing of coral samples, resulting in 77 unique bacterial metagenome-assembled genomes and 2,820 viral genomic sequences. Our analyses showed that Madracis-associated bacterial and viral communities are 12% and 20% richer than the communities of five sympatric coral species combined. The Madracis-associated bacterial community was dominated by Ruegeria and Sphingomonas, genera that have previously been associated with coral health, defense against pathogens, and bioremediation. These communities also displayed higher functional redundancy, which is often associated with ecological resilience. The viral community exhibited a 50% enrichment of proviruses relative to other corals. These proviruses had the genomic capacity to laterally transfer genes involved in antibiotic resistance, central metabolism, and oxidative stress responses, potentially enhancing the adaptive capacity of the Madracis microbiome and contributing to Madracis's success on Curaçao's reefs.

IMPORTANCE: Understanding why some coral species persist and thrive while most are in fast decline is critical. Madracis mirabilis is increasingly dominant on degraded reefs in Curaçao, yet the role of microbial communities in its success remains underexplored. This study highlights the potential role of Madracis-associated bacterial and viral communities in supporting coral resilience and competitive success. By identifying key microbial partners and viral genes that may enhance host stress tolerance and defense against pathogens, we broaden the understanding of how the coral holobiont contributes to species persistence under environmental stress. These insights are valuable for predicting key microbial community players in reef interactions and may inform microbiome-based strategies to support coral conservation and restoration.},
}

@article {pmid41099505,
year = {2025},
author = {Brubaker, L and McDonald, D and Putnam, S and Brennan, C and Fok, CS and Lewis, CE and Lowder, JL and Mueller, MG and Rickey, LM and Mueller, ER and Song, SJ and Rudser, K and Knight, R and Lukacz, ES and , },
title = {Bladder health and the urogenital microbiome in community-dwelling adult females.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0055825},
doi = {10.1128/msystems.00558-25},
pmid = {41099505},
issn = {2379-5077},
abstract = {UNLABELLED: Despite the established association with lower urinary tract symptoms, the relationship between a healthy bladder and the urogenital microbiome is unknown. This observational cohort study of 435 community-dwelling women examined bladder health and function using a validated instrument. Voided urine samples were self-collected, shipped to a repository, and underwent 16S rRNA amplicon sequencing. Two hundred seventy-four (56%) samples were retained following a limit-of-detection analysis for low biomass samples. A differential abundance analysis showed that Lactobacillus, the dominant genus, was associated with higher bladder function scores, but not global perception of bladder health, while Prevotella and Anerococcus were associated with lower scores. Associations between the female urogenital microbiome exist across the bladder health spectrum.

IMPORTANCE: There is increasing awareness that human microbiomes impact health and modulate certain health conditions. Recently, investigators developed a validated assessment of bladder health in adult women. This advance facilitated evaluation of the urogenital microbiome, across the adult lifespan and across the spectrum of bladder health in a population-based, observational study.},
}

@article {pmid41099502,
year = {2025},
author = {Serrador, D and Getz, LJ and Cao, KY and Campbell, JR and Kaul, R and Navarre, WW},
title = {Complete genome sequences of six Lactobacillus iners strains isolated from Kenyan women.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0075925},
doi = {10.1128/mra.00759-25},
pmid = {41099502},
issn = {2576-098X},
abstract = {Lactobacillus iners is one of the most common members of the vaginal microbiome, with a controversial role in vaginal health. Here, we present the complete genome sequences of six L. iners strains isolated from cervicovaginal secretions from women in Nairobi, Kenya.},
}

@article {pmid41099497,
year = {2025},
author = {Comstock, LE},
title = {Lessons from the model gut Bacteroidales Bacteroides fragilis and Bacteroides thetaiotaomicron and future opportunities.},
journal = {Journal of bacteriology},
volume = {},
number = {},
pages = {e0034625},
doi = {10.1128/jb.00346-25},
pmid = {41099497},
issn = {1098-5530},
abstract = {Bacteroidales is an order of bacteria that includes members that colonize the human gut, oral cavity, cow rumen, and other host-associated environments. Most humans become colonized with gut Bacteroidales species relatively soon after birth and later become colonized at high density with numerous diverse species. Bacteroidales strains often persist in the human gut for decades where they extensively evolve, acquiring point mutations, prophage, mobile plasmids, and integrative conjugal elements, making each person's gut Bacteroidales strains highly personalized. Much of what we have learned about basic biological properties of gut Bacteroidales comes from analyses of two species, Bacteroides fragilis and Bacteroides thetaiotaomicron, which were studied for different reasons. Three decades ago, there was only one human gut Bacteroidales genus recognized, the Bacteroides, into which all human gut Bacteroidales species were classified. Today, the human gut Bacteroidales number over 50 species with more than 14 genera and at least seven families. Studies of B. fragilis and B. thetaiotaomicron have provided a wealth of information of basic processes of these gut symbionts, many of which are generally applicable to other species of gut Bacteroidales. In this review, I provide a historical perspective as to why these two species have served as models, as well as some of the biological processes learned from studies of these two species. Finally, I discuss why present and future analyses of the gut Bacteroidales have expanded beyond these two model organisms.},
}

@article {pmid41099294,
year = {2025},
author = {Leonardi, A and Frizzo, R and Cavarzeran, F and Ozkan, J and Rosani, U},
title = {Ocular Microbiome in Dupilumab-Induced Ocular Surface Disease.},
journal = {Allergy},
volume = {},
number = {},
pages = {},
doi = {10.1111/all.70104},
pmid = {41099294},
issn = {1398-9995},
}

@article {pmid41099014,
year = {2025},
author = {Vázquez-González, L and Peña-Reyes, C and Regueira-Iglesias, A and Balsa-Castro, C and Tomás, I and Carreira, MJ},
title = {EPheClass: ensemble-based phenotype classifier from 16S rRNA gene sequences.},
journal = {Frontiers in bioinformatics},
volume = {5},
number = {},
pages = {1514880},
pmid = {41099014},
issn = {2673-7647},
abstract = {One area of bioinformatics that is currently attracting particular interest is the classification of polymicrobial diseases using machine learning (ML), with data obtained from high-throughput amplicon sequencing of the 16S rRNA gene in human microbiome samples. The microbial dysbiosis underlying these types of diseases is particularly challenging to classify, as the data is highly dimensional, with potentially hundreds or even thousands of predictive features. In addition, the imbalance in the composition of the microbial community is highly heterogeneous across samples. In this paper, we propose a curated pipeline for binary phenotype classification based on a count table of 16S rRNA gene amplicons, which can be applied to any microbiome. To evaluate our proposal, raw 16S rRNA gene sequences from samples of healthy and periodontally affected oral microbiomes that met certain quality criteria were downloaded from public repositories. In the end, a total of 2,581 samples were analysed. In our approach, we first reduced the dimensionality of the data using feature selection methods. After tuning and evaluating different machine learning (ML) models and ensembles created using Dynamic Ensemble Selection (DES) techniques, we found that all DES models performed similarly and were more robust than individual models. Although the margin over other methods was minimal, DES-P achieved the highest AUC and was therefore selected as the representative technique in our analysis. When diagnosing periodontal disease with saliva samples, it achieved with only 13 features an F1 score of 0.913, a precision of 0.881, a recall (sensitivity) of 0.947, an accuracy of 0.929, and an AUC of 0.973. In addition, we used EPheClass to diagnose inflammatory bowel disease (IBD) and obtained better results than other works in the literature using the same dataset. We also evaluated its effectiveness in detecting antibiotic exposure, where it again demonstrated competitive results. This highlights the importance and generalisation aspect of our classification approach, which is applicable to different phenotypes, study niches, and sample types. The code is available at https://gitlab.citius.usc.es/lara.vazquez/epheclass.},
}

@article {pmid41098988,
year = {2025},
author = {Bautista, J and Fuentes-Yépez, MP and Adatty-Molina, J and López-Cortés, A},
title = {Microbial signatures in metastatic cancer.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1654792},
pmid = {41098988},
issn = {2296-858X},
abstract = {Metastasis remains the leading cause of cancer-related death, yet the biological determinants that enable tumor cells to disseminate and colonize distant organs are incompletely understood. Emerging evidence identifies the microbiome, not merely as a bystander, but as an active architect of the metastatic cascade. Microbial communities residing in the gut, mucosal barriers, and within tumors shape metastatic progression by modulating immune surveillance, stromal remodeling, oncogenic signaling, and therapy response. Intratumoral and even intracellular microbes regulate epithelial-mesenchymal transition, angiogenesis, and immune escape, while gut-derived metabolites condition pre-metastatic niches and alter systemic immunity. Technological advances in spatial transcriptomics, single-cell multi-omics, and metagenomics have revealed a spatially organized, functionally integrated microbial ecosystem within tumors, challenging long-held assumptions of sterility in cancer biology. This review synthesizes five converging dimensions of this paradigm: microbial interactions in the metastatic tumor microenvironment; microbiome-mediated immunoediting and metastatic escape; the role of intratumoral and intracellular bacteria in dissemination; spatial-multi-omic approaches to map microbial niches; and microbial biomarkers predictive of metastasis and therapy outcomes. Collectively, these findings recast the microbiome as a critical and targetable determinant of metastasis. Deciphering the tumor-microbe-host triad holds transformative potential for biomarker development, therapeutic innovation, and precision oncology.},
}

@article {pmid41098902,
year = {2025},
author = {Thakur, L and Thakur, S and Rani, V and Verma, S and Kushwaha, PP},
title = {Editorial: Understanding the role of microbiome in alteration of cellular metabolism and cancer development.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1686038},
doi = {10.3389/fcimb.2025.1686038},
pmid = {41098902},
issn = {2235-2988},
}

@article {pmid41098896,
year = {2025},
author = {Primm, TP and Cannon, SR and Karki, AB},
title = {Small worms big discoveries: Galleria mellonella as a model for Campylobacter jejuni infection.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1686074},
pmid = {41098896},
issn = {2235-2988},
mesh = {Animals ; *Campylobacter jejuni/pathogenicity/genetics ; *Disease Models, Animal ; *Campylobacter Infections/microbiology/immunology ; Larva/microbiology ; Virulence Factors/metabolism ; *Moths/microbiology/immunology ; Virulence ; Host-Pathogen Interactions ; Immunity, Innate ; Humans ; },
abstract = {Galleria mellonella larva have served as a simple, cost-effective model for studying innate immunity and Campylobacter jejuni infection. The model commonly employs an acute, high-dose septic infection via hemocoel injection, with observable endpoints of death and melanization. Studies using G. mellonella have provided insights into C. jejuni virulence factors, including the capsule, transcriptional regulators, outer membrane vesicles, and a T6SS. It has revealed signals for virulence, such as pancreatic amylase and growth temperature, and also allowed for comparisons between C. jejuni strains and across multiple species in the genus. Limitations include the use of high bacterial doses that may obscure the role of specific virulence factors, lack of accounting for larval size variations, and unclear connection to the human anaerobic, microbially-rich gut environment. Future development of this model could allow oral infections for exploring pathogen-microbiome interactions and further assessing mechanisms of this important pathogen.},
}

Animals
*Campylobacter jejuni/pathogenicity/genetics
*Disease Models, Animal
*Campylobacter Infections/microbiology/immunology
Larva/microbiology
Virulence Factors/metabolism
*Moths/microbiology/immunology
Virulence
Host-Pathogen Interactions
Immunity, Innate
Humans

@article {pmid41098822,
year = {2025},
author = {Pons Salom, A and Aspillaga, E and Catalán, IA and Viver, T and Signaroli, M and Sanllehi, J and Grau, A and Martorell-Barceló, M and Barcelo-Serra, M and Alós, J},
title = {Behavioural types correlate with the gut microbiome in juvenile wild and reared gilthead seabream.},
journal = {Royal Society open science},
volume = {12},
number = {10},
pages = {250100},
pmid = {41098822},
issn = {2054-5703},
abstract = {The gut microbiome influences host behaviour through the gut-brain axis (GBA), a bidirectional network of signalling pathways. Although the GBA has been well studied in humans and other mammals, its role in shaping individual behavioural variation in fish remains largely unexplored. In this study, standardized behavioural tests were conducted on 67 juvenile gilthead seabream (Sparus aurata), consisting of 30 wild and 37 reared individuals, across five major behavioural axes-boldness, aggressiveness, sociability, activity and exploration-to determine their behavioural types using linear mixed models. High levels of repeatability of behaviour and consistent behavioural types were observed along the five studied axes. Gut samples from contrasting behavioural types were analysed for diversity, composition and structure using 16S rRNA sequencing. Statistically significant correlations and differences were found between wild and reared groups in both behavioural types and gut microbiome characteristics. These findings provide novel evidence of associations between behavioural types and the gut microbiome in juvenile marine fish, suggesting that gut microbiome may play a role in modulating fish behaviour. While this relationship could involve GBA interactions, further research is needed to confirm such mechanisms. This work could have translational significance for understanding survival, recruitment and life-history evolution in the early life stages of wild fish, as well as improving conservation management of species in both aquaculture and their natural habitats.},
}

@article {pmid41098818,
year = {2025},
author = {Pfister, CA and Stanfield, E and Bogan, M and Weigel, BL and Volbrecht, S and Scorza, K},
title = {Foundational kelp species reveal links between host traits, the environment and the associated microbial community.},
journal = {Royal Society open science},
volume = {12},
number = {10},
pages = {250637},
pmid = {41098818},
issn = {2054-5703},
abstract = {Canopy kelp are foundational species in coastal ecosystems and host diverse bacterial communities. Here, we test the association between bull kelp (Nereocystis luetkeana) host traits, blade-associated bacterial taxa and seawater environmental features across nine sites spanning more than 200 km in Washington state. Traits related to kelp fitness, environmental features and microbial community structure differed geographically. Kelp carbon fixation and tissue nitrogen content were greater at outer coast locales, compared with more inland locales in central and south Puget Sound. Geographic differences in carbon fixation rates, tissue nitrogen and bulb diameter were positively correlated with seawater nutrients and negatively correlated with sea surface temperature. Bacterial taxa showed differentiation among sites, and blade-associated bacterial densities were higher at the outer coast site compared with the most inland site. Yet, 11 bacterial genera were present in at least 80% of the samples; these taxa probably serve as core members of the N. luetkeana microbiome and show both positive and negative correlations with host health and environmental features. We show that there are strong interrelationships between kelp traits, seawater features and bacterial community composition with implications for the health of this highly productive foundational species in coastal ecosystems.},
}

@article {pmid41098770,
year = {2025},
author = {Zhou, F and Wu, Y and Ren, B and Liu, Y and Luo, K and Li, Q and Huang, F and Peng, X and Li, Y and Su, Z and Li, J},
title = {Meta-omics reveals subgingival plaque reconstruction dynamics.},
journal = {Journal of oral microbiology},
volume = {17},
number = {1},
pages = {2569528},
pmid = {41098770},
issn = {2000-2297},
abstract = {BACKGROUND: The homeostasis of the subgingival microbiome is crucial for periodontal health, although the dynamics governing its community variation remain insufficiently studied. This study aims to investigate the dynamics of subgingival microbiota reassembly after disruption, focusing on core taxa, functions, and driving forces.

METHODS: 339 subgingival plaques in periodontally healthy states were collected before and after ultrasonic cleaning across 12 timepoints for 1 year. All samples underwent full-length 16S rRNA sequencing; 30 were selected for metagenomic sequencing.

RESULTS: Our findings revealed that disturbed subgingival microbiota underwent short-term disruptions but subsequently reverted to baseline, maintaining stability within a year. Homogeneous selection dominated assembly, driving convergent structure under consistent pressure. Such a recovery process was accompanied by key taxa increased sequentially: Pseudomonas fluorescens early, Haemophilus parainfluenzae mid-stage, and Capnocytophaga spp. late. Functionally, reconstruction began with energy metabolism, expanded via biofilm formation and LPS biosynthesis mid-stage, and involved late apoptosis and complex amino acid metabolism. Microbial interactions, including positive regulation from Veillonella HMT 780 to Fusobacterium HMT 248, internally drove community assembly.

CONCLUSION: Our study clarifies species and functional dynamics during subgingival microbiota reconstruction and maps time-directed networks among stage-specific bacteria, offering a theoretical basis for targeted microbiome regulation.},
}

@article {pmid41098769,
year = {2025},
author = {Li, Y and Xin, Y and Zong, W and Li, X},
title = {The role of oral microbiota in digestive system diseases: current advances and perspectives.},
journal = {Journal of oral microbiology},
volume = {17},
number = {1},
pages = {2566403},
pmid = {41098769},
issn = {2000-2297},
abstract = {The oral microbiota is intimately linked to human health and various disease states. With the advent of the Human Microbiome Project, our comprehension of the oral microbiota has substantially improved. This microbial community is not only associated with a range of oral diseases, such as dental caries and periodontal diseases, but also with numerous digestive disorders, as demonstrated by recent clinical studies. Specific bacteria residing in the oral cavity, such as Porphyromonas gingivalis, Fusobacterium species and Streptococcus species, have been shown to translocate to the gastrointestinal tract, thereby establishing a potential connection between the oral and gut microbiota. The transfer and ectopic colonization of oral microbiota within the gastrointestinal tract may contribute to both the onset and exacerbation of gastrointestinal diseases. Following the principles of dysregulation characteristics, mechanism research and innovative treatment, this paper systematically reviews the association between the oral microbiota and various digestive system diseases. This paper explores how specific oral microbiota drive digestive system diseases mechanisms and evaluates treatments including probiotics, prebiotics, fecal microbiota transplantation, and targeted antimicrobial therapies. By clarifying the oral-gut microbiota-disease link, it highlights oral microbiota monitoring as a promising tool for early detection, diagnosis, and therapy.},
}

@article {pmid41098533,
year = {2025},
author = {Sarghie, L and Istvan, P and Aparicio, R and Walker, DW and Tacutu, R and Surleac, M},
title = {Parkin overexpression modulates gut-microbiota composition during aging in Drosophila melanogaster.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1672083},
pmid = {41098533},
issn = {1664-302X},
abstract = {BACKGROUND: The gut microbiota plays a key role in host health during aging, influencing metabolism, immune function, and lifespan. In older individuals, the microbial community often becomes less diverse and more unstable, which can contribute to chronic inflammation and increased disease risk. Parkin, an E3 ubiquitin ligase, is known to extend lifespan when overexpressed in Drosophila melanogaster, but it's still unclear whether it also influences the gut microbiota during aging and whether this might contribute to its longevity effects.

METHODS: To investigate this, we used an inducible genetic system to overexpress Parkin in adult D. melanogaster. Midguts were collected at four time points: days 10, 30, 45, and 60, and bacterial DNA was extracted for 16S rRNA amplicon sequencing to characterize microbiota composition and diversity. To assess the functional impact of these microbial communities, homogenates from Parkin-overexpressing and control flies were fed to germ-free wild-type recipients, followed by monitoring of lifespan and expression of antimicrobial peptides.

RESULTS AND DISCUSSION: Parkin overexpression resulted in age-dependent changes in gut microbiota composition and diversity. Community structure shifted significantly, with more pronounced differences observed in older flies. When fed to germ-free wild-type flies, homogenates from middle-aged and old control flies reduced the median lifespan. In contrast, the microbiome from Parkin-overexpressing flies was more similar to that of young flies. It did not reduce median lifespan and did not trigger the proinflammatory response seen with the control microbiome. Our findings suggest that Parkin promotes a gut microbial environment that is more balanced and less inflammatory, which may support healthier aging.

CONCLUSION: This study demonstrates that Parkin overexpression influences gut microbiota composition in a way that may be beneficial to host health during aging. The microbial communities associated with Parkin-overexpressing flies were not only distinct but also functionally advantageous, reducing immune activation and extending median lifespan in germ-free recipients. To our knowledge, this is the first study to use Parkin overexpression to explore potential Parkin-related changes in the gut microbial community, changes that were captured dynamically at four different stages of the D. melanogaster lifespan.},
}

@article {pmid41098531,
year = {2025},
author = {Juárez-Aragón, MC and Pantoja-Irys, JR and de la Rosa-Manzano, E and Garrido-Olvera, L and Mujica-Sánchez, H and Trejo-De León, CR and Vázquez-Lobo, A},
title = {Microbiome diversity across physicochemical gradient in low-medium enthalpy springs at the Sierra Madre Oriental eastern flank, northeastern Mexico.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1663000},
pmid = {41098531},
issn = {1664-302X},
abstract = {INTRODUCTION: Bacterial communities are fundamental to the functionality of thermal springs where they engage in essential processes such as the oxidation of sulfur, reduction of nitrates, carbon fixation, production of unique metabolites, and stabilization of microbial trophic networks. Northeastern Mexico presents a diverse array of thermal springs located within tropical karst systems situated among folded mountains and ancient inactive karstic regions. The geological complexity of these environments indicates a substantial potential for microbiome diversity; however, the composition and functional dynamics of microbial communities in these springs have not been thoroughly investigated.

METHODS: This study involved the collection of water samples from six hot springs, to characterize the planktonic microbiome using advanced metagenomic sequencing techniques. Additionally, we examined the relationship between microbial composition and physicochemical parameters.

RESULTS: Our analysis identified a total of 425 microbial species, which included 409 bacterial species, 13 eukaryotic organisms, and 3 archaeal taxa. The Ojo Caliente and Mainero Azufroso springs displayed the highest microbial diversity, whereas the Balneario El Bañito and Taninul springs exhibited the lowest. The Phyum Pseudomonadota was the predominant across the majority of springs, while Campylobacterota and Chlorobiota were specifically identified in the less diverse Balneario El Bañito and Taninul springs, respectively. A total of 30 indicator species were identified, predominantly in El Bañito and Potrero Prieto springs, emphasizing the distinctiveness of their microbial environments. Moreover, we found that electrical conductivity and bicarbonate concentration had a significant impact on the structure of this microbial communities.

DISCUSSION: This study highlights the ecological importance of these unique ecosystems in northeastern Mexico, with the Mainero Azufroso and Ojo Caliente springs identified as reservoirs of high microbial diversity.},
}

@article {pmid41098530,
year = {2025},
author = {Sharma, A and Andreani, NA and Keller, L and Herpertz-Dahlmann, B and Seitz, J and Baines, JF and Dempfle, A},
title = {Comparison of 16S ribosomal RNA hypervariable regions in microbiome studies of anorexia nervosa.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1665847},
pmid = {41098530},
issn = {1664-302X},
abstract = {INTRODUCTION: Short read sequencing of the 16S ribosomal RNA (rRNA) gene targeting specific hypervariable regions is widely employed to study the human gut microbiota. In these studies, the selection of particular 16S rRNA hypervariable regions is a crucial step. However, the results of such studies exhibit significant variability depending on the targeted hypervariable region.

METHODS: In this study, we systematically evaluated the performance of hypervariable regions V1V2 and V3V4 in a longitudinal gut microbiome study of adolescent patients with anorexia nervosa (AN) and matched controls.

RESULTS: The dominant genera, such as Bacteroides H, Faecalibacterium and Phocaeicola A 858004 were consistently detected in both hypervariable regions across timepoints. The within-sample longitudinal alpha diversity measures varied between the regions with the Chao1 index values being higher in the V1V2 region. The overall microbiome profiles based on beta diversity also differed between the regions. Bland-Altman analysis revealed a general lack of strong agreement between the two sequencing methods, except for a few taxa such as Faecalibacterium, Ruminococcus, Roseburia, Turicibacter and Anaerotruncus. While some results were similar across both hypervariable regions, most of the findings were sensitive to the chosen region.

CONCLUSION: This study underscores the importance of primer selection in microbiome studies of AN, as it can influence taxonomic resolution and diversity estimates along with downstream statistical analyses.},
}

@article {pmid41098272,
year = {2025},
author = {Kouser, M and Chaudhry, S and Sana, M},
title = {Exploring Insights Into Vaginal Microbiome Profiles in Relation to Intrauterine Insemination Success Rates.},
journal = {Cureus},
volume = {17},
number = {9},
pages = {e92244},
pmid = {41098272},
issn = {2168-8184},
abstract = {BACKGROUND: The vaginal microbiome has an essential role in female reproduction, especially during assisted reproduction treatments. The objective of the study was to examine vaginal microbiome profiles of women following intrauterine insemination (IUI) procedures and determine how they relate to clinical pregnancy outcomes.

MATERIALS AND METHODS: A prospective observational study was conducted on 100 women with IUI treatment. Before the procedure, vaginal swabs were taken and sequenced using the 16S rRNA gene to determine microbial community types. Based on microbiome profiles, patients were divided into Lactobacillus-dominant (n = 68) and non-Lactobacillus-dominant (n = 32) groups. Clinical pregnancy rates were compared between the two groups. SPSS Statistics version 26.0 (IBM Corp. Released 2019. IBM SPSS Statistics for Windows, Version 26.0. Armonk, NY: IBM Corp.) was used, with p < 0.05 considered statistically significant.

RESULTS: Overall, 68% of the participants had Lactobacillus-dominant vaginal microbiomes, whereas 32% had varied non-Lactobacillus profiles. The rate of clinical pregnancy was significantly improved in the Lactobacillus-dominant group compared to the non-dominant group, 26 (38.2%) vs. 4 (12.5%), p = 0.008. Logistic regression analysis revealed that the Lactobacillus-dominant profile was independently associated with the success of IUI (adjusted OR 3.85; 95% CI 1.28-11.58; p = 0.016). There were no significant differences in age, body mass index, and infertility duration between the two groups.

CONCLUSIONS: The success rates of IUI were significantly associated with vaginal microbiome composition, particularly the predominance of Lactobacillus. These results support that microbiome profiling may become a helpful technique to predict and enhance the success rates in fertility treatment.},
}

@article {pmid41098119,
year = {2025},
author = {Afzal, L and Dulai, AS and Khan, ZE and Nguyen, N and Afzal, N and Gunt, HB and Sivamani, RK},
title = {Open-Label, Prospective Study of a Prebiotic Gel Cream on Its Efficacy of Mild to Moderate Acne Management and Effects on the Functional Skin Microbiome.},
journal = {Journal of cosmetic dermatology},
volume = {24},
number = {10},
pages = {e70138},
doi = {10.1111/jocd.70138},
pmid = {41098119},
issn = {1473-2165},
support = {//Burt's Bees Inc/ ; },
mesh = {Humans ; *Acne Vulgaris/microbiology/drug therapy/diagnosis ; Female ; *Prebiotics/administration & dosage/adverse effects ; Male ; *Skin/microbiology/drug effects ; *Microbiota/drug effects ; Adult ; Young Adult ; Prospective Studies ; *Skin Cream/administration & dosage/adverse effects ; Treatment Outcome ; Gels ; Adolescent ; Severity of Illness Index ; Propionibacterium acnes/isolation & purification ; Skin Microbiome ; },
abstract = {BACKGROUND: Acne vulgaris is a chronic inflammatory condition, which is estimated to affect greater than 85% of the population. Acne is a multifactorial condition, which can be influenced by diet, environment, and the microbiome.

AIMS: The purpose of this clinical study is to assess the safety and effects of a prebiotic-containing gel cream on the skin microbiome of individuals with non-cystic acne-prone skin.

PATIENTS/METHODS: In this 7-week clinical trial, 30 eligible participants were recruited and enrolled from the Sacramento region. The study consisted of three visits: (1) screening; (2) week 0, baseline; (3) week 6. All participants received a standard non-comedogenic cleanser and a prebiotic-containing gel cream. The primary endpoint in this study was alteration in C. acnes abundance in mild to moderate non-cystic, acne-prone skin. The secondary endpoint in this study was functional gene analysis for skin barrier and skin inflammation-related genes from whole genome sequencing of the skin microbiome.

RESULTS: Acne lesions significantly reduced in non-inflammatory lesions, inflammatory lesions, and total lesions after treatment (-36.0%, -34.5%, and -35.9%, respectively). On the glabella, there was a 12.5 log2 fold increase in abundance of a healthy strain of C. acnes that is not associated with acne vulgaris. Furthermore, there was a wide range of functional bacterial genetic changes that may be associated with increased collagen and glutathione production. The gel cream was rated very well tolerated, and there were no adverse effects reported.

CONCLUSIONS: This prebiotic-containing gel cream can be an effective form of management for acne vulgaris by creating beneficial shifts in the skin microbiome.},
}

Humans
*Acne Vulgaris/microbiology/drug therapy/diagnosis
Female
*Prebiotics/administration & dosage/adverse effects
Male
*Skin/microbiology/drug effects
*Microbiota/drug effects
Adult
Young Adult
Prospective Studies
*Skin Cream/administration & dosage/adverse effects
Treatment Outcome
Gels
Adolescent
Severity of Illness Index
Propionibacterium acnes/isolation & purification
Skin Microbiome

@article {pmid41097974,
year = {2025},
author = {Zheng, P and Yu, C and Lyu, X and Wang, Q},
title = {[Multi-omics association among intestinal microbiome, metabolome, and histone H4 acetylation in children with asthma].},
journal = {Wei sheng yan jiu = Journal of hygiene research},
volume = {54},
number = {5},
pages = {784-804},
doi = {10.19813/j.cnki.weishengyanjiu.2025.05.012},
pmid = {41097974},
issn = {1000-8020},
mesh = {Humans ; *Asthma/microbiology/metabolism ; *Histones/metabolism ; *Gastrointestinal Microbiome ; Acetylation ; Child ; *Metabolome ; Male ; Female ; Feces/microbiology ; Metabolomics ; Multiomics ; },
abstract = {OBJECTIVE: To analyze the correlation between intestinal microbiome, metabolome and histone H4 acetylation level in children with asthma, and explore the mechanism that gut microbiome affects children with asthma.

METHODS: Histone H4 acetylation in induced sputum, 16S rRNA gene sequencing of gut microbiome, and untargeted fecal metabolomics were detected in asthmatic children and control children. Network method was used to analyze the correlation between characteristic gut microbes of asthma and histone H4 acetylation, Quantile g-computation(QGC)was used to analyze the effect of characteristic microbes on histone H4 acetylation, and the mediation model was used to analyze the mediating effect of metabolites in the process of gut microbes affecting histone H4 acetylation.

RESULTS: The mean A(optical density) value of histone H4 acetylation in sputum was 0.668±0.260 in asthmatic children(n=37), and 0.593±0.069 in control group(n=20). A total of 5 characteristic gut genera of children with asthma were significantly correlated with H4 acetylation level(adjusted P<0.05). QGC analysis showed that the 5 characteristic gut genera had a positive effect on the histone acetylation level of histone H4(P=0.001), and the A value of histone H4 acetylation increased by 0.124 for every 1 quantile increase in the relative abundance of characteristic gut genera(95%CI 0.058-0.190). By spearman analysis, 34 fecal metabolites were significantly correlated with the five characteristic gut genera and histone H4 acetylation levels. Prevotella was found have influenced the level of H4 acetylation through the mediating effect of N-delta-acetylornithine, phenethylamine, 2-hydroxy-3-methylvalerate, alpha-ketoglutaramate, gamma-glutamylglycine, and mevalonolactone.

CONCLUSION: The metabolites related with the characteristic gut bacteria in asthmatic children were associated with histone H4 acetylation, which suggested that the gut microbiome may induce childhood asthma by regulating epigenetic variation.},
}

Humans
*Asthma/microbiology/metabolism
*Histones/metabolism
*Gastrointestinal Microbiome
Acetylation
Child
*Metabolome
Male
Female
Feces/microbiology
Metabolomics
Multiomics

@article {pmid41097965,
year = {2025},
author = {Jia, X and Wang, H and Guan, F and Zhang, X and Su, C and Huang, F and Du, W and Zhang, J and Ouyang, Y and Bai, J and Wei, Y and Li, L and Zhang, B},
title = {[Association of gut microbiome and serum metabolite with dyslipidemia in Chinese adults of 4 provinces in 2018 and 2022].},
journal = {Wei sheng yan jiu = Journal of hygiene research},
volume = {54},
number = {5},
pages = {722-731},
doi = {10.19813/j.cnki.weishengyanjiu.2025.05.003},
pmid = {41097965},
issn = {1000-8020},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Dyslipidemias/microbiology/blood/epidemiology ; China/epidemiology ; Adult ; Male ; Female ; Middle Aged ; Feces/microbiology ; Lipids/blood ; },
abstract = {OBJECTIVE: To analyze the serum metabolites and gut microbiota associated with dyslipidemia in adult residents in China.

METHODS: The data were derived from the 2018 China Health and Nutrition Survey and the 2022 China Development and Nutrition Health Impact Cohort Survey, and adults(≥ 18 years) who participated in the two rounds of surveys and had completed serum metabolite and lipids data were selected. According to Chinese Guideline for Lipid Management(Primary Care Version 2024), subjects with at least one of hypertriglyceridemia, hypercholesterolemia, high LDL-C level or low HDL-C level were identified as dyslipidemia. Participants were divided into two groups: constant normal lipids(CNL) and occurred dyslipidemia(OD). Broadly targeted ultra-performance liquid chromatography-tandem mass spectrometry(UPLC-MS/MS) analysis was performed to measure serum metabolites and orthogonal partial least square discriminate analysis were used to identify different metabolites between groups. Fecal samples were collected and 16S rRNA sequencing was performed at baseline to analyze the α diversity of intestinal microbiota(Shannon and Simpson indexes), β diversity(Bray-curtis distance) and differential bacteria between groups. Spearman rank correlation was used to analyze the correlation between gut microbiota and serum metabolites.

RESULTS: A total of 1090 subjects were included during 2018-2022, of whom 226(20.7%) developed dyslipidemia at follow-up, and 864(79.3%) remained normal serum lipid levels. There were 49 differential metabolites identified between the CNL and OD groups, in which the metabolites with higher amount in the OD group was mainly lysophosphatidylcholine of glycerophospholipids. There was no significant difference in Shannon and Simpson indices between the two groups, and β diversity analysis showed that there were differences in the overall microbiota structure between the two groups. Both univariate and multivariate analyses identified eight different bacterial genera, and Veillonella, Faecalitalea, and Psychrobacter were the common differential bacteria, and the first two genera were relatively abundant in the OD group. Faecalitalea was negatively correlated with five lysophosphatidylcholine metabolites.

CONCLUSION: Serum metabolite levels of glycerophospholipids, gut Veillonella and Faecalitalea may be related to dyslipidemia in adults in China.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Dyslipidemias/microbiology/blood/epidemiology
China/epidemiology
Adult
Male
Female
Middle Aged
Feces/microbiology
Lipids/blood

@article {pmid41097963,
year = {2025},
author = {Guan, F and Huang, F and Zhang, X and Wang, L and Zhang, J and Jia, X and Du, W and Quyang, Y and Wang, H and Zhang, B},
title = {[Differential gut microbiota among adult residents of 15 provinces of China in 2018 and their relationship with blood lipids].},
journal = {Wei sheng yan jiu = Journal of hygiene research},
volume = {54},
number = {5},
pages = {707-714},
doi = {10.19813/j.cnki.weishengyanjiu.2025.05.001},
pmid = {41097963},
issn = {1000-8020},
mesh = {Humans ; *Gastrointestinal Microbiome ; China/epidemiology ; Adult ; *Lipids/blood ; Feces/microbiology ; *Inflammation/microbiology/blood ; Female ; Male ; Middle Aged ; Bacteria/classification/genetics/isolation & purification ; C-Reactive Protein/analysis ; },
abstract = {OBJECTIVE: To analyze the characteristics and differences of gut microbiota in adult residents of 15 provinces of China under different inflammation levels, and to analyze their correlation with blood lipid levels.

METHODS: A total of 4158 adult residents who participated in the 2018 China Health and Nutrition Survey and completed all the surveys were selected. Biochemical tests were performed on serum samples, and 16S amplicon sequencing was carried out on fecal samples. According to the ultra-sensitive C-reactive protein, the population was divided into a low inflammation group and a high inflammation group. The uniformity and richness of bacterial species and the overall distribution characteristics of bacterial communities between the two groups were analyzed through diversity analysis, and the differences in bacterial communities between the two groups were analyzed using linear discriminant analysis. Finally, the differences in bacterial communities between the groups were analyzed in association with the physiological and biochemical indicators of the population.

RESULTS: Compared with the low inflammation group, the bacterial diversity in the high inflammation group was lower, and there was a significant difference in the overall bacterial composition between the two groups(R~2=0.25%, P=0.01). Six genera were enriched in the samples of the low inflammation group, and four genera were enriched in the high inflammation group. Among them, Lactobacillus and Streptococcus were positively correlated with BMI, and Romboutsia was positively correlated with TC, LDL-C and HDL-C. Clostridium UCG-014, Ruminococcus and Faecalibacterium were positively correlated with TG.

CONCLUSION: The study found that there are differences in the overall structure and dominant bacteria of the gut microbiome in people with different inflammation levels, and the inflammatory response may have a certain impact on blood lipid levels through these dominant bacterial genera.},
}

Humans
*Gastrointestinal Microbiome
China/epidemiology
Adult
*Lipids/blood
Feces/microbiology
*Inflammation/microbiology/blood
Female
Male
Middle Aged
Bacteria/classification/genetics/isolation & purification
C-Reactive Protein/analysis

@article {pmid41097883,
year = {2025},
author = {Castenschiold, CDF and Mignani, C and Christiansen, S and Alsved, M and Ickes, L and Tesson, SVM and Löndahl, J and Bilde, M and Bataillon, T and Finster, K and Šantl-Temkiv, T},
title = {Atmospheric Biogenic Ice-Nucleating Particles Link to Microbial Communities in the Arctic Marine Environment in Western Greenland.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c03650},
pmid = {41097883},
issn = {1520-5851},
abstract = {Biogenic ice-nucleating particles (INPs) can significantly impact mixed-phase clouds by enhancing precipitation and reducing albedo. As Arctic sea ice diminishes, the exposure of open ocean may increase aerosolization rates of marine bioaerosols and INPs. We investigated INP concentrations and microbial communities in ambient marine air, sea bulk water (SBW), and sea surface microlayer (SML) along a transect from the Davis Strait to Baffin Bay. INP concentrations in SBW increased with latitude, regardless of the extent of terrestrial freshwater input. We further identified correlations between INP levels and abundances of specific microbial taxa, including Formosa, Lewinella, Micromonas, and Dino-Group-I-Clade-5, suggesting potential ice nucleation activity of these taxa. Air samples exhibited distinct microbiomes compared to seawater, indicating terrestrial contributions, but at the highest observed wind speeds (7-8 m/s), substantial contributions of the seawater microbiome were detected in the air. Elevated atmospheric INP concentrations at higher latitudes correlated with seawater INP levels, which was supported by laboratory sea spray experiments showing that INPs in SBW influenced aerosol INP levels. Our findings highlight the Arctic Ocean as a significant source of biogenic atmospheric INPs and enhance our understanding of marine microbes as contributors to biogenic INPs. By identification of potential ice nucleation active microbial taxa and examination of aerosolization processes, this study provides a framework for future research on Arctic marine-derived INPs and their atmospheric impact.},
}

@article {pmid41097858,
year = {2025},
author = {Chen, X and Tian, H and Han, L and Xu, W},
title = {Gut Microbiota Influences Meningioma Pathogenesis via Circulating Metabolites: A Two-Sample Mendelian Randomization Study.},
journal = {Brain and behavior},
volume = {15},
number = {10},
pages = {e70973},
doi = {10.1002/brb3.70973},
pmid = {41097858},
issn = {2162-3279},
support = {ZR2022QH335//Natural Science Foundation of Shandong Province/ ; 81902539//National Natural Science Foundation of China/ ; },
mesh = {*Meningioma/microbiology/metabolism/genetics ; Humans ; *Gastrointestinal Microbiome/physiology/genetics ; Mendelian Randomization Analysis/methods ; *Meningeal Neoplasms/microbiology/metabolism/genetics ; Female ; },
abstract = {BACKGROUND: Meningiomas are common solitary intracranial tumors without any apparent risk factors. In light of the growing interest in gut microbiome-brain tumor interactions, this investigation sought to explore potential links between intestinal microbial communities and meningioma pathogenesis, while also exploring the potential mediating role of specific metabolites.

METHODS: To investigate potential causal links between intestinal microbial communities and meningioma development, we implemented a bidirectional two-sample Mendelian randomization (MR) approach examining 196 microbial taxa. Our analytical strategy incorporated a two-stage MR methodology to pinpoint potential mediating factors. Furthermore, we performed comprehensive mediation analyses to assess the degree to which particular metabolic intermediates might influence the observed microbiota-meningioma associations.

RESULTS: Eight distinct microbial taxa exhibited potential causal associations with meningioma development. Among the identified taxa, genus Lachnoclostridium (odds ratio [OR]: 0.60; 95% confidence interval [CI]: 0.41, 0.89; p = 0.010) and class Lentisphaeria (OR: 0.73; 95% CI: 0.57, 0.95; p = 0.017) were suggestively associated with a reduced risk of meningioma, whereas family Oxalobacteraceae (OR: 1.28; 95% CI: 1.04, 1.58; p = 0.018) suggested a positive association with the risk of meningioma. An exploratory mediation analysis suggested that the relationships between genus Lachnoclostridium, class Lentisphaeria, and family Oxalobacteraceae and meningioma were mediated by the histidine to pyruvate ratio, hydroxymalonate, and 1-linoleoylglycerol. Each of these accounted for 10.65%, 10.78%, and 11.82%, respectively.

CONCLUSION: This investigation provides preliminary evidence that intestinal microbial communities play a contributory role in meningioma pathogenesis, with circulating metabolites potentially serving as key intermediaries in this microbiota-meningioma axis.},
}

*Meningioma/microbiology/metabolism/genetics
Humans
*Gastrointestinal Microbiome/physiology/genetics
Mendelian Randomization Analysis/methods
*Meningeal Neoplasms/microbiology/metabolism/genetics
Female

@article {pmid41097775,
year = {2025},
author = {Jaye, K and Alsherbiny, MA and Chang, D and Li, CG and Bhuyan, DJ},
title = {Guardians in the Gut: Mechanistic Insights into a Hidden Ally Against Triple-Negative Breast Cancer.},
journal = {Cancers},
volume = {17},
number = {19},
pages = {},
doi = {10.3390/cancers17193248},
pmid = {41097775},
issn = {2072-6694},
abstract = {The gut microbiome possesses a diverse range of biological properties that play a role in maintaining host health and preventing disease. Gut microbial metabolites, including short-chain fatty acids, natural purine nucleosides, ellagic acid derivatives, and tryptophan metabolites, have been observed to have complex and multifaceted roles in the gut and in wider body systems in the management of disease, including cancer. Triple-negative breast cancer is the most aggressive subtype of breast cancer, with restricted treatment options and poor prognoses. Recently, preclinical research has investigated the antiproliferative potential of gut microbial metabolites against this type of breast cancer with promising results. However, little is understood about the mechanisms of action and molecular pathways driving this antiproliferative potential. Understanding the complex mechanisms of action of gut microbial metabolites on triple-negative breast cancer will be instrumental in the investigation of the combined administration with standard chemotherapeutic drugs. To date, there is a paucity of research studies investigating the potential synergistic interactions between gut microbial metabolites and standard chemotherapeutic drugs. The identification of synergistic potential between these compounds may provide alternate and more effective therapeutic options in the treatment and management of triple-negative breast cancer. Further investigation into the mechanistic action of gut microbial metabolites against this breast cancer subtype may support the administration of more cost-effective treatment options for breast cancer, with an aim to reduce side effects associated with standard treatments. Additionally, future research will aim to identify more potent metabolite-drug combinations in the mitigation of triple-negative breast cancer progression and metastasis.},
}

@article {pmid41097753,
year = {2025},
author = {Łatkiewicz, T and Rasoul-Pelińska, K and Kułak, K and Tarkowski, R and Kułak, A and Puzio, I},
title = {Gynecological Cancer Oncobiome Systematic Review.},
journal = {Cancers},
volume = {17},
number = {19},
pages = {},
doi = {10.3390/cancers17193227},
pmid = {41097753},
issn = {2072-6694},
abstract = {Objective: The primary objective of this systematic review is to present current knowledge about the oncobiome of gynecological cancers. Methods: Our systematic review contains data about the oncobiome of uterine corpus cancer, ovarian cancer and cervical cancer. Articles about other gynecological cancers were excluded. Results: A total of 72 articles were included in our systematic review. In uterine corpus cancer, cervical cancer and ovarian cancer, representatives of bacteria, fungi, viruses and parasites can be found. The oncobiome of ovarian cancer is connected with the oncobiome of head and neck cancers. Our systematic review proved that the human papilloma virus is connected with ovarian and cervical cancer. Gut dysbiosis can be used as a marker of ovarian cancer. In cervical cancer, we found the difference between the microbiota of healthy patients and patients with cervical cancer. Methylobacter, Robignitomaculum, Klebsiella, Micromonospora and Microbispora have an impact on overall survival. The microbiome of uterine corpus cancer is more differentiated than in cancer-free samples. Chronic endometrial inflammation has an impact on endometrial microbiome. Discussion: Treatment of gynecological cancers is changing permanently. Chemotherapy, as a systematic treatment, is being left in the past. Modern methods of therapy are addressed to specific genes. In the past, researchers claimed that tumors are sterile. However, the newest research indicates that malignancies were found to have genetic fragments of pathogens, which can be used as vectors for medications or as markers for the detection of a specific malignancy. Three most common gynecological cancers are as follows: endometrial cancer, ovarian cancer and cervical cancer. Each of these has their specific microbiome, which can be used for oncological treatment. These discoveries create possibilities for new, efficient methods of treatment. This systematic review analyzes publications about the composition of the gynecological tumor microenvironment, correlation between microbiomes of different organs, the female reproductive tract and the microbiome of the female reproductive tract during malignancy. Moreover, we provide information on the influence of some pathogens on the treatment.},
}

@article {pmid41097535,
year = {2025},
author = {Mulet, JM and Benito, P and Celdrán, M and Yenush, L and Porcel, R},
title = {Impact of Different Microbial Biostimulants and Salt Stress on the Endophytome of the Edible Part of Lettuce and Tomato Plants.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {19},
pages = {},
doi = {10.3390/foods14193366},
pmid = {41097535},
issn = {2304-8158},
support = {PAID-06-22//Universitat Politècnica de València/ ; MCIN/AEI/10.13039/501100011033//Ministerio de Ciencia, Innovación y Universidades/ ; },
abstract = {The human gut microbiota plays a critical role in health throughout life. While fruits and vegetables are well-known sources of nutrients and prebiotics, recent studies suggest they may also contribute viable microorganisms to the gut microbiome, particularly when consumed raw. However, the impact of agricultural practices-such as the use of microbial biostimulants or exposure to salt stress-on the composition of the edible plant microbiome remains poorly understood. In this study, we performed a comprehensive metataxonomic analysis of the endophytic microbiome in the edible tissues (leaves or fruits) of lettuce (Lactuca sativa) and tomato (Solanum lycopersicum), cultivated under standard conditions with or without microbial biostimulants and salt stress. Our results show that microbial biostimulants-Priestia megaterium (PGPB) and Rhizophagus irregularis (AMF)-as well as moderate salt stress, significantly reshape the composition and diversity of endophytes in both crops. Notably, the PGPB and NaCl treatments enhanced the abundance of bacterial genera such as Pantoea, Stenotrophomonas, and Massilia, which are associated with plant health and may have probiotic potential. Salt stress also increased alpha-diversity indices and favored the presence of Firmicutes and Bacteroidota, phyla commonly linked to a healthy human gut microbiome. Agronomic inputs used in organic and conventional farming, such as microbial biostimulants or controlled salt exposure, may represent novel strategies to enhance the microbial quality of fresh produce and promote gut microbial diversity through diet.},
}

@article {pmid41097330,
year = {2025},
author = {Sikora, E and Łętocha, A and Michalczyk, A and Kozik, A},
title = {Encapsulation of Acid Whey in Alginate Microspheres for Application in Skin Microbiome-Friendly Topical Formulations: Optimization Through a Design of Experiments Approach.},
journal = {Molecules (Basel, Switzerland)},
volume = {30},
number = {19},
pages = {},
doi = {10.3390/molecules30193907},
pmid = {41097330},
issn = {1420-3049},
mesh = {*Alginates/chemistry ; *Microspheres ; *Skin/microbiology ; *Microbiota/drug effects ; Probiotics/chemistry ; *Whey/chemistry ; Drug Compounding ; Emulsions ; Humans ; *Whey Proteins/chemistry ; Particle Size ; Cosmetics/chemistry ; Animals ; Skin Microbiome ; },
abstract = {Skin microbiome-friendly preparations are gaining increasing popularity in the cosmetics and pharmaceutical industries. Fermented plants, lysates, and heat-treated products are used as probiotic ingredients in cosmetics. This is due to the presence of Lactobacillus bacteria, such as acid or acid-rennet whey, which are natural probiotics that can positively impact the skin microbiome. However, due to technological difficulties, the direct use of whey as a cosmetic ingredient is limited. An optimized emulsification method was used to obtain alginate microspheres as carriers of whey. The process parameters were optimized using the Design of Experiments (DoEs) methodology. The effect of three key variables, including the type of probiotic raw material (whey from 1-cows, 2-goats, and 3-mixed), the alginate-to-raw material ratio (1-3%), and sonication time (0.5-1.5 min), on parameters such as encapsulation efficiency, bacterial survival, viscosity, and microspheres size was analyzed. The results obtained demonstrated that the optimal process parameters were the sonication time of 0.5 min and the alginate-to-whey mass ratio of 1.5% for all types of whey material studied. However, the most important factor influencing the properties and functionality of the microspheres was sonication time. The optimized whey-loaded microspheres were incorporated into a preservative-containing emulsion system, in which the viability of whey-derived bacteria was monitored over time. The whey encapsulation process effectively maintained the bacteria's probiotic properties, protecting their viability despite the presence of preservatives (at a level of 4.92 ± 0.9 log CFU/g after 30 days of formulation storage), thus confirming the feasibility of incorporating liquid whey into skincare formulations.},
}

*Alginates/chemistry
*Microspheres
*Skin/microbiology
*Microbiota/drug effects
Probiotics/chemistry
*Whey/chemistry
Drug Compounding
Emulsions
Humans
*Whey Proteins/chemistry
Particle Size
Cosmetics/chemistry
Animals
Skin Microbiome

@article {pmid41097290,
year = {2025},
author = {Zaborowska, M and Wyszkowska, J and Słaba, M and Borowik, A and Kucharski, J and Bernat, P},
title = {The Effect of Organic Materials on the Response of the Soil Microbiome to Bisphenol A.},
journal = {Molecules (Basel, Switzerland)},
volume = {30},
number = {19},
pages = {},
doi = {10.3390/molecules30193868},
pmid = {41097290},
issn = {1420-3049},
support = {30.610.006-110//University of Warmia and Mazury in Olsztyn, Faculty of Agriculture and Forestry, Department of Soil Science and Microbiology/ ; NGR/319/2022//he Minister of Science under "the Regional Initiative of Excellence Program/ ; Rector's Scientific Grant - Edition II"//University of Warmia and Mazury in Olsztyn/ ; },
mesh = {*Soil Microbiology ; *Benzhydryl Compounds/pharmacology ; *Phenols/pharmacology ; *Microbiota/drug effects ; Soil/chemistry ; Bacteria/drug effects/genetics/classification ; *Soil Pollutants ; Fungi/drug effects/genetics ; RNA, Ribosomal, 16S/genetics ; Zea mays/growth & development ; Bisphenol A Compounds ; },
abstract = {In view of the increasing environmental pollution caused by bisphenol A (BPA), understanding its impact on the microbiological properties of soil, which play a key role in maintaining soil fertility and consequently ecosystem stability, is particularly important. Therefore, the aim of this study was to assess the sensitivity of the soil microbiome to this xenobiotic and to evaluate the potential of organic materials such as starch (St), grass compost (Co), and fermented bark (B) to restore the balance of soil cultivated with Zea mays. The negative effects of BPA on the abundance, diversity, and structure of bacterial and fungal communities in soil contaminated with 500 and 1000 mg kg[-1] d.m. of soil were confirmed. Changes in the phospholipid profile, including phosphatidylethanolamine (PE), phosphatidylcholine (PC), phosphatidylglycerol (PG), and ergosterol (E), were also assessed. BPA applied at 1000 mg kg[-1] d.m. of soil inhibited the proliferation of organotrophic bacteria and actinomycetes, while stimulating fungal growth. This xenobiotic's impact is also reflected by a decrease in PC and PG levels in soil under BPA pressure. Through amplification of the V3-V4 16S rRNA region (for bacteria) and the ITS1 region (for fungi), the dominant bacterial phylum Proteobacteria was identified, with genera including Cellulosimicrobium, Caulobacter, Rhodanobacter, Sphingomonas, Mucilaginibacter, and Pseudomonas. Among fungi, Ascomycota dominated, primarily represented by the genus Penicillium. Of all the organic materials tested for mitigating BPA's negative effects, grass compost was identified as the most promising, not only restoring soil homeostasis but also enhancing the growth and development of Zea mays cultivated in BPA-contaminated soil.},
}

*Soil Microbiology
*Benzhydryl Compounds/pharmacology
*Phenols/pharmacology
*Microbiota/drug effects
Soil/chemistry
Bacteria/drug effects/genetics/classification
*Soil Pollutants
Fungi/drug effects/genetics
RNA, Ribosomal, 16S/genetics
Zea mays/growth & development
Bisphenol A Compounds

@article {pmid41097262,
year = {2025},
author = {Ebrahim, Z and Proost, S and Tito, RY and Raes, J and Glorieux, G and Moosa, MR and Blaauw, R},
title = {Correction: Ebrahim et al. The Effect of ß-Glucan Prebiotic on Kidney Function, Uremic Toxins and Gut Microbiome in Stage 3 to 5 Chronic Kidney Disease (CKD) Predialysis Participants: A Randomized Controlled Trial. Nutrients 2022, 14, 805.},
journal = {Nutrients},
volume = {17},
number = {19},
pages = {},
doi = {10.3390/nu17193054},
pmid = {41097262},
issn = {2072-6643},
abstract = {After a thorough review of our data and methodology, we identified an issue related to assigning enterotypes to samples from "The Effect of ß-Glucan Prebiotic on Kidney Function, Uremic Toxins and Gut Microbiome in Stage 3 to 5 Chronic Kidney Disease (CKD) Predialysis Participants: A Randomized Controlled Trial" [...].},
}

@article {pmid41097233,
year = {2025},
author = {Karekezi, J and Kim, H and Dusabimana, T and Nugroho, TA and Ndahigwa, EN and So, YJ and Kim, J and Kim, TR and Sohn, M and Miao, J and Moon, Y and Park, SW},
title = {Lactiplantibacillus plantarum LM1001 Supplementation Attenuates Muscle Atrophy and Function Decline in Aged Mice.},
journal = {Nutrients},
volume = {17},
number = {19},
pages = {},
doi = {10.3390/nu17193156},
pmid = {41097233},
issn = {2072-6643},
support = {RS-2023-00273563//National Research Foundation of Korea/ ; 2021R1A5A8029490//National Research Foundation of Korea/ ; Fund for Professors on Sabbatical Leave, 2025//Gyeongsang National University/ ; },
mesh = {Animals ; *Probiotics/pharmacology/administration & dosage ; Male ; Gastrointestinal Microbiome/drug effects ; Mice, Inbred C57BL ; *Sarcopenia ; *Aging/physiology ; *Muscular Atrophy/prevention & control ; Mice ; Diet, High-Fat/adverse effects ; *Dietary Supplements ; *Lactobacillus plantarum ; Muscle, Skeletal/physiopathology ; Muscle Strength/drug effects ; Insulin-Like Growth Factor I/metabolism ; Proto-Oncogene Proteins c-akt/metabolism ; },
abstract = {Background/Objectives: Aging and metabolic disorders are associated with a decline in muscle function, referred to as age-related sarcopenia. The underlying mechanisms of sarcopenia include cellular senescence, imbalanced protein homeostasis, accumulation of oxidative and inflammatory stressors, and mitochondrial dysfunction. Probiotic supplementation improves the gut microbiome and enhances muscle function via the gut-muscle axis. However, details of molecular mechanisms and the development of an appropriate treatment are under active investigation. Methods: We have examined the effects of Lactiplantibacillus plantarum LM1001, a probiotic that reportedly improves the digestibility of branched-chain amino acids in myocyte cultures, but exactly how it contributes to muscle structure and function remains unclear. Results: We show that aged mice (male C57BL6/J) fed a high-fat diet (HFD) exhibit weak muscle strength, as reflected by a reduction in grip strength. LM1001 supplementation increases muscle strength and restores myofibril size, which has been altered by HFD in aged mice. Expression of myogenic proteins is increased, while protein markers for muscle atrophy are downregulated by LM1001 treatment via the IGF-1/Akt/FoxO3a pathway. LM1001 improves gut microbiota that are altered in aged HFD-fed mice, by increasing their abundance in beneficial bacteria, and efficiently maintains the epithelial lining integrity of the large intestine. Conclusions: We conclude that LM1001 supplementation serves a beneficial role in patients suffering from sarcopenia and metabolic disorders, improving their muscle function, gut microbiota, and intestinal integrity.},
}

Animals
*Probiotics/pharmacology/administration & dosage
Male
Gastrointestinal Microbiome/drug effects
Mice, Inbred C57BL
*Sarcopenia
*Aging/physiology
*Muscular Atrophy/prevention & control
Mice
Diet, High-Fat/adverse effects
*Dietary Supplements
*Lactobacillus plantarum
Muscle, Skeletal/physiopathology
Muscle Strength/drug effects
Insulin-Like Growth Factor I/metabolism
Proto-Oncogene Proteins c-akt/metabolism

@article {pmid41097227,
year = {2025},
author = {Mao, JS and Cui, HY and Zhou, XZ and Zhang, SW},
title = {Recent Progress in Exploring Dietary Nutrition and Dietary Patterns in Periodontitis with a Focus on SCFAs.},
journal = {Nutrients},
volume = {17},
number = {19},
pages = {},
doi = {10.3390/nu17193150},
pmid = {41097227},
issn = {2072-6643},
support = {82401128//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Periodontitis/prevention & control/epidemiology/microbiology ; *Dietary Fiber/administration & dosage ; *Fatty Acids, Volatile/metabolism ; *Diet ; *Nutritional Status ; Diet, Mediterranean ; },
abstract = {Dietary patterns greatly affect periodontitis, a chronic inflammatory disease that compromises both dental and systemic health. According to the emerging evidence, periodontal risk is more strongly associated with the overall dietary quality, especially fiber density intake, than any one micronutrient. While the average intake in industrialized countries is only half of the recommended 30 g day[-1], high-fiber diets such as the Mediterranean diet, the Dietary Approaches to Stop Hypertension (DASH), and whole-food plant-based diets are consistently associated with a 20-40% lower periodontitis prevalence. Dietary fiber plays a central role in regulating immune responses, strengthening tissue barriers, improving metabolic homeostasis, and shaping a healthy microbiome through its microbial fermentation products: short-chain fatty acids (SCFAs). This makes it a biologically rational and clinical evidence-supported strategy for the prevention and management of periodontitis. Integrating high-fiber diet recommendations into routine periodontal care and public health policies could be a crucial step towards more comprehensive oral and systemic health management. This narrative review elaborates on the mechanistic, observational, and intervention data highlighting the role of dietary fiber, especially SCFAs, in periodontal health.},
}

Humans
*Periodontitis/prevention & control/epidemiology/microbiology
*Dietary Fiber/administration & dosage
*Fatty Acids, Volatile/metabolism
*Diet
*Nutritional Status
Diet, Mediterranean

@article {pmid41097199,
year = {2025},
author = {Dey, P},
title = {All That Glitters Ain't Gold: The Myths and Scientific Realities About the Gut Microbiota.},
journal = {Nutrients},
volume = {17},
number = {19},
pages = {},
doi = {10.3390/nu17193121},
pmid = {41097199},
issn = {2072-6643},
mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; Dysbiosis/microbiology ; Probiotics ; Diet ; Fecal Microbiota Transplantation ; },
abstract = {Gut microbial modulation through diet is central to human health and disease. Despite tremendous effort in understanding the impact of nutrients and drugs on the gut microbiota, and attempts to develop dietary strategies that facilitate gut-beneficial effects, several erroneous gut microbiota-associated concepts remain prevalent in popular belief. This article discusses widespread misconceptions about the gut microbiota, contrasting them with contemporary scientific facts. In this article, ten prevalent myths, including the obsolete 10:1 bacteria-to-human-cell ratio, the reductive categorization of microbes as 'good' or 'bad', and the discredited universal biomarker status of the Firmicutes/Bacteroidetes ratio in relation to metabolic diseases, have been debunked. Essential facts highlighting the context-dependency of the microbiome, considerable inter-individual heterogeneity, and dynamic reactivity to dietary changes are discussed. This questions the assumptions that increased diversity always signifies health, that probiotics are intrinsically safe, that fecal microbiota transplantation is a universal remedy, or that leaky gut syndrome constitutes a clearly defined diagnosis. It is highlighted that eubiosis and dysbiosis do not possess uniform criteria, and microbiome-drug interactions are extremely individualized. The gut microbiota operates as a dynamic, adaptive ecosystem, necessitating sophisticated, evidence-based methodologies for study and therapeutic application, transcending simplistic misconceptions in favor of tailored insights and therapies.},
}

*Gastrointestinal Microbiome/physiology
Humans
Dysbiosis/microbiology
Probiotics
Diet
Fecal Microbiota Transplantation

@article {pmid41097131,
year = {2025},
author = {Ochocińska, AM and Podstawka, I and Kępka, A and Waszkiewicz, N},
title = {Diet as a Modulator of Gut Microbiota May Reduce Alzheimer's Disease Risk.},
journal = {Nutrients},
volume = {17},
number = {19},
pages = {},
doi = {10.3390/nu17193053},
pmid = {41097131},
issn = {2072-6643},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Alzheimer Disease/prevention & control/microbiology ; Diet, Mediterranean ; Diet, Ketogenic ; Diet, Western/adverse effects ; Dysbiosis ; *Diet ; Risk Factors ; },
abstract = {The aging process, along with an inadequate diet and an inflammatory gut response resulting from dysbiosis, contributes to the pathogenesis of Alzheimer's disease (AD). Modifying the composition of the gut microbiota through appropriate pre/probiotic-rich diets may act as a preventive option for AD. The variety of functions performed by the gut microbiota makes this ecosystem one of the most important systems in the human body. The Mediterranean diet (MedDiet), the Dietary Approaches to Stop Hypertension (DASH), the Mediterranean-DASH Intervention for Neurodegenerative Delay diet (MIND), and the modified ketogenic-Mediterranean diet (MKD) positively affect the intestinal microflora and may reduce the risk of dementia. A ketogenic diet has a neuroprotective effect and improves cognitive function but leads to a significant decrease in the abundance and diversity of bacterial species in favor of harmful bacteria. A Western-style diet (Western diet, WD) rich in processed products, red meat, simple sugars, and saturated fatty acids has a negative impact on gut microbiota function, increasing the risk of AD. Our review supports the hypothesis that factors like a proper diet and a healthy gut microbiota have a positive impact on the prevention of neurodegenerative diseases, including AD. A thorough understanding of the role the microbiota plays in the proper functioning of the nervous system can aid in the prevention of AD by developing new dietary strategies and dietary lifestyles.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Alzheimer Disease/prevention & control/microbiology
Diet, Mediterranean
Diet, Ketogenic
Diet, Western/adverse effects
Dysbiosis
*Diet
Risk Factors

@article {pmid41097128,
year = {2025},
author = {Wu, Y and Chen, Q and Fan, R and Song, L and Wang, S and You, M and Cai, M and Li, Y and Xu, M},
title = {Association Between the Dietary Inflammatory Index and Life's Essential 8 in Older Adults Based on Gut Microbiota Profiles.},
journal = {Nutrients},
volume = {17},
number = {19},
pages = {},
doi = {10.3390/nu17193050},
pmid = {41097128},
issn = {2072-6643},
mesh = {Humans ; *Gastrointestinal Microbiome ; Aged ; Male ; Female ; *Inflammation ; *Diet/adverse effects ; *Cardiovascular Diseases/prevention & control/etiology ; RNA, Ribosomal, 16S/genetics ; Aged, 80 and over ; Middle Aged ; },
abstract = {BACKGROUND/OBJECTIVES: As the global population ages, cardiovascular disease (CVD) emerges as a critical challenge for public health, with chronic inflammation identified as a key contributing risk factor. As a modifiable lifestyle factor, diet plays a critical role in the prevention of CVD. Given the established link between diet and inflammation, clarifying the relationship between dietary inflammatory potential and cardiovascular health (CVH) is of significant public health importance. This study aimed to evaluate the association between dietary inflammatory potential and CVH in an elderly population, and to explore the related role of the gut microbiota.

METHODS: Dietary inflammatory potential was quantified using the Dietary Inflammatory Index (DII), CVH was assessed by the American Heart Association's Life's Essential 8 (LE8) score, and gut microbiome analysis was profiled by 16S rRNA gene sequencing.

RESULTS: Results showed that higher DII scores, indicative of a pro-inflammatory dietary pattern, were significantly linked to reduced LE8 scores, suggesting an inverse association between dietary inflammatory potential and CVH. Based on the gut microbiome, participants with high CVH exhibited greater α diversity compared with those with low CVH, while both α and β diversity were higher in the anti-inflammatory diet group than in the pro-inflammatory diet group. These results indicate that anti-inflammatory diets may be associated with better CVH, possibly through the preservation of the ecological balance of the gut microbiota. Correlation analyses further pointed to several genera potentially associated with both dietary inflammatory potential and CVH. Functional predictions suggested that variation in dietary inflammatory potential could be linked to differences in microbial metabolic functions relevant to energy, lipid and glucose metabolism, and inflammatory processes.

CONCLUSIONS: In conclusion, this study provides novel evidence linking dietary inflammatory potential, gut microbiota, and CVH in older adults, and offers preliminary insights for dietary interventions and microbiota-targeted strategies in CVD prevention.},
}

Humans
*Gastrointestinal Microbiome
Aged
Male
Female
*Inflammation
*Diet/adverse effects
*Cardiovascular Diseases/prevention & control/etiology
RNA, Ribosomal, 16S/genetics
Aged, 80 and over
Middle Aged

@article {pmid41097077,
year = {2025},
author = {So, MT and Ullah, A and Waris, A and Alhumaydhi, FA},
title = {The Etiological Role of Impaired Neurogenesis in Schizophrenia: Interactions with Inflammatory, Microbiome and Hormonal Signaling.},
journal = {International journal of molecular sciences},
volume = {26},
number = {19},
pages = {},
doi = {10.3390/ijms26199814},
pmid = {41097077},
issn = {1422-0067},
support = {QUAPC-2025//Deanship of Graduate Studies and Scientific Research at Qassim University for financial support (QU-APC-2025)./ ; },
mesh = {Humans ; *Schizophrenia/etiology/metabolism/pathology/microbiology ; *Neurogenesis ; Signal Transduction ; Animals ; *Microbiota ; Inflammation/metabolism ; },
abstract = {Schizophrenia is a prevailing yet severely debilitating psychiatric disorder characterized by a convoluted etiology. Although antipsychotics have been available for over half a century, they primarily mitigate symptoms rather than providing definitive care. This limitation suggests that the neurotransmitter systems targeted by these medications are not the root cause of the disorder. Ongoing research seeks to elucidate the cellular, molecular, and circuitry pathways that contribute to the development of schizophrenia. Unfortunately, its precise pathogenesis remains incompletely understood. Accumulating evidence implicates dysregulated neurogenesis and aberrant neurodevelopmental processes as key contributors to disease progression. Recent advances in proteomics and imaging technology have facilitated the emergence of novel models of schizophrenia, emphasizing the roles of neuroinflammation, sex steroids, and cortisol. This paper aims to organize and map the intercorrelations and potential causal effects between various mechanistic models to gain deeper insight on how these mechanisms contribute to the cause, risks, and symptoms of the disorder. Furthermore, we discuss the potential therapeutic strategies that target these pathological pathways. Elucidating these mechanisms may ultimately advance our understanding of schizophrenia's etiological foundations and guide the development of curative interventions.},
}

Humans
*Schizophrenia/etiology/metabolism/pathology/microbiology
*Neurogenesis
Signal Transduction
Animals
*Microbiota
Inflammation/metabolism

@article {pmid41097043,
year = {2025},
author = {Chernevskaya, E and Sorokina, E and Polyakov, P and Gorshkov, K and Kovaleva, N and Zakharchenko, V and Beloborodova, N},
title = {Evaluation and Modulation of Gut Microbiome Dysfunction in Chronically Critically Ill Patients: A Prospective Pilot Study.},
journal = {International journal of molecular sciences},
volume = {26},
number = {19},
pages = {},
doi = {10.3390/ijms26199778},
pmid = {41097043},
issn = {1422-0067},
mesh = {Humans ; *Critical Illness/therapy ; *Gastrointestinal Microbiome/drug effects ; Pilot Projects ; Male ; Female ; Prospective Studies ; Middle Aged ; Aged ; Anti-Bacterial Agents/therapeutic use ; Chronic Disease ; Adult ; },
abstract = {Assessing gut microbiota disturbances for subsequent modulation remains a challenge. This study aims to evaluate the safety and efficacy of a microbiota-oriented strategy in treating patients with chronic critical illness (CCI). This single-center prospective study included chronically critically ill patients, stratified into three groups by severity of microbiota dysfunction. Three different microbiota modulation regimens including metabiotics, enteral, and anaerobic-safe systemic antibiotics were applied subsequently. Forty-three patients with chronic critical illness were included. Mild microbiota dysfunction was present in 49% patients, moderate in 19% and severe in 32%. Monitoring of biomarkers for 14 days confirmed the safety of reducing the pharmacological load in mild to moderate microbiota dysfunction. The microbiota-oriented strategy demonstrated improvements in neurological condition, a decrease in inflammation, and normalization of several hematological and biochemical parameters, without contributing to the activation of opportunistic microorganisms in the intestinal microbiota. The incidence of pneumonia in patients with CCI was reduced significantly during the 28-day observation period. The results of the pilot study suggest the potential benefits of a microbiota-oriented strategy in preventing nosocomial pneumonia in CCI patients.},
}

Humans
*Critical Illness/therapy
*Gastrointestinal Microbiome/drug effects
Pilot Projects
Male
Female
Prospective Studies
Middle Aged
Aged
Anti-Bacterial Agents/therapeutic use
Chronic Disease
Adult

@article {pmid41097031,
year = {2025},
author = {Chen, Y and Han, L and Ye, T and Xie, C},
title = {Research Progress on Diseases and Pests of Chrysanthemum (2015-2025).},
journal = {International journal of molecular sciences},
volume = {26},
number = {19},
pages = {},
doi = {10.3390/ijms26199767},
pmid = {41097031},
issn = {1422-0067},
support = {CSTB2024TIAD-LUX0004//Basic Research and Key Technology Integration and Application of Functional Flowers/ ; 2024LYXZ024//Basic Research and Key Technology Integration and Application of Functional Flowers/ ; 2024YFD1600900//National Key R&D Program of China/ ; },
mesh = {*Chrysanthemum/genetics/parasitology/microbiology/virology ; *Plant Diseases/microbiology/parasitology/genetics ; Animals ; Disease Resistance/genetics ; Pest Control, Biological ; },
abstract = {Chrysanthemum morifolium Ramat. is a major ornamental crop that suffers from diverse fungal, bacterial, viral, and insect pests, causing significant yield and quality losses. Between 2015 and 2025, rapid progress in molecular biology, genomics, and ecological regulation has advanced both fundamental research and applied control strategies. Multi-locus sequencing, multiplex PCR, and next-generation sequencing refined the identification of fungal and bacterial pathogens, while functional studies of WRKY, MYB, and NAC transcription factors revealed key resistance modules. Hormone-mediated signaling pathways, particularly those of salicylic acid, jasmonic acid, and abscisic acid, were shown to play central roles in host defense. Despite these advances, durable genetic resistance against bacterial pathogens and broad-spectrum defense against viruses remains limited. Novel technologies, including virus-free propagation, RNA interference, and spray-induced gene silencing, have shown promising outcomes. For insect pests, studies clarified the damage and virus-vectoring roles of aphids and thrips, and resistance traits linked to trichomes, terpenoids, and lignin have been identified. Biocontrol agents such as Trichoderma spp., Bacillus spp., predatory mites, and entomopathogenic fungi have also demonstrated efficacy. Future efforts should integrate molecular breeding, genome editing, RNA-based tools, and microbiome management to achieve sustainable chrysanthemum protection.},
}

*Chrysanthemum/genetics/parasitology/microbiology/virology
*Plant Diseases/microbiology/parasitology/genetics
Animals
Disease Resistance/genetics
Pest Control, Biological

@article {pmid41097012,
year = {2025},
author = {Yu, H and Niu, X and Niu, B and Lei, P and Xu, N and Yang, S and Yu, Q and Li, G and Wang, L},
title = {Liver-Targeted Scutellarin Nanoemulsion Alleviates Fibrosis with Ancillary Modulation of the Gut-Liver Microbiota.},
journal = {International journal of molecular sciences},
volume = {26},
number = {19},
pages = {},
doi = {10.3390/ijms26199746},
pmid = {41097012},
issn = {1422-0067},
support = {2021-I2M-1-070; 2023-I2M-2-006//CAMS Innovation Fund for Medical Sciences/ ; },
mesh = {*Apigenin/pharmacology/administration & dosage/chemistry ; Animals ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Glucuronates/pharmacology/administration & dosage/chemistry ; *Liver Cirrhosis/drug therapy/pathology/metabolism/microbiology ; Emulsions/chemistry ; *Liver/drug effects/microbiology/metabolism/pathology ; Hepatic Stellate Cells/drug effects/metabolism ; Male ; Mice, Inbred C57BL ; *Nanoparticles/chemistry ; Humans ; Disease Models, Animal ; Transforming Growth Factor beta1/metabolism ; },
abstract = {Liver fibrosis, a progressive condition with limited pharmacotherapies, poses a global health challenge. Scutellarin (SCU), a flavonoid derived from Erigeron breviscapus, has demonstrated anti-fibrotic activity and modulates gut microbiota. Emerging evidence suggests that SCU may also influence the hepatic microbiome. However, its clinical utility is constrained by poor water solubility and low oral bioavailability. Here, we developed an SCU-loaded nanoemulsion (SCE) to enhance solubility and liver-targeted delivery. In vitro, SCE increased SCU uptake in hepatic stellate cells (HSCs) and significantly inhibited TGF-β1-induced fibrogenesis. In a bile duct ligation (BDL) mouse model, oral administration of SCE improved hepatic SCU accumulation and produced superior anti-fibrotic efficacy. SCE treatment attenuated fibrosis and collagen deposition in the liver and improved liver function markers. Mechanistic investigations using 16S rRNA sequencing revealed that SCU treatment was associated with beneficial microbiota changes, although its main therapeutic effects were achieved through enhanced hepatic targeting. Notably, the SCE formulation was well-tolerated, showing no significant toxicity in vitro or in vivo. In conclusion, the SCU-loaded nanoemulsion achieved enhanced hepatic delivery of SCU and exerted potent anti-fibrotic effects via multiple mechanisms, including direct suppression of fibrogenesis and ancillary modulation of the gut-liver microbiome, offering a promising therapeutic strategy for liver fibrosis.},
}

*Apigenin/pharmacology/administration & dosage/chemistry
Animals
*Gastrointestinal Microbiome/drug effects
Mice
*Glucuronates/pharmacology/administration & dosage/chemistry
*Liver Cirrhosis/drug therapy/pathology/metabolism/microbiology
Emulsions/chemistry
*Liver/drug effects/microbiology/metabolism/pathology
Hepatic Stellate Cells/drug effects/metabolism
Male
Mice, Inbred C57BL
*Nanoparticles/chemistry
Humans
Disease Models, Animal
Transforming Growth Factor beta1/metabolism

@article {pmid41096928,
year = {2025},
author = {Yang, B and Wu, J and Hou, X and Bai, T and Liu, S},
title = {Memory in Misfire: The Gut Microbiome-Trained Immunity Circuit in Inflammatory Bowel Diseases.},
journal = {International journal of molecular sciences},
volume = {26},
number = {19},
pages = {},
doi = {10.3390/ijms26199663},
pmid = {41096928},
issn = {1422-0067},
support = {2022YFC2504005//National Key Research and Development Program of China/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; *Inflammatory Bowel Diseases/immunology/microbiology/therapy ; Animals ; *Immunologic Memory ; Immunity, Innate ; Probiotics/therapeutic use ; Fecal Microbiota Transplantation ; Trained Immunity ; },
abstract = {Inflammatory bowel disease (IBD) demonstrates chronic relapsing inflammation extending beyond adaptive immunity dysfunction. "Trained immunity"-the reprogramming of innate immune memory in myeloid cells and hematopoietic progenitors-maintains intestinal inflammation; however, the mechanism by which gut microbiome orchestration determines protective versus pathological outcomes remains unclear. Microbial metabolites demonstrate context-dependent dual effects along the gut-bone marrow axis. Short-chain fatty acids typically induce tolerogenic immune memory, whereas metabolites like succinate and polyamines exhibit dual roles: promoting inflammation in certain contexts while enhancing barrier integrity in others, influenced by cell-specific receptors and microenvironmental factors. Interventions include precision probiotics and postbiotics delivering specific metabolites, fecal microbiota transplantation addressing dysbiotic trained immunity, targeted metabolite supplementation, and pharmacologic reprogramming of pathological myeloid training states. Patient stratification based on microbiome composition and host genetics enhances therapeutic precision. Future research requires integration of non-coding RNAs regulating trained immunity, microbiome-immune-neuronal axis interactions, and host genetic variants modulating microbiome-immunity crosstalk. Priorities include developing companion diagnostics, establishing regulatory frameworks for microbiome therapeutics, and defining mechanistic switches for personalized interventions.},
}

Humans
*Gastrointestinal Microbiome/immunology
*Inflammatory Bowel Diseases/immunology/microbiology/therapy
Animals
*Immunologic Memory
Immunity, Innate
Probiotics/therapeutic use
Fecal Microbiota Transplantation
Trained Immunity

@article {pmid41096907,
year = {2025},
author = {Murillo-Cancho, AF and Lozano-Paniagua, D and Nievas-Soriano, BJ},
title = {Dietary and Pharmacological Modulation of Aging-Related Metabolic Pathways: Molecular Insights, Clinical Evidence, and a Translational Model.},
journal = {International journal of molecular sciences},
volume = {26},
number = {19},
pages = {},
doi = {10.3390/ijms26199643},
pmid = {41096907},
issn = {1422-0067},
mesh = {Humans ; *Aging/metabolism/drug effects ; *Caloric Restriction ; *Metabolic Networks and Pathways/drug effects ; Animals ; Longevity ; Fasting ; Translational Research, Biomedical ; *Diet ; },
abstract = {Advances in geroscience suggest that aging is modulated by molecular pathways that are amenable to dietary and pharmacological intervention. We conducted an integrative critical review of caloric restriction (CR), intermittent fasting (IF), and caloric restriction mimetics (CR-mimetics) to compare shared mechanisms, clinical evidence, limitations, and translational potential. Across modalities, CR and IF consistently activate AMP-activated protein kinase and sirtuins, inhibit mTOR (mechanistic target of rapamycin) signaling, and enhance autophagy, aligning with improvements in insulin sensitivity, lipid profile, low-grade inflammation, and selected epigenetic aging measures in humans. CR-mimetics, such as metformin, resveratrol, rapamycin, and spermidine, partially reproduce these effects; however, long-term safety and efficacy in healthy populations remain incompletely defined. Methodological constraints-short trial duration, selective samples, intermediate (nonclinical) endpoints, and limited adherence monitoring-impede definitive conclusions on hard outcomes (frailty, disability, hospitalization, mortality). We propose the Active Management of Aging and Longevity (AMAL) model, a three-level biomarker-guided framework that integrates personalized diet, chrono-nutrition, exercise, and the selective use of CR-mimetics, along with digital monitoring and decision support. AMAL emphasizes epigenetic clocks, multi-omics profiling, inflammatory and microbiome metrics, and adaptive protocols to enhance adherence and clinical relevance. Overall, CR, IF, and CR mimetics constitute promising, complementary strategies to modulate biological aging; rigorous long-term trials with standardized biomarkers and clinically meaningful endpoints are needed to enable their scalable implementation.},
}

Humans
*Aging/metabolism/drug effects
*Caloric Restriction
*Metabolic Networks and Pathways/drug effects
Animals
Longevity
Fasting
Translational Research, Biomedical
*Diet

@article {pmid41096891,
year = {2025},
author = {Sheikh, MY and Younus, MF and Shergill, A and Hasan, MN},
title = {Diet and Lifestyle Interventions in Metabolic Dysfunction-Associated Fatty Liver Disease: A Comprehensive Review.},
journal = {International journal of molecular sciences},
volume = {26},
number = {19},
pages = {},
doi = {10.3390/ijms26199625},
pmid = {41096891},
issn = {1422-0067},
mesh = {Humans ; *Life Style ; Insulin Resistance ; Exercise ; *Diet ; *Fatty Liver/metabolism/therapy ; Gastrointestinal Microbiome ; *Non-alcoholic Fatty Liver Disease ; },
abstract = {Metabolic dysfunction-associated steatotic liver disease (MASLD) and its progressive form, metabolic dysfunction-associated steatohepatitis (MASH), have become the leading causes of chronic liver disease worldwide, with increasing rates of cirrhosis, hepatocellular carcinoma, and cardiovascular complications. Pathogenesis involves a complex interplay of dietary excess, sedentary lifestyle, insulin resistance, adipose tissue dysfunction, and alterations in the gut microbiome, which collectively lead to hepatocellular stress, inflammation, and fibrogenesis. Despite ongoing advances in pharmacotherapy, lifestyle intervention remains the cornerstone of management. Evidence shows that sustained weight loss of ≥5% reduces hepatic steatosis, ≥7% improves necroinflammation, and ≥10% stabilizes or reverses fibrosis. Dietary strategies, including Mediterranean-style patterns, high-protein approaches, and intermittent fasting, have been shown to be effective in improving insulin sensitivity and reducing intrahepatic triglycerides. Exercise interventions, focusing on both aerobic fitness and resistance training, enhance metabolic flexibility and combat sarcopenia, thereby improving hepatic and systemic outcomes. Equally important are behavioral support, digital health tools, and multidisciplinary approaches that enhance adherence and address barriers such as socioeconomic disparities, limited access, and patient engagement issues. Personalized nutrition plans, integrating physical activity, and ongoing support for behavioral change are essential for long-term disease management. This review synthesizes current evidence on the roles of macronutrients, micronutrients, dietary quality, physical activity, and adjunctive behavioral strategies in managing MASLD. By translating mechanistic insights into practical, evidence-based recommendations, we aim to provide clinicians, dietitians, and exercise professionals with effective frameworks to slow disease progression and improve outcomes across diverse patient populations.},
}

Humans
*Life Style
Insulin Resistance
Exercise
*Diet
*Fatty Liver/metabolism/therapy
Gastrointestinal Microbiome
*Non-alcoholic Fatty Liver Disease