@article {pmid42014682,
year = {2026},
author = {Lee, EM and McNulty, NP and Hibberd, MC and Cheng, J and Ahsan, K and Chang, HW and Cohen, BA and Gordon, JI},
title = {Enhancing inference of differential gene expression in metatranscriptomes from human microbial communities.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42014682},
issn = {2041-1723},
support = {F30 DK142304/DK/NIDDK NIH HHS/United States ; DK30292//Foundation for the National Institutes of Health (Foundation for the National Institutes of Health, Inc.)/ ; },
mesh = {Humans ; Animals ; Mice ; Metagenome/genetics ; *Microbiota/genetics ; *Transcriptome ; *Gene Expression Profiling/methods ; Bacteria/genetics/classification ; *Metagenomics/methods ; Germ-Free Life ; },
abstract = {Metatranscriptomic (MTX) sequencing quantifies gene expression from the collective genomes of microbial communities (microbiomes), enabling assessment of functional activity rather than functional potential. While differential expression testing is essential for RNA-sequencing analysis, current metatranscriptomic approaches have only been benchmarked on simulated data, resulting in a lack of standard practices for analysis of real datasets. Here, we use mock communities (defined mixtures of microbial cells with known properties) to quantitatively assess robustness and susceptibility of current approaches to various confounders including organisms' low relative abundance, differential abundance, low prevalence, global transcriptional output changes, and compositional effects. We show that no current method is robust to all confounders and method performance on simulated data does not generalize to real datasets. We then apply the same approaches to MTX datasets generated from gnotobiotic mice colonized with defined consortia of human bacterial strains and show that the method nominated by the mock community comparisons successfully inferred cross-feeding dynamics that were subsequently validated in vitro. Finally, using metagenome-assembled genomes from a human clinical study, we leverage genome-level sequencing depth and detection of genes to exclude low information samples on a per-organism basis to overcome confounding low prevalence and enhance differential expression inference. We conclude that MTX benchmarking on real, non-simulated datasets can and should guide choice of methods and their implementation, enabling inference and validation of microbial metabolic strategies and interactions in vivo.},
}

Humans
Animals
Mice
Metagenome/genetics
*Microbiota/genetics
*Transcriptome
*Gene Expression Profiling/methods
Bacteria/genetics/classification
*Metagenomics/methods
Germ-Free Life

@article {pmid42014730,
year = {2026},
author = {Wang, Y and Yu, P and Huang, ES and Lu, DC and Zhang, W},
title = {Decoding a Microbial Community for Healthy Kelp: 403 MAGs from the World's Largest Kelp Farming Region.},
journal = {Scientific data},
volume = {13},
number = {1},
pages = {},
pmid = {42014730},
issn = {2052-4463},
support = {2023-004//2023 Weihai Key Postdoctoral Research Funding Program/ ; },
mesh = {*Kelp/microbiology ; Aquaculture ; *Microbiota ; *Metagenome ; Phylogeny ; Bacteria/classification/genetics ; Archaea/genetics/classification ; },
abstract = {Kelp is economically and ecologically significant, with its organic nutrient-rich aquaculture water harboring diverse microbial communities that critically influence kelp health and productivity. To characterize these communities, we collected ten water samples from major kelp farming areas and reconstructed 403 medium- to high-quality Metagenome-Assembled Genomes (MAGs). Of these, 110 (27.3%) met high-quality criteria (completeness >90%, contamination <5%). Phylogenomic analysis classified these MAGs into 21 archaeal and 382 bacterial species across 19 phyla, with Pseudomonadota (n = 217), Bacteroidota (n = 74), and Patescibacteria (n = 24) as the dominant groups. UpSet plot analysis revealed the presence of a core set of 30 MAGs across all sampling sites. Notably, diseased samples exhibited a marked increase in Pseudomonadota MAGs, suggesting their potential as biomarkers for disease monitoring. Together, these findings provide foundational insights into the microbial ecology of kelp aquaculture systems, supporting improved disease management and sustainable practices.},
}

*Kelp/microbiology
Aquaculture
*Microbiota
*Metagenome
Phylogeny
Bacteria/classification/genetics
Archaea/genetics/classification

@article {pmid42034087,
year = {2026},
author = {Liao, S and Lin, X and Wang, X and Lin, J and Lu, Y and Deng, W and He, Q and Chi, Y and Xu, Z},
title = {Insights into the salt-dependent mechanisms of physicochemical changes, microbial succession, and biogenic amine formation during Doubanjiang fermentation.},
journal = {Food chemistry},
volume = {516},
number = {},
pages = {149287},
doi = {10.1016/j.foodchem.2026.149287},
pmid = {42034087},
issn = {1873-7072},
mesh = {*Biogenic Amines/metabolism ; Fermentation ; *Bacteria/metabolism/genetics/classification/isolation & purification ; *Sodium Chloride/metabolism/analysis ; *Wine/microbiology/analysis ; Microbiota ; },
abstract = {Excessive biogenic amine formation is a major safety concern in salt-reduced Doubanjiang fermentation. This study compared high- (12%), medium- (9%), and low-salt (6%) systems to elucidate physicochemical dynamics, microbial succession, and mechanisms promoting biogenic amine accumulation. Salt reduction accelerated acidification and proteolysis, with the low-salt system showing the highest total acidity (0.73 g/100 g) and free amino acids (2684.86 mg/100 g), accompanied by excessive biogenic amine accumulation (1456.95 mg/kg). Microbial communities responded strongly to salinity, with Weissella and Bacillus dominating under low-salt conditions, whereas Tetragenococcus and Millerozyma prevailed at higher salinities. Metagenomic and culturomic analyses further identified key functional strains associated with biogenic amine metabolism. Microbially driven acid accumulation and increased amino acid availability, together with activation of decarboxylases induced by acid stress, jointly promoted biogenic amine formation in the low-salt system. These findings clarify salt-dependent mechanisms of biogenic amine formation and provide guidance for designing safe reduced-salt fermentation strategies.},
}

*Biogenic Amines/metabolism
Fermentation
*Bacteria/metabolism/genetics/classification/isolation & purification
*Sodium Chloride/metabolism/analysis
*Wine/microbiology/analysis
Microbiota

@article {pmid42069617,
year = {2026},
author = {Yuan, H and Song, Y and Nie, L and Yang, Z and Yang, L and Yang, K and Yang, Y and Li, W and Wang, X and Zhang, XX and Hua, Y and Yuan, ZG},
title = {The gut metabolite arachidonic acid alleviates intestinal injury induced by a Toxoplasma gondii strain isolated from a wild rodent.},
journal = {Parasites & vectors},
volume = {19},
number = {1},
pages = {},
pmid = {42069617},
issn = {1756-3305},
support = {2025A1515012622//Natural Science Foundation of Guangdong Province/ ; },
mesh = {Animals ; *Toxoplasma/isolation & purification/pathogenicity/genetics ; *Arachidonic Acid/metabolism/pharmacology ; *Toxoplasmosis, Animal/parasitology/pathology ; Mice, Inbred C57BL ; Mice ; Gastrointestinal Microbiome ; *Intestines/pathology/parasitology ; Female ; Virulence ; Animals, Wild/parasitology ; },
abstract = {BACKGROUND: Wild isolates of Toxoplasma gondii may exhibit different virulence characteristics and host adaptability compared with those of laboratory strains. In this study, we isolated a novel rodent-derived T. gondii strain, denoted TgRodGz1, and evaluated its pathogenic features.

METHODS: TgRodGz1 was isolated from T. gondii-positive wild rodents in Guangdong Province and compared with the RH and Me49 strains in C57BL/6 mice. Virulence and intestinal injury were evaluated by survival analysis, brain cyst quantification, histopathology, tight junction assessment and qPCR. Gut microbiota and metabolic alterations were analyzed by metagenomic sequencing and LC-MS/MS-based metabolomics.

RESULTS: Compared with theT. gondii laboratory strains RH and Me49, TgRodGz1 was associated with more pronounced intestinal injury, including villus atrophy, barrier disruption and downregulation of tight junction proteins and increased gut permeability and inflammation. Metagenomic analysis revealed significant intestinal flora dysbiosis, with a marked reduction in beneficial bacteria and expansion of pathogenic bacteria. Metabolomic analysis revealed suppression of arachidonic acid (ARA) metabolism during TgRodGz1 infection. Supplementation with ARA did not directly inhibit parasite growth but significantly alleviated intestinal lesions, reduced brain cyst burden and attenuated inflammatory responses, including microglial activation.

CONCLUSIONS: These findings suggest that TgRodGz1 represents a distinct T. gondii genotype associated with pronounced intestinal pathology and suggest that ARA supplementation may alleviate intestinal and neuroinflammatory changes associated with T. gondii infection.},
}

Animals
*Toxoplasma/isolation & purification/pathogenicity/genetics
*Arachidonic Acid/metabolism/pharmacology
*Toxoplasmosis, Animal/parasitology/pathology
Mice, Inbred C57BL
Mice
Gastrointestinal Microbiome
*Intestines/pathology/parasitology
Female
Virulence
Animals, Wild/parasitology

@article {pmid42207030,
year = {2026},
author = {Ren, P and Kan, Z and Wei, B and Qin, W and Lu, S},
title = {Yellow tea extract ameliorates dexamethasone-induced hepatic steatosis by modulating the gut-liver axis and reshaping microbial metabolites: a multi-omics insight.},
journal = {Food & function},
volume = {17},
number = {12},
pages = {5410-5424},
doi = {10.1039/d6fo01620k},
pmid = {42207030},
issn = {2042-650X},
mesh = {Animals ; Mice ; Liver/metabolism/drug effects ; *Plant Extracts/pharmacology ; Male ; *Gastrointestinal Microbiome/drug effects ; *Dexamethasone/adverse effects ; *Fatty Liver/chemically induced/drug therapy/metabolism ; *Tea/chemistry ; Mice, Inbred C57BL ; Multiomics ; Camellia sinensis/chemistry ; },
abstract = {Long-term glucocorticoid therapy, exemplified by dexamethasone (DEX), frequently induces hepatic steatosis, posing a significant clinical challenge. Yellow tea (YT), a lightly fermented tea, is rich in polyphenols and polysaccharides, yet its protective effects against DEX-induced liver injury remain underexplored. This study investigated the hepatoprotective mechanisms of a yellow tea water extract (YT) using a DEX-induced mouse model, integrated with transcriptomic, metagenomic, and metabolomic analyses. YT intervention (500 mg[-1] kg[-1] day[-1] for 6 weeks) significantly attenuated DEX-induced hepatocellular injury, as evidenced by reduced serum alanine aminotransferase (ALT) and aspartate aminotransferase (AST) levels, decreased hepatic triglyceride (TG) and total cholesterol (TC) accumulation, and suppressed systemic inflammation (lipopolysaccharide (LPS) and tumor necrosis factor-alpha (TNF-α)). Hepatic transcriptomics and subsequent reverse transcription quantitative PCR (RT-qPCR) validation revealed that YT upregulated the antioxidant genes nuclear factor erythroid 2-related factor 2 (Nrf2) and heme oxygenase-1 (HO-1) while downregulating the lipogenic gene sterol regulatory element-binding protein 1c (SREBP-1c) and upregulating the fatty acid oxidation gene peroxisome proliferator-activated receptor alpha (PPAR-α). Gut microbiota analysis showed that YT reshaped the microbial community, notably enriching beneficial taxa such as Bifidobacterium pseudolongum and members of the Muribaculaceae family. Serum metabolomics indicated that this microbiota remodeling was associated with the restoration of perturbed metabolic pathways, notably tryptophan metabolism. Correlation analysis further linked specific microbial shifts with improved metabolic and inflammatory markers. Collectively, these integrated transcriptomic, metagenomic, and metabolomic findings demonstrate that YT alleviates DEX-induced hepatic steatosis through dual mechanisms involving direct hepatic antioxidant and lipid metabolic regulation and systemic modulation via the gut-liver axis, positioning it as a promising dietary strategy against glucocorticoid-associated metabolic complications.},
}

Animals
Mice
Liver/metabolism/drug effects
*Plant Extracts/pharmacology
Male
*Gastrointestinal Microbiome/drug effects
*Dexamethasone/adverse effects
*Fatty Liver/chemically induced/drug therapy/metabolism
*Tea/chemistry
Mice, Inbred C57BL
Multiomics
Camellia sinensis/chemistry

@article {pmid41566339,
year = {2026},
author = {Fernández-Trapote, E and Cobo-Díaz, JF and Oliveira, M and Puente, A and Berdejo, D and Puente, H and Cordero-García, R and López, M and Prieto, M and Argüello, H and Alvarez-Ordóñez, A},
title = {Microbiome and resistome successions in pig carcasses and fresh pork meat throughout slaughtering, processing and shelf-life.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {67},
pmid = {41566339},
issn = {2049-2618},
support = {FPU21/03421//Ministerio de Ciencia, Innovación y Universidades, Spain/ ; PRE2021-098910//Ministerio de Ciencia, Innovación y Universidades, Spain/ ; CNS2022-136066//Ministerio de Ciencia, Innovación y Universidades, Spain/ ; No 818368//European Commission under the European Union´s Horizon 2020/ ; PID2020-118813GB-I00//Ministerio de Ciencia, Innovación y Universidades/ ; },
mesh = {Animals ; Swine/microbiology ; *Microbiota/genetics ; *Bacteria/genetics/classification/isolation & purification/drug effects ; Acinetobacter/isolation & purification/genetics ; Abattoirs ; *Pork Meat/microbiology ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; Metagenomics ; Food Storage ; Metagenome ; Food Handling ; Food, Processed ; Pseudomonas/isolation & purification/genetics ; Brochothrix/isolation & purification/genetics ; Food Microbiology ; },
abstract = {BACKGROUND: Slaughterhouses and meat cutting plants represent potential hotspots for the spread and transfer of spoilage and pathogenic, including antimicrobial resistant, bacteria to meat and meat products. Here, we characterise the progression of the microbiome and resistome of two pork cuts (loin and sirloin) at different stages of processing, from the slaughter line to the end of shelf-life. To this end, we analysed samples from facility surfaces, carcasses, and meat cuts using whole metagenome sequencing.

RESULTS: The taxonomic and antimicrobial resistance gene (ARG) profiles of carcasses and meat cuts were significantly influenced by the point of sampling and the processing room. The facility surfaces were found to be the main source of some abundant genera, such as Anoxybacillus, Acinetobacter, Pseudomonas, and Brochothrix, in carcasses and meat cuts. A total of 1,291 metagenome-assembled genomes were reconstructed, corresponding to the most prevalent species identified in the taxonomic analysis at the read level. A reduction in bacterial and ARGs richness and diversity was observed for carcasses and meat cuts along the production chain, which suggests that processing procedures are effective in reducing bacterial and ARGs loads. Nonetheless, an increase in the ARGs load was observed at two sampling points: the carcass after evisceration and the sirloin at the end of its shelf-life (in this case linked to the increase of a single gene, tet(L)). The ARGs most frequently detected were those associated with resistance to tetracyclines, aminoglycosides, and lincosamides. Acinetobacter (in processing environments and carcass/meat samples) and Staphylococcus (in carcasses and meat) were identified as the main genera associated with the ARGs found.

CONCLUSIONS: Overall, our results provide the most detailed metagenomics-based perspective on the microbial successions of pig carcasses and fresh meat cuts during slaughtering, processing, and commercialisation. The observations made suggest that selection pressures imposed by processing steps and contact with facility surfaces contribute to shaping the microbiome and resistome of the two pork products throughout their production line and shelf-life. Video Abstract.},
}

Animals
Swine/microbiology
*Microbiota/genetics
*Bacteria/genetics/classification/isolation & purification/drug effects
Acinetobacter/isolation & purification/genetics
Abattoirs
*Pork Meat/microbiology
Anti-Bacterial Agents/pharmacology
Drug Resistance, Bacterial/genetics
Metagenomics
Food Storage
Metagenome
Food Handling
Food, Processed
Pseudomonas/isolation & purification/genetics
Brochothrix/isolation & purification/genetics
Food Microbiology

@article {pmid41567008,
year = {2026},
author = {Zhao, S and Rogers, MJ and Ding, C and He, J},
title = {Stable Function, Dynamic Phylotypes: Microdiversity as a Reservoir for Resilience in Dehalococcoides.},
journal = {Environmental science & technology},
volume = {60},
number = {4},
pages = {3364-3373},
doi = {10.1021/acs.est.5c14525},
pmid = {41567008},
issn = {1520-5851},
mesh = {*Dehalococcoides/metabolism/genetics ; Phylogeny ; Biodiversity ; },
abstract = {Organohalide-respiring bacteria (OHRB) are key contributors to global halogen cycling and mitigation of anthropogenic halogenated pollutants, yet their persistence is challenged by slow growth and restricted metabolic capacity. The mechanisms supporting long-term functional stability remain unclear. As a key OHRB, Dehalococcoides faces similar constraints, including declining abundance and loss or divergence of functional genes in bioaugmentation. Here we demonstrate that strain-level microdiversity within Dehalococcoides supports the resilience of community-scale dehalogenation. In AEDhc, a reconstructed consortium derived from eight Dehalococcoides-containing enrichment cultures, sequencing of a Dehalococcoides-specific marker gene revealed 30 distinct Dehalococcoides phylotypes coexisting within the community. Despite fluctuations in phylotype abundance over successive transfers, AEDhc consistently debrominated tetra- and pentabrominated diphenyl ethers (0.39 ± 0.06 - 0.45 ± 0.05 μM Br[-]/d), producing no detectable accumulation of intermediates. Proteomics analyses revealed that among 71 putative reductive dehalogenase (RDase) genes identified in metagenomic analysis, expression was consistently dominated by PcbA1-like and TceA-like RDases across transfers. These findings demonstrated that Dehalococcoides phylotypes can coexist and fluctuate dynamically even under constant cultivation conditions, with genetic variation serving as a reservoir of metabolic potential. Such microdiversity enhances functional stability and ecological resilience, highlighting the need to consider strain-level heterogeneity in bioremediation strategies.},
}

*Dehalococcoides/metabolism/genetics
Phylogeny
Biodiversity

@article {pmid41568034,
year = {2025},
author = {Yu, F and Song, J and Qi, L and Liu, J and Yang, Y and Li, W and Li, L and Ma, ZS},
title = {Gene and function diversity-area relationships in the inflammatory bowel disease fecal and mucosal microbiome.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1660973},
pmid = {41568034},
issn = {1664-302X},
abstract = {The diversity-area relationship (DAR), an extension of the classic species-area relationship (SAR), provides a powerful framework for understanding how biodiversity scales across space. In this study, we applied DAR and its metagenomic counterpart (m-DAR) to investigate the spatial scaling of metagenomic genes (MGs) and metagenomic functional gene clusters (MFGCs) of seven functional databases in the gut microbiomes of individuals with inflammatory bowel disease (IBD) and healthy cohorts. Using shotgun sequencing data from 42 mucosal and 22 fecal samples from both healthy and IBD cohorts, we modeled how this MGs and MFGCs accrues with area (samples), estimating diversity scaling parameters (z), pair-wise diversity overlap (PDO), and maximal accrual diversity (MAD), which reflects the total potential diversity. We found that mucosal communities exhibited greater dissimilarity (less pair-wise diversity overlap) between individuals than fecal cowmmunities at the levels of gene richness and evenness (q = 1, 2), whereas fecal communities showed a stronger influence from dominant, abundant genes (q = 2, 3). Furthermore, healthy gut microbiomes showed greater similarity than those of IBD at the level of gene richness (q = 0), but showed greater dissimilarity at the level of abundant genes and dominant genes. Healthy gut microbiomes generally demonstrated a higher potential total diversity compared to those from IBD patients. Notably, fecal samples captured a broader range of microbial diversity than mucosal samples. Additionally, mucosal communities showed greater dissimilarity than fecal communities in almost all the MFGCs of the seven databases except ARDB, which showed the same trend as MGs. We also identified that specific functional clusters related to antibiotic resistance, such as genes for chloramphenicol and vancomycin resistance, displayed distinct scaling behaviors, suggesting their potential role in IBD pathogenesis. These findings demonstrate that the gut microbiome in IBD is not merely less diverse but is fundamentally restructured in its spatial architecture. The application of DAR provides a novel, quantitative insight to diagnose and understand this dysbiosis, moving beyond simple diversity metrics to capture the spatial diversity scaling of microbial genes and functions.},
}

@article {pmid41568738,
year = {2026},
author = {Warren, A and Wynia, Z and Corr, PG and Devin, MF and Celikkol, Z and Gordon, L and Farah, M and Karam, M and Villarreal, D and Jackson, SA and Frame, LA},
title = {The microbiota-gut-brain axis in mild cognitive impairment and Alzheimer's disease: a scoping review of human studies.},
journal = {Alzheimer's & dementia : the journal of the Alzheimer's Association},
volume = {22},
number = {1},
pages = {e71023},
pmid = {41568738},
issn = {1552-5279},
support = {//TMCity/ ; },
mesh = {Humans ; *Cognitive Dysfunction/microbiology ; *Alzheimer Disease/microbiology ; *Gastrointestinal Microbiome/physiology ; *Dysbiosis/microbiology ; Probiotics/therapeutic use ; *Brain ; },
abstract = {Alzheimer's disease (AD) is projected to become the highest-burden neurological disorder globally. Mounting evidence implicates the gut microbiome in AD pathogenesis. This scoping review of gut microbiomes in mild cognitive impairment (MCI) and AD included dietary and probiotic interventions. We included original research and systematic reviews/meta-analyses. Animal and non-English studies were excluded. We searched PubMed, Scopus, and Cochrane Library through February 2023. Using Arksey and O'Malley's framework and the Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA)-Extension for Scoping Reviews (ScR) checklist, we screened 4751 articles, with 58 meeting predefined inclusion criteria. Our results demonstrated that gut dysbiosis was frequently reported in MCI and AD, including increased Pseudomonadota and Actinomycetota in AD and reduced diversity in some cases. Probiotic and dietary interventions showed promise in modulating cognition and microbiota, inconsistently. Emerging evidence links dysbiosis to cognitive decline; however, methodological heterogeneity and limited follow-up impede causal inference. Research should prioritize standardized protocols, functional microbiome analysis, and longitudinal human studies to clarify therapeutic potential. HIGHLIGHTS: Gut dysbiosis is a common feature of MCI and AD, with phylum-level microbial shifts frequently observed. Pseudomonadota and Actinomycetota are enriched in AD across multiple human studies. Beneficial genera like Faecalibacterium and Roseburia are consistently reduced in MCI and AD in a small number of studies. Probiotic and dietary interventions are promising to modulate the microbiota-cognition axis. More longitudinal human studies are needed to assess causal microbiome relationships.},
}

Humans
*Cognitive Dysfunction/microbiology
*Alzheimer Disease/microbiology
*Gastrointestinal Microbiome/physiology
*Dysbiosis/microbiology
Probiotics/therapeutic use
*Brain

@article {pmid41569365,
year = {2026},
author = {Duarte, M and Mansilha, C and Melo, A and Sobral, D and Ferreira, R and Gomes, JP and Rebelo, H and Veber, A and Puskar, L and Schade, U and Jordao, L},
title = {Detection of polycyclic aromatic hydrocarbons, microplastic presence and characterization of microbial communities in the soil of touristic zones at Alqueva's edges (Alentejo, Portugal).},
journal = {Environmental science and pollution research international},
volume = {33},
number = {4},
pages = {1447-1458},
pmid = {41569365},
issn = {1614-7499},
mesh = {Portugal ; *Polycyclic Aromatic Hydrocarbons/analysis ; *Soil Pollutants/analysis ; *Microplastics/analysis ; Environmental Monitoring ; *Soil Microbiology ; Bacteria ; Soil/chemistry ; Microbiota ; },
abstract = {Environmental pollution is a growing concern. Here, we assessed the occurrence of two groups of persistent organic pollutants (POPs-polycyclic aromatic hydrocarbons (PAHs) and microplastics (MPs)) and bacterial populations in the topsoil of three tourist spots located at the Alqueva's edges during 1 year, once per season. Soil chemical analysis revealed low content of total organic carbon, pH close to neutrality, and nitrogen and phosphorus levels consistent with acquisition of these nutrients only by atmospheric deposition. PAH's concentrations were in the range of ng/kg, being significantly below the "reference values" for contaminated soils. Nevertheless, potentially carcinogenic PAHs, detected at all locations, raise ecotoxicological concerns. Polyamide, polyester, polystyrene, and styrene acrylonitrile resin MPs were found. Six bacterial phyla constitute the core microbiome in the three locations and include genera of bacteria reported as plastic degraders, such as Bacillus, Exiguobacterium, Paenibacillus, and Pseudomonas. The presence of POPs, even at low levels, in the soil at the edges of a water reservoir should be monitored. The identification of bacteria reported as plastic degraders in the soil, and previously in the water, is promising, and their ability to spontaneously ensure the detoxification of the ecosystem should be further investigated.},
}

Portugal
*Polycyclic Aromatic Hydrocarbons/analysis
*Soil Pollutants/analysis
*Microplastics/analysis
Environmental Monitoring
*Soil Microbiology
Bacteria
Soil/chemistry
Microbiota

@article {pmid41570402,
year = {2026},
author = {Nitert, MD and Sternes, PR and Altemani, F and Callaway, LK and McIntyre, H and Tyson, GW and Barrett, HL},
title = {Gut microbiota is different before the development of preeclampsia.},
journal = {Pregnancy hypertension},
volume = {43},
number = {},
pages = {101415},
doi = {10.1016/j.preghy.2026.101415},
pmid = {41570402},
issn = {2210-7797},
mesh = {Humans ; Female ; Pregnancy ; *Pre-Eclampsia/microbiology/physiopathology ; *Gastrointestinal Microbiome ; Adult ; Feces/microbiology ; Blood Pressure ; Case-Control Studies ; },
abstract = {OBJECTIVES: The gut microbiota contributes to the regulation of blood pressure during and outside pregnancy. Preeclampsia (PE) is characterised by the development of hypertension along with renal, liver or other systemic complications. In women with PE, alterations in the gut microbiota composition have been reported.

STUDY DESIGN: We investigated whether changes in the gut microbiota composition were present before the onset of symptoms in a group of 10 women who developed late-onset PE and 24 women who remained normotensive throughout pregnancy. Faecal samples were obtained at 28 weeks' gestation from a subset of participants of the Study of PRobiotics IN Gestational diabetes (SPRING) and sequenced by metagenomic sequencing.

MAIN OUTCOME MEASURES: Taxonomic and functional characteristics were compared between the groups.

RESULTS: There were no taxonomic or functional differences in alpha diversity; however, for beta diversity, women who developed PE demonstrated a different taxonomic composition compared to women who remained normotensive. Women who developed PE had lower abundance of numerous taxa and functions. Both systolic and diastolic blood pressure were correlated with the abundances of specific species, though members of the same genus did not show consistency in the direction of correlation.

CONCLUSION: Despite a limited sample size, this study demonstrates numerous taxonomic and functional alterations in the gut microbiota composition. However, a clear signature to identify women at high risk of developing late-onset PE remains to be uncovered. The species-level data indicate that the regulation of blood pressure by the gut microbiota in pregnancy is complex and needs further investigation.},
}

Humans
Female
Pregnancy
*Pre-Eclampsia/microbiology/physiopathology
*Gastrointestinal Microbiome
Adult
Feces/microbiology
Blood Pressure
Case-Control Studies

@article {pmid41570486,
year = {2026},
author = {Lahariya, R and Anand, G and Kumari, B and Priyadarshi, K},
title = {Postbiotics and the gut-brain axis: A mechanistic review on modulating neuroinflammation and cognitive aging.},
journal = {Journal of neuroimmunology},
volume = {413},
number = {},
pages = {578870},
doi = {10.1016/j.jneuroim.2026.578870},
pmid = {41570486},
issn = {1872-8421},
mesh = {Humans ; Animals ; *Neuroinflammatory Diseases/metabolism/microbiology ; *Brain-Gut Axis/physiology/drug effects ; *Gastrointestinal Microbiome/physiology/drug effects ; *Cognitive Aging/physiology ; *Probiotics/administration & dosage ; *Brain/metabolism ; *Dysbiosis/metabolism ; *Aging ; },
abstract = {Aging triggers gut microbiota dysbiosis that disrupts the gut-brain axis (GBA), promoting neuroinflammation and neurodegeneration. Elderly exhibit reduced microbial diversity, depleted beneficial bacteria, and expanded pathobionts, elevating neurotoxic metabolites-lipopolysaccharides (LPS), trimethylamine-N-oxide, kynurenine derivatives, and secondary bile acids. These drive "inflammaging," blood-brain barrier breakdown, microglial activation, mitochondrial impairment, and proteinopathies in Alzheimer's and Parkinson's disease. Conversely, neuroprotective metabolites from commensals-short-chain fatty acids, indole-3-propionic acid, and urolithins-preserve gut integrity, suppress inflammation, upregulate BDNF for synaptic plasticity, and enhance mitophagy. Postbiotics, stable probiotic-derived bioactives (butyrate, polyphenol metabolites, and lactate derivatives), surpass live probiotics in safety and precision. They modulate GBA via histone deacetylase inhibition, GPR41/43 signaling, NF-κB blockade, and microglial M2 shift, blocking LPS translocation and bolstering neuronal resilience. Preclinical rodent studies demonstrate robust neuroprotection, but human translation reveals challenges: inter-individual microbiota variability (diet/genetics/comorbidities), inconsistent metabolite absorption/brain penetration between species, methodological limitations (16S rRNA vs. functional metagenomics), postbiotic standardization barriers, and sparse Phase I/II trials showing biomarker benefits without cognitive endpoints. This review synthesizes gut dysbiosis-metabolite-brain aging mechanisms, positioning postbiotics as precision therapeutics. Multi-omics stratified controlled trials are essential to validate long-term efficacy for delaying neurodegeneration and extending cognitive health.},
}

Humans
Animals
*Neuroinflammatory Diseases/metabolism/microbiology
*Brain-Gut Axis/physiology/drug effects
*Gastrointestinal Microbiome/physiology/drug effects
*Cognitive Aging/physiology
*Probiotics/administration & dosage
*Brain/metabolism
*Dysbiosis/metabolism
*Aging

@article {pmid41570514,
year = {2026},
author = {Yan, S and Ahmad, HA and Xie, Y and Liu, S and Wu, J and Cui, J and Yang, B and Su, L and Ding, T and Liu, T},
title = {Metagenomic insights into the trophic gradient influence on nitrogen cycling microbiomes in plateau lakes.},
journal = {Marine pollution bulletin},
volume = {225},
number = {},
pages = {119288},
doi = {10.1016/j.marpolbul.2026.119288},
pmid = {41570514},
issn = {1879-3363},
mesh = {*Lakes/microbiology ; *Nitrogen Cycle ; *Microbiota ; Nitrogen ; Metagenomics ; Metagenome ; Proteobacteria ; Denitrification ; Bacteria ; },
abstract = {The increasing prevalence of nitrogen (Nr) pollution in lake ecosystems is a growing global concern. Understanding the dynamics of Nr-cycling microbial communities in these environments is crucial for assessing how ecosystem processes and functions respond to trophic gradients. This study investigates the microbial Nr-metabolism in plateau lakes with varying trophic states across a broad geographical range. A detailed metagenomic study revealed that increasing trophic status index (TSI) reduced the α-diversity of Nr-cycling microbial communities, while TSI and altitude jointly shaped the β-diversity patterns. The Nr-cycling microorganisms predominantly belonged to the phylum Proteobacteria, with the most abundant functional genes associated with organic Nr degradation and synthesis, dissimilatory/assimilatory nitrate reduction to ammonium (DNRA and ANRA), and denitrification processes (DNiF). Key Nr functional genes exhibited differential enrichment across lakes, indicating changes in Nr-metabolism strategies along the trophic gradient. A total of 126 metagenome-assembled genomes (MAGs) contributed to Nr-cycling, with the majority assigned to Proteobacteria (36) and Planctomycetes (25). Among these, MAG110 was enriched in eutrophic lakes and possessed near-complete DNiF and ANRA pathways, while MAG115, predominant in oligotrophic lakes, relied solely on ANRA. This functional divergence reflects trophic-specific ecological adaptations, that denitrification is favored in nutrient-rich, low-oxygen conditions and Nr- retention is prioritized under Nr-limited environments. Moreover, enzymes like nitronate monooxygenase (encoded by both genomes) and nitroalkane oxidase highlight a novel metabolic interaction between Nr-transformations and organic C1 compound oxidation in freshwater ecosystems. Overall, this study highlights the complex relationship among trophic status, microbial diversity, and Nr-metabolism in lake ecosystems.},
}

*Lakes/microbiology
*Nitrogen Cycle
*Microbiota
Nitrogen
Metagenomics
Metagenome
Proteobacteria
Denitrification
Bacteria

@article {pmid41570777,
year = {2026},
author = {Wang, Z and Lu, J and Wang, X and An, W and Zhao, Y and Han, B and Tao, H and Liu, J and Guo, J and Wang, J},
title = {Long-term pet ownership promotes resistome similarity between cats and their owners.},
journal = {Environment international},
volume = {208},
number = {},
pages = {110074},
doi = {10.1016/j.envint.2026.110074},
pmid = {41570777},
issn = {1873-6750},
mesh = {Animals ; Cats/microbiology ; *Pets/microbiology ; Humans ; *Ownership ; *Drug Resistance, Microbial/genetics ; Feces/microbiology ; Interspersed Repetitive Sequences ; *Gastrointestinal Microbiome ; Drug Resistance, Bacterial/genetics ; },
abstract = {Pet ownership offers physical and mental health benefits, but the risks of antibiotic resistance genes (ARGs) transmission between pets and humans remain underexplored. In this study, we used metagenomics analysis of fecal samples to compare resistome profiles among four groups: owned cats and their owners, and caged cats and non-cat owners. Our findings show significant similarities in gut microbial composition, ARGs, and mobile genetic elements (MGEs) between owned cats and their owners, identifying 73 shared core ARGs and 80 shared MGEs. In contrast, caged cats and non-cat owners shared only 30 ARGs and 73 MGEs. Long-term contact was positively correlated with a higher number of shared ARGs (from 20 + to 60 +) and MGEs (from 10 + to 40 +), as well as increased resistome risk (2.47- to 4.92-fold) between pet cats and owners. The gut microbiota played a key role in shaping the ARGs and MGEs profiles, with Escherichia coli and Klebsiella pneumoniae identified as primary carriers, each genome harboring 20 to 62 ARGs and 6 to 29 MGEs. ARGs transfer events were more frequent between pet cats and their owners than in other groups. These findings underscore a potential risk of shared antimicrobial resistance between companion animals and humans within the studied population in China.},
}

Animals
Cats/microbiology
*Pets/microbiology
Humans
*Ownership
*Drug Resistance, Microbial/genetics
Feces/microbiology
Interspersed Repetitive Sequences
*Gastrointestinal Microbiome
Drug Resistance, Bacterial/genetics

@article {pmid41572308,
year = {2026},
author = {Zakharevich, N and Strokach, A and Shitikov, E and Klimina, K},
title = {Bacteriophages in gut metagenomes: from analysis to application.},
journal = {Virology journal},
volume = {23},
number = {1},
pages = {40},
pmid = {41572308},
issn = {1743-422X},
support = {23-75-10125//Russian Science Foundation/ ; },
mesh = {Humans ; *Bacteriophages/genetics/classification/isolation & purification/physiology ; *Metagenome ; *Gastrointestinal Microbiome ; Metagenomics/methods ; Computational Biology/methods ; Virome ; Genome, Viral ; },
abstract = {Bacteriophages constitute a major component of the human gut virome, playing very important roles in shaping of the structure and function of the gut microbiota. Moreover, bacteriophages interact with the human immune system, thereby influencing various disease processes. Recent advancements in metagenomic sequencing and computational analysis have substantially expanded our understanding of gut phage diversity and the scale of the so-called 'viral dark matter'. In this review, we summarize current bioinformatic approaches for identifying and annotating bacteriophage sequences in metagenomic data, discuss key challenges in taxonomic classification and host prediction of phages, as well as the limitations associated with the assembly and analysis of viral metagenome-assembled genomes (vMAGs). We also analyze the therapeutic potential of bacteriophages, including their application in cancer immunotherapy, inflammatory diseases, and liver diseases, and their promise as diagnostic and prognostic biomarkers.},
}

Humans
*Bacteriophages/genetics/classification/isolation & purification/physiology
*Metagenome
*Gastrointestinal Microbiome
Metagenomics/methods
Computational Biology/methods
Virome
Genome, Viral

@article {pmid41572438,
year = {2026},
author = {Maes, M and Almulla, AF and Vasupanrajit, A and Jirakran, K and Tunvirachaisakul, C and Maes, A and Chanchaem, P and Klomkliew, P and Payungporn, S and Zhang, Y},
title = {Functional shotgun metagenomic insights into gut microbial pathway and enzyme disruptions linking metabolism, affect, cognition, and suicidal ideation in major depressive disorder.},
journal = {Acta neuropsychiatrica},
volume = {38},
number = {},
pages = {e16},
pmid = {41572438},
issn = {1601-5215},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics/physiology ; *Major Depressive Disorder/microbiology/metabolism/psychology/genetics ; Metagenomics/methods ; Female ; Dysbiosis/microbiology ; Male ; Adult ; *Cognition/physiology ; Oxidative Stress ; Middle Aged ; },
abstract = {BACKGROUND: Major depression (MDD) is linked to neuro-immune, metabolic, and oxidative stress (NIMETOX) pathways. The gut microbiome may contribute to these pathways via leaky gut and immune–metabolic processes.

AIMS: To identify gut microbial alterations in MDD and to quantify functional pathways and enzyme gene families and integrate these with the clinical phenome and immune–metabolic biomarkers of MDD.

METHODS: Shotgun metagenomics with taxonomic profiling was performed in MDD versus controls using MetaPhlAn v4.0.6, and functional profiling was conducted using HUMAnN v3.9, aligning microbial reads to species-specific pangenomes (Bowtie2 v2.5.4) followed by alignment to the UniRef90 v201901 protein database (DIAMOND v2.1.9).

RESULTS: Gut microbiome diversity, both species richness and evenness, is quite similar between MDD and controls. The top enriched taxa in the multivariate discriminant profile of MDD reflect gut dysbiosis associated with leaky gut and NIMETOX mechanisms, that is, Ruminococcus gnavus, Veillonella rogosaem, and Anaerobutyricum hallii. The top four protective taxa enriched in controls indicate an anti-inflammatory ecosystem and microbiome resilience, that is, Vescimonas coprocola, Coprococcus, Faecalibacterium prausnitzii, and Faecalibacterium parasitized. Pathway analysis indicates loss of barrier protection, antioxidants, and short-chain fatty acids, and activation of NIMETOX pathways. The differential abundance of gene families suggests that there are metabolic distinctions between both groups, indicating aberrations in purine, sugar, and protein metabolism. The gene and pathway scores explain a larger part of the variance in suicidal ideation, recurrence of illness, neurocognitive impairments, immune functions, and atherogenicity.

CONCLUSION: The gut microbiome changes might contribute to activated peripheral NIMETOX pathways in MDD.},
}

Humans
*Gastrointestinal Microbiome/genetics/physiology
*Major Depressive Disorder/microbiology/metabolism/psychology/genetics
Metagenomics/methods
Female
Dysbiosis/microbiology
Male
Adult
*Cognition/physiology
Oxidative Stress
Middle Aged

@article {pmid41572814,
year = {2026},
author = {Fathima, N and Mascarenhas, R and Umar, D and Rekha, PD and Shetty, S and Amin, V},
title = {Impact of removing fixed orthodontic appliances on oral microbial dysbiosis: A longitudinal study and metagenomic sequencing analysis.},
journal = {Journal of orthodontics},
volume = {53},
number = {1},
pages = {34-44},
doi = {10.1177/14653125251408048},
pmid = {41572814},
issn = {1465-3133},
mesh = {Humans ; Longitudinal Studies ; *Orthodontic Appliances, Fixed/adverse effects ; *Microbiota/genetics ; *Dysbiosis/microbiology/etiology ; Metagenomics ; Female ; RNA, Ribosomal, 16S/genetics ; Male ; Saliva/microbiology ; *Mouth/microbiology ; Adolescent ; *Dental Debonding ; },
abstract = {OBJECTIVE: To investigate the impact of appliance removal on oral microbial diversity, composition, and abundance using metagenomic sequencing. It aims to identify the core microbiome and assess changes between mid-treatment and 2 weeks after debonding to understand the relationship between orthodontic therapy and oral health better.

METHODS: This longitudinal cohort study recruited 26 patients undergoing fixed orthodontic treatment between January 2022 and June 2023. Saliva samples were collected at two predefined time points: mid-treatment (T0, defined as before appliance removal) and 2 weeks after debonding (T1). Microbial DNA was extracted and the V1-V3 hypervariable regions of the 16S rRNA gene were sequenced using Illumina NovaSeq. Bioinformatics analysis was performed using QIIME and the SILVA database to evaluate microbial diversity and composition at T0 and T1. Beta diversity metrics and statistical tests, including PERMANOVA and Wilcoxon signed-rank tests, were applied to identify significant differences (P < 0.05). Effect sizes with 95% confidence intervals (CIs) were reported.

RESULTS: The analysis revealed significant shifts in microbial diversity and composition between T0 and T1. A total of 189 species across 63 genera were identified, with Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, and Fusobacteria as dominant phyla. Genera such as Fusobacterium periodonticum (↑ 12.4%, 95% CI = 10.1-14.7) and Veillonella parvula (↑ 9.8%, 95% CI = 7.6-11.3) increased after debonding, while Prevotella melaninogenica (↓ 10.2%, 95% CI = 8.1-12.0) and Rothia dentocariosa (↓ 7.9%, 95% CI = 6.3-9.2) decreased. Beta diversity analysis confirmed a statistically significant microbial community shift (P < 0.05).

CONCLUSION: This study demonstrated significant microbial shifts between mid-treatment and 2 weeks after debonding, including increases in potentially pathogenic genera and alterations in the core microbiome. These findings indicate microbial changes persist for at least 2 weeks after appliance removal. Further research with pre-treatment baselines and extended follow-up is required to better define the long-term trajectory of these changes.},
}

Humans
Longitudinal Studies
*Orthodontic Appliances, Fixed/adverse effects
*Microbiota/genetics
*Dysbiosis/microbiology/etiology
Metagenomics
Female
RNA, Ribosomal, 16S/genetics
Male
Saliva/microbiology
*Mouth/microbiology
Adolescent
*Dental Debonding

@article {pmid41572827,
year = {2025},
author = {Xu, B and Liu, P and Yan, N and Wang, T and Liu, L and Cheng, Y},
title = {Multi-omics insights into gut microbial dysbiosis and metabolic alterations in immune checkpoint inhibitor-induced thrombocytopenia.},
journal = {Immunotherapy},
volume = {17},
number = {17-18},
pages = {1231-1239},
pmid = {41572827},
issn = {1750-7448},
mesh = {Humans ; Multiomics ; *Dysbiosis/metabolism ; *Thrombocytopenia/chemically induced/metabolism ; *Gastrointestinal Microbiome ; *Immune Checkpoint Inhibitors/adverse effects ; Proteomics ; Metabolomics ; Female ; Male ; Middle Aged ; Aged ; *Neoplasms/drug therapy ; },
abstract = {BACKGROUND: Immune checkpoint inhibitors-induced thrombocytopenia (ICIs-TCP) is a rare immune-related adverse events (irAEs). The physiological changes underlying ICIs-TCP remain incompletely elucidated.

METHODS: We performed multi-omics analysis (gut microbiome, plasma metabolomics/proteomics) comparing microbial/metabolic alterations in cancer patients with (n = 8) and without ICIs-TCP (n = 8). Fecal metagenomic shotgun sequencing was performed to assess microbial composition and function, while plasma metabolomics and proteomics analyses identified systemic metabolic and protein expression changes associated with ICIs-TCP.

RESULTS: Patients with ICIs-TCP exhibited distinct gut microbiota profiles, with an increased abundance of Segatella, Prevotella, and Clostridium, alongside a depletion of Bacteroides and Roseburia. Functional analysis revealed significant downregulation of metabolic pathways, including arginine biosynthesis, alanine, aspartate, and glutamate metabolism. Plasma metabolomics identified reduced arginine levels and disruptions in key amino acid and energy metabolism pathways, suggesting systemic arginine depletion. Proteomic analysis further demonstrated down-regulation of folate hydrolase 1 (FOLH1), a key enzyme in glutamate metabolism, implicating metabolic dysregulation in TCP pathogenesis.

CONCLUSION: The depletion of arginine and associated metabolic disruptions are associated with ICIs-TCP and may represent a potential therapeutic target for mitigating TCP risk in patients receiving ICIs.},
}

Humans
Multiomics
*Dysbiosis/metabolism
*Thrombocytopenia/chemically induced/metabolism
*Gastrointestinal Microbiome
*Immune Checkpoint Inhibitors/adverse effects
Proteomics
Metabolomics
Female
Male
Middle Aged
Aged
*Neoplasms/drug therapy

@article {pmid41574290,
year = {2025},
author = {Chen, J and Gong, G and Su, X and Song, X and Zhang, J and Wu, P and Wang, H and Shan, T and Zhang, W},
title = {Viral metagenomic analysis of fecal samples from Bos grunniens on the Qinghai-Tibet Plateau reveals novel picornaviruses and diverse CRESS-DNA viruses.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1719300},
pmid = {41574290},
issn = {2235-2988},
mesh = {Animals ; Phylogeny ; *Metagenomics ; Tibet ; *Feces/virology ; *DNA Viruses/genetics/classification/isolation & purification ; Cattle/virology ; *Virome/genetics ; Genome, Viral ; *Picornaviridae/genetics/classification/isolation & purification ; },
abstract = {INTRODUCTION: The Qinghai-Tibet Plateau (QTP), one of the most extreme environments on Earth, provides a unique natural setting for exploring viral diversity and evolution under conditions of high altitude, hypoxia, and intense ultraviolet radiation. The yak (Bos grunniens), a key endemic ruminant species of the QTP, plays an essential ecological and economic role, yet its fecal virome remains poorly characterized.

METHODS: In this study, we analyzed 43 yak fecal samples collected from Yushu, Qinghai Province, and constructed nine metagenomic libraries to investigate the composition, diversity, and phylogenetic characteristics of the yak fecal virome.

RESULTS: Metagenomic sequencing generated approximately 463 million raw reads, of which 2.87 million were classified as viral. The viral reads in the sequenced libraries were primarily composed of single-stranded DNA viruses (92.46%), particularly members of Smacoviridae, Circoviridae, and Genomoviridae, whereas RNA viruses such as Picornaviridae accounted for a minor fraction (0.71%). Phylogenetic analyses revealed that several circular single-stranded DNA (CRESS-DNA) virus and picornavirus genomes share high similarity with known ruminant-associated viruses, while forming independent evolutionary clades, suggesting potential cross-species transmission among plateau animals. The large-scale divergence within Smacoviridae further reflects extensive lineage expansion under the plateau's extreme environmental pressures.

DISCUSSION: Compared with our previous yak virome study, this work provides independent and complementary insights into the genomic and evolutionary characteristics of key viral taxa. Overall, our findings expand the genomic landscape of the yak fecal virome and highlight the Qinghai-Tibet Plateau as an important reservoir for exploring viral diversity, evolution, and host-environment interactions in extreme ecosystems.},
}

Animals
Phylogeny
*Metagenomics
Tibet
*Feces/virology
*DNA Viruses/genetics/classification/isolation & purification
Cattle/virology
*Virome/genetics
Genome, Viral
*Picornaviridae/genetics/classification/isolation & purification

@article {pmid41575223,
year = {2026},
author = {Han, N and Peng, X and Zhang, T and Qiang, Y and Li, X and Zhang, W},
title = {Hidden reservoir of highly adaptable multi-host plasmids that propagate antibiotic genes in healthy human populations.},
journal = {The ISME journal},
volume = {20},
number = {1},
pages = {},
pmid = {41575223},
issn = {1751-7370},
support = {//The National Key Research and Development Program of China/ ; Project32098//National Science and Technology Major Project/ ; },
mesh = {Humans ; *Plasmids/genetics ; Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; Anti-Bacterial Agents/pharmacology ; *Bacteria/genetics/drug effects ; Gene Transfer, Horizontal ; *Drug Resistance, Bacterial/genetics ; Metagenome ; Extrachromosomal DNA ; },
abstract = {Plasmids are key vectors for disseminating antibiotic resistance genes, yet their diversity and dynamics in the healthy human gut microbiome remain largely unexplored. Using fecal metagenomes from two cohorts (n = 498 samples), we constructed a comprehensive atlas of the healthy human gut plasmidome. We observed a polarization: while 97.4% of 19 151 plasmid clusters exhibited low prevalence (<5%), we identified 17 plasmid clusters that were detected in >30% of individuals. Among these, the plasmid pGut1 emerged as a paradigm of a stealth vector. Prevalent globally (>50% in independent cohorts), pGut1 possesses a minimal 4-kb conserved backbone ensuring stability and a hypervariable region acting as a "plug-and-play" module. We documented 40 distinct cargo inserts, including multiple antibiotic resistance genes such as cfr(C), erm(B), and aphA, across individuals, within individuals over time, and even within single fecal samples- validated by single-cell and long-read Nanopore sequencing. Screening of 2.3 million bacterial genomes revealed pGut1 in 93 strains across 49 genera and 2 phyla, including pathogenic Clostridioides difficile and three distinct Salmonella enterica strains. This pattern suggests potential repeated cross-species transmission events, equipping diverse pathogens with new antibiotic resistance genes. Our study exposes a hidden reservoir of highly adaptable, multi-host plasmids like pGut1 silently propagating antibiotic resistance genes in healthy populations. These plasmids, pre-adapted for cross-boundary dissemination, may pose a threat by fueling the emergence of multidrug-resistant pathogens.},
}

Humans
*Plasmids/genetics
Feces/microbiology
*Gastrointestinal Microbiome/genetics
Anti-Bacterial Agents/pharmacology
*Bacteria/genetics/drug effects
Gene Transfer, Horizontal
*Drug Resistance, Bacterial/genetics
Metagenome
Extrachromosomal DNA

@article {pmid41576514,
year = {2026},
author = {Hao, Y and Li, Y and Liu, F and Long, J and Yang, H},
title = {Metagenomic insights into the influence of goose farming on the gut microbiome and antibiotic resistome of workers.},
journal = {Poultry science},
volume = {105},
number = {4},
pages = {106487},
pmid = {41576514},
issn = {1525-3171},
mesh = {Animals ; *Geese/microbiology ; *Gastrointestinal Microbiome ; Humans ; *Drug Resistance, Microbial/genetics ; *Bacteria/drug effects/genetics ; *Metagenome ; *Animal Husbandry ; Metagenomics ; Feces/microbiology ; *Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; Farmers ; },
abstract = {Antimicrobial resistance (AMR) seriously threatens the health of humans and animals. Antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) were enriched in the goose farms. However, the influence of goose farming exposure on the gut microbiota and ARGs of workers was unclear. In this study, metagenomic analysis was used to characterize gut microbiome structures, annotate bacterial taxa, and quantify the abundances of ARGs and MGEs in geese and human samples. Results showed that goose feces harbored more abundant ARGs and ARB than human feces. Significantly higher abundances of special ARGs (such as vanY, lsaE, AAC3-IId and ampC) were identified in workers compared to villagers. Compositions of gut bacteria were significantly different between workers and villagers, and some certain gut pathogens were abundant in the feces of workers, including Bacillus anthracis, Clostridium perfringens, and Escherichia coli O45:K1:H7. A total of 51 ARGs were pinpointed in the metagenome-assembled genomes (MAGs). Based on ARG-MGE associations and co-occurrence signals in MAGs, the potential for horizontal gene transfer (HGT) was inferred. With this transfer capacity and ubiquitous gut colonization, E. coli carrying 38 ARGs is proposed as a putative AMR indicator for the goose farm. This study demonstrates that goose farming had non-ignorable influences on the gut microbiome and antibiotic resistome of workers. More efforts should be made to control the ARGs and ARB in the goose farm.},
}

Animals
*Geese/microbiology
*Gastrointestinal Microbiome
Humans
*Drug Resistance, Microbial/genetics
*Bacteria/drug effects/genetics
*Metagenome
*Animal Husbandry
Metagenomics
Feces/microbiology
*Drug Resistance, Bacterial/genetics
Anti-Bacterial Agents/pharmacology
Genes, Bacterial
Farmers

@article {pmid41576933,
year = {2026},
author = {Hernandez-Leyva, AJ and Berna, AZ and Bui, MH and Liu, Y and Rosen, AL and Lint, MA and Whiteside, SA and Jaeger, N and McDonough, RT and Joardar, N and Santiago-Borges, J and Tomera, CP and Luo, W and Odom John, AR and Kau, AL},
title = {The gut microbiota shapes the human and murine breath volatilome.},
journal = {Cell metabolism},
volume = {38},
number = {4},
pages = {779-793.e8},
pmid = {41576933},
issn = {1932-7420},
support = {T32 GM007200/GM/NIGMS NIH HHS/United States ; R01 HD109963/HD/NICHD NIH HHS/United States ; R21 AI154370/AI/NIAID NIH HHS/United States ; R33 HD105594/HD/NICHD NIH HHS/United States ; F30 DK127584/DK/NIDDK NIH HHS/United States ; },
mesh = {Animals ; Humans ; *Volatile Organic Compounds/metabolism/analysis ; Breath Tests ; Mice ; *Gastrointestinal Microbiome ; Child ; Female ; Male ; Asthma/microbiology/metabolism ; Gas Chromatography-Mass Spectrometry ; Germ-Free Life ; Child, Preschool ; Mice, Inbred C57BL ; },
abstract = {The gut microbiota is crucial to health, yet implementation of microbiota-based therapeutics is limited by the lack of rapid diagnostics. We hypothesize that breath contains gut microbe-derived volatile organic compounds (VOCs) reflecting microbiota composition and metabolism. In healthy children, we found that breath VOC composition (or volatilome), assessed by gas chromatography-mass spectrometry, correlates with gut microbiome composition and function. By capturing exhaled breath from human-stool-colonized and monocolonized gnotobiotic mice, we profiled breath VOCs and discovered that murine breath is also significantly influenced by the gut microbiome. VOCs from cultured gut microbes were identified in vivo in monocolonized gnotobiotic colonized mice. As a proof of principle, we demonstrated that exhaled breath predicts the abundance of a disease-associated bacterium, Eubacterium siraeum, in children with asthma. Altogether, our studies identify microbe-derived VOCs in breath, show that gut bacterial metabolism directly contributes to mammalian breath VOC profiles, and inform the development of non-invasive microbiome diagnostics.},
}

Animals
Humans
*Volatile Organic Compounds/metabolism/analysis
Breath Tests
Mice
*Gastrointestinal Microbiome
Child
Female
Male
Asthma/microbiology/metabolism
Gas Chromatography-Mass Spectrometry
Germ-Free Life
Child, Preschool
Mice, Inbred C57BL

@article {pmid41576939,
year = {2026},
author = {Nalapareddy, K and Haslam, DB and Kissmann, AK and Alenghat, T and Stahl, S and Rosenau, F and Zheng, Y and Geiger, H},
title = {Microbiota from young mice restore the function of aged ISCs.},
journal = {Stem cell reports},
volume = {21},
number = {2},
pages = {102788},
pmid = {41576939},
issn = {2213-6711},
support = {R01 DK137771/DK/NIDDK NIH HHS/United States ; },
mesh = {Animals ; *Stem Cells/metabolism/cytology ; Wnt Signaling Pathway ; *Aging ; Mice ; *Intestinal Mucosa/cytology/metabolism/microbiology ; Regeneration ; *Gastrointestinal Microbiome ; *Microbiota ; Basic Helix-Loop-Helix Proteins/metabolism ; Homeostasis ; Akkermansia ; },
abstract = {Homeostasis in the intestinal epithelium depends on intestinal stem cells (ISCs). A reduction in the function of ISCs, caused by a decline of canonical Wnt signaling in ISCs, contributes to a reduced regenerative potential of the aged intestine. The composition of the intestinal microbiota changes upon aging. We report here that aging-associated changes in the composition of the microbiota result in reduced canonical Wnt signaling through Ascl2 in ISCs, which causes a decline in the regenerative potential of aged ISCs in vivo. We demonstrate, using microbiota transfer experiments, that interestingly, elevated levels of Akkermansia muciniphila in the intestine cause a reduction of Ascl2-mediated canonical Wnt signaling in ISCs and thus reduced regeneration of the aged epithelium. The composition of the intestinal microbiota thus plays a critical role in regulating the function of ISCs. Our data imply potential therapeutic approaches via modulation of the composition of microbiota for aging-associated changes in the function of ISCs.},
}

Animals
*Stem Cells/metabolism/cytology
Wnt Signaling Pathway
*Aging
Mice
*Intestinal Mucosa/cytology/metabolism/microbiology
Regeneration
*Gastrointestinal Microbiome
*Microbiota
Basic Helix-Loop-Helix Proteins/metabolism
Homeostasis
Akkermansia

@article {pmid41576942,
year = {2026},
author = {Masi, D and Watanabe, M and Clément, K},
title = {Gut microbiome and obesity care: Bridging dietary, surgical, and pharmacological interventions.},
journal = {Cell reports. Medicine},
volume = {7},
number = {2},
pages = {102573},
pmid = {41576942},
issn = {2666-3791},
mesh = {*Obesity/microbiology/therapy/metabolism/drug therapy ; Humans ; Animals ; *Gastrointestinal Microbiome/physiology/drug effects ; Multiomics ; *Diet ; },
abstract = {In the mid-2000s, mouse studies suggested that the gut microbiome might influence energy harvest, fat storage, appetite, insulin sensitivity, and inflammation. Since then, our understanding of the gut microbiome's role in obesity has advanced significantly. Mechanistic studies identified microbial metabolites, such as short-chain fatty acids, bile acids, branched-chain amino acids, tryptophan catabolites, and imidazole propionate, as key modulators of metabolism, inflammation, and gut-brain communication. Metagenomic and multi-omics technologies now provide deeper insights into the intricate interactions between microbes, metabolites, and host factors, reshaping obesity research and reinforcing the need for phenotype stratification by recognizing microbiome-driven metabolic profiles. Integrating gut microbiome data into clinical strategies may enable targeted interventions for specific obesity subtypes, advancing prevention and personalized care. However, as new anti-obesity medications emerge, it is imperative to determine how microbiome-based therapies can complement them, considering efficacy, cost, and patient-specific variability.},
}

*Obesity/microbiology/therapy/metabolism/drug therapy
Humans
Animals
*Gastrointestinal Microbiome/physiology/drug effects
Multiomics
*Diet

@article {pmid41577947,
year = {2026},
author = {Kettenburg, G and Ranaivoson, HC and Andrianiaina, A and Andry, S and Henry, AR and Davis, RL and Laboune, F and Longtine, ER and Godbole, S and Horigan, S and Ruhs, EC and Raharinosy, V and Randriambolamanantsoa, TH and Lacoste, V and Heraud, JM and Dussart, P and Douek, DC and Brook, CE},
title = {Co-speciation and host-switching drives diversity of picornaviruses and sapoviruses in Malagasy fruit bats.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {6583},
pmid = {41577947},
issn = {2045-2322},
support = {P200A210054/NH/NIH HHS/United States ; 1R01AI129822-01/NH/NIH HHS/United States ; 5DP2AI171120-S1/NH/NIH HHS/United States ; OPP1211841//Bill and Melinda Gates Foundation/ ; D18AC00031//Defense Sciences Office, DARPA/ ; P200A210054/NH/NIH HHS/United States ; 1R01AI129822-01/NH/NIH HHS/United States ; 5DP2AI171120-S1/NH/NIH HHS/United States ; },
abstract = {UNLABELLED: Bats are reservoir hosts for numerous well-known zoonotic viruses, but their broader virus-hosting capacities remain understudied. Picornavirales are an order of enteric viruses that cause disease across a wide range of mammalian hosts, including Hepatitis A in humans and foot-and-mouth disease in ungulates. Host-switching and recombination drive the diversification of Picornavirales worldwide. Picornaviridae and Caliciviridae (families within Picornavirales) have been described in bats across mainland Africa, but surveillance for these viruses has been rare in the Southwest Indian Ocean Islands. Prior work in Madagascar has described numerous bat viruses, some with zoonotic potential, that demonstrate both high identity to and extreme divergence from viruses found in sister bat species in Africa. Using metagenomic Next Generation Sequencing of urine and fecal samples obtained from three species of endemic Malagasy fruit bats (Eidolon dupreanum, Pteropus rufus, and Rousettus madagascariensis), we identify and describe 13 full-length and 38 partial-length genomic sequences within the Picornaviridae and Caliciviridae families (36 picornavirus and 15 Sapovirus sequences). We find evidence that host-switching between Madagascar and mainland African bat picornaviruses and sapoviruses, followed by host-parasite co-speciation, likely shaped the diversification pattens of these novel sequences, with little evidence for cross-species transmission among Malagasy bat species in close contact.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-025-34969-2.},
}

@article {pmid41578124,
year = {2026},
author = {Candeliere, F and Sola, L and Busi, E and Pedroni, S and Raimondi, S and Amaretti, A and Greco, S and Dominici, M and Rossi, M},
title = {Altered abundance in cancer patients gut of diadenylate cyclase-encoding bacteria.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {6070},
pmid = {41578124},
issn = {2045-2322},
support = {Progetto identificato con codice PE00000019, Titolo "HEAL ITALIA" - Spoke 5 - CUP E93C22001860006//PIANO NAZIONALE DI RIPRESA E RESILIENZA(PNRR) - MISSIONE 4 COMPONENTE 2/ ; },
mesh = {Humans ; *Bacteria/enzymology/genetics ; *Gastrointestinal Microbiome/genetics ; *Neoplasms/microbiology/immunology/therapy ; *Phosphorus-Oxygen Lyases/genetics/metabolism ; Dinucleoside Phosphates/metabolism ; },
abstract = {c-di-AMP is a bacterial second messenger recognized by host immune sensors such as the STING pathway, linking gut microbiota activity to tumor immunity. This interaction holds significant therapeutic potential particularly for oncologic patients, given the increasingly recognized relationship between gut microbiota and tumor immunity. Recent evidence shows that microbial c-di-AMP can enhance anti-tumor responses and improve the efficacy of PD-1/PD-L1 blockade and radiotherapy. This study identified gut microbial species capable of synthesizing c-di-AMP by mining the Unified Human Gastrointestinal Protein catalogue for diadenylate cyclases (DACs), generating a database of 4,228 DACs across 3,901 species out of 4,744 presents in the Unified Human Gastrointestinal Genome catalogue. Analysis of metagenomic data from 190 healthy subjects and 569 cancer patients (melanoma, NSCLC, renal carcinoma) revealed a significantly higher abundance of DAC-encoding species in healthy microbiota, with no differences between responders and non-responders to immunotherapy. These findings indicate that c-di-AMP-producing bacteria are depleted in cancer-associated microbiota, supporting further studies on their role in modulating anti-tumor immunity.},
}

Humans
*Bacteria/enzymology/genetics
*Gastrointestinal Microbiome/genetics
*Neoplasms/microbiology/immunology/therapy
*Phosphorus-Oxygen Lyases/genetics/metabolism
Dinucleoside Phosphates/metabolism

@article {pmid41578762,
year = {2025},
author = {Shen, F and Xu, C and Wang, C},
title = {Gut Microbiome Diagnostic Biomarkers for Colorectal Cancer.},
journal = {The Turkish journal of gastroenterology : the official journal of Turkish Society of Gastroenterology},
volume = {37},
number = {1},
pages = {62-74},
pmid = {41578762},
issn = {2148-5607},
mesh = {Humans ; *Colorectal Neoplasms/diagnosis/microbiology ; Feces/microbiology ; Female ; Male ; *Biomarkers, Tumor/analysis ; *Adenoma/microbiology/diagnosis ; Middle Aged ; *Gastrointestinal Microbiome/genetics ; Case-Control Studies ; Fusobacterium nucleatum/isolation & purification/genetics ; Aged ; Peptostreptococcus/isolation & purification/genetics ; Disease Progression ; Adult ; Prognosis ; Early Detection of Cancer/methods ; Sensitivity and Specificity ; },
abstract = {BACKGROUND/AIMS: Gold standard diagnostic methods, such as invasive procedures and serum biomarkers, have limited sensitivity and specificity for the detection of colorectal cancer (CRC). Thus, the development of more accurate and noninvasive detection approaches is imperative. Emerging research elucidating the intricate role of the gut microbiota in CRC pathogenesis underscores the need for precision screening tailored to high-risk cohorts to improve early detection and intervention strategies and comprehensively address this challenging clinical problem.

MATERIALS AND METHODS: Fecal metagenomic sequencing datasets were employed to identify potential bacterial biomarkers for CRC diagnosis and selected relevant microbial taxa for subsequent validation. A total of 180 participants were enrolled: 65 healthy controls (HC), 65 colorectal adenoma patients, and 50 CRC patients, and fecal samples were analyzed using fluorescence quantitative polymerase chain reaction to confirm biomarker relative abundance, culminating in the establishment of an evolutionary model for CRC progression; furthermore, a treatment efficacy and prognostication model supported by comprehensive statistical methodologies was established.

RESULTS: This study analyzed fecal microbial biomarkers associated with CRC progression and identified differentially abundant bacterial species across HCs, adenoma, and CRC patient groups. Notably, Fusobacterium nucleatum (Fn) and Peptostreptococcus anaerobius (P. anaerobius) showed significant correlations with CRC stage and metastasis, highlighting their potential as diagnostic biomarkers. Among individual microbes, P. anaerobius exhibited the highest diagnostic value when combined with Fn.

CONCLUSION: The results underscore the potential application of fecal microbial markers, particularly Fn and P. anaerobius, for diagnosing CRC and monitoring its progression.   Cite this article as: Shen F, Xu C, Wang C. Gut microbiome diagnostic biomarkers for colorectal cancer. Turk J Gastroenterol. 2026;37(1):62-74.},
}

Humans
*Colorectal Neoplasms/diagnosis/microbiology
Feces/microbiology
Female
Male
*Biomarkers, Tumor/analysis
*Adenoma/microbiology/diagnosis
Middle Aged
*Gastrointestinal Microbiome/genetics
Case-Control Studies
Fusobacterium nucleatum/isolation & purification/genetics
Aged
Peptostreptococcus/isolation & purification/genetics
Disease Progression
Adult
Prognosis
Early Detection of Cancer/methods
Sensitivity and Specificity

@article {pmid41579975,
year = {2026},
author = {Ferrero, G and Mastrocola, R and Tarallo, S and Pardini, B and Scheijen, J and van de Waarenburg, M and Gallo, G and Chatziioannou, AC and Robinot, N and Keski-Rahkonen, P and Piccinno, G and Segata, N and Aglago, EK and Hughes, DJ and Jenab, M and Schalkwijk, CG and Naccarati, A},
title = {Integrative analyses of dicarbonyls and advanced glycation end-products with multiomic profiles across tissue, plasma and stool samples reveal methylglyoxal accumulation in colon cancer.},
journal = {Free radical biology & medicine},
volume = {246},
number = {},
pages = {518-530},
pmid = {41579975},
issn = {1873-4596},
support = {001/WHO_/World Health Organization/International ; },
mesh = {Humans ; *Colonic Neoplasms/metabolism/pathology/genetics ; *Pyruvaldehyde/metabolism ; *Glycation End Products, Advanced/metabolism ; Multiomics ; Feces/chemistry/microbiology ; Male ; Female ; Glyoxal/metabolism ; Deoxyglucose/analogs & derivatives/metabolism ; Aged ; Middle Aged ; Lactoylglutathione Lyase/genetics/metabolism ; Metabolomics ; Gastrointestinal Microbiome ; },
abstract = {Advanced Glycation Endproducts (AGEs) arise from the reaction of proteins with highly reactive dicarbonyl compounds such as methylglyoxal (MGO), glyoxal (GO) and 3-deoxyglucosone (3-DG), which have been implicated in inflammation and carcinogenesis. How dicarbonyls and AGEs are distributed across tumor tissue and surrogate specimens, and how they relate to systemic metabolism, AGE-related pathways, and alterations in gut microbiota in colon cancer, remains poorly understood. An integrative multi-specimen analysis of MGO, GO, 3-DG and major AGEs was performed using targeted tandem mass spectrometry in matched tumor tissue, adjacent normal mucosa, plasma, and stool from 26 sporadic colon cancer patients. These measurements were combined with tumor RNA-sequencing, untargeted plasma metabolomics, and stool shotgun metagenomics generated from the same individuals. A marked accumulation of MGO was observed in tumor tissue when compared with adjacent mucosa, accompanied by higher levels of the MGO-derived AGE Nδ-[5-hydro-5-methyl-4-imidazolon-2-yl]-ornithine (MG-H1). Tissue MG-H1 concentrations significantly correlated with corresponding plasma levels. Elevated tumor MGO levels were associated with up-regulation of GLO1 (encoding for the detoxifying enzyme glyoxalase-1), DDOST (coding for the AGE-clearance receptor AGE-R1), and the glycolytic flux marker triose phosphate isomerase (TPI), alongside down-regulation of the AGE-scavenger receptor CD36. These findings suggest a candidate remodeling of dicarbonyl-handling pathways. The MGO/GO ratio in tumors was positively associated with the relative abundances of Fusobacterium nucleatum and Parvimonas micra, two bacterial species related to colorectal carcinogenesis, and with metagenomic signatures of oral-derived taxa colonizing the gut. This pilot integrative analysis highlighted novel coherent associations among tissue, circulating, and stool levels of MGO-derived AGEs, the expression of AGE-related metabolic pathways, and microbial signatures in colon cancer. If confirmed in larger studies, these candidate molecular and microbial interactions may provide novel insights into the dicarbonyl stress involvement in tumor biology.},
}

Humans
*Colonic Neoplasms/metabolism/pathology/genetics
*Pyruvaldehyde/metabolism
*Glycation End Products, Advanced/metabolism
Multiomics
Feces/chemistry/microbiology
Male
Female
Glyoxal/metabolism
Deoxyglucose/analogs & derivatives/metabolism
Aged
Middle Aged
Lactoylglutathione Lyase/genetics/metabolism
Metabolomics
Gastrointestinal Microbiome

@article {pmid41581112,
year = {2026},
author = {Lett, JM and Scussel, S and Chéhida, SB and Hoareau, M and Filloux, D and Fernandez, E and Roumagnac, P and Parvedy, E and Quirin, E and Clain, C and Minatchy, J and Roux, E and Teycheney, PY and Lefeuvre, P},
title = {Metagenomic screening of the virome of symptomatic tomato plants from La Réunion Island uncovers a complex of viruses including a newly identified whitefly-transmitted polerovirus.},
journal = {Archives of virology},
volume = {171},
number = {2},
pages = {62},
pmid = {41581112},
issn = {1432-8798},
mesh = {*Solanum lycopersicum/virology ; Animals ; *Hemiptera/virology ; Reunion ; Phylogeny ; *Plant Diseases/virology ; Metagenomics ; *Luteoviridae/genetics/classification/isolation & purification ; *Virome ; Genome, Viral ; Insect Vectors/virology ; },
abstract = {Using unbiased high-throughput sequencing for metagenomic screening of viruses in diseased tomato plants, we identified a viral complex that includes viruses previously reported in tomato crops on La Réunion Island as well as a novel polerovirus, tentatively named "tomato necrotic yellowing virus" (ToNYV, proposed species, "Polerovirus ToNYV"). Molecular characterization and phylogenetic analysis revealed that ToNYV is closely related to two recently described poleroviruses from Africa and the Middle East, one of which is transmitted by the whitefly Bemisia tabaci, a trait uncommon among poleroviruses. Our transmission experiments demonstrated that ToNYV is also transmitted by B. tabaci and is prevalent across major tomato-growing regions of La Réunion. These findings highlight the value of metagenomic virome analysis in diseased plants for identifying novel viruses potentially involved in emerging plant diseases, either individually or as components of viral complexes.},
}

*Solanum lycopersicum/virology
Animals
*Hemiptera/virology
Reunion
Phylogeny
*Plant Diseases/virology
Metagenomics
*Luteoviridae/genetics/classification/isolation & purification
*Virome
Genome, Viral
Insect Vectors/virology

@article {pmid41581442,
year = {2026},
author = {Chen, Y and Huang, S and Zhang, S and Wang, H and Song, X and Ji, L and Shen, Q and Yang, S and Liu, Y and Wang, X and Wu, P and Yang, H and Shan, T and Wang, X and Zhang, W},
title = {Viral metagenomics reveals the RNA viral composition of herbivorous wildlife on the Qinghai-Tibet Plateau.},
journal = {Virology},
volume = {617},
number = {},
pages = {110814},
doi = {10.1016/j.virol.2026.110814},
pmid = {41581442},
issn = {1096-0341},
mesh = {Animals ; *Metagenomics ; Phylogeny ; *RNA Viruses/genetics/classification/isolation & purification ; *Animals, Wild/virology ; Tibet ; Feces/virology ; *Virome ; RNA, Viral/genetics ; Genetic Variation ; Genome, Viral ; },
abstract = {RNA viruses, a widely distributed group of pathogens in nature, possess exceptionally high genetic diversity and rapid evolutionary potential. High-altitude ecosystems, represented by the Qinghai-Tibet Plateau, with their unique environmental conditions, may harbor distinct viral communities. However, there remains a lack of systematic understanding regarding the composition and distribution of RNA viruses in wildlife under such extreme environments. In this study, a total of 741 fecal samples were collected from three regions on the Qinghai-Tibet Plateau, and viral metagenomics technology was used to reveal the composition and diversity of RNA viruses in the fecal samples of six species of herbivorous wild animals on the plateau. We identified a substantial abundance of RNA viruses, classified into 18 distinct viral families. Furthermore, the structure of the viral communities varied among different host species. Through assembly, 28 viral sequences belonging to the families Astroviridae, Picornaviridae, Picobirnaviridae, Tobaniviridae, and Caliciviridae were identified. Phylogenetic analysis revealed that the newly identified viral strains share close relationships with viruses found in humans, marmots, and other mammals. The results indicate that wildlife in this region are reservoirs of unidentified RNA viruses, some of which may pose potential threats to public health and the animal husbandry. These findings provide crucial scientific evidence and data support for future virus surveillance, ecological risk assessment, and the prevention and control of emerging infectious diseases at their source.},
}

Animals
*Metagenomics
Phylogeny
*RNA Viruses/genetics/classification/isolation & purification
*Animals, Wild/virology
Tibet
Feces/virology
*Virome
RNA, Viral/genetics
Genetic Variation
Genome, Viral

@article {pmid41581489,
year = {2026},
author = {Liu, Z and Zhao, F and Li, Q and Shang, Q and Fang, D and Li, X and Li, H and He, Q and Zhang, D and Cheng, J and Zhu, Y and Li, Z and Silva, AS and Chen, J},
title = {Multi-omics chemical and biochemical profiling reveals ellagic acid enhances insulin sensitivity via gut microbiota-tryptophan-indole signaling mechanism.},
journal = {Food chemistry},
volume = {505},
number = {},
pages = {147984},
doi = {10.1016/j.foodchem.2026.147984},
pmid = {41581489},
issn = {1873-7072},
mesh = {*Indoles/metabolism ; Animals ; *Insulin Resistance ; *Gastrointestinal Microbiome/drug effects ; *Tryptophan/metabolism ; *Ellagic Acid/metabolism/chemistry ; Signal Transduction/drug effects ; Multiomics ; Bacteria/isolation & purification/classification/genetics/metabolism ; Male ; Humans ; Mice ; },
abstract = {Ellagic acid (EA) is a dietary polyphenol with limited systemic bioavailability, resulting in substantial intestinal exposure. However, the biochemical mechanisms by which EA modulates gut microbiota and metabolism remain unclear. Here, EA improved glucose tolerance and enhanced insulin sensitivity, with histology confirming reduced lipid accumulation and restored tissue architecture in liver, skeletal muscle, brown adipose tissue, and mesenteric fat. Consistently, metagenomic analysis showed that EA enriched Akkermansia muciniphila, Muribaculum intestinale, and Duncaniella dubosii, while reducing Lachnoclostridium phocaeense. These microbial shifts were accompanied by elevated levels of tryptophan-derived metabolites-indole-3-propionic acid, indole, and indole-3-acrylic acid-known to enhance insulin sensitivity. Lipidomics revealed EA decreased triacylglycerols and ceramides, along with restored phosphatidylcholine, phosphatidylethanolamine and phosphatidylserine levels. Transcriptomics revealed EA suppressed hepatic lipogenesis, inhibited MAPK signaling in skeletal muscle, activated thermogenic and oxidative phosphorylation in adipose tissues. Our findings highlight EA, a food-derived polyphenol, might alleviate insulin resistance through a gut microbiota-indole metabolite-multi-tissue axis.},
}

*Indoles/metabolism
Animals
*Insulin Resistance
*Gastrointestinal Microbiome/drug effects
*Tryptophan/metabolism
*Ellagic Acid/metabolism/chemistry
Signal Transduction/drug effects
Multiomics
Bacteria/isolation & purification/classification/genetics/metabolism
Male
Humans
Mice

@article {pmid41581932,
year = {2026},
author = {Selvaraj, C and Desai, D and Santos-Villalobos, SL and Jayaprakashvel, M and Muthezhilan, R and Singh, SK},
title = {Marine-derived antimicrobial peptides (AMPs): Blue biotechnological assets for sustainable healthcare and circular bioeconomy.},
journal = {Advances in protein chemistry and structural biology},
volume = {149},
number = {},
pages = {171-201},
doi = {10.1016/bs.apcsb.2025.08.002},
pmid = {41581932},
issn = {1876-1631},
mesh = {*Antimicrobial Peptides/chemistry/pharmacology/economics ; *Biotechnology/economics ; *Aquatic Organisms/chemistry ; Animals ; Humans ; },
abstract = {The global antimicrobial resistance (AMR) crisis drives the demand for novel therapeutics, positioning marine-derived antimicrobial peptides (AMPs) as sustainable alternatives with unique structural and functional advantages. These cationic, amphipathic molecules, from the source of diverse marine organisms, such as invertebrates, extremophiles, and cyanobacteria, exhibit broad-spectrum activity against drug-resistant pathogens through mechanisms like membrane disruption and immunomodulation. Their low resistance propensity and multifunctional bioactivity (eg., antioxidant, antimicrobial, anticancer) underscore therapeutic potential beyond the conventional antibiotics. Advances in genomic and metagenomic tools, machine learning, and synthetic biology are revolutionizing AMP discovery, enabling targeted mining of marine biodiversity and peptide optimization for enhanced stability and specificity. Biotechnological innovations support scalable production through heterologous expression and marine biomass valorization, which aligns with the principles of the circular economy. Marine-sourced AMPs demonstrate transformative applications across various healthcare, aquaculture, food safety, and environmental remediation, that majorly reduce the dependence on synthetic chemicals. Their integration into blue bioeconomy frameworks is promoting sustainable bio-prospects, marine ecosystem conservation, and progress towards the United Nations Sustainable Development Goals. This review narrates the collective research and also addresses the critical challenges, including production scalability and regulatory frameworks, to outline a clear pathway for the marine sourced AMP commercialization. By bridging the antimicrobial innovation with circular biotechnology, marine-sourced AMPs are exemplifying the ocean's role as a reservoir of sustainable solutions for global health and bioeconomic resilience.},
}

*Antimicrobial Peptides/chemistry/pharmacology/economics
*Biotechnology/economics
*Aquatic Organisms/chemistry
Animals
Humans

@article {pmid41582242,
year = {2026},
author = {Chethan, D and Kavya, BS and Arati, and Chandana, R and Gowtham, HP and Ashika, S and Chanchala, S and Nagaraju, N and Reddy, CNL and Kunjeti, SG and Ningaraju, TM},
title = {Endophyte profiling of tomato leaf curl virus (ToLCV) resistant and susceptible tomato genotypes: Insights into microbial diversity and growth promotion.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {5348},
pmid = {41582242},
issn = {2045-2322},
mesh = {*Solanum lycopersicum/virology/genetics/growth & development/microbiology ; *Endophytes/genetics/isolation & purification/classification ; *Begomovirus/pathogenicity ; *Disease Resistance/genetics ; *Plant Diseases/virology/genetics/microbiology ; Genotype ; Bacteria/isolation & purification/classification/genetics ; Fungi/isolation & purification/genetics/classification ; Biodiversity ; },
abstract = {Tomato (Solanum lycopersicum L.) is one of the most widely cultivated vegetable crops globally. Still, its productivity is significantly constrained by tomato leaf curl virus (ToLCV), a devastating begomovirus transmitted by whiteflies. This study examined the diversity and plant growth-promoting potential of culturable endophytes associated with tomato cultivars differing in resistance to tomato leaf curl virus (ToLCV). A total of 59 fungal and bacterial endophytes were isolated. Resistant cultivars (Nandi, Sankranthi, and Vybhav) harboured more diverse and compositionally distinct communities than the susceptible cultivar Arka Vikas, as indicated by Shannon, Simpson, and Chao-1 indices and multivariate analyses. Several isolates, particularly from the genera Xylaria, Fusarium, Arcopilus, Epicoccum, Bacillus, Pseudomonas, Stutzerimonas, and Paenibacillus, displayed strong nutrient-solubilizing traits in vitro, highlighting their potential as plant growth-promoting candidates. Eleven promising isolates were further evaluated on the susceptible cultivar Arka Vikas. At 30 days after sowing, Epicoccum nigrum and Bacillus subtilis significantly increased seedling height, biomass, and leaf number relative to the control. Overall, the study reveals that resistant cultivars are associated with greater culturable endophyte diversity and identifies several isolates with strong potential for promoting plant growth. Future research should assess the antiviral potential of these endophytes under ToLCV challenge and employ metagenomic studies to elucidate their functional roles in enhancing plant health.},
}

*Solanum lycopersicum/virology/genetics/growth & development/microbiology
*Endophytes/genetics/isolation & purification/classification
*Begomovirus/pathogenicity
*Disease Resistance/genetics
*Plant Diseases/virology/genetics/microbiology
Genotype
Bacteria/isolation & purification/classification/genetics
Fungi/isolation & purification/genetics/classification
Biodiversity

@article {pmid41582543,
year = {2026},
author = {Tang, ZH and Lin, ZN and Li, JX and Liu, FC and Cao, J and Chen, SF and Huang, KY and Li, HF and Hu, DS and Huang, JF and Gu, DF and Lu, XF},
title = {Plasma Metabolites Mediate the Associations of Gut Microbial Diversity with Ambulatory Blood Pressure and Its Variability.},
journal = {Biomedical and environmental sciences : BES},
volume = {39},
number = {1},
pages = {26-35},
doi = {10.3967/bes2025.089},
pmid = {41582543},
issn = {2214-0190},
mesh = {Humans ; *Blood Pressure ; *Hypertension/microbiology/blood ; *Gastrointestinal Microbiome ; Male ; Female ; Middle Aged ; Adult ; Blood Pressure Monitoring, Ambulatory ; China ; Prospective Studies ; *Metabolome ; },
abstract = {OBJECTIVE: Evidence suggests that depleted gut microbial α-diversity is associated with hypertension; however, whether metabolic markers affect this relationship remains unknown. We aimed to determine the potential metabolites mediating the associations of α-diversity with blood pressure (BP) and BP variability (BPV).

METHODS: Metagenomics and plasma targeted metabolomics were conducted on 523 Chinese participants from the MetaSalt study. The 24-hour, daytime, and nighttime BP and BPV were calculated based on ambulatory BP measurements. Linear mixed models were used to characterize the relationships between α-diversity (Shannon and Chao1 index) and BP indices. Mediation analyses were performed to assess the contribution of metabolites to the observed associations. The influence of key metabolites on hypertension was further evaluated in a prospective cohort of 2,169 participants.

RESULTS: Gut microbial richness (Chao1) was negatively associated with 24-hour systolic BP, daytime systolic BP, daytime diastolic BP, 24-hour systolic BPV, and nighttime systolic BPV (P < 0.05). Moreover, 26 metabolites were strongly associated with richness (Bonferroni P < 0.05). Among them, four key metabolites (imidazole propionate, 2-hydroxy-3-methylbutyric acid, homovanillic acid, and hydrocinnamic acid) mediated the associations between richness and BP indices (proportions of mediating effects: 14.1%-67.4%). These key metabolites were also associated with hypertension in the prospective cohort. For example, each 1-standard deviation unit increase in hydrocinnamic acid significantly reduced the risk of prevalent (OR [95% CI] = 0.90 [0.82, 0.99]; P = 0.03) and incident hypertension (HR [95% CI] = 0.83 [0.71, 0.96]; P = 0.01).

CONCLUSION: Our results suggest that gut microbial richness correlates with lower BP and BPV, and that certain metabolites mediate these associations. These findings provide novel insights into the pathogenesis and prevention of hypertension.},
}

Humans
*Blood Pressure
*Hypertension/microbiology/blood
*Gastrointestinal Microbiome
Male
Female
Middle Aged
Adult
Blood Pressure Monitoring, Ambulatory
China
Prospective Studies
*Metabolome

@article {pmid41582602,
year = {2026},
author = {Hernani, R and Albert, E and Hernani-Morales, C and Zúñiga, S and Benzaquén, A and González-Castillo, L and Colomer, E and Morell, J and Català-Senent, JF and Piñana, JL and Giménez, E and Pérez, A and Hernández-Boluda, JC and Arroyo, I and Rivada, M and Barber, T and Alemany, T and Santacatalina, E and Rentero-Garrido, P and Terol, MJ and Díaz, R and Navarro, D and Solano, C},
title = {Microbiome-Based Modeling of CAR-T Therapy Response in Lymphoma: Insights From Shotgun Metagenomics Sequencing.},
journal = {European journal of haematology},
volume = {116},
number = {5},
pages = {646-662},
pmid = {41582602},
issn = {1600-0609},
support = {//Fundación FERO and the Fundación para la Promoción de Acciones Solidarias/ ; //European Union through the Operational Program of the European Regional Development Fund/ ; CA23/00007//bioinformatics technician/ ; //2023 Strategic Action in Health/ ; //Instituto de Salud Carlos III/ ; //European Union/ ; },
mesh = {Humans ; *Metagenomics/methods ; Shotgun Sequencing ; Female ; Treatment Outcome ; *Microbiota ; *Immunotherapy, Adoptive/adverse effects/methods ; Male ; Middle Aged ; Adult ; *Receptors, Chimeric Antigen/genetics/metabolism ; Aged ; *Lymphoma/therapy/diagnosis/mortality ; Machine Learning ; },
abstract = {The interplay between the commensal microbiota and the mammalian immune system may influence the outcomes of T cell-driven cancer immunotherapies. However, clinical studies supporting microbiota-based interventions in chimeric antigen receptor T-cell (CAR-T) therapy remain scarce. This study included 30 adult patients with B-cell lymphoma treated with axicabtagene ciloleucel (axi-cel) or 4-1BB investigational product. Shotgun metagenomics sequencing (SMS) of fecal samples, collected before lymphodepletion and 1 month post infusion, enabled species-level resolution. We also trained 25 microbiome-based machine-learning (ML) models for response prediction. Neither prior "high-risk" antibiotics exposure nor alpha diversity influenced toxicity, response, or survival. However, dysbiosis was observed between 11 healthy controls and patients, particularly in those treated with axi-cel. SMS identified species associated with clinical outcomes. Increased abundance of Alistipes senegalensis and Alistipes onderdonkii correlated with lower neurotoxicity and improved survival, respectively. Bifidobacterium longum was associated with reduced cytokine release syndrome, whereas Bifidobacterium adolescentis , Bifidobacterium bifidum , and Bifidobacterium breve correlated with poorer survival. ML models demonstrated strong predictive performance, with some identifying non-responders using only six species selected by the Boruta method (Bacteroides xylanisolvens , Bifidobacterium bifidum , Bifidobacterium breve , Eubacteriaceae bacterium Marseille-Q4139, Negativibacillus massiliensis, and Sellimonas intestinalis). These findings deepen current knowledge and support prospective microbiota-based strategies in CAR-T therapy.},
}

Humans
*Metagenomics/methods
Shotgun Sequencing
Female
Treatment Outcome
*Microbiota
*Immunotherapy, Adoptive/adverse effects/methods
Male
Middle Aged
Adult
*Receptors, Chimeric Antigen/genetics/metabolism
Aged
*Lymphoma/therapy/diagnosis/mortality
Machine Learning

@article {pmid41582618,
year = {2026},
author = {Wu, X and Lim, KJ and Ma, Y and Gu, J and Jiang, Y and Zhu, L and Chen, Y and Sun, J},
title = {The Effects of Soy Protein-Rich Meals on Muscle Health of Older Adults Are Linked to Gut Microbiome Modifications.},
journal = {Journal of cachexia, sarcopenia and muscle},
volume = {17},
number = {1},
pages = {e70212},
pmid = {41582618},
issn = {2190-6009},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; Aged ; Female ; Male ; *Soybean Proteins/administration & dosage/pharmacology ; *Sarcopenia/diet therapy ; *Muscle, Skeletal/physiology ; Aged, 80 and over ; Fatty Acids, Volatile ; Feces/microbiology ; },
abstract = {BACKGROUND: Sarcopenia is characterized by accelerated muscle mass and function loss in older adults. The role of nutritional interventions in sarcopenia is uncertain. This study investigates whether a soy protein-rich diet can enhance muscle health in older adults via gut microbiota changes.

METHODS: A 12-week randomized controlled trial was conducted with 84 older adults from a long-term care facility. Participants in the intervention group consumed three daily meals containing 10 g of soy protein (totalling 30 g/day), while the control group maintained their usual diets. Faecal samples from 53 participants were collected at Weeks 0, 6 and 12. We assessed changes in muscle function, gut microbiota composition and faecal short-chain fatty acids (SCFA).

RESULTS: The intervention group showed preserved calf circumference, while the control group experienced a decrease (W12-W0: Intervention, 0.56 ± 0.22 cm; Control, -0.91 ± 0.26 cm, p(interaction) < 0.001). Metagenomic analysis revealed significant alterations in gut microbiota among intervention participants who showed improvement in muscle performance parameters. The intervention increased SCFA-producing bacteria (Roseburia faecis, Intervention: 0.42 ± 0.21%, Control: -0.06 ± 0.16, p(interaction) < 0.05; Agathobaculum butyriciproducens, Intervention: 0.02 ± 0.007%, p(time) < 0.01, Control: -0.04 ± 0.01) and decreased species associated with poorer muscle outcomes (Alistipes putredinis, Intervention: -0.88 ± 0.40%, Control: 0.62 ± 0.63, p(interaction) < 0.05; Eubacterium_sp_CAG_38, Intervention: -0.64 ± 0.28%, Control: 0.10 ± 0.22, p(interaction) < 0.05). Functional pathway analysis showed enrichment of anaerobic amino acid degradation pathways and vitamin biosynthesis, with depletion of inflammatory pathways, particularly lipopolysaccharide biosynthesis. Microbiome phenotype prediction revealed a decrease in aerobic bacteria abundance in the intervention group (W12-W0, Intervention: -0.004 ± 0.002; Control: 0.001 ± 0.001, p(interaction) < 0.05). Interaction (group × time) for SCFA was not statistically significant; within-group increases at Week 6 were observed in only the intervention group (butyric acid, Intervention: 0.74 ± 0.34 mg/g, p(time) < 0.05, Control: 0.12 ± 0.43 mg/g; isobutyric acid, Intervention: 0.14 ± 0.08 mg/g, p(time) < 0.05, Control: 0.08 ± 0.10 mg/g; isovaleric acid, Intervention: 0.27 ± 0.14 mg/g, p(time) < 0.05; Control: 0.16 ± 0.20 mg/g), with partial reversal by Week 12. These changes, positively correlated with improved muscle function parameters, suggest intervention benefits on gut health and muscle function.

CONCLUSION: A soy protein-rich intervention improved muscle health in older adults through beneficial gut microbiota. These findings support the gut-muscle axis hypothesis and suggest dietary soy protein may alleviate sarcopenia by promoting a healthier gut microbiome.},
}

Humans
*Gastrointestinal Microbiome/drug effects
Aged
Female
Male
*Soybean Proteins/administration & dosage/pharmacology
*Sarcopenia/diet therapy
*Muscle, Skeletal/physiology
Aged, 80 and over
Fatty Acids, Volatile
Feces/microbiology

@article {pmid41586308,
year = {2025},
author = {Wang, X and Ye, L and Liu, Y and Li, H and Shi, H and Zheng, L},
title = {Metagenomic analysis reveals severity-dependent microbial succession and correlation with host inflammatory response in oral and maxillofacial space infections.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1695928},
pmid = {41586308},
issn = {2235-2988},
mesh = {Humans ; *Metagenomics ; Female ; Cross-Sectional Studies ; Retrospective Studies ; *Microbiota ; Male ; *Inflammation/microbiology ; *Abscess/microbiology ; Severity of Illness Index ; Middle Aged ; *Bacteria/classification/genetics/isolation & purification ; Adult ; Aged ; },
abstract = {BACKGROUND: Oral and maxillofacial space infections (OMSI) vary widely in clinical severity, yet the relationships between microbial community patterns in the abscess niche and host inflammatory responses remain incompletely characterized.

METHODS: We conducted a retrospective, cross-sectional, severity-stratified study of 197 patients diagnosed with OMSI between January 2020 and November 2023. Patients were stratified into mild (n=90), moderate (n=41), and severe (n=66) groups based on established clinical criteria. We performed mNGS on abscess pus samples to characterize the microbial community composition and assessed associations between these features and systemic inflammatory markers.

RESULTS: Although α-diversity did not differ significantly among severity groups, β-diversity analysis revealed distinct microbial communities. Pairwise analyses indicated a threshold-like community shift, characterized by a significant divergence between mild and severe infections, while the moderate group exhibited an intermediate composition that overlapped with both. Severe infections were characterized by an enrichment of Prevotella. Furthermore, analysis of predominant taxa (>30% abundance) revealed considerable microbial heterogeneity, challenging a simple monoinfection model. Notably, a machine learning-identified microbial profile comprising Streptococcus, Corynebacterium, and Pseudomonas was significantly correlated with elevated systemic inflammatory markers.

CONCLUSION: This study characterizes associations between abscess-site microbial communities and host inflammatory profiles across OMSI severity strata. Given the cross-sectional design and the lack of an external validation cohort, the present findings should be interpreted as exploratory and non-causal. Future multicenter prospective studies including independent validation cohorts are warranted to test reproducibility and to evaluate whether any candidate features possess generalizable predictive value.},
}

Humans
*Metagenomics
Female
Cross-Sectional Studies
Retrospective Studies
*Microbiota
Male
*Inflammation/microbiology
*Abscess/microbiology
Severity of Illness Index
Middle Aged
*Bacteria/classification/genetics/isolation & purification
Adult
Aged

@article {pmid41586370,
year = {2025},
author = {Zeng, B and Peng, X and Xiao, P and Nie, K and Zhang, G and Xia, L},
title = {Salt sensitivity potentiates high-salt diet-induced intestinal barrier disruption and gut microbiome dysbiosis in rats.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1718782},
pmid = {41586370},
issn = {1664-302X},
abstract = {INTRODUCTION: The high-salt diet is a prevalent eating habit associated with health risks. This study investigated the impact of high salt on intestinal barrier disruption and gut microbiome dysbiosis using Wistar and Dahl salt-sensitive rat models.

METHODS: Rats were fed a normal diet or a high-salt diet for eight weeks. Body weight and plasma inflammatory cytokines were monitored in the study. Colon tissue damage was assessed via histopathological examination, and metagenomic sequencing was utilized to analyze alterations in microbial composition, functional pathways, and biodiversity.

RESULTS: The results indicated that high salt significantly elevated pro-inflammatory cytokine levels and induced structural damage in the colon. Metagenomic analysis revealed that high salt concentrations resulted in approximately a 15% difference in microbial species composition. And led to a decrease in Alpha diversity, along with an increase in the Firmicutes/Bacteroidetes ratio. Taxon-specific alterations included reduced abundance of Lactobacillus and Clostridium, and increased abundance of Enterobacter and Bifidobacterium. Correlation analyses further revealed a positive correlation between Bifidobacterium abundance and tumor necrosis factor-α level in Dahl salt-sensitive rats.

DISCUSSION: This study illuminates the gut microbiota's role in salt-sensitivity and provides a foundational basis for developing microbiota-targeted interventions for at-risk individuals.},
}

@article {pmid41586524,
year = {2026},
author = {Bloemen, B and Delvoye, M and Hoffman, S and Marchal, K and Vanneste, K and Fraiture, M-A and Roosens, NHC and De Keersmaecker, SCJ},
title = {Recovery and microbial host assignment of mobile genetic elements in complex microbiomes: insights from a spiked gut sample.},
journal = {mSystems},
volume = {11},
number = {2},
pages = {e0128225},
pmid = {41586524},
issn = {2379-5077},
mesh = {*Interspersed Repetitive Sequences/genetics ; DNA Methylation ; *Gastrointestinal Microbiome/genetics ; Plasmids/genetics ; Humans ; *Bacillus/genetics ; Gene Transfer, Horizontal ; Bacteriophages/genetics ; Genome, Bacterial ; Bioreactors/microbiology ; },
abstract = {UNLABELLED: Mobile genetic elements (MGEs) are major drivers of horizontal gene transfer, including the spread of antimicrobial resistance (AMR) genes. However, determining the microbial host of an MGE in complex microbiomes remains challenging. Here, we spike a niche-aspecific Bacillus velezensis strain carrying a plasmid and linear phage-plasmid into a batch bioreactor simulating the human gut, and use it as a spike-in control to assess the performance of Hi-C sequencing and Oxford Nanopore Technologies (ONT)-enabled DNA methylation detection to identify MGE-host pairs. To improve recovery of low-abundance genomes, we used a novel ONT adaptive sampling (AS) strategy that depletes de novo assembled, sample-specific high-abundance contigs, rather than relying on reference genomes. This approach led to an approximately twofold enrichment of low-abundance replicons, including the spike-in strain. Methylation-based host assignment failed for the B. velezensis MGEs, likely due to the absence of DNA methylation. In contrast, Hi-C successfully linked the phage-plasmid to its host, but not the plasmid, likely due to non-intact cells, and only after removing artefactual signals through bioinformatic processing. For a native Escherichia coli strain, Hi-C and methylation data linked it to two plasmids. Selective isolation and whole-genome sequencing of both the native E. coli and spike-in B. velezensis then confirmed the metagenomic observations. Our results highlight that Hi-C and methylation data can provide powerful insights into MGE-host associations, but their interpretation requires careful computational analysis and biological validation. Moreover, our AS strategy offers a cost-efficient method to boost coverage of low-abundance genomes, improving metagenomic investigation of MGEs in complex microbiomes.

IMPORTANCE: Mobile genetic elements are important contributors to horizontal gene transfer, including of antimicrobial resistance genes. Understanding which microbes carry these mobile elements is vital to assess the spread of resistance. Here, we use a nanopore adaptive sampling approach to increase detection of low-abundance bacteria and mobile elements and use DNA methylation detection and Hi-C sequencing to determine mobile element hosts. By introducing a known bacterium and isolating a native strain, we could evaluate the performance of these methods, indicating that although powerful, they require careful experimental design, interpretation, and validation. However, when combined, these approaches enable a comprehensive investigation of mobile elements and gene transfer dynamics in complex environments.},
}

*Interspersed Repetitive Sequences/genetics
DNA Methylation
*Gastrointestinal Microbiome/genetics
Plasmids/genetics
Humans
*Bacillus/genetics
Gene Transfer, Horizontal
Bacteriophages/genetics
Genome, Bacterial
Bioreactors/microbiology

@article {pmid41587576,
year = {2026},
author = {Mburu, D and Kumar, S and Wang, Y and Namagerdi, AA and Bai, K and Ali, B and Minalla, A and Gonzales, KO and Abdelhalim, KA},
title = {The oxalobiome: unraveling the role of gut microbiota in oxalate metabolism and its implications for kidney health and disease management.},
journal = {Clinica chimica acta; international journal of clinical chemistry},
volume = {584},
number = {},
pages = {120852},
doi = {10.1016/j.cca.2026.120852},
pmid = {41587576},
issn = {1873-3492},
mesh = {Humans ; *Oxalates/metabolism ; *Gastrointestinal Microbiome ; *Kidney/metabolism ; Disease Management ; Oxalobacter formigenes/metabolism ; Hyperoxaluria/metabolism/therapy ; Animals ; },
abstract = {The oxalobiome, comprising microbial communities involved in oxalate metabolism, plays a critical role in maintaining oxalate homeostasis and preventing associated health issues, particularly calcium oxalate nephrolithiasis. Key organisms, notably Oxalobacter formigenes, are essential for degrading oxalate, yet their abundance is influenced by factors such as diet, genetics, and antibiotic use. Recent advances in research have elucidated the complex interactions between the gut microbiome and oxalate metabolism, highlighting the potential for therapeutic interventions. Innovative strategies, including RNA interference therapies (e.g., lumasiran, nedosiran), engineered probiotics, and gene-editing technologies, show promise in managing conditions like primary hyperoxaluria. However, challenges remain, including limitations in oxalate measurement techniques and variability in microbial populations. Multi-omics approaches and metagenomic analyses have enhanced our understanding of the oxalobiome, revealing novel microbial taxa and metabolic pathways involved in oxalate degradation. Despite the potential of emerging therapies, clinical translation is still in its infancy, necessitating further research to establish efficacy and safety. Future studies should focus on mechanistic insights, standardized methodologies, and targeted microbiome-based therapies to optimize management strategies for hyperoxaluria and related systemic diseases. A comprehensive understanding of the oxalobiome is essential for developing precision medicine approaches that effectively address oxalate dysregulation and improve patient outcomes.},
}

Humans
*Oxalates/metabolism
*Gastrointestinal Microbiome
*Kidney/metabolism
Disease Management
Oxalobacter formigenes/metabolism
Hyperoxaluria/metabolism/therapy
Animals

@article {pmid41588069,
year = {2026},
author = {Muñoz-Hisado, V and Bartolomé, M and Osácar, MC and Giménez, R and Cazenave, G and Garcia-Lopez, E and Moreno, A and Cid, C},
title = {Microbial communities and biomineralization potential within mountain permafrost of the Devaux ice cave in the Central Pyrenees.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {6232},
pmid = {41588069},
issn = {2045-2322},
support = {HORIZON-MSCA-2022-PF-01 (01107943)//European Union/ ; PTA2022-021737-I//the Spanish Ministry of Science and Innovation/State Agency of Research MCIN/ ; },
mesh = {*Permafrost/microbiology ; *Biomineralization ; *Caves/microbiology ; *Microbiota ; Bacteria/genetics/classification ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Metagenome ; Metagenomics ; },
abstract = {Ice caves constitute one of the last cryospheric environments studied in the meridional regions. They are undergoing a pronounced ice reduction, and are an important example of ecosystems that have not yet been thoroughly explored from a microbiological point of view. The Devaux cave, in the Central Pyrenees, still hosts perennial ice. To test whether this ice contained microbial communities, prokaryotic and eukaryotic microorganisms were searched by sequencing their 16S and 18S rRNA genes. From the taxonomic information, the potential functional pathways of these communities were predicted using bioinformatic techniques. In addition, the genome of the microorganisms housed in the perennial ice samples was investigated, and through metagenomic studies their metabolic capacity was elucidated. The cryogenic mineralization of the Devaux cave leads to the production of various Ca and Mg carbonates: calcite, aragonite, vaterite, Mg-rich calcite, and nesquehonite, whose formation may have been favored by the microorganisms in the cave. Among the genes encoding enzymes that enable reactions involved in biomineralization, those belonging to the nitrate and sulfate reduction dissimilatory pathways as well as ureases, ammonia lyases, and carbonic anhydrases were identified. This research takes a further step in the investigation of biomineralization, using the Devaux cave as a model.},
}

*Permafrost/microbiology
*Biomineralization
*Caves/microbiology
*Microbiota
Bacteria/genetics/classification
Phylogeny
RNA, Ribosomal, 16S/genetics
Metagenome
Metagenomics

@article {pmid41588163,
year = {2026},
author = {Young, V and Dohai, B and Halder, H and Fernandez-Macgregor, J and van Heusden, NS and Hitch, TCA and Weller, B and Hyden, P and Saha, D and Pieren, DKJ and Rittchen, S and Lambourne, L and Maseko, SB and Lin, CW and Tun, YM and Bibus, J and Pletschacher, L and Boujeant, M and Choteau, SA and Bergogne, L and Perrin, J and Ober, F and Schwehn, P and Rothballer, ST and Altmann, M and Altmann, S and Strobel, A and Rothballer, M and Tofaute, M and Kotlarz, D and Heinig, M and Clavel, T and Calderwood, MA and Vidal, M and Twizere, JC and Vincentelli, R and Krappmann, D and Boes, M and Falter, C and Rattei, T and Brun, C and Zanzoni, A and Falter-Braun, P},
title = {Effector-host interactome map links type III secretion systems in healthy gut microbiomes to immune modulation.},
journal = {Nature microbiology},
volume = {11},
number = {2},
pages = {442-460},
pmid = {41588163},
issn = {2058-5276},
support = {01EA1803//Bundesministerium für Bildung und Forschung (Federal Ministry of Education and Research)/ ; 101003633//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 210592381//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 403224013//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 11819559//Österreichische Forschungsförderungsgesellschaft (Austrian Research Promotion Agency)/ ; ANR-16-CONV-0001//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-17-HDIM-000//Agence Nationale de la Recherche (French National Research Agency)/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; *Type III Secretion Systems/metabolism/genetics/immunology ; Bacterial Proteins/metabolism/genetics ; Crohn Disease/microbiology/immunology ; NF-kappa B/metabolism ; *Immunomodulation ; Host-Pathogen Interactions ; Colitis, Ulcerative/microbiology/immunology ; Host Microbial Interactions ; Protein Interaction Maps ; Metagenomics ; },
abstract = {Pseudomonadota (formerly Proteobacteria) are prevalent in the commensal human gut microbiota, but also include many pathogens that rely on secretion systems to support pathogenicity by injecting proteins into host cells. Here we show that 80% of Pseudomonadota from healthy gut microbiomes also have intact type III secretion systems (T3SS). Candidate effectors predicted by machine learning display sequence and structural features that are distinct from those of pathogen effectors. Towards a systems-level functional understanding, we experimentally constructed a protein-protein meta-interactome map between human proteins and commensal effectors. Network analyses uncovered that effector-targeted neighbourhoods are enriched for genetic variation linked to microbiome-associated conditions, including autoimmune and metabolic diseases. Metagenomic analysis revealed effector enrichment in Crohn's disease but depletion in ulcerative colitis. Functionally, commensal effectors can translocate into human cells and modulate NF-κB signalling and cytokine secretion in vitro. Our findings indicate that T3SS contribute to microorganism-host cohabitation and that effector-host protein interactions may represent an underappreciated route by which commensal gut microbiota influences health.},
}

Humans
*Gastrointestinal Microbiome/immunology
*Type III Secretion Systems/metabolism/genetics/immunology
Bacterial Proteins/metabolism/genetics
Crohn Disease/microbiology/immunology
NF-kappa B/metabolism
*Immunomodulation
Host-Pathogen Interactions
Colitis, Ulcerative/microbiology/immunology
Host Microbial Interactions
Protein Interaction Maps
Metagenomics

@article {pmid41589071,
year = {2026},
author = {Caserta, MT and Mariani, TJ and Walsh, EE and Gill, SR and Gill, AL and Corbett, A and Harrington, D and Chu, C and Qiu, X},
title = {Nasal Biomarkers of Acute Illness Severity and Predictors of Recurrent Wheeze in Infants Infected With Respiratory Syncytial Virus.},
journal = {The Journal of infectious diseases},
volume = {233},
number = {6},
pages = {1027-1035},
doi = {10.1093/infdis/jiag049},
pmid = {41589071},
issn = {1537-6613},
support = {58711//Merck Investigator Studies Program/ ; //Merck and Co, Inc/ ; },
mesh = {Humans ; *Respiratory Syncytial Virus Infections/diagnosis/virology ; *Respiratory Sounds/etiology ; Infant ; Male ; Severity of Illness Index ; Female ; *Biomarkers/analysis ; Recurrence ; Microbiota ; Respiratory Syncytial Virus, Human ; Acute Disease ; },
abstract = {BACKGROUND: Respiratory syncytial virus (RSV) is a leading cause of hospitalization in infants, and those with RSV disease appear more likely to develop recurrent wheeze. We examined nasal airway gene expression and microbiome composition during primary RSV infection to test associations with illness severity and identify infants with recurrent wheeze.

METHODS: Previously healthy infants with RSV infection were enrolled (December 2019-December 2023). Clinical and demographic data were collected, as were 2 anterior nasal swabs and a nasal wash for metagenome and transcriptome sequencing. Disease severity was measured by the improved Global Respiratory Severity Score (iGRSS). Participants were followed for approximately 1 year to identify recurrent wheeze. Multivariate regression models were developed to identify correlates and predictors of disease severity and recurrent wheeze, respectively.

RESULTS: One hundred infants (90 hospitalized) were enrolled (mean ± SD age, 3.2 ± 2.3 months; 61% male). An overall 405 genes (false discovery rate, 0.10) were significantly and consistently associated with illness severity (iGRSS), implicating innate immune and interleukin signaling pathways. The abundance of nasal Dolosigranulum was inversely associated with iGRSS, while the abundance of Haemophilus was directly associated with iGRSS. Predictive models based on nasal gene expression during infection had the power to classify recurrent wheeze (in-sample area under the curve, 0.992; cross-validated area under the curve, 0.882), while metagenomic features did not improve predictive performance.

CONCLUSIONS: We prospectively followed infants with primary RSV infection and identified associations among nasal gene expression, microbiome composition/function, and acute disease severity and recurrent wheeze. Host transcriptional profiles during infection were predictive of recurrent wheeze within the following year.},
}

Humans
*Respiratory Syncytial Virus Infections/diagnosis/virology
*Respiratory Sounds/etiology
Infant
Male
Severity of Illness Index
Female
*Biomarkers/analysis
Recurrence
Microbiota
Respiratory Syncytial Virus, Human
Acute Disease

@article {pmid41589896,
year = {2026},
author = {Conrad, RE and Tsementzi, D and Meziti, A and Hatt, JK and Montoya, J and Konstantinidis, KT},
title = {Metagenome-based vertical profiling of the Gulf of Mexico highlights its uniqueness and far-reaching effects of freshwater input.},
journal = {Applied and environmental microbiology},
volume = {92},
number = {2},
pages = {e0258925},
pmid = {41589896},
issn = {1098-5336},
support = {ECOGIG Consortium//Gulf of Mexico Research Initiative/ ; 1831582//National Science Foundation/ ; 2129823//National Science Foundation/ ; },
mesh = {Gulf of America ; *Metagenome ; *Fresh Water/microbiology ; *Seawater/microbiology ; *Bacteria/genetics/classification/isolation & purification ; Metagenomics ; Phylogeny ; },
abstract = {Genomic and metagenomic explorations of the oceans have identified well-structured microbial assemblages showing endemic genomic adaptations with increasing depth. However, deep water column surveys have been limited, especially of the Gulf of Mexico (GoM) basin, despite its importance for human activities. To fill this gap, we report on 19 deeply sequenced (~5 Gbp/sample) shotgun metagenomes collected along a vertical gradient, from the surface to about 2,000 m deep, at three GoM stations. Beta diversity analysis revealed strong clustering by depth, and not by station. However, a community-level pangenome style gene content analysis revealed ~54% of predicted gene sequences to be station-specific within our GoM samples. Of the 154 medium-to-high-quality MAGs recovered, 145 represent novel species compared with the NCBI genomes and Tara Oceans MAGs databases. Two of these MAGs were relatively abundant at both surface and deep samples, revealing remarkable versatility across the water column. A few MAGs of freshwater origin (~6% of total detected) were relatively abundant at 600 m deep and 270 miles from the coast at one station, revealing that the effects of freshwater input in the GoM can sometimes be far-reaching and long-lasting. Notably, 1,447/16,068 of the total COGs detected were positively (Pearson's r ≥ 0.5) or negatively (Pearson's r ≤ -0.5) correlated with depth, including beta-lactamases, dehydrogenases, and CoA-associated oxidoreductases. Taken together, our results reveal substantial novel genome and gene diversity across the GoM's water column, and testable hypotheses for some of the diversity patterns observed.IMPORTANCETo what extent microbial communities are similar between different ocean basins at similar depths, and what the impact of freshwater input by major rivers may be on these communities, remain poorly understood issues with potentially important implications for modeling and managing marine biodiversity. In this study, we performed metagenomic sequencing and recovered 154 medium-to-high-quality metagenome-assembled genomes (MAGs) from three stations in the Gulf of Mexico (GoM) and from various depths up to about 2,000 m. Comparison to MAGs recovered from other ocean basins highlighted the unique diversity harbored by the GoM, which could be driven by more substantial input from the Mississippi River and by human activities, including offshore oil drilling. The data and results provided by this study should be useful for future comparative analysis of marine biodiversity and contribute to its more complete characterization.},
}

Gulf of America
*Metagenome
*Fresh Water/microbiology
*Seawater/microbiology
*Bacteria/genetics/classification/isolation & purification
Metagenomics
Phylogeny

@article {pmid41590723,
year = {2026},
author = {Atak, E and Tavčar Verdev, P and Petek, M and Coll, A and Bosch, D and Dolinar, M and Komarysta, V and Glavaš, N and Rotter, A},
title = {Identification and Cultivation of Biotechnologically Relevant Microalgal and Cyanobacterial Species Isolated from Sečovlje Salt Pans, Slovenia.},
journal = {Marine drugs},
volume = {24},
number = {1},
pages = {},
pmid = {41590723},
issn = {1660-3397},
support = {L4-4564//The Slovenian Research and Innovation Agency/ ; Euro-MED 0200514//Interreg Euro-MED Program/ ; },
mesh = {*Cyanobacteria/isolation & purification/genetics/growth & development ; *Microalgae/isolation & purification/genetics/growth & development ; Slovenia ; Salinity ; Metagenomics ; Biotechnology ; Biodiversity ; Ecosystem ; },
abstract = {Studies of complex natural environments often focus on either biodiversity or on isolating organisms with specific properties. In this study, we sought to widen this perspective and achieve both. In particular, hypersaline ecosystems, such as the Sečovlje salt pans (Slovenia), are particularly promising sources of novel bioactive compounds, as their microorganisms have evolved adaptations to desiccation and high light intensity stress. We applied shotgun metagenomics to assess microbial biodiversity under low- and high-salinity conditions, complemented by isolation and cultivation of photosynthetic microorganisms. Metagenomic analyses revealed major shifts in community composition with increasing salinity: halophilic Archaea became dominant, while bacterial abundance decreased. Eukaryotic assemblages also changed, with greater representation of salt-tolerant genera such as Dunaliella sp. Numerous additional microorganisms with biotechnological potential were identified. Samples from both petola and brine led to the isolation and cultivation of Dunaliella sp., Tetradesmus obliquus, Tetraselmis sp. and cyanobacteria Phormidium sp./Sodalinema stali, Leptolyngbya sp., and Capilliphycus guerandensis. The newly established cultures are the first collection from this hypersaline environment and provide a foundation for future biodiscovery, production optimization, and sustainable bioprocess development. The methods developed in this study constitute a Toolbox Solution that can be easily replicated in other habitats.},
}

*Cyanobacteria/isolation & purification/genetics/growth & development
*Microalgae/isolation & purification/genetics/growth & development
Slovenia
Salinity
Metagenomics
Biotechnology
Biodiversity
Ecosystem

@article {pmid41591576,
year = {2026},
author = {Robayo, MIG and Armijo, JHC and Rosa, LH and Passarini, MRZ},
title = {Metagenomic analysis of the fungal community present in unimpacted and oil-impacted soil, South Shetland Islands, maritime Antarctica.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {2},
pages = {62},
pmid = {41591576},
issn = {1573-0972},
support = {440218/2023-3//CNPq PROANTAR/ ; PRPPG Nº 118/2024//Institutional Program to Support Research Groups/ ; CNPq 18/2024//National Council for Scientific and Technological Development/ ; },
mesh = {Antarctic Regions ; *Soil Microbiology ; *Fungi/classification/genetics/isolation & purification/metabolism ; *Metagenomics ; Islands ; Soil/chemistry ; Biodiversity ; Phylogeny ; *Mycobiome/genetics ; Nitrogen/analysis ; Ascomycota/genetics/classification/isolation & purification ; },
abstract = {We assessed the fungal diversity and functional profile of two soils collected in contrasting environments: one unimpacted soil, Hennequin Point, King George Island, and the other impacted by whale oil, Whalers Bay, Deception Island, Maritime Antarctica, using metagenomic approaches. Taxonomic assignment revealed a predominance of Ascomycota in both soils. A total of 20 and 23 fungal genera were identified at King George and Deception islands, respectively. The rare genera Thermothielavioides, Pyricularia, Fulvia, and Coccidioides were detected in the Antarctic environment. The highest fungal diversity was observed in the soil of Deception Island. Canonical analysis of King George Island soil displayed higher values of total organic carbon, sulfur, and lead, which may have favored the presence of the genera Puccinia, Lachancea, and Akanthomyces. The soil of Deception Island presented correlations with higher levels of nitrogen, chromium, and iron, with a predominance of genera such as Aspergillus, Trichoderma, and Malassezia. Functional analysis revealed distinct adaptive strategies among the soils. Domains related to translation, gene regulation, and metabolic efficiency were observed for fungi in Hennequin Point soil, King George Island, suggesting resource optimization in a cold, moss-covered environment. In Deception Island soil, fungal redox metabolism, iron acquisition, and the degradation of nitrogen compounds were highlighted, reflecting adaptation to an anthropogenic soil rich in metal oxides. Both soils exhibited functional fungal networks involved in hydrolytic enzymatic pathways that may act in the decomposition of organic compounds. New sequencing must be performed due to the insufficient depth of the data. Our results indicated that the soil from Hennequin Point and Whalers Bay exhibited distinct fungal communities, which can be influenced by environmental and ecological factors such as moss, oil, and heavy metals encountered in pristine and oil-impacted soils resulting from anthropogenic activities over the years.},
}

Antarctic Regions
*Soil Microbiology
*Fungi/classification/genetics/isolation & purification/metabolism
*Metagenomics
Islands
Soil/chemistry
Biodiversity
Phylogeny
*Mycobiome/genetics
Nitrogen/analysis
Ascomycota/genetics/classification/isolation & purification

@article {pmid41591867,
year = {2026},
author = {Petraro, S and Tarracchini, C and Mancabelli, L and Lugli, GA and Turroni, F and Ventura, M and Milani, C},
title = {Microbial BioRemediation Database: A Comprehensive Database of Genes Involved in Microbial Bioremediation Processes.},
journal = {MicrobiologyOpen},
volume = {15},
number = {1},
pages = {e70215},
doi = {10.1002/mbo3.70215},
pmid = {41591867},
issn = {2045-8827},
support = {//European Union, NextGeneration EU, PNRR-M4C2- I1.1, PRIN 2022 - Project Code 20229LEB99 - CUP Code D53D23014150006/ ; T5-AN-11//Piano di Sviluppo e Coesione of the Italian Ministry of Health 2014-2020/ ; },
mesh = {*Biodegradation, Environmental ; *Bacteria/genetics/metabolism/classification ; *Databases, Genetic ; *Environmental Pollutants/metabolism ; Metagenomics ; Biocuration ; Microbiota/genetics ; Metagenome ; },
abstract = {Environmental pollution from a wide range of compounds poses serious ecological and health risks. While bioremediation offers a promising solution, its application is limited by fragmented genomic resources and unsatisfactory understanding of microbial biodegradation pathways. Here, we developed the Microbial BioRemediation (MBR) database, freely accessible at https://probiogenomics.unipr.it/cmu, a comprehensive and manually curated repository comprising over 643,351 bacterial protein sequences associated with the degradation of 564 pollutant compounds across 25 chemical classes. Optimized for both genomic and metagenomic analyses, the Microbial BioRemediation database enables high-resolution functional and taxonomic profiling of microbial communities and individual bacterial strains. Validation using public genome and metagenome datasets from contaminated environments confirmed the database ability to detect both conserved and environment-specific biodegradation functions. Its application to host-associated microbiomes further confirmed the suitability of MBR for assessing how environmental exposures shape microbial catabolic potential across ecological contexts. The MBR database thus serves as a strategic tool for the early-stage identification and prioritization of microbial candidates for bioremediation. By enabling the in silico selection of key microbial taxa and enzymatic functions, it supports a rational pipeline that progresses toward targeted in vitro validation and experimental characterization. This integrative approach facilitates development of next-generation, tailored strategies for the remediation of complex polluted ecosystems.},
}

*Biodegradation, Environmental
*Bacteria/genetics/metabolism/classification
*Databases, Genetic
*Environmental Pollutants/metabolism
Metagenomics
Biocuration
Microbiota/genetics
Metagenome

@article {pmid41592403,
year = {2026},
author = {Zhang, B and Wang, M and Zheng, J and Yu, C and Wei, C and Ren, J and Sun, S and Wang, G and Wang, J and Lu, Y and Lin, L and Zhang, C},
title = {Strain-specific impacts of Pichia kudriavzevii on metabolite profiles and microbial community dynamics in Chinese Baijiu fermentation: Integrated metabolomics and metagenomics analysis.},
journal = {International journal of food microbiology},
volume = {450},
number = {},
pages = {111660},
doi = {10.1016/j.ijfoodmicro.2026.111660},
pmid = {41592403},
issn = {1879-3460},
mesh = {Fermentation ; *Pichia/metabolism/genetics/classification ; Metabolomics ; Metagenomics ; *Microbiota ; *Alcoholic Beverages/microbiology/analysis ; Metabolome ; Bacteria/genetics/classification/metabolism/isolation & purification ; Food Microbiology ; },
abstract = {Pichia kudriavzevii is a dominant yeast species in Chinese baijiu fermentation, yet its intraspecific diversity remains underexplored. This study used metabolomics and metagenomics analysis to investigate the impact of four distinct P. kudriavzevii strains (PK12, PK25, PK97, and PK360) on the metabolite profiles and microbial community structure in a controlled baijiu solid-state fermentation. Metabolomics analysis identified 49 key volatile compounds and 2792 non-volatile metabolites. Strain PK97 exhibited exceptional capacity for butanoic acid metabolism, inducing a 55.27-fold increase in butanoic acid and a 30.54-fold enhancement in ethyl butanoate production. Strain PK25 specialized in acetoin biosynthesis, while PK360 maximized 2-phenylethanol production. Metagenomic analysis uncovered that strains PK12, PK25, and PK360 promoted Lactobacillus acetotolerans population, increasing its relative abundance to 67.39%, 58.57%, and 71.79%, respectively. In contrast, strain PK97 orchestrated a dramatic ecological shift, elevating Enterobacter mori abundance from 0.56% to 17.60%, transforming the community from Lactobacillus-dominated to Enterobacteriaceae-enriched. Integration of metabolomic and metagenomic data revealed that strain PK97's promotion of Enterobacter mori correlated with significant upregulation of key enzymes including α-amylase (EC 3.2.1.1), enoyl-CoA hydratase (EC 4.2.1.17), and succinyl-CoA synthetase (EC 6.2.1.5), creating a metabolic environment favoring enhanced starch hydrolysis, altered TCA cycle flux, and butanoic acid accumulation. Strain PK25 specifically upregulated acetyl-CoA hydrolase (EC 3.1.2.1), facilitating acetic acid and acetoin formation. Strain PK360 enhanced glucose pyrophosphorylase (EC 2.7.7.9) and asparagine synthetase (EC 6.3.1.1) activities, accelerating galactose metabolism and amino acid transformations. These findings illustrate the impact of P. kudriavzevii intraspecific diversity on reshaping microbial ecology and flavor chemistry in Chinese baijiu, offering novel insights for targeted fermentation control and quality enhancement strategies in baijiu production.},
}

Fermentation
*Pichia/metabolism/genetics/classification
Metabolomics
Metagenomics
*Microbiota
*Alcoholic Beverages/microbiology/analysis
Metabolome
Bacteria/genetics/classification/metabolism/isolation & purification
Food Microbiology

@article {pmid41593363,
year = {2026},
author = {Sorensen, PO and Karaoz, U and Beller, HR and Bill, M and Bouskill, NJ and Banfied, JF and Chu, RK and Hoyt, DW and Eder, E and Eloe-Fadrosh, E and Sharrar, A and Tfaily, MM and Toyoda, J and Tolic, N and Wang, S and Wong, AR and Williams, KH and Zhong, Y and Brodie, EL},
title = {Multi-omics reveals nitrogen dynamics associated with soil microbial blooms during snowmelt.},
journal = {Nature microbiology},
volume = {11},
number = {2},
pages = {359-374},
pmid = {41593363},
issn = {2058-5276},
support = {DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; DE-AC05-76RL01830//U.S. Department of Energy (DOE)/ ; DBI-1315705//National Science Foundation (NSF)/ ; },
mesh = {*Bacteria/metabolism ; Biomass ; Bradyrhizobium/metabolism ; Climate Change ; Metagenome ; Microbiota ; Nitrogen/metabolism ; *Nitrogen Compounds/metabolism ; *Nitrogen Cycle ; *Seasons ; *Snow ; *Soil Microbiology ; Ecosystem ; Multiomics ; },
abstract = {Snowmelt triggers a soil microbial bloom and crash that affects nitrogen (N) export in high-elevation watersheds. The mechanisms underlying these microbial dynamics are uncertain, making soil nitrogen processes difficult to predict as snowpack declines globally. Here, integration of genome-resolved metagenomics, metatranscriptomics and metabolomics in a high-elevation watershed revealed ecologically distinct soil microorganisms linked across the snowmelt time-period by their unique nitrogen cycling capacities. The molecular properties and transformations of dissolved organic N suggested that degradation or recycling of microbial biomass provided N for biosynthesis during the microbial bloom. Winter-adapted Bradyrhizobia spp. oxidized amino acids anaerobically and had the highest gene expression for denitrification during the microbial bloom. A pulse of nitrate was driven by spring-adapted Nitrososphaerales after snowmelt, but dissimilatory nitrate reduction to ammonia (DNRA) gene expression indicated significant nitrate retention potential. These findings inform our understanding of nitrogen cycling in environments sensitive to snowpack decline due to global change.},
}

*Bacteria/metabolism
Biomass
Bradyrhizobium/metabolism
Climate Change
Metagenome
Microbiota
Nitrogen/metabolism
*Nitrogen Compounds/metabolism
*Nitrogen Cycle
*Seasons
*Snow
*Soil Microbiology
Ecosystem
Multiomics

@article {pmid41593438,
year = {2026},
author = {Wang, X and Tian, D and Han, B and Zhao, K and Hao, W and Du, K and Li, X and Duan, Z},
title = {Exploring the impact of rumen microbiome on ovine flavor-related compounds and comparing flavor profiles between Tibetan sheep and Small-tail Han sheep.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {41593438},
issn = {1471-2180},
support = {2024YFF0728800//National Key Research and Development Program of China/ ; 2024-ZJ-949//the Natural Science Foundation of Qinghai Province/ ; XDA26040305//the Strategic Priority Research Program of the Chinese Academy of Sciences/ ; },
mesh = {Animals ; *Rumen/microbiology ; *Microbiota ; Sheep/microbiology ; Fatty Acids, Volatile/analysis/metabolism ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Tibet ; Metagenomics ; Taste ; Meat/analysis ; Tandem Mass Spectrometry ; *Flavoring Agents/analysis ; Metagenome ; },
abstract = {The characteristic 'mutton flavor', primarily attributed to branched-chain fatty acids (BCFAs), is influenced by various factors including rumen microbes. This study aims to elucidate the disparities in meat flavor compounds and their underlying regulatory mechanisms mediated by rumen microbes between two important sheep breeds on the Qinghai-Tibetan Plateau. We used LC-MS/MS to analyze BCFAs and rumen short-chain fatty acids (SCFAs), along with metagenomic sequencing to characterize the rumen microbiome. Compared to Tibetan sheep, Small Tail Han sheep exhibited significantly higher concentrations of BCFAs, including 4-ethyloctanoic acid (EOA) and 4-methyloctanoic acid (MOA), as well as SCFAs such as pentanoate, glutarate, and propionate. In contrast, acetate levels were inversely correlated with these fatty acids. Metagenomics revealed a predominance of Bacteroidota (formerly Bacteroidetes) and Bacillota (formerly Firmicutes) in sheep. Furthermore, random forest and LEfSe analyses identified seven bacterial biomarkers, including Lactobacillus, Ligilactobacillus, Blautia, Anaerovibrio, Selenomonas, Phocaeicola, Sodaliphilus. Functional analysis indicated differences in carbohydrate degradation capabilities of two breeds. Likewise, strong positive correlations of propionate with MOA, and glutarate with EOA were observed, respectively. The findings are expected to provide critical insights into the potential for modulating meat flavor through nutritional strategies targeting rumen microbes.},
}

Animals
*Rumen/microbiology
*Microbiota
Sheep/microbiology
Fatty Acids, Volatile/analysis/metabolism
*Bacteria/classification/genetics/isolation & purification/metabolism
Tibet
Metagenomics
Taste
Meat/analysis
Tandem Mass Spectrometry
*Flavoring Agents/analysis
Metagenome

@article {pmid41593440,
year = {2026},
author = {Lv, J and Liu, R and Sun, Z and Zhang, J and Zhang, Y and Zhao, X and Liu, J and Zhou, X and Zhang, M and Liu, Q and Gao, F},
title = {Gut Microbiota as Neuroimmune Modulators in Myasthenia Gravis: Mechanistic Insights from the Gut-Brain Axis to Therapeutic Innovations.},
journal = {The American journal of Chinese medicine},
volume = {54},
number = {1},
pages = {65-85},
doi = {10.1142/S0192415X26500023},
pmid = {41593440},
issn = {1793-6853},
mesh = {Humans ; *Myasthenia Gravis/immunology/therapy/microbiology ; *Gastrointestinal Microbiome/immunology/physiology ; Animals ; *Brain/immunology ; Fecal Microbiota Transplantation ; *Neuroimmunomodulation ; Cytokines/metabolism ; Dysbiosis ; Probiotics ; },
abstract = {Myasthenia gravis (MG) is a chronic autoimmune disorder characterized by an immune-mediated attack on neuromuscular junction acetylcholine receptors (AChRs), and its pathogenesis is closely linked to immune dysregulation. Emerging evidence has highlighted the pivotal role of the gut microbiota in the pathophysiology of MG through immunomodulation, microbial metabolite signaling, and gut-brain axis interactions. This review combines 16S rRNA sequencing, metagenomic, and metabolomic data to reveal distinct gut microbial signatures in patients with MG. These signatures include reduced α-diversity, depletion of beneficial taxa like Bacteroides and Bifidobacterium, enrichment of pathobionts such as Escherichia and Enterococcus, and diminished levels of the short-chain fatty acids (SCFA), which were inversely correlated with disease severity. Experimental models have demonstrated that fecal microbiota transplantation (FMT) and probiotic supplementation with strains like Bifidobacterium ameliorate symptoms by restoring Th17/Treg equilibrium, suppressing the expression of pro-inflammatory cytokines including IL-6 and TNF-α, and enhancing intestinal barrier integrity. Mechanistically, gut dysbiosis exacerbates autoimmunity via NF-αB pathway activation, disrupts tryptophan metabolism and impairs gut-brain signaling. While existing studies have established microbiota-MG associations, further causal validation, personalized therapeutic strategies, and multi-omics integration remain critical priorities. Microbiota-targeted interventions, including precision FMT and metabolite delivery, hold translational potential, but their validation via large-scale randomized controlled trials and interdisciplinary approaches like AI-driven microbiota profiling is essential if they are to advance precision medicine for MG management.},
}

Humans
*Myasthenia Gravis/immunology/therapy/microbiology
*Gastrointestinal Microbiome/immunology/physiology
Animals
*Brain/immunology
Fecal Microbiota Transplantation
*Neuroimmunomodulation
Cytokines/metabolism
Dysbiosis
Probiotics

@article {pmid41593747,
year = {2026},
author = {Lin, L and Zheng, X and Tao, Y and Zhu, W and Guan, LL and Mao, S},
title = {Genome-resolved metagenomics uncovers diversity and functional landscapes of the gastrointestinal epithelium-associated microbiome in cattle.},
journal = {Genome biology},
volume = {27},
number = {1},
pages = {44},
pmid = {41593747},
issn = {1474-760X},
support = {U2202203//NSFC-Regional Innovation and Development Joint Fund/ ; 3236114378//NSFC-International (Regional) Cooperation Research and Exchange Programme/ ; },
mesh = {Animals ; *Metagenomics/methods ; Cattle/microbiology ; *Gastrointestinal Microbiome/genetics ; *Metagenome ; Rumen/microbiology ; Biodiversity ; },
abstract = {BACKGROUND: The ruminant gastrointestinal epithelium harbors a diverse and functionally critical remains poorly characterized microbial community due to persistent host-derived DNA contamination in metagenomic studies.

RESULTS: We develop Dilute-MetaSeq (dilution-based metagenomic sequencing), a novel, metagenomic workflow integrating gradient dilution with multiple displacement amplification. Dilute-MetaSeq reduces host DNA interference by 52.4-fold and achieves > 90% microbial sequencing efficiency to assess gastrointestinal epithelium-associated microbiome. This enables the construction of the microbial genome atlas of gastrointestinal epithelium (MGA-GE). This comprehensive resource, comprising 1,907 nonredundant prokaryotic and 5,603 viral genomes, reveals extraordinary microbial diversity and novelty, with 41.4% of prokaryotic and 99.9% of viral genomes representing taxonomically unclassified lineages. Spatial profiling identifies the rumen and reticulum as a biodiversity hotspot dominated by epithelium-adapted Butyrivibrio and methylotrophic Methanomassiliicoccales, while functional annotation uncovers 1,200 biosynthetic gene clusters (primarily RiPPs and NRPSs) and 1,212 viral auxiliary metabolic genes linked to host metabolism modulation. Pangenome analysis of 987 strains, including a novel Butyrivibrio clade with reduced genome sizes, elevated GC content, and butyrate synthesis from amino acid-derived substrates (e.g., glutarate, lysine), highlights metabolic adaptations to the nutrient-scarce epithelial niche compared to digesta-associated microbes.

CONCLUSIONS: Collectively, the MGA-GE provides transformative insights into host-microbe-virus interactions and establishes a foundation for developing microbiome-based intervention strategies to enhance ruminant health, agricultural productivity, and bioactive discovery.},
}

Animals
*Metagenomics/methods
Cattle/microbiology
*Gastrointestinal Microbiome/genetics
*Metagenome
Rumen/microbiology
Biodiversity

@article {pmid41594560,
year = {2025},
author = {Dissanayaka, DMS and Jayasinghe, TN and Sohrabi, HR and Rainey-Smith, SR and Taddei, K and Masters, CL and Martins, RN and Fernando, WMADB},
title = {Gut Microbial Composition and Short-Chain Fatty Acid Metabolism in Cognitively Unimpaired Adults Stratified by Amyloid-β Status.},
journal = {Biomolecules},
volume = {16},
number = {1},
pages = {},
pmid = {41594560},
issn = {2218-273X},
mesh = {Humans ; *Fatty Acids, Volatile/metabolism ; *Amyloid beta-Peptides/metabolism ; *Gastrointestinal Microbiome ; Female ; Aged ; Male ; Feces/microbiology/chemistry ; Alzheimer Disease/metabolism/microbiology ; Middle Aged ; },
abstract = {Short-chain fatty acids (SCFAs) produced by gut microbial fermentation influence host metabolism and neuroinflammatory processes implicated in Alzheimer's disease (AD). However, the relationship between fecal SCFAs, microbial taxa, and cerebral amyloid-β (Aβ) burden in cognitively unimpaired individuals remains unclear. Fecal SCFAs were quantified using GC-MS, and microbial species were profiled by shotgun metagenomics in 87 participants. Associations between SCFAs, demographics, APOE ε4 status, and Aβ burden were tested using nonparametric statistics and multivariable regression. Microbial-SCFA links were evaluated using Spearman correlations and multivariate ordinations, with mediation analysis exploring potential indirect pathways. Acetate was the predominant SCFA and demonstrated the most robust microbial associations. Higher acetate concentrations were positively associated with Bacteroides ovatus and Faecalibacterium prausnitzii, whereas lower acetate levels were linked to species such as Bifidobacterium animalis and Lachnoclostridium scindens. Stratified analyses indicated that individuals with elevated Aβ burden exhibited more pronounced species-SCFA relationships, including a notable association between Bacteroides thetaiotaomicron and butyrate. Multivariate ordination further identified a significant overall coupling between SCFA profiles and microbial community structure. Mediation analysis suggested that an Oscillospiraceae species may represent a potential intermediary linking valerate concentrations with Aβ status. SCFA concentrations were not strongly influenced by demographic or genetic factors, but specific species demonstrated robust associations with acetate levels. Distinct SCFA-microbial interaction patterns in Aβ High individuals suggest subtle early gut microbial alterations linked to amyloid burden. These findings highlight the potential role of SCFA-related microbial pathways in preclinical AD.},
}

Humans
*Fatty Acids, Volatile/metabolism
*Amyloid beta-Peptides/metabolism
*Gastrointestinal Microbiome
Female
Aged
Male
Feces/microbiology/chemistry
Alzheimer Disease/metabolism/microbiology
Middle Aged

@article {pmid41594879,
year = {2026},
author = {Han, H and Yang, Y and Zhu, X and Wangdwei, M and Yang, L},
title = {Age-Specific Composition and Predicted Function of Gut Microbiota in Plateau Pikas (Ochotona curzoniae).},
journal = {Biology},
volume = {15},
number = {2},
pages = {},
pmid = {41594879},
issn = {2079-7737},
support = {202401ZR0101//Natural Science Foundation of the Xizang Autonomous Region/ ; 2021-GSP-B015//High-level Personnel Training Program of Xizang University/ ; },
abstract = {Gut microbes play a crucial role in regulating physiological processes such as host energy metabolism, nutrient absorption, and environmental adaptation. The predicted functions of gut microbes can be influenced by many factors, both extrinsic and intrinsic to the hosts. The plateau pika is a key species in the alpine ecosystem of the Qinghai-Tibet Plateau. Previous research on the plateau pika primarily examined how extrinsic factors affected its gut microbiota. However, studies on intrinsic factors are scarce. Here, we used live-trapping to capture plateau pikas and collect cecum contents. Using metagenomic sequencing of cecum content samples, we characterized and compared the gut microbial composition and predicted function of plateau pika in adult (n = 9) and juvenile (n = 9) populations. The results indicated that Bacillota and Bacteroidete were the major bacterial phyla. The core gut microbial genera were the same, but the relative abundance of Oscillospira in juveniles was significantly lower than that in adults. The changes in the proportion of cellulose-degradation-related bacterial communities in juveniles suggest that they tend to choose low-fiber diets. In this study, we found no significant differences in the gut microbial composition and diversity, KEGG level 1 metabolic pathways, or CAZy class level between adult and juvenile plateau pikas. In total, the composition and predicted functions of cecal microorganisms in juvenile and adult male plateau pikas were not different. Regarding KEGG level 2 metabolic pathways, the juvenile group had a higher relative abundance of metabolic pathways for cofactors and vitamins, terpenoids, and polyketides, whereas the adult group had a higher relative abundance of energy metabolism. However, the resulting differences remain unclear. Therefore, future research should validate the above findings on a broader spatio-temporal scale and conduct cross-species comparisons to construct a microbial ecological framework for the health management of plateau wild animals.},
}

@article {pmid41595438,
year = {2025},
author = {Vougiouklaki, D and Letsiou, S and Ladias, K and Tsakni, A and Mavrokefalidou, I and Siateli, Z and Halvatsiotis, P and Houhoula, D},
title = {Lactobacillus-Dominated Cervical Microbiota Revealed by Long-Read 16S rRNA Sequencing: A Greek Pilot Study.},
journal = {Genes},
volume = {17},
number = {1},
pages = {},
pmid = {41595438},
issn = {2073-4425},
mesh = {Humans ; Female ; *RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; *Cervix Uteri/microbiology ; Greece ; Pilot Projects ; *Lactobacillus/genetics/classification/isolation & purification ; Vagina/microbiology ; Human Papillomavirus Viruses/genetics ; },
abstract = {Background/Objectives: The vaginal microbiota constitutes a highly dynamic microbial ecosystem shaped by the distinct mucosal, hormonal, and immunological environment of the female genital tract. Accumulating evidence suggests that shifts in cervical microbial composition and function may influence host-microbe interactions and contribute to gynecological disease risk. Within this framework, the present study aimed to perform an in-depth genomic characterization of the cervical microbiota in a well-defined cohort of Greek women. The primary objective was to explore the functional microbial landscape by identifying dominant bacterial taxa, taxon-specific signatures, and potential microbial pathways implicated in cervical epithelial homeostasis, immune modulation, and disease susceptibility. Methods: Microbial genomic DNA was isolated from 60 cervical samples using the Magcore Bacterial Automated Kit and analyzed through full-length 16S rRNA gene sequencing using the Nanopore MinION™ platform, allowing high-resolution taxonomic assignment and enhanced functional inference. In parallel, cervical samples were screened for 14 HPV genotypes using a real-time PCR-based assay. Results: The cervical microbial communities were dominated by Lactobacillus iners, Lactobacillus crispatus, and Aerococcus christensenii, collectively representing over 75% of total microbial abundance and suggesting a functionally protective microbiota profile. A diverse set of low-abundance taxa-including Stenotrophomonas maltophilia, Stenotrophomonas pavanii, Acinetobacter septicus, Rhizobium spp. (Rhizobium rhizogenes, Rhizobium tropici, Rhizobium jaguaris), Prevotella amnii, Prevotella disiens, Brevibacterium casei, Fannyhessea vaginae, and Gemelliphila asaccharolytica-was also detected, potentially reflecting niche-specific metabolic functions or environmental microbial inputs. No HPV genotypes were detected in any of the cervical samples. Conclusions: This genomic profiling study underscores the functional dominance of Lactobacillus spp. within the cervical microbiota and highlights the contribution of low-abundance taxa that may participate in metabolic cross-feeding, immune signaling, or epithelial barrier modulation. Future large-scale, multi-omics studies integrating metagenomics and host transcriptomic data are warranted to validate microbial functional signatures as biomarkers or therapeutic targets for cervical health optimization.},
}

Humans
Female
*RNA, Ribosomal, 16S/genetics
*Microbiota/genetics
*Cervix Uteri/microbiology
Greece
Pilot Projects
*Lactobacillus/genetics/classification/isolation & purification
Vagina/microbiology
Human Papillomavirus Viruses/genetics

@article {pmid41595535,
year = {2026},
author = {Ma, Y and Wang, L and Hu, H and Shieh, AR and Li, E and He, D and He, L and Liu, Z and Paing, TM and Chen, X and Cao, Y},
title = {Composition and Function of Gut Microbiome: From Basic Omics to Precision Medicine.},
journal = {Genes},
volume = {17},
number = {1},
pages = {},
pmid = {41595535},
issn = {2073-4425},
mesh = {Humans ; *Precision Medicine/methods ; Multiomics ; Animals ; *Gastrointestinal Microbiome/genetics/physiology ; Genomics ; Host Microbial Interactions ; },
abstract = {The gut microbiome is defined as the collective assembly of microbial communities inhabiting the gut, along with their genes and metabolic products. The gut microbiome systematically regulates host metabolism, immunity, and neuroendocrine homeostasis via interspecies interaction networks and inter-organ axes. Given the importance of the gut microbiome to the host, this review integrates the composition, function, and genetic basis of the gut microbiome with host genomics to provide a systematic overview of recent advances in microbiome-host interactions. This encompasses a complete technological pipeline spanning from in vitro to in vivo models to translational medicine. This technological pipeline spans from single-bacterium CRISPR editing, organoid-microbiome co-culture, and sterile/humanized animal models to multi-omics integrated algorithms, machine learning causal inference, and individualized probiotic design. It aims to transform microbiome associations into precision intervention strategies that can be targeted and predicted for clinical application through interdisciplinary research, thereby providing the cornerstone of a new generation of precision treatment strategies for cancer, metabolic, and neurodegenerative diseases.},
}

Humans
*Precision Medicine/methods
Multiomics
Animals
*Gastrointestinal Microbiome/genetics/physiology
Genomics
Host Microbial Interactions

@article {pmid41596486,
year = {2026},
author = {Sá, L and Machado, E and Ginani, V and Timbó, R and Romiti, R and Kurizky, P and Gomes, C},
title = {Species-Level Comparative Metagenomic Analysis of the Bacterial Abundance of the Gut Microbiome in Psoriasis, Hidradenitis Suppurativa, and Pemphigus Foliaceous Patients Using Shotgun Next-Generation Sequencing.},
journal = {International journal of molecular sciences},
volume = {27},
number = {2},
pages = {},
pmid = {41596486},
issn = {1422-0067},
support = {00193-00000279/2023-70//Fundação de Apoio à Pesquisa do Distrito Federal (FAP-DF)/ ; 445040/2023-8//National Council for Scientific and Technological Development/ ; 21/2023//Departamento de Ciência e Tecnologia, da Secretaria de Ciência, Tecnologia, Inovação e Com-plexo da Saúde, do Ministério da Saúde (Decit/SECTICS/MS)/ ; },
mesh = {Humans ; *Psoriasis/microbiology ; *Hidradenitis Suppurativa/microbiology ; Female ; Male ; Adult ; High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; *Pemphigus/microbiology ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; Middle Aged ; *Bacteria/genetics/classification ; Metagenome ; },
abstract = {Recent studies have revealed a specific relationship between gut bacteria and inflammatory skin profiles. We aimed to perform a species-level comparative metagenomic analysis of the gut microbiome in patients with psoriasis, hidradenitis suppurativa (HS), and pemphigus foliaceus (PF). We included omnivorous nonsmokers and nondrinkers with psoriasis (n = 24), HS (n = 10), and PF (n = 11), as well as healthy controls (n = 10). We collected faecal samples from all patients for classic parasitological analysis. Gut microbiome analysis was conducted using shotgun next-generation sequencing. We used the Deseq2, Limma_voom, LinDA, and MaAMaAsLin 2 bioinformatics tools to evaluate concordance and differential abundance between patients. Thirteen patients (23.64%) were diagnosed with active intestinal parasitosis. The presence of intestinal parasitosis was significantly related to immunosuppression (p = 0.009). The most abundant microorganism species found in the faeces of the patients evaluated was Escherichia coli. Psoriasis patients presented a greater abundance of bacteria from the Veillonellaceae family, whereas PF patients presented a greater abundance of Firmicutes bacteria. Patients with PF showed increased E. coli virulence and antibiotic resistance functional markers. Immunosuppression significantly influenced the presence of intestinal parasitosis as well as increased the virulence of functional markers in patients with PF receiving systemic corticosteroid therapy.},
}

Humans
*Psoriasis/microbiology
*Hidradenitis Suppurativa/microbiology
Female
Male
Adult
High-Throughput Nucleotide Sequencing/methods
*Metagenomics/methods
*Pemphigus/microbiology
*Gastrointestinal Microbiome/genetics
Feces/microbiology
Middle Aged
*Bacteria/genetics/classification
Metagenome

@article {pmid41596659,
year = {2026},
author = {Sánchez-Recillas, E and Almanza-Aguilera, E and Bars-Cortina, D and Zamora-Ros, R and Godínez-Santillán, RI and Sánchez-Tusié, AA and Vergara-Castañeda, HA},
title = {Effect of Garambullo (Myrtillocactus geometrizans) Consumption on the Intestinal Microbiota Profile in an Early-Phase Rat Model of Colon Cancer.},
journal = {International journal of molecular sciences},
volume = {27},
number = {2},
pages = {},
pmid = {41596659},
issn = {1422-0067},
support = {1560335//Secretaría de Ciencia, Humanidades, Tecnología e Innovación/ ; FME202404//Autonomous University of Queretaro - FONFIVE/ ; },
mesh = {Animals ; *Colonic Neoplasms/microbiology/chemically induced ; Male ; *Gastrointestinal Microbiome/drug effects ; Rats ; Rats, Sprague-Dawley ; Azoxymethane ; Disease Models, Animal ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; Dextran Sulfate ; *Plant Extracts/pharmacology ; Bacteria/genetics/classification ; },
abstract = {Bioactive compounds in food contribute to reducing the risk of developing colon cancer by modulating the gut microbiota. We have recently demonstrated that garambullo (Myrtillocactus geometrizans), an endemic fruit of Mexico rich in bioactive compounds, attenuates aberrant crypt foci in an animal model. However, its potential to modulate the gut microbiota is unknown. The main objective of this study was to evaluate whether its consumption modulates colon carcinogenesis by altering the microbiota in an in vivo model induced by azoxymethane and dextran sulfate sodium (AOM/DSS). Fecal samples were collected from twelve male Sprague-Dawley rats and analyzed for microbiota composition after 0, 8, and 16 weeks of treatment with saline (control), AOM/DSS, garambullo (G), or residue of garambullo (RG) with AOM/DSS (G+AOM/DSS and RG+AOM/DSS, respectively). Characterization of the microbiome was based on the conserved region of the 16S rRNA V3-V4 gene, and analyzed by the ZymoBIOMICS' Targeted Metagenomics Sequencing (Zymo Research) service. In an animal model induced with AOM/DSS for 8 weeks, consumption of G and its residue increased the bacterial genera Shuttleworthiia, Subdoligranulum, Lactobacillus, Faecalibacterium, and Alloprevotella (p < 0.05). Consumption of G and its residue allowed the proliferation of bacteria that produce short-chain fatty acids and are associated with protective mechanisms of the colon.},
}

Animals
*Colonic Neoplasms/microbiology/chemically induced
Male
*Gastrointestinal Microbiome/drug effects
Rats
Rats, Sprague-Dawley
Azoxymethane
Disease Models, Animal
RNA, Ribosomal, 16S/genetics
Feces/microbiology
Dextran Sulfate
*Plant Extracts/pharmacology
Bacteria/genetics/classification

@article {pmid41597216,
year = {2026},
author = {Mamun, MAA and Rakib, A and Mandal, M and Li, W and Miller, DD and Chen, H and Nagarkatti, M and Nagarkatti, P and Singh, UP},
title = {VERU-111 Promotes an Anti-Tumor Response Through Restoration of Gut Microbial Homeostasis and Associated Metabolic Dysregulation.},
journal = {Cells},
volume = {15},
number = {2},
pages = {},
pmid = {41597216},
issn = {2073-4409},
support = {AI140405//National Institute of Allergy and Infectious Diseases/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Homeostasis/drug effects ; Mice ; *Colorectal Neoplasms/drug therapy/microbiology/metabolism ; RNA, Ribosomal, 16S/genetics ; *Antineoplastic Agents/pharmacology ; Dextran Sulfate ; Mice, Inbred C57BL ; Azoxymethane ; Male ; },
abstract = {The rising global burden of colorectal cancer (CRC) has now positioned it as the third most common cancer worldwide. Chemotherapy regimens are known to disrupt the composition of the gut microbiota and lead to long-term health consequences for cancer patients. However, the alteration of gut microbiota by specific chemotherapeutic agents has been insufficiently explored until now. The purpose of this study was to assess changes in the gut microbiota following treatment with VERU-111 as a chemotherapy agent for the treatment of CRC. We thus performed a metagenomic study using 16S rRNA gene amplicon sequencing of fecal samples from different experimental groups in the azoxymethane (AOM) and dextran sodium sulfate (DSS)-induced murine model of CRC. To predict the functional potential of microbial communities, we used the resulting 16S rRNA gene sequencing data to perform Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. We found that the administration of VERU-111 led to a restructured microbial community that was characterized by increased alpha and beta diversity. Compared to the mice treated with DSS alone, VERU-111 treatment significantly increased the relative abundance of several bacterial species, including Verrucomicrobiota species, Muribaculum intestinale, Alistipes finegoldii, Turicibacter, and the well-known gut-protective bacterial species Akkermansia muciniphila. The relative abundance of Ruminococcus, which is negatively correlated with immune checkpoint blockade therapy, was diminished following VERU-111 administration. Overall, this metagenomic study suggests that the microbial shift after administration of VERU-111 is associated with suppression of several metabolic and cancer-related pathways that might, at least in part, facilitate the suppression of CRC. These favorable shifts in gut microbiota suggest a novel therapeutic dimension of using VERU-111 to treat CRC and emphasize the need for further mechanistic exploration.},
}

Animals
*Gastrointestinal Microbiome/drug effects
*Homeostasis/drug effects
Mice
*Colorectal Neoplasms/drug therapy/microbiology/metabolism
RNA, Ribosomal, 16S/genetics
*Antineoplastic Agents/pharmacology
Dextran Sulfate
Mice, Inbred C57BL
Azoxymethane
Male

@article {pmid41597231,
year = {2026},
author = {Feng, Y and Geng, Y and Liu, S and Huang, X and Mou, C and Zhao, H and Zhou, J and Li, Q and Deng, Y},
title = {Overwinter Syndrome in Grass Carp (Ctenopharyngodon idellus) Links Enteric Viral Proliferation to Mucosal Disruption via Multiomics Investigation.},
journal = {Cells},
volume = {15},
number = {2},
pages = {},
pmid = {41597231},
issn = {2073-4409},
support = {2024YFD2401102//National Key R&D ProgramNational Key R&D Program/ ; 2025ZNSFSC1081//Sichuan Provincial Natural Science Foundation/ ; NKYRCZX2025031//Research Initiation Funding from the Sichuan Academy of Agricultural Sciences/ ; SCCXTD-2025-15//Sichuan Freshwater Fish Innovation Team of the National Modern Agricultural Industrial Technology System/ ; },
mesh = {Animals ; *Carps/virology/microbiology/genetics ; Multiomics ; *Intestinal Mucosa/virology/pathology ; *Fish Diseases/virology/microbiology ; Gastrointestinal Microbiome ; *Virus Replication ; },
abstract = {Overwinter Syndrome (OWS) affects grass carp (Ctenopharyngodon idellus) aquaculture in China, causing high mortality and economic losses under low temperatures. Failure of antibiotic therapies shows limits of the 'low-temperature-pathogen' model and shifts focus to mucosal barrier dysfunction and host-microbiome interactions in OWS. We compared healthy and diseased grass carp collected from the same pond using histopathology, transcriptomics, proteomics, and metagenomics. This integrated approach was used to characterize intestinal structure, microbial composition, and host molecular responses at both taxonomic and functional levels. Results revealed a three-layer barrier failure in OWS fish: the physical barrier was compromised, with structural damage and reduced mucosal index; microbial dysbiosis featured increased richness without changes in diversity or evenness, and expansion of the virobiota, notably uncultured Caudovirales phage; and mucosal immune dysregulation indicated loss of local immune balance. Multi-omics integration identified downregulation of lysosome-related and glycosphingolipid biosynthesis pathways at transcript and protein levels, with disrupted nucleotide metabolism. Overall gut microbial richness, rather than individual taxa abundance, correlated most strongly with host gene changes linked to immunity, metabolism, and epithelial integrity. Although biological replicates were limited by natural outbreak sampling, matched high-depth multi-omics datasets provide exploratory insights into OWS-associated intestinal dysfunction. In summary, OWS entails a cold-triggered breakdown of intestinal barrier integrity and immune homeostasis. This breakdown is driven by a global restructuring of the gut microbiome, which is marked by increased richness, viral expansion, and functional shifts, ultimately resulting in altered host-microbe crosstalk. This ecological perspective informs future mechanistic and applied studies for disease prevention.},
}

Animals
*Carps/virology/microbiology/genetics
Multiomics
*Intestinal Mucosa/virology/pathology
*Fish Diseases/virology/microbiology
Gastrointestinal Microbiome
*Virus Replication

@article {pmid41597665,
year = {2026},
author = {Khachatryan, A and Vardanyan, A and Zhang, R and Zhang, Y and Shi, X and Willscher, S and Nguyen, NHA and Vardanyan, N},
title = {Metagenome Insights into Armenian Acid Mine Drainage: A Novel Thermoacidophilic Iron-Oxidizing Bacterium with Perspectives for Copper Bioleaching.},
journal = {Microorganisms},
volume = {14},
number = {1},
pages = {},
pmid = {41597665},
issn = {2076-2607},
support = {22rl-031//Higher Education Science Committee of Armenia/ ; 23-YSIP-012//Higher Education Science Committee of Armenia/ ; },
abstract = {The microbial ecology of acid mine drainage (AMD) systems in Armenia, with a long mining history, remains unexplored. This study aimed to characterize the microbial diversity and functional potential of AMD in the Syunik region and to isolate novel microorganisms with biotechnological value. A comprehensive analysis of the microbial communities' structure of Kavart abandoned, Kapan exploring mines effluent, and Artsvanik tailing was conducted. Metagenomics revealed bacterial-dominated communities, comprising Pseudomonadota (previously "Proteobacteria") (68-72%), with site-specific variations in genus abundance. A high abundance and diversity of metal resistance genes (MRGs), particularly for copper and arsenic, were identified. Carbohydrate-active enzyme (CAZy) analysis showed a dominance of GT2 and GT4 genes, suggesting a high potential for extracellular polymeric substances (EPS) production and biofilm formation. A novel strain of iron-oxidizing bacteria Arm-12 was isolated that shares only ~90% similarity with known Leptospirillum type species, indicating it may represent a new genus without culturable representatives. The strain exhibits enhanced copper extraction from concentrate. This study provides the first metagenomic insights into Armenian AMD systems and tailing, revealing a unique community rich in metal resistance and biofilm-forming genes. The isolation of a novel highly effective iron-oxidizer Arm-12 highlights the potential of AMD environments as a source of novel taxa with significant applications in biomining and bioremediation processes.},
}

@article {pmid41599039,
year = {2026},
author = {Wang, Z and Chen, G and Yang, M and Wang, S and Fang, J and Shi, C and Gu, Y and Ning, Z},
title = {Host-Filtered Blood Nucleic Acids for Pathogen Detection: Shared Background, Sparse Signal, and Methodological Limits.},
journal = {Pathogens (Basel, Switzerland)},
volume = {15},
number = {1},
pages = {},
pmid = {41599039},
issn = {2076-0817},
support = {2024-PWXZ-04//New Quality Clinical Specialty Program of High-end Medical Disciplinary Construction in Shanghai Pudong New Area/ ; 2024ZDXK0019//Shanghai Municipal Health Commission, Key Discipline of Shanghai Health System, Cardiology/ ; PW2025D-01//The Scientific Research Program of Shanghai Pudong New Area Health Commission (the Joint Research and Development Program)/ ; },
mesh = {Humans ; Microbiota ; *Cell-Free Nucleic Acids/blood/genetics ; *Metagenomics/methods ; Coronary Artery Disease/microbiology/blood/diagnosis ; *Tuberculosis/diagnosis/microbiology/blood ; },
abstract = {Plasma cell-free RNA (cfRNA) metagenomics is increasingly explored for blood-based pathogen detection, but the structure of the shared background "blood microbiome", the reproducibility of reported signals, and the practical limits of this approach remain unclear. We performed a critical re-analysis and benchmarking ("stress test") of host-filtered blood RNA sequencing data from two cohorts: a bacteriologically confirmed tuberculosis (TB) cohort (n = 51) previously used only to derive host cfRNA signatures, and a coronary artery disease (CAD) cohort (n = 16) previously reported to show a CAD-shifted "blood microbiome" enriched for periodontal taxa. Both datasets were processed with a unified pipeline combining stringent human read removal and taxonomic profiling using the latest versions of specialized tools Kraken2 and MetaPhlAn4. Across both cohorts, only a minority of non-host reads were classifiable; under strict host filtering, classified non-host reads comprised 7.3% (5.0-12.0%) in CAD and 21.8% (5.4-31.5%) in TB, still representing only a small fraction of total cfRNA. Classified non-host communities were dominated by recurrent, low-abundance taxa from skin, oral, and environmental lineages, forming a largely shared, low-complexity background in both TB and CAD. Background-derived bacterial signatures showed only modest separation between disease and control groups, with wide intra-group variability. Mycobacterium tuberculosis-assigned reads were detectable in many TB-positive samples but accounted for ≤0.001% of total cfRNA and occurred at similar orders of magnitude in a subset of TB-negative samples, precluding robust discrimination. Phylogeny-aware visualization confirmed that visually "enriched" taxa in TB-positive plasma arose mainly from background-associated clades rather than a distinct pathogen-specific cluster. Collectively, these findings provide a quantitative benchmark of the background-dominated regime and practical limits of plasma cfRNA metagenomics for pathogen detection, highlighting that practical performance is constrained more by a shared, low-complexity background and sparse pathogen-derived fragments than by large disease-specific shifts, underscoring the need for transparent host filtering, explicit background modeling, and integration with targeted or orthogonal assays.},
}

Humans
Microbiota
*Cell-Free Nucleic Acids/blood/genetics
*Metagenomics/methods
Coronary Artery Disease/microbiology/blood/diagnosis
*Tuberculosis/diagnosis/microbiology/blood

@article {pmid41599943,
year = {2026},
author = {Rocha, HR and Ribeiro, P and Rodrigues, PM and Gomes, AM and Pintado, M and Coelho, MC},
title = {Bioinformatic Insights into the Carotenoids' Role in Gut Microbiota Dynamics.},
journal = {Nutrients},
volume = {18},
number = {2},
pages = {},
pmid = {41599943},
issn = {2072-6643},
mesh = {*Carotenoids/pharmacology/chemistry ; *Computational Biology ; *Gastrointestinal Microbiome/drug effects ; Fermentation ; Humans ; Antioxidants/pharmacology ; Lutein/pharmacology ; Lycopene/pharmacology ; *Bacteria/classification/drug effects/metabolism ; beta Carotene/pharmacology ; },
abstract = {Background/Objectives: Carotenoids are bioactive pigments with well-established antioxidant and immunomodulatory properties, yet their impact on gut microbiota remains poorly understood from a chemical standpoint. This study explores how carotenoid structure and gastrointestinal stability shape microbial responses combining in vitro fermentation with bioinformatic analyses. Methods: Individual carotenoids (beta (β)-carotene, lutein, lycopene) and combined carotenoids, as well as algal-derived extracts were subjected to 48 h in vitro fermentation, and microbial composition and activity were assessed through sequencing and computational analysis. Results: β-carotene and lycopene promoted acid-tolerant taxa such as Escherichia-Shigella, whereas lutein, due to its higher polarity, supported more transient fluctuations. Mixtures and algal carotenoids exhibited synergistic effects, sustaining beneficial genera including Bifidobacterium and Bacteroides and promoting structured ecological trajectories. Conclusions: These findings provide a chemistry-driven perspective on how carotenoids act as modulators of microbial ecosystems, with direct implications for the formulation of carotenoid-enriched functional foods and dietary interventions.},
}

*Carotenoids/pharmacology/chemistry
*Computational Biology
*Gastrointestinal Microbiome/drug effects
Fermentation
Humans
Antioxidants/pharmacology
Lutein/pharmacology
Lycopene/pharmacology
*Bacteria/classification/drug effects/metabolism
beta Carotene/pharmacology

@article {pmid41601218,
year = {2025},
author = {Li, CT},
title = {[Applications and challenges of forensic microbiomics].},
journal = {Fa yi xue za zhi},
volume = {41},
number = {5},
pages = {441-442},
doi = {10.12116/j.issn.1004-5619.2025.551105},
pmid = {41601218},
issn = {1004-5619},
mesh = {Humans ; *Metagenomics/methods ; *Microbiota/genetics ; *Forensic Medicine/methods ; *Gastrointestinal Microbiome ; China ; Genomics ; Human Genome Project ; *Forensic Sciences ; Metagenome ; },
}

Humans
*Metagenomics/methods
*Microbiota/genetics
*Forensic Medicine/methods
*Gastrointestinal Microbiome
China
Genomics
Human Genome Project
*Forensic Sciences
Metagenome

@article {pmid41602101,
year = {2025},
author = {Deng, Q and Liu, Y and Zhang, J and Zhang, H and Zhang, Y and Wang, M and Jia, M and Ding, D and Fang, Y and Wang, Y and Gu, H and Wang, H},
title = {Clinical validation and utility of targeted nanopore sequencing for rapid pathogen diagnosis and precision therapy in lung cancer patients with pulmonary infections.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1730098},
pmid = {41602101},
issn = {2235-2988},
mesh = {Humans ; *Lung Neoplasms/complications/microbiology ; Female ; *Nanopore Sequencing/methods ; Aged ; Male ; Sputum/microbiology ; Middle Aged ; *Respiratory Tract Infections/diagnosis/microbiology/drug therapy ; High-Throughput Nucleotide Sequencing ; Microbiota ; *Precision Medicine/methods ; Metagenomics ; Sensitivity and Specificity ; Bacteria/genetics/classification/isolation & purification ; Aged, 80 and over ; },
abstract = {BACKGROUND: Pulmonary infections are common in patients with lung cancer (LC), complicating diagnosis and treatment. This study explored the diagnostic performance and clinical utility of targeted nanopore sequencing (TNPseq) for detecting pathogens in LC-related pulmonary infections.

METHODS: A total of 143 patients with LC or benign pulmonary diseases complicated by pulmonary infections were included and stratified into diagnostic and therapeutic cohorts. Sputum samples underwent conventional culture, metagenomic next-generation sequencing (mNGS), and TNPseq analyses. Microbiota profiles were compared across disease groups and correlated with tumor therapy responses. In the therapeutic cohort, clinical outcomes were assessed between empirical therapy and TNPseq-guided therapy.

RESULTS: TNPseq identified a significantly higher proportion of clinically relevant pathogens compared to mNGS (48.76% vs. 16.80%, p < 0.001) and demonstrated superior sensitivity (81.25% vs. 68.75%), with a 40.7% reduction in turnaround time (16 hours vs. 27 hours). Both sequencing methods revealed an enrichment of Lactobacillus species in non-initial diagnosis lung cancer (NDLC) patients (p < 0.01). Patients exhibiting partial response or stable disease (PR/SD) showed increased abundance of Neisseria, Veillonella, and Prevotella species (p < 0.05). Clinical remission was achieved in all patients; however, 68.4% of those initially receiving empirical therapy subsequently required a switch to TNPseq-guided treatment due to its ineffectiveness. Compared to this empirical-to-TNPseq group, the median treatment duration was significantly shorter under direct TNPseq guidance (total: 6 days vs. 13 days, p < 0.01; LC subgroup: 5 days vs. 15.5 days, p < 0.05), thereby reducing unnecessary antibiotic exposure.

CONCLUSIONS: By enabling rapid pathogen detection and profiling of the pulmonary microbiome, TNPseq facilitates targeted therapy and reduces antibiotic overuse in LC patients. These findings highlight the potential of TNPseq as a promising, rapid, and non-invasive diagnostic candidate for first-line use, offering a comprehensive view of both infection and host-microbe interactions in immunocompromised patients.},
}

Humans
*Lung Neoplasms/complications/microbiology
Female
*Nanopore Sequencing/methods
Aged
Male
Sputum/microbiology
Middle Aged
*Respiratory Tract Infections/diagnosis/microbiology/drug therapy
High-Throughput Nucleotide Sequencing
Microbiota
*Precision Medicine/methods
Metagenomics
Sensitivity and Specificity
Bacteria/genetics/classification/isolation & purification
Aged, 80 and over

@article {pmid41602774,
year = {2025},
author = {Zhang, M and Zhu, Y and Sun, Z and Wang, B and Chen, J and Zhou, F and Zeng, J and Li, M and Zou, D and Jiang, Z},
title = {Correction: Chemoautotrophic Thermodesulfobacteriota as a key genomic potential group in the hypoxic diazotrophic community of the Changjiang (Yangtze River) estuary.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1766907},
doi = {10.3389/fmicb.2025.1766907},
pmid = {41602774},
issn = {1664-302X},
abstract = {[This corrects the article DOI: 10.3389/fmicb.2025.1671267.].},
}

@article {pmid41603333,
year = {2026},
author = {Tiwari, P and Gupta, A and Kaushik, M and Dwivedi, R and Tripathi, M and Dada, R},
title = {Association of yoga with cognitive and gut microbiome changes in Alzheimer's disease: An exploratory case-control study.},
journal = {Journal of Alzheimer's disease : JAD},
volume = {110},
number = {2},
pages = {562-575},
doi = {10.1177/13872877261415612},
pmid = {41603333},
issn = {1875-8908},
mesh = {Humans ; *Yoga/psychology ; *Alzheimer Disease/psychology/microbiology/therapy ; Male ; Female ; *Gastrointestinal Microbiome/physiology ; Case-Control Studies ; *Cognition/physiology ; Aged ; Depression/psychology ; Middle Aged ; },
abstract = {BackgroundAlzheimer's disease (AD) is marked by cognitive decline, depressive symptoms, and gut microbial dysbiosis. Yoga may support cognitive and emotional health while modulating gut microbiota, but integrative clinical evidence is limited.ObjectiveTo evaluate the effects of a 12-week yoga intervention on cognition, depressive symptoms, and gut microbial diversity, composition, and function in Indian patients with mild AD.MethodsIn this hospital-based case-control study, 16 AD patients and 17 cognitively healthy controls (HCs) were recruited at AIIMS, New Delhi. AD diagnosis followed NIA-AA criteria, supported by Montreal Cognitive Assessment (MoCA) and Patient Health Questionnaire-9 (PHQ-9) assessments. AD participants underwent 60-min supervised yoga sessions daily for 12 weeks. Cognitive performance, depressive symptoms, and stool microbiota were assessed pre- and post-intervention. Metagenomic sequencing enabled taxonomic and functional profiling, with alpha diversity, beta diversity (Bray-Curtis distance), and differential abundance analyses performed using standard bioinformatics tools.ResultsYoga was associated with improved cognition (MoCA: 22.33 ± 2.34 → 25.44 ± 2.01; p = 0.001) and reduced depressive symptoms (PHQ-9: 5.78 ± 3.11 → 2.22 ± 1.71; p = 0.007). Alpha diversity remained stable, while beta diversity shifted post-yoga AD samples toward the HC cluster. Beneficial taxa (Faecalibacterium prausnitzii, Roseburia intestinalis, Bifidobacterium, Akkermansia) increased, whereas pro-inflammatory taxa (Collinsella aerofaciens, Klebsiella spp.) decreased. Functional analysis showed partial recovery of metabolic and short-chain fatty acid pathways.ConclusionsA 12-week yoga intervention was associated with cognitive and mood improvements and partial normalization of gut microbial function in mild AD. Larger randomized trials with lifestyle monitoring and multi-omics integration are warranted to confirm causal mechanisms.},
}

Humans
*Yoga/psychology
*Alzheimer Disease/psychology/microbiology/therapy
Male
Female
*Gastrointestinal Microbiome/physiology
Case-Control Studies
*Cognition/physiology
Aged
Depression/psychology
Middle Aged

@article {pmid41604303,
year = {2026},
author = {Guo, Z and Cheng, H and Shi, H and Liu, D and Zhai, X and Li, X and Zhang, X and Liu, L and Zhang, XH and Zhang, Y},
title = {Potential for microbial methanethiol-dependent dimethylsulfide production in different marine sediments.},
journal = {Cell reports},
volume = {45},
number = {2},
pages = {116891},
doi = {10.1016/j.celrep.2025.116891},
pmid = {41604303},
issn = {2211-1247},
mesh = {*Geologic Sediments/microbiology ; *Sulfides/metabolism ; *Sulfhydryl Compounds/metabolism ; Hydrogen Sulfide/metabolism ; *Bacteria/metabolism/genetics ; Phylogeny ; },
abstract = {Dimethyl sulfide (DMS) plays a pivotal role in sulfur cycling and climate regulation. This study investigates microbial DMS production via the methylation of hydrogen sulfide (H2S) and methanethiol (MeSH) in nearshore, pelagic deep-sea, and cold-seep sediments using culture-dependent and -independent methods. DMS production is detected in all sediments with exogenous MeSH addition. High mdd abundance is found in pelagic deep-sea sediments (24.55%-26.73%) from the Kuroshio-Oyashio Extension region, as well as in the nearshore sediments (25.78%). Metagenomic analyses reveal previously unrecognized Mdd-encoding taxa, such as Polyangia, and eight Bacteroidota and Bacillota isolates may possess unknown Mdd enzymes. Importantly, a widespread alternative pathway that converts H2S to MeSH is identified, representing a significant source of MeSH. These findings reveal a prevalent and diverse microbial pathway for DMS production in marine sediments, underscoring the need for further investigation to discover Mdd[+] microbial contributors.},
}

*Geologic Sediments/microbiology
*Sulfides/metabolism
*Sulfhydryl Compounds/metabolism
Hydrogen Sulfide/metabolism
*Bacteria/metabolism/genetics
Phylogeny

@article {pmid41605932,
year = {2026},
author = {Raethong, N and Patumcharoenpol, P and Vongsangnak, W},
title = {Modeling diet-gut microbiome interactions and prebiotic responses in Thai adults.},
journal = {NPJ biofilms and microbiomes},
volume = {12},
number = {1},
pages = {},
pmid = {41605932},
issn = {2055-5008},
support = {N42A660907//National Research Council of Thailand/ ; },
mesh = {Humans ; Thailand ; *Prebiotics/administration & dosage ; *Diet ; *Gastrointestinal Microbiome ; Adult ; Fatty Acids, Volatile/metabolism ; Metagenomics ; Systems Biology ; *Bacteria/classification/metabolism/genetics ; },
abstract = {The impact of diet on gut microbial metabolism is essential for advancing microbiome-based health interventions. This study introduces a novel systems biology pipeline that integrates genome-scale metabolic models (GSMMs) with Thai dietary intake data to simulate gut microbiome metabolism and assess prebiotic responses. Utilizing metagenomic data from healthy Thai adults and an average Thai diet derived from national surveys, community-scale metabolic models (CSMMs) were developed and simulated under both typical dietary and prebiotic-supplemented condition. Flux variability analysis was employed to assess metabolic capacities, short-chain fatty acids (SCFAs) production in relation to microbial taxonomy. The results promisingly revealed inter-individual variability in SCFA profiles, with Bacteroides and Phocaeicola notably linked to isobutyrate production and Bifidobacterium emerged as a key responder to prebiotic supplementation. This integrative framework offers biological insights into diet-gut microbiome interactions and provides a foundation for the development of precision nutrition strategies tailored to the Thai population.},
}

Humans
Thailand
*Prebiotics/administration & dosage
*Diet
*Gastrointestinal Microbiome
Adult
Fatty Acids, Volatile/metabolism
Metagenomics
Systems Biology
*Bacteria/classification/metabolism/genetics

@article {pmid41606218,
year = {2026},
author = {Abdelhameed, A and Hussein, RH and Hatem, ZA and Bağcı, C and Ziemert, N},
title = {From niche to niche: investigating microbial communities and their specialised metabolite gene clusters in human microbiomes.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {2},
pages = {65},
pmid = {41606218},
issn = {1573-0972},
mesh = {Humans ; *Microbiota/genetics ; *Multigene Family ; Metagenomics ; *Bacteria/genetics/classification/metabolism/isolation & purification ; Biosynthetic Pathways/genetics ; Metagenome ; Skin Microbiome ; Phylogeny ; },
abstract = {Diverse microbial communities within the human microbiome perform vital functions which influence both health and disease in hosts. Specialized metabolites produced by microbes via biosynthetic gene clusters (BGCs) drive ecological interactions and offer possibilities for therapeutic application. The biosynthetic capabilities of microorganisms present in human microbiomes are still mostly unexplored despite metagenomics advancements. The study examines the variety of microbial communities and BGC locations through metagenomic data from 1,191 samples across eight human microbiomes taken from the IMG/M database. Kraken2 executed taxonomic classification while antiSMASH v6.1.1 identified BGCs. The study used BiG-SCAPE to build a sequence similarity network while Bracken and Pavian tools analyzed microbial diversity. A total of 25,681 BGCs were identified, of which 97.5%, showed no significant match to existing clusters in MIBIG database, indicating substantial potential for novel biosynthetic discoveries . Showing no match to existing clusters in the MIBiG database which shows huge potential for new biosynthetic discoveries. New strains were discovered that produce unique RiPPs, NRPs, and siderophores primarily within the microbiomes of the large intestine, oral cavity, and skin. The large intestine showed maximum microbial and biosynthetic diversity compared to other areas while the biliary tract and nasal cavity displayed minimal diversity. New BGCs associated with antibiotic, cytotoxic, and immune-modulating functions present potential therapeutic uses. The investigation uncovers essential information about how microbial communities develop specific functions within various body regions. Uncharacterized BGC discoveries present new opportunities for drug development and treatments that target microbiomes.},
}

Humans
*Microbiota/genetics
*Multigene Family
Metagenomics
*Bacteria/genetics/classification/metabolism/isolation & purification
Biosynthetic Pathways/genetics
Metagenome
Skin Microbiome
Phylogeny

@article {pmid41606854,
year = {2025},
author = {Okoye, CO and Abhadiomhen, SE and Ezenwanne, BC and Chen, X and Jiang, H and Wu, Y and Jiang, J},
title = {Machine learning-based predictive modeling of foodborne pathogens and antimicrobial resistance in food microbiomes using omics techniques: A systematic review.},
journal = {Food research international (Ottawa, Ont.)},
volume = {221},
number = {Pt 1},
pages = {117255},
doi = {10.1016/j.foodres.2025.117255},
pmid = {41606854},
issn = {1873-7145},
mesh = {*Machine Learning ; *Food Microbiology ; *Foodborne Diseases/microbiology ; *Microbiota ; *Drug Resistance, Bacterial/genetics ; Animals ; Genomics/methods ; Metagenomics ; Salmonella/pathogenicity/genetics ; Food Safety ; Humans ; },
abstract = {The globalization of food systems has heightened the risk of foodborne pathogens such as Salmonella, Listeria monocytogenes, and Campylobacter, exacerbated by rising antimicrobial resistance (AMR). Traditional pathogen identification and AMR risk surveillance methods are often labor-intensive and low-throughput, while single-omics approaches fail to capture microbial complexity. Moreover, reliance on individual machine learning (ML) models limits predictive robustness, posing challenges to food safety and public health. This systematic review evaluates ML-based predictive modeling integrated with omics techniques (genomics, metagenomics, and transcriptomics) for foodborne pathogen and AMR risk surveillance. Following PRISMA guidelines, 1245 articles from PubMed, Scopus, and other databases (2015-2025) were screened, selecting 13 relevant studies. These studies applied ML algorithms, including Random Forest (RF), Extreme Gradient Boosting (XGBoost), and Support Vector Machines (SVM), to enhance predictive accuracy. The selected studies demonstrated predictive accuracies up to 99 % and AUROC scores above 0.90. Key discoveries include genetic markers for Salmonella virulence, Listeria attribution to fruits and dairy, and 145 mobile antimicrobial resistance genes (ARGs) in poultry. Despite these advancements, limitations such as small sample sizes, inconsistent metadata, overfitting, and computational scalability hinder real-world implementation. This review underscores the potential of ML-driven omics frameworks to revolutionize foodborne pathogen and AMR risk monitoring, paving the way for smarter, more resilient food safety systems. However, methodological inconsistencies necessitate standardized protocols, larger datasets, and explainable AI (XAI) to improve reliability and applicability in global food safety monitoring.},
}

*Machine Learning
*Food Microbiology
*Foodborne Diseases/microbiology
*Microbiota
*Drug Resistance, Bacterial/genetics
Animals
Genomics/methods
Metagenomics
Salmonella/pathogenicity/genetics
Food Safety
Humans

@article {pmid41609167,
year = {2026},
author = {Koo, WLY and Thng, KX and Tiew, PY and Chotirmall, SH},
title = {The Airway Microbiome in Chronic Obstructive Pulmonary Disease (COPD): A Guide for Clinicians.},
journal = {British journal of hospital medicine (London, England : 2005)},
volume = {87},
number = {1},
pages = {50163},
doi = {10.31083/BJHM50163},
pmid = {41609167},
issn = {1759-7390},
support = {MOH-001636//National Research Foundation Singapore/ ; MOH-001356//Singapore Ministry of Health's National Medical Research Council/ ; MOH-000710//Singapore Ministry of Health's National Medical Research Council/ ; MOH-001275-00//Singapore Ministry of Health's National Medical Research Council/ ; MOH-000955//Singapore Ministry of Health's National Medical Research Council/ ; RT1/22//Singapore Ministry of Education/ ; },
mesh = {Humans ; *Pulmonary Disease, Chronic Obstructive/microbiology/physiopathology ; *Microbiota ; Dysbiosis ; Disease Progression ; },
abstract = {Chronic obstructive pulmonary disease (COPD) is a progressive and debilitating respiratory condition marked by chronic symptoms and frequent exacerbations, contributing to significant morbidity and mortality. The advent of molecular microbiology and next-generation sequencing (NGS) has expanded our understanding of the lung microbiome, and integration of microbiome datasets with other omics reveals important microbial-metabolic-immuno-inflammatory interactions that influence COPD pathogenesis. Recent studies have highlighted dysbiosis of the airway microbiome, with shifts in bacterial, viral, and fungal communities playing a crucial role in disease progression, exacerbations and clinical outcomes. Moreover, microbiome changes are observed in COPD associated overlap syndromes, complicating diagnosis and treatment. This review synthesizes current microbiome research in COPD, focusing on its clinical relevance, including its potential as a diagnostic and prognostic tool. We additionally discuss the challenges of integrating microbiome data into clinical practice, emphasizing the need for personalized, precision medicine approaches to optimize COPD management and improve patient outcomes.},
}

Humans
*Pulmonary Disease, Chronic Obstructive/microbiology/physiopathology
*Microbiota
Dysbiosis
Disease Progression

@article {pmid41609355,
year = {2026},
author = {Li, Y and Li, Q and Quan, K and Xie, Y and Yang, N and Ma, T and Zheng, L and Zhou, W and Li, Y and Jin, H and Sun, Z and Chen, Y and Kwok, L-Y and Lu, N and Zhu, W and Liu, W and Zhang, H},
title = {Adjunctive probiotic therapy sustains symptom relief in gastroesophageal reflux disease through gut microbiome-metabolome remodeling.},
journal = {mSystems},
volume = {11},
number = {2},
pages = {e0156825},
pmid = {41609355},
issn = {2379-5077},
support = {No.2022LJRC0003//the Inner Mongolia Autonomous Region Science and Technology Leading Talent Team Project/ ; No. U22A20540//National Natural Science Foundation of China/ ; No. 2022YFD2100700//National Key Research and Development Program of China/ ; CARS-36//the Earmarked Fund for China Agriculture Research System/ ; BX20250337//the China National Postdoctoral Program for Innovative Talents/ ; },
mesh = {Humans ; *Probiotics/therapeutic use/administration & dosage ; *Gastroesophageal Reflux/microbiology/metabolism/drug therapy/therapy ; Female ; Male ; *Gastrointestinal Microbiome/drug effects ; *Metabolome/drug effects ; Double-Blind Method ; Adult ; Middle Aged ; Rabeprazole/therapeutic use ; Proton Pump Inhibitors/therapeutic use ; Treatment Outcome ; Metabolomics ; },
abstract = {Proton pump inhibitors (PPIs) are standard therapy for gastroesophageal reflux disease (GERD), but long-term use causes dysbiosis, gastrointestinal side effects, and symptom relapse after discontinuation. Probiotics may offer adjunctive benefits by modulating the gut ecosystem. The study aimed to evaluate the efficacy of a multi-strain probiotic (Lihuo) with rabeprazole in GERD and its impact on gut microbiota and metabolome. A randomized, double-blind, placebo-controlled trial was conducted in 120 GERD patients assigned to receive rabeprazole with either Lihuo (n = 64) or placebo (n = 56) for 8 weeks, followed by 4 weeks of probiotic or placebo alone. The primary outcome was change in the Reflux Disease Questionnaire (RDQ) score. Secondary outcomes included Gastrointestinal Symptom Rating Scale, endoscopic healing, and multi-omics profiling (shotgun metagenomics, phageome, and untargeted/targeted metabolomics). Compared with the placebo group, the probiotic group exhibited a pronounced 36.51% reduction in RDQ scores after 12 weeks of intervention (P = 0.017), alongside a higher numerical endoscopic healing rate (36.84% vs 12.50%; P = 0.365). Metagenomics revealed enrichment of Bifidobacterium animalis, Lactiplantibacillus plantarum, and Clostridium sp900540255, with reductions in Bacteroides uniformis and Clostridium Q fessum. Metabolomics showed increased γ-aminobutyric acid, succinate, citrulline, and short-chain fatty acids levels, with interesting microbe-metabolite correlations such as Bifidobacterium animalis-γ-aminobutyric acid and Bacteroides fragilis-succinate (r ≥ 0.30, P < 0.01). Our findings support that adjunctive probiotic therapy sustains post-PPI symptom relief, associated with targeted modulation of gut microbiota and bioactive metabolites.IMPORTANCELong-term proton pump inhibitor use in gastroesophageal reflux disease (GERD) may disrupt gut microbiota and cause symptom relapse after discontinuation. We found that adjunctive probiotic therapy sustained reflux reduction post-proton pump inhibitor. Probiotic use enriched beneficial taxa (Bifidobacterium and Lactiplantibacillus plantarum) and increased γ-aminobutyric acid, succinate, citrulline, and short-chain fatty acids. Strong correlations linked microbial shifts to metabolic and clinical improvements. This study demonstrates that adjunctive probiotic therapy enhances symptom control and supports microbial-metabolic homeostasis in GERD.CLINICAL TRIALSThis study is registered with the Chinese Clinial Trial Registry as ChiCTR2000038409.},
}

Humans
*Probiotics/therapeutic use/administration & dosage
*Gastroesophageal Reflux/microbiology/metabolism/drug therapy/therapy
Female
Male
*Gastrointestinal Microbiome/drug effects
*Metabolome/drug effects
Double-Blind Method
Adult
Middle Aged
Rabeprazole/therapeutic use
Proton Pump Inhibitors/therapeutic use
Treatment Outcome
Metabolomics

@article {pmid41609371,
year = {2026},
author = {Panattoni, A and De Boeck, I and Wittouck, S and Deffner, P and Lillie-Jaschniski, K and Stadler, J and Lebeer, S and Theuns, S},
title = {Exploring the functional microbiome of pigs within the porcine respiratory disease complex: viral-bacterial co-infections and virulence factor profiling.},
journal = {Microbiology spectrum},
volume = {14},
number = {3},
pages = {e0191025},
pmid = {41609371},
issn = {2165-0497},
support = {HBC.2023.0154//Agentschap Innoveren en Ondernemen/ ; },
mesh = {Animals ; Swine ; *Virulence Factors/genetics ; *Microbiota/genetics ; *Coinfection/veterinary/microbiology/virology ; *Bacteria/genetics/classification/isolation & purification/pathogenicity ; RNA, Ribosomal, 16S/genetics ; *Swine Diseases/microbiology/virology ; *Respiratory Tract Infections/veterinary/microbiology/virology ; Porcine respiratory and reproductive syndrome virus/genetics/isolation & purification ; *Bacterial Infections/veterinary/microbiology ; Influenza A virus/genetics/isolation & purification ; Respiratory System/microbiology/virology ; Porcine Reproductive and Respiratory Syndrome/microbiology/virology ; },
abstract = {Respiratory infections are among the most impacting on pigs' health and economic productivity. Despite this, detailed insights into the microbial community of the lower respiratory tract (LRT) are currently lacking, mainly because of difficulties in the processing of respiratory samples. In this study, we characterized the microbiota of the LRT of finisher pigs aged 3-5 months with respiratory symptoms for both the viral and bacterial components, using a previously validated metagenomic diagnostic assay and a full-length 16S rRNA gene sequencing approach, respectively. Functional characterization was carried out using metagenomic shotgun sequencing, revealing the presence of specific virulence factors (VFs). Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) and swine Influenza A Virus (swIAV) were the most prevalent viruses, being detected in 30% and 23% of the tested samples, respectively. Mesomycoplasma hyopneumoniae, Glaesserella parasuis, and Pasteurella multocida were the three most abundant bacterial taxa based on both sequencing approaches, while other detected bacterial taxa consisted mainly of Streptococcus, Clostridium, and Rothia species. Detected virulence factors belonged mainly to Mesomycoplasma and Pasteurella and consisted of adhesion factors such as p102, p97, p146, mhp108, mhp107 and the hemolysin-encoding gene hlyA for Mesomycoplasma, and adhesin-encoding ptfA and endoxtoxin-related gene lpxC for Pasteurella. Our data show how the microbial community of the lower respiratory tract in pigs with respiratory symptoms includes key viral (PRRSV, swIAV) and bacterial pathogens (M. hyopneumoniae, G. parasuis, and P. multocida), along with specific virulence factors likely contributing to disease.IMPORTANCEThe obtained results offer insights into the composition of the swine respiratory tract microflora, opening new perspectives on its correlation with viral infections, functional characteristics, and overall health conditions. Moreover, the present study provides technical advancement on the possibility of extracting and amplifying bacterial DNA from low-biomass respiratory samples, with the resulting possibility of identifying virulence factors and better understanding their contribution to the disease state. These discoveries pave the way for future studies aimed at improving diagnostic accuracy and treatment strategies for respiratory disease in both veterinary and human medicine.},
}

Animals
Swine
*Virulence Factors/genetics
*Microbiota/genetics
*Coinfection/veterinary/microbiology/virology
*Bacteria/genetics/classification/isolation & purification/pathogenicity
RNA, Ribosomal, 16S/genetics
*Swine Diseases/microbiology/virology
*Respiratory Tract Infections/veterinary/microbiology/virology
Porcine respiratory and reproductive syndrome virus/genetics/isolation & purification
*Bacterial Infections/veterinary/microbiology
Influenza A virus/genetics/isolation & purification
Respiratory System/microbiology/virology
Porcine Reproductive and Respiratory Syndrome/microbiology/virology

@article {pmid41610602,
year = {2026},
author = {Phusathian, B and Pongmanee, K and Theapparat, Y and Saikhwan, N and Trairatapiwan, T and Chaosap, C and Seemacharoensri, A and Tactacan, GB and Wong, LY and Ruangpanit, Y},
title = {Bacterial xylanase supplementation improves nutrient utilization, gut integrity, and microbial metabolism in broilers fed energy-reduced diets.},
journal = {Poultry science},
volume = {105},
number = {4},
pages = {106515},
pmid = {41610602},
issn = {1525-3171},
mesh = {Animals ; *Chickens/physiology/microbiology/growth & development/metabolism ; Male ; Animal Feed/analysis ; Diet/veterinary ; Dietary Supplements/analysis ; *Endo-1,4-beta Xylanases/administration & dosage/metabolism ; Animal Nutritional Physiological Phenomena/drug effects ; Digestion/drug effects ; Random Allocation ; Nutrients/metabolism ; *Gastrointestinal Microbiome/drug effects ; Energy Metabolism ; Intestines/drug effects/physiology ; *Bacterial Proteins/administration & dosage/metabolism ; },
abstract = {This study evaluated the effects of bacterial xylanase supplementation on growth performance, nutrient digestibility, intestinal integrity, and microbial metabolic function in broilers fed energy-reduced diets. A total of 1,050 one-day-old male Ross 308 broiler chicks were randomly assigned to three dietary treatments, each comprising 14 replicates of 25 birds: a positive control (CON; standard corn-soybean meal diet), a negative control with reduced energy (NC; -85 kcal/kg), and an energy-reduced diet supplemented with bacterial xylanase (NCX; 100 g/ton Belfeed Xylanase™). During the starter phase, broilers fed the NC diet exhibited higher feed intake and FCR compared with those fed the CON and NCX diets (P < 0.05), with no significant difference between the CON and NCX diets. Apparent digestibility of dry matter, crude protein, and fat did not differ among dietary treatments (P > 0.05). However, broilers fed the NCX diet showed higher (P < 0.05) digestibility of crude fiber, NDF, and ADF than those fed the CON or NC diets. Apparent metabolizable energy was higher in broilers fed the CON and NCX diets compared with the NC diet. Furthermore, broilers receiving the CON and NCX diets exhibited significantly lower serum fluorescein isothiocyanate-dextran concentrations than those fed the NC diet, indicating improved intestinal barrier integrity. Bacterial xylanase supplementation increased microbial alpha diversity and altered beta diversity clustering, with enrichment of beneficial taxa such as Bifidobacteriaceae and Lactobacillaceae. Functional metagenomic prediction suggested greater representation of carbohydrate metabolism and energy production pathways in the NCX diet, whereas the NC diet was associated with enrichment of stress-related and xenobiotic degradation pathways. Overall, bacterial xylanase supplementation mitigated the adverse effects of dietary energy reduction by improving fiber utilization, maintaining gut integrity, and modulating the cecal microbiota toward a more favorable metabolic profile.},
}

Animals
*Chickens/physiology/microbiology/growth & development/metabolism
Male
Animal Feed/analysis
Diet/veterinary
Dietary Supplements/analysis
*Endo-1,4-beta Xylanases/administration & dosage/metabolism
Animal Nutritional Physiological Phenomena/drug effects
Digestion/drug effects
Random Allocation
Nutrients/metabolism
*Gastrointestinal Microbiome/drug effects
Energy Metabolism
Intestines/drug effects/physiology
*Bacterial Proteins/administration & dosage/metabolism

@article {pmid41611051,
year = {2026},
author = {Shi, J and Sun, C and Su, Y and Wu, Y and Zhan, M and Ji, C and Wang, R and Lv, B},
title = {Ecosystem-specific composition and drivers of plastisphere resistome in freshwater and marine environments.},
journal = {Environmental research},
volume = {294},
number = {},
pages = {123858},
doi = {10.1016/j.envres.2026.123858},
pmid = {41611051},
issn = {1096-0953},
mesh = {*Seawater/microbiology ; *Fresh Water/microbiology ; *Microplastics/analysis ; *Ecosystem ; *Bacteria/genetics/drug effects ; *Water Pollutants, Chemical/analysis/toxicity ; *Drug Resistance, Microbial/genetics ; Genes, Bacterial ; *Microbiota ; },
abstract = {Microplastics in aquatic environments facilitate the formation of specific plastisphere microbiomes and serve as potential hotspots for antibiotic resistance genes (ARGs) propagation. However, the systematic comparisons of ARG profiles on microplastics from different aquatic ecosystems remain limited, particularly the prevalent ARGs and their bacterial hosts. This study performed a comparative meta-analysis of existing metagenomic datasets to investigate the resistome between freshwater and seawater microplastics (FMP and SMP) and their driving factors. Our results revealed that the ARG profiles on both FMP and SMP were significantly distinct from their surrounding waterbody. Moreover, FMP exhibited a higher diversity and abundance of ARGs rather than SMP. Ten core ARGs were shared on FMP and SMP, while 23 core ARGs were exclusively detected on FMP. The bacterial community on microplastics exhibited an ecosystem-specific composition, and was identified as the primary determinant shaping the ARG profiles. Notably, more complex bacteria-ARG co-occurrence pattern was identified on FMP, involving a broader spectrum of core genera and potential pathogenic hosts (e.g., Mycobacterium, Streptomyces). Furthermore, a significant and specific correlation between mobile genetic elements and ARGs was identified on FMP but not SMP, suggesting a markedly elevated horizontal gene transfer potential, with mechanistic support from the concurrent enrichment of oxidative stress and SOS response genes on FMP. These findings provide a comprehensive characterization of ARGs on aquatic microplastics, and especially highlight the role of FMP in the ARG dissemination.},
}

*Seawater/microbiology
*Fresh Water/microbiology
*Microplastics/analysis
*Ecosystem
*Bacteria/genetics/drug effects
*Water Pollutants, Chemical/analysis/toxicity
*Drug Resistance, Microbial/genetics
Genes, Bacterial
*Microbiota

@article {pmid41611767,
year = {2026},
author = {Jain, AG and Agwan, D and Kumar, A and Pancha, I and Rathod, J and Mohapatra, B},
title = {Mixing regimes shape microbial community composition, nutrient regimes, and plant growth attributes in Jeevamrit: metagenomics and culturomics-based insights.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {6603},
pmid = {41611767},
issn = {2045-2322},
support = {GSBTM/JD(R&D)/661/2022-23/00173054//GSBTM/ ; },
mesh = {*Metagenomics/methods ; *Soil Microbiology ; *Nutrients/metabolism ; *Plant Development ; *Microbiota ; *Bacteria/genetics/classification ; Soil/chemistry ; Nitrogen/metabolism ; },
abstract = {Jeevamrit, a microbial inoculant widely used in zero-budget natural farming (ZBNF) that relies on local farm-based resources to enhance overall biological health of soil, is reported for inconsistent crop yield enhancements. This is mainly due to variability in its preparation methods, e.g., mixing intensity, incubation regimes, and quality of ingredients used. Hence, the current study aimed to decipher the effect of mixing intensity (extent of oxygenation) on microbial community composition, nutrient transformation, and plant growth attributes of Jeevamrit, using a combined metagenomics-culturomics approach. Frequent mixing (Constant/Intermediate) enhanced nutrient solubilization (Fe, Zn, Cu, Mn) with higher total N and dissolved organic carbon, while less mixing (Anoxic/No-mix) led to accumulation of soluble Fe and NH4[+]-N with higher microbial diversity. Mixing-driven differential enrichment of taxa were noted, i.e., constant mixing (CM) dominated by Acinetobacter (~ 40%), Comamonas, Pseudomonas, and Lysinibacillus, linked to oxidative C/N cycling and metal dissolution. Whereas, anoxic (AO) favored Clostridium sensu stricto, Lactobacillales, Enterococcus, and Enterobacterales (> 60%), correlating to fermentative metabolism-driven reductive elemental cycling. Co-occurrence network analysis identified Acinetobacter, Pseudomonas, Comamonas, Trichococcus, and Stenotrophomonas as hubs, indicating keystone functions in structuring metabolic interactions. The metagenome-recovered MAGs belonged to Acinetobacter sp., Clostridium saccharobutylicum, Trichococcus flocculiformis, and Enterococcus gallinarum with potential to participate in multiple nutrient cycling. Cultivable members of Shigella, Rhodococcus, and Bacillus spp. showed high IAA production (135-145 µg mL[-][1]), NH3 release (~ 0.12 µg mL[-][1]), and K and P solubilization (~ 55.2 µg mL[-][1]). We hypothesize that oxygenation drives the Jeevamrit's microbial guild assembly, where mixing intensity modulates oxido-reductive metabolism and nutrient mobilization efficiency, indicating the requirement for standardization of formulation aligned to soil-specific conditions.},
}

*Metagenomics/methods
*Soil Microbiology
*Nutrients/metabolism
*Plant Development
*Microbiota
*Bacteria/genetics/classification
Soil/chemistry
Nitrogen/metabolism

@article {pmid41611865,
year = {2026},
author = {Ulloa, MA and Serrano, AV and Camelo, LC and Guyot, R and Vela, D and Muñoz, AR},
title = {Bacterial genome reconstruction and community profiling in Neotropical Drosophila.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {6601},
pmid = {41611865},
issn = {2045-2322},
mesh = {Animals ; *Drosophila/microbiology ; *Genome, Bacterial ; *Microbiota/genetics ; Phylogeny ; Metagenomics/methods ; Metagenome ; *Bacteria/genetics/classification ; Ecuador ; },
abstract = {Drosophila species serve as key models for microbiota research due to their relatively simple microbial communities. However, microbial diversity and dynamics in Neotropical Andean Drosophila remain underexplored. Here we applied shotgun metagenomics to characterize the microbiota of 24 Neotropical Drosophila species from Ecuador, reconstructing 64 high-quality bacterial genomes predominantly from Acetobacteraceae and Enterobacterales. Microbial communities were consistently dominated by yeasts, lactic acid bacteria, acetic acid bacteria, and Wolbachia. Comparative analyses revealed no strong correlation between host phylogeny and microbial community composition, suggesting environmental factors and microbial interactions shape these communities. Notably, shifts in relative abundances indicate dynamic ecological succession and metabolic cooperation among microbes. These findings expand genomic resources for Drosophila-associated bacteria and highlight the complex ecological processes influencing host-microbiota relationships in natural populations.},
}

Animals
*Drosophila/microbiology
*Genome, Bacterial
*Microbiota/genetics
Phylogeny
Metagenomics/methods
Metagenome
*Bacteria/genetics/classification
Ecuador

@article {pmid41615027,
year = {2025},
author = {Jiménez, DJ and Marasco, R and Schultz, J and Díaz Rodríguez, CA and Nogales, J and Rodriguez-R, LM and Overmann, J and Rosado, AS},
title = {Discovery and cultivation of prokaryotic taxa in the age of metagenomics and artificial intelligence.},
journal = {The ISME journal},
volume = {20},
number = {1},
pages = {},
pmid = {41615027},
issn = {1751-7370},
support = {MCIN/AEI/10.13039/501100011033//Spanish Ministry of Science and Innovation/ ; 101081782 (deCYPher)//European Union/ ; 101036768 (PROMISEANG)//European Union/ ; PID2022-139247OB-I00 (Rob3D)//European Union/ ; BAS/1/1096-01-01//King Abdullah University of Science and Technology/ ; },
mesh = {*Metagenomics/methods ; *Artificial Intelligence ; *Bacteria/genetics/classification/isolation & purification/growth & development ; Microbiota ; },
abstract = {Despite advances in sequencing, microbial genomics, and cultivation techniques, the vast majority of prokaryotic species remain uncultured, which is a persistent bottleneck in microbiology and microbial ecology. This perspective outlines a conceptual framework to improve the transition from genome-resolved metagenomics to the targeted isolation of yet-uncultured prokaryotic taxa. The proposed framework integrates the induced reshaping of microbiomes, genome-based inferences of physiological and phenotypic traits, culture media design, and targeted culturomics, enabling hypothesis-driven cultivation. In addition, this manuscript addresses the critical limitations in the field, including the sequence-to-function gap, and emphasizes the synergistic potential of experimental microbiology, microbial ecology, metagenomics, and artificial intelligence-based predictions to enhance rational and actionable roadmaps for discovering and cultivating novel prokaryotic lineages.},
}

*Metagenomics/methods
*Artificial Intelligence
*Bacteria/genetics/classification/isolation & purification/growth & development
Microbiota

@article {pmid41615149,
year = {2026},
author = {Mora-Martínez, C and Molina-Mendoza, G and Cenit, MC and Medina-Rodríguez, EM and Larroya-García, A and Sanchez-Carro, Y and Gonzalez-Blanco, L and Bobes, J and Lopez-Garcia, P and Zandio-Zorrilla, M and Lahortiga-Ramos, F and Gili, M and Garcia-Toro, M and Barcelo, B and Ibarra, O and Sanz, Y},
title = {Gut microbiome signatures associated with depression and obesity.},
journal = {mSystems},
volume = {11},
number = {3},
pages = {e0126325},
pmid = {41615149},
issn = {2379-5077},
support = {EarlyCause 848158//Horizon 2020 Framework Programme/ ; Centro de Excelencia Severo Ochoa CEX2021-001189-S/MCIN/AEI/10.13039/501100011033//Ministerio de Ciencia e Innovación/ ; FPI PRE2018-083895//Ministerio de Ciencia e Innovación/ ; Miguel Servet CP22/00031//Instituto de Salud Carlos III/ ; },
mesh = {Humans ; *Obesity/microbiology ; *Major Depressive Disorder/microbiology ; *Gastrointestinal Microbiome/genetics ; Case-Control Studies ; Female ; Male ; Middle Aged ; Adult ; Body Mass Index ; Metagenomics ; Metagenome ; Bacteria/classification/genetics ; },
abstract = {UNLABELLED: Depression and obesity are highly comorbid and likely involve common risk factors and pathophysiological mechanisms, which could crosslink to gut microbiome dysfunction. Here, we performed a case-control study with a total of 105 subjects, 43 with major depressive disorder (MDD) and 62 non-depressed controls free from psychiatric comorbidities, to identify gut microbiome signatures associated with MDD and dissect its relation to body mass index (BMI) and lifestyle (diet and exercise). We performed shotgun metagenomics, followed by taxonomic and functional annotations. Using different machine learning methods, we were able to classify subjects into depressed and non-depressed controls with a balanced accuracy of 0.90 and into depressed or non-depressed and normal weight or overweight with a balanced accuracy of 0.78 based solely on taxonomic profiles. We identify novel bacterial taxa associated with depression, including reductions in Butyrivibrio hungatei and Anaerocolumna sedimenticola, and also replicate previously reported associations, such as decreased Faecalibacterium prausnitzii in patients with MDD. Functional annotation of metagenomes shows differences in pathways linked to the synthesis of fundamental nutrients, which have been associated with diet, as well as inflammation. Strikingly, we found an increase in tryptophan degradation and a decrease in queuosine synthesis pathways, both of which are directly related to a decrease in monoaminergic neurotransmitter availability. Additionally, our functional analysis shows that most of the functions that are more abundant in controls than in depressed subjects are encoded by F. prausnitzii. These findings reveal distinct microbial and functional signatures associated with depression, including taxa and pathways linked to neurotransmitter metabolism and independent of other covariates. This suggests that gut microbiome profiling could support diagnosis and the development of gut-directed depression treatments.

IMPORTANCE: This study identifies gut microbiome signatures that are predictive of major depressive disorder (MDD) and explores their links to body mass index (BMI). We uncover bacterial species and metabolic pathways that are associated with MDD, some of them related to neurotransmitter metabolism and inflammation. Among the differences identified, depletion of Faecalibacterium prausnitzii stands out as an important feature in the MDD microbiome, which suggests the possible use of this species to improve depression symptoms. Importantly, we demonstrate shared microbiome features between MDD and BMI, suggesting common underlying mechanisms. This research not only provides a framework for developing microbiome-based diagnostics but also informs future stratified interventions targeting gut microbial functions to improve mental health outcomes.},
}

Humans
*Obesity/microbiology
*Major Depressive Disorder/microbiology
*Gastrointestinal Microbiome/genetics
Case-Control Studies
Female
Male
Middle Aged
Adult
Body Mass Index
Metagenomics
Metagenome
Bacteria/classification/genetics

@article {pmid41616624,
year = {2026},
author = {Sun, Y and Zhang, M and Teng, Y and Yin, Y and Ran, J and Su, H and Li, H and Huang, X and Long, Z and Sun, X and Pan, H and Wang, X and Li, M},
title = {Human activities and horizontal gene transfer shape the resistome landscapes of non-human primates.},
journal = {Journal of hazardous materials},
volume = {504},
number = {},
pages = {141276},
doi = {10.1016/j.jhazmat.2026.141276},
pmid = {41616624},
issn = {1873-3336},
mesh = {Animals ; *Gene Transfer, Horizontal ; *Drug Resistance, Microbial/genetics ; *Primates/microbiology/genetics ; Humans ; *Human Activities ; Soil Microbiology ; Bacteria/genetics/drug effects ; China ; Metagenome ; *Drug Resistance, Bacterial/genetics ; },
abstract = {Antibiotic resistance represents a growing threat to human, animal, and ecosystem health, yet its dynamics in wildlife remain poorly understood. We conducted a systematic analysis of the gut resistomes in non-human primates (NHPs) and environmental soils in Guizhou Province, China, a biodiversity hotspot. Metagenomic analyses reveal that human activities and horizontal gene transfer (HGT) influence primate resistome landscapes and enhance their dissemination potential. A total of 1927 antibiotic resistance ontologies (AROs) distributed across 1477 species-level genome bins (SGBs), providing a comprehensive genomic catalog of the NHPs resistome. Bacterial genera such as Pseudomonas, Stenotrophomonas, and Comamonas drive ARG mobilization, with a core subset of ARGs that reliably predict overall resistance burdens. Notably, widely distributed primate species, with large habitat ranges and frequent interspecies interactions exhibit the most potential for ARG dissemination. Ecological modeling identifies current and future hotspot regions requiring prioritized monitoring amid ongoing human disturbance and climate change. These findings provide a molecular-indicator-based framework for environmental antibiotic resistance (AR) monitoring and conservation strategies for endangered species. Despite limitations in temporal and spatial coverage, our study highlights the need to integrate wildlife, particularly NHPs, as sentinel species into "One Health" AR surveillance and policy. This approach will strengthen our understanding of ARG transmission dynamics and their long-term impacts on host adaptation, ecosystem stability, and public health.},
}

Animals
*Gene Transfer, Horizontal
*Drug Resistance, Microbial/genetics
*Primates/microbiology/genetics
Humans
*Human Activities
Soil Microbiology
Bacteria/genetics/drug effects
China
Metagenome
*Drug Resistance, Bacterial/genetics

@article {pmid41616686,
year = {2026},
author = {Sattari Khavas, D and Schwartz, SK and Bird, P and Truong, A and Silberg, JJ},
title = {Microbial spies and bloggers: programming cells to convert environmental information into discernible signals.},
journal = {Current opinion in biotechnology},
volume = {98},
number = {},
pages = {103436},
doi = {10.1016/j.copbio.2026.103436},
pmid = {41616686},
issn = {1879-0429},
mesh = {*Biosensing Techniques/methods ; Synthetic Biology ; *Bacteria/metabolism/genetics ; *Microbiota ; },
abstract = {Microbes regulate their dynamic behaviors using the chemical and physical characteristics of their environment. The ability of microbes to continuously convert this physicochemical information into biochemical information and to use organic matter in the environment as a power source makes these organisms attractive as chassis for building sensors. However, most biosensors have severe limitations when considering applications in hard-to-image settings like soils, sediments, and wastewater. Emerging technologies at the interface of biomolecular design, microbiome engineering, and synthetic biology offer new tools to program cells and communities as biosensors for these settings. In this review, we describe innovations in biosensor outputs that are enabling new applications in complex environments, including reporters that are read out using electrochemical, gas chromatography, hyperspectral imaging, and next-generation sequencing methods. We also discuss computational advances that are accelerating the diversification of sensing components by mining metagenomics data for new transcriptional regulators and by designing allosteric protein switches that directly regulate reporter outputs using analytes. We highlight emerging opportunities for programming undomesticated microbes in communities to function as distributed sensors in the environment. Finally, we discuss the need for responsible biosensor development and to modernize regulatory frameworks to support evidence-based assessment of environmental biosensors.},
}

*Biosensing Techniques/methods
Synthetic Biology
*Bacteria/metabolism/genetics
*Microbiota

@article {pmid41616716,
year = {2026},
author = {Breyer, GM and Torres, MC and Rebelatto, R and Wuaden, CR and Pastore, J and Lazzarotti, M and Nicoloso, RDS and Dorn, M and Kich, JD and Siqueira, FM},
title = {From farm to environment: the microbiome and the silent spread of antimicrobial resistance genes in soil despite manure management in swine farms.},
journal = {Journal of environmental management},
volume = {400},
number = {},
pages = {128747},
doi = {10.1016/j.jenvman.2026.128747},
pmid = {41616716},
issn = {1095-8630},
mesh = {Animals ; *Manure/microbiology ; *Soil Microbiology ; *Microbiota ; Swine ; Farms ; Soil ; Bacteria/genetics ; },
abstract = {The swine industry generates large amounts of organic waste containing antimicrobial residues, requiring efficient manure management to reduce environmental risks. Covered lagoon biodigesters (CLBs) and waste stabilization ponds (WSPs) are commonly used digestion systems, with digestates subsequently applied as organic fertilizers. Although these systems successfully reduce pathogenic bacteria, their effectiveness in removing antimicrobial resistance genes (ARGs) remains unclear. In this study, we compared microbiome and resistome profiles from CLB- (n = 23) and WSP-farms (n = 20) using shotgun metagenomic sequencing of raw and digested manure, as well as fertilized and non-fertilized soils. Our findings indicate that digestate application slightly shifted soil microbial communities and significantly increased bacterial diversity, suggesting the introduction of diverse manure-derived bacteria. Reads from taxonomic markers associated with clinically important pathogens, including Enterobacterales, streptococci (groups A and B), Enterococcus faecium, Staphylococcus aureus, Pseudomonas aeruginosa, Acinetobacter baumannii, Klebsiella pneumoniae, and Salmonella enterica were still detected in digestates and fertilized soils, regardless of the digestion system. Moreover, DNA sequences associated with ARGs against critical antimicrobials, such as carbapenems, cephalosporins, and glycopeptides persisted. Notably, WSPs exhibited greater accumulation of some ARGs, including OXA-347 and vanG. Overall, although CLBs exerted a lower impact on soil microbial communities and resistomes compared to WSPs, neither system effectively eliminated ARGs. These findings highlight the potential for environmental dissemination of ARGs through manure fertilization and underscore the urgent transition toward more sustainable production practices, including eliminating non-therapeutic antimicrobial use in the swine industry, as well as the need for improved digestion technologies and continuous monitoring under the One Health framework.},
}

Animals
*Manure/microbiology
*Soil Microbiology
*Microbiota
Swine
Farms
Soil
Bacteria/genetics

@article {pmid41616776,
year = {2026},
author = {Liu, C and Sun, S and Ren, X and Geisen, S and Wang, S and Jiang, G and Xu, Y and Shen, Q and Jousset, A and Wei, Z and Xiong, W},
title = {Predation by soil protists shifts bacterial metabolism from competitive to cooperative interactions.},
journal = {Cell host & microbe},
volume = {34},
number = {2},
pages = {201-211.e6},
doi = {10.1016/j.chom.2026.01.006},
pmid = {41616776},
issn = {1934-6069},
mesh = {*Soil Microbiology ; *Bacteria/metabolism/genetics ; Rhizosphere ; *Eukaryota/physiology ; *Microbial Interactions ; Microbiota ; Metagenomics ; Soil/parasitology ; },
abstract = {Many soil protists are bacterivores, yet how protist predation reshapes bacterial metabolic interactions and functions remains poorly understood. Here, we combine global soil samples with microbial metabolic simulations, along with soil microcosm-pot validations, to investigate the influence of protists on bacterial metabolic interactions. Across 3,785 metabolic simulations spanning 757 soils, increased protists predicted higher bacterial metabolic interaction potential and cross-feeding but lower metabolic resource overlap and competition. These patterns were confirmed using an independent rhizosphere dataset and metagenomic analysis. Protist predation selected bacterial communities containing GC-rich genomes, acid-carbon-preferring taxa, and enhanced metabolite exchange. Additionally, exposing a synthetic community (SynCom) to protist predation elevated the expression of bacterial genes associated with plant growth-promoting functions. Consistently, microcosm- and pot-based experiments showed that protist addition increased bacterial cross-feeding over time and improved plant performance. Together, we establish a scalable framework to evaluate protist-driven bacterial cooperation and function to guide rational rhizosphere microbiome engineering.},
}

*Soil Microbiology
*Bacteria/metabolism/genetics
Rhizosphere
*Eukaryota/physiology
*Microbial Interactions
Microbiota
Metagenomics
Soil/parasitology

@article {pmid41617120,
year = {2026},
author = {Hu, S and Wang, X and Xu, H and Xiong, J and Gu, Y and Cao, X and Zhou, L and Fan, Y and Wang, S and Bai, X and Shi, H and Zhu, Q and Chen, L and Shi, Z},
title = {Vaginal microbiota in late pregnancy associates with the outcomes of planned induced labor: a multicenter prospective cohort study.},
journal = {American journal of obstetrics and gynecology},
volume = {234},
number = {6},
pages = {1740-1758},
doi = {10.1016/j.ajog.2026.01.026},
pmid = {41617120},
issn = {1097-6868},
mesh = {Female ; Humans ; Pregnancy ; *Labor, Induced/methods ; *Vagina/microbiology ; *Microbiota ; Prospective Studies ; Adult ; Cervical Ripening ; Animals ; Lactobacillus crispatus ; Pregnancy Outcome ; Genome-Wide Association Study ; Lactobacillus ; Cesarean Section/statistics & numerical data ; Oxytocin/therapeutic use ; },
abstract = {BACKGROUND: Induction of labor is a commonly used obstetric method for terminating pregnancy in cases of delayed or expired pregnancy or complications, with cervical maturity being a key determinant of success. Balloon-induced labor is a safe, effective, and cost-effective induction of labor method. While clinical factors such as parity, cervical Bishop score, prepregnancy body mass index, are known to influence outcomes. Emerging evidence suggests that vaginal microbiota may also play a critical role through activation of local complement mediators and inflammatory signalling that accelerates cervical ripening. Additionally, genetic factors may influence both preterm birth risk and vaginal microbiota composition. However, the specific impact of vaginal microbiota and genetic factors on balloon-induced labor outcomes remains unclear and requires further investigation.

OBJECT: To explore the impact of the vaginal microbiota prior to delivery on the maternal and fetal outcomes of planned induced labor through metagenomic sequencing and genome-wide association studies.

STUDY DESIGN: A multicenter prospective cohort study was conducted from October 2022 to June 2024 across 5 hospitals, enrolling 635 pregnant women undergoing planned sequential induction of labor using cervical balloons combined with oxytocin. The clinical data throughout the entire pregnancy and labor period, as well as samples of vaginal and cervical secretions before the induction of labor, were collected. Firstly, the characteristics of the vaginal microbiota in all pregnant women were analyzed through metagenomic sequencing, and then the impact of vaginal microbiota differences on the maternal and fetal outcomes of planned induced labor was studied. Subsequently, a nested case-control study was performed, based on human whole genome sequencing combined with genome-wide association studies analysis on vaginal secretion samples, to investigate the role of genetic factors in planned induced labor. Finally, vaginal microbiota transplantation in pregnant rats was conducted to verify the effects of vaginal microbiota on the maternal and fetal outcomes of labor.

RESULTS: Among the participants, 167 delivered within 24 hours, 318 delivered within 24-72 hours, 50 failed induction, and 100 underwent cesarean section for miscellaneous indications. Vaginal microbiota analysis in parturients revealed that the probability of delivery within 24 hours is negatively correlated with Lactobacillus iners (L. iners) abundance, while failed induction is negatively correlated with Ralstonia mannitolilytica abundance. Cesarean section probability is positively correlated with Lactobacillus crispatus (P=0.03). Additionally, the time from balloon placement to delivery is positively correlated with L. iners (P=0.002) and negatively correlated with Lactobacillus crispatus (P=0.08, not fully significant). Genome-wide association studies analysis shows that single-nucleotide polymorphisms associated with adverse pregnancy outcomes are mainly concentrated on chromosomes 1, 4, 8, and 10. Vaginal microbiota transplantation experiments showed that pregnant rats transplanted with vaginal bacteria from women who delivered within 24 hours had the shortest delivery time, while those transplanted with vaginal bacteria from women who failed to induced labor had the longest delivery time and some experienced dystocia.

CONCLUSION: This study reveals that, in addition to genetic factors, the outcomes of planned labor induction, especially the total duration of labor and the success rate of induction, are closely related to the vaginal microbiota in women during the late stages of pregnancy. The study provides new evidence to explain the different outcomes of labor induction.},
}

Female
Humans
Pregnancy
*Labor, Induced/methods
*Vagina/microbiology
*Microbiota
Prospective Studies
Adult
Cervical Ripening
Animals
Lactobacillus crispatus
Pregnancy Outcome
Genome-Wide Association Study
Lactobacillus
Cesarean Section/statistics & numerical data
Oxytocin/therapeutic use

@article {pmid41617723,
year = {2026},
author = {Pratama, AA and Pérez-Carrascal, O and Sullivan, MB and Küsel, K},
title = {Diversity and ecological roles of hidden viral players in groundwater microbiomes.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {41617723},
issn = {2041-1723},
support = {EXC 2051, Project-ID 390713860//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; DE-SC0023307//U.S. Department of Energy (DOE)/ ; },
mesh = {*Groundwater/virology/microbiology ; *Microbiota/genetics ; Archaea/genetics/virology ; Bacteria/genetics/virology/classification ; *Virome/genetics ; *Viruses/genetics/classification/isolation & purification ; Metagenomics ; Metagenome ; Phylogeny ; },
abstract = {Groundwater ecosystems harbor diverse microbial communities adapted to energy-limited, light-deprived conditions, yet the role of viruses in these environments remains poorly understood. Here, we analyzed 1.24 terabases of metagenomic and metatranscriptomic data from seven wells in the Hainich Critical Zone Exploratory (CZE) to characterize groundwater viromes. We identified 257,252 viral operational taxonomic units (vOTUs) (≥ 5 kb), with 99% novel at order, family and genus levels against global ocean, freshwater and/or other publicly available datasets. In silico host predictions suggest that vOTUs primarily targeted Proteobacteria, Candidate Phyla Radiation (CPR) bacteria, and DPANN archaea, which reflects abundant and active groundwater microbial members. Patterns of virus-host abundance ratios, CRISPR-spacers, and prophage screening suggest the potential for multi-layer interactions involving CPR/DPANN lineages, their hosts, and viruses. Additionally, we identified 289 KEGG metabolic modules, 31.1% of which were targeted by 3378 vOTUs encoded auxiliary metabolic genes (AMGs) linked to carbon, nitrogen, and sulfur cycling. These findings provide a baseline for exploring how viruses influence microbial community dynamics, metabolic reprogramming and nutrient cycling in groundwater.},
}

*Groundwater/virology/microbiology
*Microbiota/genetics
Archaea/genetics/virology
Bacteria/genetics/virology/classification
*Virome/genetics
*Viruses/genetics/classification/isolation & purification
Metagenomics
Metagenome
Phylogeny

@article {pmid41617724,
year = {2026},
author = {Dong, Z and Sun, MS and He, YD and Zhou, L and Xiang, W and Li, X and Huang, P and Zeng, JG},
title = {Fungal photobiont and microbiome genome composition in the Cladonia uncialis tripartite symbiosis.},
journal = {Scientific data},
volume = {13},
number = {1},
pages = {},
pmid = {41617724},
issn = {2052-4463},
mesh = {*Symbiosis ; *Lichens/microbiology/genetics ; *Microbiota ; *Ascomycota/genetics ; *Genome, Fungal ; Genome, Bacterial ; Metagenome ; },
abstract = {As symbiotic complexes formed through the association of bacteria or algae with fungi, lichens exhibit exceptional adaptability to extreme environments and function as pioneer species in rocky habitat ecological succession. The absence of high quality chromosome-level genome has constrained investigations into lichen adaptive evolution, while functional contributions of symbiotic bacterial communities remain inadequately explored. This study presents the chromosome-level genome assembly of the mycobiont Cladonia uncialis, comprising 28 chromosomes with a total size of 43.49 Mb, generated through integrated PacBio HiFi and Hi-C methodologies. We characterized the symbiotic microbiota using integrated short and long-read sequencing and constructed 31 metagenome-assembled genomes. The community was dominated by Ascomycota (41.16%), Proteobacteria (17.61%), and Bacteroidota (14.20%). Long-read sequencing significantly enhanced detection sensitivity for low-abundance taxa. This study provides essential genomic resources and comprehensive profiles of the symbiotic microbiota, enabling mechanistic exploration of adaptive evolution within lichen symbiotic systems under extreme environmental conditions.},
}

*Symbiosis
*Lichens/microbiology/genetics
*Microbiota
*Ascomycota/genetics
*Genome, Fungal
Genome, Bacterial
Metagenome

@article {pmid41618383,
year = {2026},
author = {Pérez-Pérez, L and Arguello, H and Cobo-Díaz, JF and Galisteo, C and Puente, H and Gómez-Martínez, S and Carvajal, A},
title = {From predisposition to recovery: field evidence of interactions between the gut microbiota and Brachyspira hyodysenteriae infection.},
journal = {Veterinary research},
volume = {57},
number = {1},
pages = {25},
pmid = {41618383},
issn = {1297-9716},
support = {PRE2020-093762//Ministerio de Ciencia, Innovación y Universidades/ ; JDC2023-051122-I//Ministerio de Ciencia, Innovación y Universidades/ ; EDU-1868-2022//Junta de Castilla y León/ ; },
mesh = {Animals ; Swine ; *Swine Diseases/microbiology ; *Brachyspira hyodysenteriae/physiology ; *Gram-Negative Bacterial Infections/veterinary/microbiology ; Feces/microbiology ; *Gastrointestinal Microbiome ; Disease Susceptibility/veterinary/microbiology ; Sus scrofa ; },
abstract = {Restrictions on antibiotics use have increased interest in the gut microbiota relationship to host health, particularly in enteric infections. The present field study, performed on two farms with endemic swine dysentery (SD) infection, characterises the faecal microbiota in 102 faecal samples from 13 diseased and 13 non-diseased pigs by shotgun metagenomic sequencing. The samples were collected during four samplings, which allowed us to monitor the animals before, during and after the clinical disease to investigate the role of the gut microbiota in disease outcome, assess the impact of infection on microbial composition and evaluate the microbiota evolution following recovery. Samples collected before disease demonstrated that SD susceptible pigs had lower microbial diversity, with significantly lower abundance of Treponema rectale, Prevotella spp. or Ruminiclostridium E compared with SD resistant pigs, which remained healthy. Marked alterations in microbial species composition and their functional profiles were evident during clinical disease. Brachyspira hyodysenteriae, Dysosmobacter sp. BX15, Acetivibrio ethanolgignens and Mucispirillum sp. 910586745 were significantly increased in abundance, which was associated with an increase of functions such as Bacteroides capsular polysaccharide transcription antitermination proteins or pterin carbinolamine dehydratase. No changes in the microbiota were observed after the disease when compared with non-diseased pigs, thus evidencing a restoration of the microbiota composition after therapeutic treatment and recovery. The study demonstrates that the microbiota may play a relevant role in SD disease outcome and evidences the changes that occur during clinical disease do not persist over time after pig therapeutic treatment.},
}

Animals
Swine
*Swine Diseases/microbiology
*Brachyspira hyodysenteriae/physiology
*Gram-Negative Bacterial Infections/veterinary/microbiology
Feces/microbiology
*Gastrointestinal Microbiome
Disease Susceptibility/veterinary/microbiology
Sus scrofa

@article {pmid41618437,
year = {2026},
author = {Chong-Nguyen, C and Fuentes Artiles, R and Pilgrim, T and Yilmaz, B and Döring, Y},
title = {The gut-heart axis in coronary artery disease: a scoping and narrative review of sex-based microbial and metabolic disparities.},
journal = {Biology of sex differences},
volume = {17},
number = {1},
pages = {24},
pmid = {41618437},
issn = {2042-6410},
mesh = {Humans ; *Coronary Artery Disease/microbiology/metabolism ; *Sex Characteristics ; *Gastrointestinal Microbiome ; Female ; Male ; },
abstract = {BACKGROUND: The gut microbiota significantly influences cardiovascular health by regulating host metabolism and generating bioactive compounds like trimethylamine-N-oxide (TMAO) and indoxyl sulfate (IS), both linked to coronary artery disease (CAD). Emerging research indicates sex-based differences in microbial composition and metabolite production, yet their impact on CAD pathophysiology remains unclear. This scoping review summarizes current findings on sex-specific microbial and metabolic differences in individuals with CAD.

METHODS: A systematic search of PubMed and EMBASE was conducted through March 2025 for peer-reviewed studies comparing gut microbiota or metabolite profiles between male and female patients with CAD. Eligible studies used 16S rRNA sequencing, shotgun metagenomics, or metabolite profiling to analyze microbial communities and atherosclerosis-associated metabolites. Mechanistic links from genetics, epigenetics, and hormone-microbiota interactions were integrated to provide a more comprehensive understanding of how gut microbiota may contribute to sex differences in CAD.

RESULTS: Eleven studies met the inclusion criteria for this review. Men with CAD exhibited increased relative abundances of taxa such as Prevotella, Clostridia_UCG_014, UCG_010, and other pro-inflammatory genera, whereas women microbiota was comparatively enriched in Barnesiella, Bifidobacteriales, and other potentially beneficial taxa. Parallel differences emerged in microbial metabolite profiles: men demonstrated elevated plasma levels of TMAO and IS, both associated with heightened cardiovascular risk and disease burden. Conversely, women with CAD had higher circulating levels of secondary bile acids and lower TMAO concentrations.

CONCLUSION: Preliminary studies suggest sex-related differences in gut microbiota composition and metabolite profiles in CAD patients. Integrating mechanistic links from microbial metabolism, genetics, epigenetics, and hormones supports a potential role of the microbiota in sex-dependent disease pathways. Current evidence is limited and mostly observational; well-designed studies are needed to clarify mechanisms, clinical relevance of sex-specific microbiome signatures and specifically assess whether these sex-specific microbial and metabolic differences influence CAD progression and outcomes.},
}

Humans
*Coronary Artery Disease/microbiology/metabolism
*Sex Characteristics
*Gastrointestinal Microbiome
Female
Male

@article {pmid41618858,
year = {2026},
author = {Yang, T and Gao, Z and Huang, H and Zhang, C and Tang, Y and Qu, Q and Li, H and Ke, J and Chen, Z and Feng, M and Zhou, H and Shu, Y and Yuan, W},
title = {Gut-Metabolome-Proteome Interactions in Age-Related Hearing Loss: Insights from Fecal Microbiota Transplantation and Multi-Omics Analyses.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {13},
number = {18},
pages = {e14269},
pmid = {41618858},
issn = {2198-3844},
support = {81873702//National Natural Science Foundation of China/ ; 81470694//National Natural Science Foundation of China/ ; 82225014//National Natural Science Foundation of China/ ; 82171114//National Natural Science Foundation of China/ ; 2024NF008//National Clinical Research Center for Otolaryngologic Diseases/ ; CSTB2023TIAD-KPX0059//Chongqing Technology Innovation and Application Development Special Project/ ; 2022DBXM006//Major Programs of Chongqing Science and Health Union/ ; cstc2022ycjh-bgzxm0126//Chongqing Talent Project/ ; CSTB2022NSCQ-MSX0553//Chongqing Natural Science Foundation/ ; },
mesh = {Animals ; Mice ; Multiomics ; *Gastrointestinal Microbiome/physiology ; *Fecal Microbiota Transplantation/methods ; *Metabolome/physiology/genetics ; *Proteome/metabolism ; *Aging ; Disease Models, Animal ; Proteomics/methods ; Male ; *Hearing Loss/metabolism ; Metabolomics ; *Presbycusis/metabolism ; },
abstract = {Age-related hearing loss (ARHL) is a prevalent sensory disorder lacking disease-modifying interventions. The biological drivers, particularly the contribution of the gut microbiota and gut-inner ear crosstalk, remain poorly defined. Here, we utilize germ-free (GF) mice and fecal microbiota transplantation (FMT) to isolate microbiota-dependent effects on ARHL progression. Through integrated metagenomic, metabolomic, and proteomic profiling, we map molecular signatures of auditory aging and uncover functional gut-inner ear network, prioritizing 5-hydroxytryptophan (5-HTP) as a key intermediate metabolite within this network. Furthermore, in an aging-like House Ear Institute-Organ of Corti 1 (HEI-OC1) model, 5-HTP exhibits protective effects, potentially mediated through the PI3K/Akt-antioxidant signaling axis. Collectively, this study provides a valuable multi-omics resource and highlights microbiota-derived metabolic regulation as a promising avenue for biomarker discovery and therapeutic development in ARHL.},
}

Animals
Mice
Multiomics
*Gastrointestinal Microbiome/physiology
*Fecal Microbiota Transplantation/methods
*Metabolome/physiology/genetics
*Proteome/metabolism
*Aging
Disease Models, Animal
Proteomics/methods
Male
*Hearing Loss/metabolism
Metabolomics
*Presbycusis/metabolism

@article {pmid41619209,
year = {2026},
author = {Tang, R and Wang, J and Wang, X and Zeng, M and Gao, W and Yang, K and Xu, L and Li, Y and Zhou, C and Yue, B and Fan, Z and Song, Z},
title = {Large-scale metagenomic analysis reveals host genetics shapes microbiomes in wild freshwater fish gut and skin.},
journal = {Cell reports},
volume = {45},
number = {2},
pages = {116930},
doi = {10.1016/j.celrep.2026.116930},
pmid = {41619209},
issn = {2211-1247},
mesh = {*Metagenomics ; *Microbiota/genetics ; *Fishes/classification/microbiology ; Fresh Water ; *Gastrointestinal Tract/microbiology ; *Skin/microbiology ; Gastrointestinal Microbiome/genetics ; Phylogeny ; Animals ; *Host Microbial Interactions ; Cyprinidae/classification/microbiology ; Symbiosis ; Aquaculture/methods ; Probiotics ; },
abstract = {Wild freshwater fish microbiomes remain underexplored despite their ecological and economic importance. Through metagenomic sequencing of 903 gut/skin samples from 121 species in southwest China, we constructed the Wild Freshwater Fish Microbiome Catalog, comprising 705 metagenome-assembled genomes and 3,271 viral operational taxonomic units. Host phylogeny dominates microbial community variation, explaining 48.2% (skin) and 22.28% (gut) of the variation. Significant phylosymbiosis occurs in wild freshwater fish, particularly Cyprinidae, with a stronger skin than gut signal. Deterministic selection underpins phylosymbiosis via host-specific ecological filtering. Lifestyle factors (diet, living water layer) and geographical location also impact microbial communities. Notably, wild freshwater fish microbiota harbor a complete set of vitamin B12de novo biosynthesis genes, with Cetobacterium as a keystone genus with probiotic potential. Our work expands gut and skin microbial genome resources, reveals host-microbe coevolution in freshwater fishes, and provides probiotic resources for aquaculture.},
}

*Metagenomics
*Microbiota/genetics
*Fishes/classification/microbiology
Fresh Water
*Gastrointestinal Tract/microbiology
*Skin/microbiology
Gastrointestinal Microbiome/genetics
Phylogeny
Animals
*Host Microbial Interactions
Cyprinidae/classification/microbiology
Symbiosis
Aquaculture/methods
Probiotics

@article {pmid41619244,
year = {2025},
author = {Zahanuddin, A and Rahim, FF and Lau, YL and Mokhtar, AS},
title = {Genetic diversity, microbiome composition and socio-sanitary predictors of head lice (Pediculus humanus capitis) among disadvantaged children in Klang Valley, Malaysia.},
journal = {Tropical biomedicine},
volume = {42},
number = {4},
pages = {435-445},
doi = {10.47665/tb.42.4.010},
pmid = {41619244},
issn = {2521-9855},
mesh = {Humans ; Malaysia/epidemiology ; *Pediculus/genetics/microbiology ; Animals ; *Genetic Variation ; *Lice Infestations/epidemiology/parasitology ; Female ; Male ; Child ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Child, Preschool ; *Bacteria/classification/genetics/isolation & purification ; Vulnerable Populations ; },
abstract = {Pediculosis capitis remains a neglected public health issue in Malaysia, particularly among disadvantaged children. While the genetic diversity of head lice is well studied, their associated microbiome and links to socio-sanitary conditions remain unclear. This study examined 266 children from ten children's establishments in Klang Valley and Greater Kuala Lumpur, of whom 89 (33.46%) were positive for pediculosis capitis. Cytochrome c oxidase subunit I (COI) barcoding identified two clades: A (36%) and C (64%). 16S rRNA metagenomic profiling of pooled samples revealed higher microbial diversity in Clade C compared to Clade A, with opportunistic bacteria, including Propionibacterium acnes, Streptococcus spp., Bacteroides fragilis, and Staphylococcus aureus being detected. Logistic regression identified age, head lice awareness, and eating with hands as significant predictors of infection. These findings demonstrate that head lice not only cluster genetically but also may harbour clade-dependent microbiomes, with potential health implications. The integration of genetic diversity, microbial variation, and socio-sanitary data highlights the multifactorial risks of pediculosis capitis in vulnerable populations, underscoring the importance of combined ectoparasite control and hygiene interventions.},
}

Humans
Malaysia/epidemiology
*Pediculus/genetics/microbiology
Animals
*Genetic Variation
*Lice Infestations/epidemiology/parasitology
Female
Male
Child
RNA, Ribosomal, 16S/genetics
*Microbiota
Child, Preschool
*Bacteria/classification/genetics/isolation & purification
Vulnerable Populations

@article {pmid41619464,
year = {2026},
author = {Umunnawuike, C and Abutu, D and Nwaichi, PI and Nyah, F and Agi, A},
title = {Thermophilic biohydrogen production from reservoir residual hydrocarbons using palm oil mill effluent-derived microbial consortia.},
journal = {The Science of the total environment},
volume = {1016},
number = {},
pages = {181482},
doi = {10.1016/j.scitotenv.2026.181482},
pmid = {41619464},
issn = {1879-1026},
mesh = {Palm Oil ; *Hydrogen/metabolism ; *Microbial Consortia ; Oil and Gas Fields ; *Hydrocarbons/metabolism ; Bioreactors ; *Petroleum/metabolism ; *Waste Disposal, Fluid/methods ; *Biofuels ; Biodegradation, Environmental ; Plant Oils ; },
abstract = {Residual crude oil remaining in depleted reservoirs represents a largely untapped carbon source for biological hydrogen generation. Previous studies have relied on indigenous bacteria present in oil reservoirs but reported low hydrogen yields, as not all reservoir microorganisms are hydrogen-producing. Therefore, in this study, external mixed culture bacterial consortia obtained from palm oil mill effluent (POME) were used to degrade crude oil for hydrogen production. Morphological changes in microbial communities were assessed using field emission scanning electron microscopy. Metagenomic profiling was conducted to identify the dominant microbial taxa capable of producing biohydrogen. Thereafter, a high-temperature and high-pressure (800 °C/30 MPa) stainless-steel bioreactor containing crude oil was inoculated with mixed culture consortia to simulate an oilfield reservoir for hydrogen production. Box-Behnken design was applied to systematically examine the effects of exposure time (6-90 h), crude oil volume (10-40 mL), and temperature (35-70 °C) on continuous hydrogen production. Statistical analysis of variance was used to evaluate model parameters. Heat pretreatment selectively enriched hydrogenogenic spore-formers (Clostridium and Bacillus), resulting in a ~ 4-fold increase (97.40 ± 0.02 mL/L) in hydrogen yield compared to 25.68 ± 0.04 mL/L POME for untreated sludge. In the presence of crude oil, the optimum hydrogen production was 152.50 ± 0.01 mL/L at 50 °C, compared to 125.45 ± 0.03 mL/L and 29.95 ± 0.01 mL/L crude oil at 35 °C and 70 °C, respectively. Predicted hydrogen production, with R[2] value of 97.4% close to unity, indicates that the model was highly consistent with the experimental results, with high precision and reliability. Thermodynamic analysis shows negative Gibbs free energy changes of -122 to -236 kJ/mol, demonstrating that hydrocarbon-to‑hydrogen conversion was energetically favorable and feasible across all tested temperatures. Overall, the experimental, statistical, and thermodynamic analyses establish the technical and energetic feasibility of microbial enhanced hydrogen recovery in depleted oil reservoirs.},
}

Palm Oil
*Hydrogen/metabolism
*Microbial Consortia
Oil and Gas Fields
*Hydrocarbons/metabolism
Bioreactors
*Petroleum/metabolism
*Waste Disposal, Fluid/methods
*Biofuels
Biodegradation, Environmental
Plant Oils

@article {pmid41619482,
year = {2026},
author = {Wang, M and Ye, X and Hsu, CY and Fugate, H and Zhang, X and Adhikari, PA and Fan, P and Elliott, K and Macklin, K and Zhang, L},
title = {Application of culturomics to explore the cultivable microbiota and enable targeted bacterial isolation from the ceca of broiler chickens.},
journal = {Poultry science},
volume = {105},
number = {4},
pages = {106527},
pmid = {41619482},
issn = {1525-3171},
mesh = {Animals ; *Chickens/microbiology ; *Cecum/microbiology ; *Bacteria/isolation & purification/classification/genetics ; RNA, Ribosomal, 16S/analysis ; *Gastrointestinal Microbiome ; *Metagenomics/methods ; RNA, Bacterial/analysis ; },
abstract = {Metagenomic analyses have significantly advanced our understanding of microbial composition in the poultry gut. However, many microbes identified through metagenomic studies remain uncultured, largely due to the lack of understanding of their cultivation conditions, which hinders efforts to explore their functional roles in gut health and metabolism. In this study, we performed culturomics, a culture-dependent approach that combines diverse culture conditions with high-throughput 16S rRNA gene sequencing, to comprehensively assess the cultivability of chicken cecal microbiota and provide guidance for isolating target species of interest. Microbial profiling was performed using both culture-dependent (CD) and culture-independent (CI) approaches. For CI, genomic DNA (gDNA) was directly extracted from six broiler chicken cecal samples and subjected to full-length 16S rRNA gene sequencing. For CD, the same samples were cultured under 28 conditions, yielding 161 colony mixtures for sequencing. Based on diversity profiles of the colony mixtures, 10 conditions were selected for single-colony isolation and analysis. Results showed that CD and CI approaches identified 350 and 502 bacterial species, respectively, with 160 species detected by both methods. The dominant species recovered by the CD approach,including Escherichia coli, Proteus mirabilis, Limosilactobacillus reuteri, Enterococcus faecalis, and Ligilactobacillus salivarius, were detected at much lower abundances in the CI analysis, highlighting the capacity of culturomics to enrich and recover minority taxa that are often poorly detected by CI apparoach. Cultivation profiling showed that MRS selectively enriched Limosilactobacillus and Ligilactobacillus as well as Lactobacillus, whereas CNAB and MSA enriched Enterococcus and Bacillus, respectively. Community diversity and structure were significantly influenced by culture conditions (P < 0.01), with medium as the primary factor and air condition as a secondary factor. Subsequent single-colony analysis from 10 selected culture conditions identified 150 single-species isolates belonging to 14 distinct bacterial species. This study provides foundational insight into the cultivability of chicken cecal microbiota, facilitating future research to isolate specific strains and characterize their roles in poultry health and nutrition.},
}

Animals
*Chickens/microbiology
*Cecum/microbiology
*Bacteria/isolation & purification/classification/genetics
RNA, Ribosomal, 16S/analysis
*Gastrointestinal Microbiome
*Metagenomics/methods
RNA, Bacterial/analysis

@article {pmid41619490,
year = {2026},
author = {Deng, S and Zheng, X and Chu, H and Hong, L and Zhang, J and Yang, H and Gu, L and Pu, L},
title = {Antibiotic-free Wenchang chickens may promote blood levels of B vitamins by modulating the gut microbiota: An integrated analysis of cecal content metagenomics and serum metabolomics.},
journal = {Poultry science},
volume = {105},
number = {4},
pages = {106506},
pmid = {41619490},
issn = {1525-3171},
mesh = {Animals ; *Chickens/microbiology/blood/genetics ; Cecum/microbiology ; *Gastrointestinal Microbiome/drug effects ; Metagenomics ; *Metabolome ; Metabolomics ; Diet/veterinary ; Male ; Anti-Bacterial Agents ; },
abstract = {Through the selective breeding of superior strains, livestock and poultry can achieve enhanced disease resistance and production performance, thereby improving farming efficiency and increasing chicken meat yield. This study analyzed the expression of gut health-related genes, cecal microbiota, and untargeted serum metabolomics in Wenchang chickens from the NS strain (Normal strain) and the AFS strain (Antibiotic-free strain), and explored the relationships between their cecal microbiota and serum metabolites. Our results show that in the ileum, antioxidant-related indicators T-AOC (P < 0.05), T-SOD (P < 0.05), and GSH-PX (P < 0.05) were significantly higher in the AFS strain than in the NS strain, while MDA (P < 0.05) was significantly lower in the AFS strain than in the NS strain. The mRNA expression level of RORγt/FoxP3, which is related to immune regulation, was significantly lower in the AFS strain than in the NS strain (P < 0.05). The differential microorganisms in the cecum primarily included Muribaculum, Cryptobacteroides, Blautia, Enterocloster, Lachnoclostridium, Hydrogenoanaerobacterium, Ruminococcus, Subdoligranulum, Clostridioides, and Evtepia. The main differential metabolites in serum included folinic acid, biotin, lysophosphatidic acid (LPA), 3-hydroxy-3-methylbutanoic acid, 3-hydroxybutyric acid, and others. The differential metabolites are primarily enriched in the following metabolic pathways: gap junction, glycolipid metabolism, and fatty acid biosynthesis. In addition, the Pearson correlation analysis between the gut microbiota and serum metabolites showed that Blautia was positively correlated with folinic acid (P < 0.05) and biotin (P < 0.05); Lachnoclostridium was positively correlated with biotin (P < 0.01); and Ruminococcus was positively correlated with 3-hydroxybutyric acid (P < 0.05). This study mainly elucidates the metabolic characteristics of the antibiotic-free Wenchang chicken strain by analyzing gut microbiota and serum metabolites.},
}

Animals
*Chickens/microbiology/blood/genetics
Cecum/microbiology
*Gastrointestinal Microbiome/drug effects
Metagenomics
*Metabolome
Metabolomics
Diet/veterinary
Male
Anti-Bacterial Agents

@article {pmid41619556,
year = {2026},
author = {Xiao, Y and Ke, C and Wang, D and Chen, N and Chen, G and Qu, L and Liu, Y},
title = {Atractyloside-A ameliorates spleen deficiency diarrhea in mice via modulating Lactobacillus johnsonii-butyric acid-GPR43 axis and NF-κB -NLRP3 signaling pathway.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {152},
number = {},
pages = {157875},
doi = {10.1016/j.phymed.2026.157875},
pmid = {41619556},
issn = {1618-095X},
mesh = {Animals ; NLR Family, Pyrin Domain-Containing 3 Protein/metabolism ; *Receptors, G-Protein-Coupled/metabolism ; Signal Transduction/drug effects ; NF-kappa B/metabolism ; *Diarrhea/drug therapy/microbiology/metabolism ; Mice ; *Lactobacillus johnsonii/drug effects ; Male ; Butyric Acid/metabolism ; Gastrointestinal Microbiome/drug effects ; Spleen ; *Sesquiterpenes/pharmacology ; Disease Models, Animal ; Fatty Acids, Volatile/metabolism ; Mice, Inbred C57BL ; *Lactones/pharmacology ; Intestinal Barrier Function ; },
abstract = {BACKGROUND: Spleen deficiency diarrhea (SDD) is regarded as a common gastrointestinal dysfunction in Traditional Chinese Medicine (TCM), which may lead to intestinal barrier damage and trigger intestinal inflammation. Previous studies have shown that Atractylenolide-A (AA) can effectively treat SDD by regulating intestinal flora. However, it remains uncertain whether AA can increase the levels of short-chain fatty acids (SCFAs) by restoring intestinal microbiota, thereby activating specific signaling pathways to regulate target protein and subsequently alleviate issues related to intestinal barrier function and inflammation.

PURPOSE: This study focused on examining the function of the signaling pathway involving microbiota, SCFAs, and G protein-coupled receptors (GPRs) in the anti-SDD effects of AA.

METHODS: The effects of AA on the Senna (SE) - induced SDD mouse model were assessed through various methods, including diarrhea scoring, H&E staining, qRT-PCR, and ELISA analysis. Subsequently, targeted metabolomics was employed to pinpoint essential metabolites that influence the intestinal microenvironment, while western blotting was utilized to measure the expression of GPRs and the NLRP3 inflammasome. Additionally, experiments involving dietary supplementation with SCFAs and AAV-shGPR43 were performed to determine whether the pharmacological effects of AA operate through SCFAs and rely on GPR43. Key bacterial species that play a role in AA's modulation of SCFAs' pharmacological effects were identified through metagenomic sequencing and single-strain experiments.

RESULTS: The findings of this research revealed that AA is capable of significantly reducing the intestinal inflammatory response, reversing damage to mucin synthesis, and alleviating the pathological symptoms linked to SDD. Furthermore, the use of Lactobacillus johnsonii, sodium butyrate (NaB), and SCFAs individually can lead to notable enhancements in various phenotypes related to SDD. In terms of mechanism, AA achieves its anti-SDD effects by elevating the levels of Lactobacillus johnsonii, facilitating the concentration of butyric acid, boosting GPR43 expression, and modulating the TLR4/NF-κB signaling pathway, which in turn inhibits the assembly of the NLRP3 inflammasome. Nonetheless, following the injection of AAV-shGPR43, the advantageous effects of both AA and NaB were negated, underscoring the significance of this target.

CONCLUSIONS: Gut microbiota-SCFAs-GPRs axis and NF-κB-NLRP3 pathway involve in the alleviation of diarrhea and inflammation in SDD mice intervened with AA, AA promotes the production of butyrate by influencing Lactobacillus johnsonii, stimulates GPR43, and suppresses the formation of the NLRP3 inflammasome via the regulation of the TLR4/NF-κB signaling pathway, which subsequently improves SDD in mice.},
}

Animals
NLR Family, Pyrin Domain-Containing 3 Protein/metabolism
*Receptors, G-Protein-Coupled/metabolism
Signal Transduction/drug effects
NF-kappa B/metabolism
*Diarrhea/drug therapy/microbiology/metabolism
Mice
*Lactobacillus johnsonii/drug effects
Male
Butyric Acid/metabolism
Gastrointestinal Microbiome/drug effects
Spleen
*Sesquiterpenes/pharmacology
Disease Models, Animal
Fatty Acids, Volatile/metabolism
Mice, Inbred C57BL
*Lactones/pharmacology
Intestinal Barrier Function

@article {pmid41620544,
year = {2026},
author = {Kirsche, L and Leary, P and Blaser, MJ and Scharl, M and Negussie, A and Müller, A},
title = {Gut microbial signatures expose the westernized lifestyle of urban Ethiopian children.},
journal = {Communications biology},
volume = {9},
number = {1},
pages = {},
pmid = {41620544},
issn = {2399-3642},
support = {310030_192490//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; },
mesh = {Humans ; Child, Preschool ; Ethiopia ; *Urban Population ; *Gastrointestinal Microbiome/genetics ; Female ; Feces/microbiology ; *Life Style ; Male ; RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics ; Metagenomics ; },
abstract = {Gut microbiota composition has been extensively studied in European and North American pediatric cohorts, as well as in rural African children. Much less attention has been paid to urban African children, whose families have transitioned to a "Western" lifestyle characterized by smaller family sizes, access to perinatal care including C-section delivery, non-traditional food sources and widespread availability of antibiotics. We analyzed fecal samples from ~200 Ethiopian children aged 2-5 years from Adama, Ethiopia, using 16S rRNA gene sequencing and shotgun metagenomics. We found that well-studied factors such as delivery mode, breastfeeding and family size have only minor effects on α-diversity, whereas household crowding (single vs. multiple rooms) and consumption of the traditional fermented cereal Eragrostis tef predict higher α-diversity. Stunted growth and absence of Helicobacter pylori infection were additional factors associated with increased fecal microbial diversity. Metagenomic profiling revealed that rural African signature genera such as Segatella and Prevotella were largely absent; instead, urban Ethiopian children displayed a high Firmicutes/Bacteroidota ratio and enrichment of metabolic pathways linked to a westernized diet, resembling European rather than rural Ethiopian children. These results indicate that an urban westernized lifestyle alters gut microbiota composition, which may be partially offset by a traditional fermented diet.},
}